1
|
Johnson M, Lazarus SK, Bennett AE, Tovar-Salazar A, Robertson CE, Kofonow JM, Li S, McCollister B, Nunes MC, Madhi SA, Frank DN, Weinberg A. Gut Microbiota and Other Factors Associated With Increased Regulatory T Cells in Hiv-exposed Uninfected Infants. Res Sq 2024:rs.3.rs-3909424. [PMID: 38352510 PMCID: PMC10862973 DOI: 10.21203/rs.3.rs-3909424/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
HIV-exposed uninfected infants (HEU) have higher infectious morbidity than HIV-unexposed infants (HUU). HEU have multiple immune defects of unknown origin. We hypothesized that HEU have higher regulatory T cells (Treg) than HUU, which may dampen their immune defenses against pathogens. We compared 25 Treg subsets between HEU and HUU and sought the factors that may affect Treg frequencies. At birth, 3 Treg subsets, including CD4 + FOXP3 + and CD4 + FOXP3 + CD25+, had higher frequencies in 123 HEU than 117 HUU and 3 subsets were higher in HUU. At 28 and 62 weeks of life, 5 Treg subsets were higher in HEU, and none were higher in HUU. The frequencies of the discrepant Treg subsets correlated at birth with differential abundances of bacterial taxas in maternal gut microbiome and at subsequent visits in infant gut microbiomes. In vitro, bacterial taxa most abundant in HEU expanded Treg subsets with higher frequencies in HEU, recapitulating the in vivo observations. Other factors that correlated with increased Treg were low maternal CD4 + T cells in HEU at birth and male sex in HUU at 28 weeks. We conclude that maternal and infant gut dysbiosis are central to the Treg increase in HEU and may be targeted by mitigating interventions.
Collapse
|
2
|
Seymour BJ, Trent B, Allen BE, Berlinberg AJ, Tangchittsumran J, Jubair WK, Chriswell ME, Liu S, Ornelas A, Stahly A, Alexeev EE, Dowdell AS, Sneed SL, Fechtner S, Kofonow JM, Robertson CE, Dillon SM, Wilson CC, Anthony RM, Frank DN, Colgan SP, Kuhn KA. Microbiota-dependent indole production stimulates the development of collagen-induced arthritis in mice. J Clin Invest 2023; 134:e167671. [PMID: 38113112 PMCID: PMC10866668 DOI: 10.1172/jci167671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/13/2023] [Indexed: 12/21/2023] Open
Abstract
Altered tryptophan catabolism has been identified in inflammatory diseases like rheumatoid arthritis (RA) and spondyloarthritis (SpA), but the causal mechanisms linking tryptophan metabolites to disease are unknown. Using the collagen-induced arthritis (CIA) model, we identified alterations in tryptophan metabolism, and specifically indole, that correlated with disease. We demonstrated that both bacteria and dietary tryptophan were required for disease and that indole supplementation was sufficient to induce disease in their absence. When mice with CIA on a low-tryptophan diet were supplemented with indole, we observed significant increases in serum IL-6, TNF, and IL-1β; splenic RORγt+CD4+ T cells and ex vivo collagen-stimulated IL-17 production; and a pattern of anti-collagen antibody isotype switching and glycosylation that corresponded with increased complement fixation. IL-23 neutralization reduced disease severity in indole-induced CIA. Finally, exposure of human colonic lymphocytes to indole increased the expression of genes involved in IL-17 signaling and plasma cell activation. Altogether, we propose a mechanism by which intestinal dysbiosis during inflammatory arthritis results in altered tryptophan catabolism, leading to indole stimulation of arthritis development. Blockade of indole generation may present a unique therapeutic pathway for RA and SpA.
Collapse
Affiliation(s)
| | - Brandon Trent
- Division of Rheumatology, Department of Medicine, and
| | | | | | | | | | | | - Sucai Liu
- Division of Rheumatology, Department of Medicine, and
| | - Alfredo Ornelas
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Andrew Stahly
- Division of Rheumatology, Department of Medicine, and
| | - Erica E. Alexeev
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alexander S. Dowdell
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sunny L. Sneed
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Stephanie M. Dillon
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cara C. Wilson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Robert M. Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sean P. Colgan
- Mucosal Inflammation Program and Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | |
Collapse
|
3
|
Francis D, Chawla A, LaComb JF, Markarian K, Robertson CE, Frank DN, Gathungu GN. Gastroesophageal reflux and PPI exposure alter gut microbiota in very young infants. Front Pediatr 2023; 11:1254329. [PMID: 38027267 PMCID: PMC10651085 DOI: 10.3389/fped.2023.1254329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023] Open
Abstract
Importance Infants with symptomatic Gastroesophageal reflux are treated with pharmacological therapy that includes proton pump inhibitors (PPI) with clinical improvement. The alterations to gut microbiome profiles in comparison to infants without reflux is not known. Objective To determine the effect of PPI therapy on gut bacterial richness, diversity, and proportions of specific taxa in infants when compared to infants not exposed to acid suppressive therapy. Design setting and participants This cohort study was conducted at the Stony Brook Hospital in Stony Brook, NY between February 2016, and June 2019. Infants meeting inclusion criteria were enrolled in a consecutive fashion. Results A total of 76 Infants were recruited and 60 were enrolled in the study, Twenty nine infants met clinical criteria for reflux and were treated with PPI therapy: median [IQR] gestation: 38.0 weeks [34.7-39.6 weeks]; median [IQR] birthweight: 2.95 Kg [2.2-3.4]; 14 [46.7%] male) and 29 infant were healthy controls median [IQR] gestation: 39.1 weeks [38-40 weeks]; median [IQR] birthweight: 3.3 Kg [2.2-3.4]; 17 [58.6%] male); 58 stool samples from 58 infants were analyzed. There were differences in Shannon diversity between the reflux and control groups. The reflux group that was exposed to PPI therapy had increased relative abundance of a diverse set of genera belonging to the phylum Firmicutes. On the other hand, the control group microbiota was dominated by Bifidobacterium, and a comparatively lower level of enrichment and abundance of microbial taxa was observed in this group of infants. Conclusions and relevance We observed significant differences in both α- and β-diversity of the microbiome, when the two groups of infants were compared. The microbiome in the reflux group had more bacterial taxa and the duration of PPIs exposure was clearly associated with the diversity and abundance of gut microbes. These findings suggest that PPI exposure among infants results in early enrichment of the intestinal microbiome.
Collapse
Affiliation(s)
- Denease Francis
- Department of Pediatrics, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Anupama Chawla
- Department of Pediatrics, Stony Brook University Hospital, Stony Brook, NY, United States
| | - Joseph F. LaComb
- Department of Pediatrics, Stony Brook University Hospital, Stony Brook, NY, United States
| | - Katherine Markarian
- Department of Pediatrics, Stony Brook University Hospital, Stony Brook, NY, United States
| | - Charles E. Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N. Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Grace N. Gathungu
- Department of Pediatrics, Stony Brook University Hospital, Stony Brook, NY, United States
| |
Collapse
|
4
|
Wagner BD, Zemanick ET, Sagel SD, Robertson CE, Stevens MJ, Mayer-Hamblett N, Retsch-Bogart G, Ramsey BW, Harris JK. Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection. BMC Microbiol 2023; 23:312. [PMID: 37891457 PMCID: PMC10612347 DOI: 10.1186/s12866-023-03073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Tobramycin inhalation solution (TIS) and chronic azithromycin (AZ) have known clinical benefits for children with CF, likely due to antimicrobial and anti-inflammatory activity. The effects of chronic AZ in combination with TIS on the airway microbiome have not been extensively investigated. Oropharyngeal swab samples were collected in the OPTIMIZE multicenter, randomized, placebo-controlled trial examining the addition of AZ to TIS in 198 children with CF and early P. aeruginosa infection. Bacterial small subunit rRNA gene community profiles were determined. The effects of TIS and AZ were assessed on oropharyngeal microbial diversity and composition to uncover whether effects on the bacterial community may be a mechanism of action related to the observed changes in clinical outcomes. RESULTS Substantial changes in bacterial communities (total bacterial load, diversity and relative abundance of specific taxa) were observed by week 3 of TIS treatment for both the AZ and placebo groups. On average, these shifts were due to changes in non-traditional CF taxa that were not sustained at the later study visits (weeks 13 and 26). Bacterial community measures did not differ between the AZ and placebo groups. CONCLUSIONS This study provides further evidence that the mechanism for AZ's effect on clinical outcomes is not due solely to action on airway microbial composition.
Collapse
Affiliation(s)
- Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA.
- Children's Hospital Colorado, Aurora, CO, USA.
| | - Edith T Zemanick
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Scott D Sagel
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | | | - Mark J Stevens
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Nicole Mayer-Hamblett
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | | | - Bonnie W Ramsey
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | - J Kirk Harris
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| |
Collapse
|
5
|
Seymour BJ, Trent B, Allen B, Berlinberg AJ, Tangchittsumran J, Jubair WK, Chriswell ME, Liu S, Ornelas A, Stahly A, Alexeev EE, Dowdell AS, Sneed SL, Fechtner S, Kofonow JM, Robertson CE, Dillon SM, Wilson CC, Anthony RM, Frank DN, Colgan SP, Kuhn KA. Microbiota-dependent indole production is required for the development of collagen-induced arthritis. bioRxiv 2023:2023.10.13.561693. [PMID: 37873395 PMCID: PMC10592798 DOI: 10.1101/2023.10.13.561693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Altered tryptophan catabolism has been identified in inflammatory diseases like rheumatoid arthritis (RA) and spondyloarthritis (SpA), but the causal mechanisms linking tryptophan metabolites to disease are unknown. Using the collagen-induced arthritis (CIA) model we identify alterations in tryptophan metabolism, and specifically indole, that correlate with disease. We demonstrate that both bacteria and dietary tryptophan are required for disease, and indole supplementation is sufficient to induce disease in their absence. When mice with CIA on a low-tryptophan diet were supplemented with indole, we observed significant increases in serum IL-6, TNF, and IL-1β; splenic RORγt+CD4+ T cells and ex vivo collagen-stimulated IL-17 production; and a pattern of anti-collagen antibody isotype switching and glycosylation that corresponded with increased complement fixation. IL-23 neutralization reduced disease severity in indole-induced CIA. Finally, exposure of human colon lymphocytes to indole increased expression of genes involved in IL-17 signaling and plasma cell activation. Altogether, we propose a mechanism by which intestinal dysbiosis during inflammatory arthritis results in altered tryptophan catabolism, leading to indole stimulation of arthritis development. Blockade of indole generation may present a novel therapeutic pathway for RA and SpA.
Collapse
Affiliation(s)
- Brenda J. Seymour
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brandon Trent
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brendan Allen
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Adam J. Berlinberg
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jimmy Tangchittsumran
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Widian K. Jubair
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Meagan E. Chriswell
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sucai Liu
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alfredo Ornelas
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Stahly
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Erica E. Alexeev
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alexander S. Dowdell
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sunny L. Sneed
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sabrina Fechtner
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephanie M. Dillon
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Cara C. Wilson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Robert M. Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sean P. Colgan
- Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristine A. Kuhn
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
6
|
Walrath T, Najarro KM, Giesy LE, Khair S, Frank DN, Robertson CE, Orlicky DJ, Quillinan N, Idrovo JP, McMahan RH, Kovacs EJ. REMOTE BURN INJURY IN AGED MICE INDUCES COLONIC LYMPHOID AGGREGATE EXPANSION AND DYSBIOSIS OF THE FECAL MICROBIOME WHICH CORRELATES WITH NEUROINFLAMMATION. Shock 2023; 60:585-593. [PMID: 37548929 PMCID: PMC10581426 DOI: 10.1097/shk.0000000000002202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/02/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023]
Abstract
ABSTRACT The Earth's population is aging, and by 2050, one of six people will be 65 years or older. Therefore, proper treatment of injuries that disproportionately impact people of advanced age will be more important. Clinical studies reveal people 65 years or older account for 16.5% of all burn injuries and experience higher morbidity, including neurocognitive decline, and mortality that we and others believe are mediated, in part, by heightened intestinal permeability. Herein, we used our clinically relevant model of scald burn injury in young and aged mice to determine whether age and burn injury cooperate to induce heightened colonic damage, alterations to the fecal microbiome, and whether resultant changes in the microbiome correlate with neuroinflammation. We found that aged, burn-injured mice have an increase in colonic lymphoid aggregates, inflammation, and proinflammatory chemokine expression when compared with young groups and sham-injured aged mice. We then performed fecal microbiota sequencing and found a striking reduction in gut protective bacterial taxa, including Akkermansia , in the aged burn group compared with all other groups. This reduction correlated with an increase in serum fluorescein isothiocyanate-Dextran administered by gavage, indicating heightened intestinal permeability. Furthermore, loss of Akkermansia was highly correlated with increased messenger RNA expression of neuroinflammatory markers in the brain, including chemokine ligand 2, TNF-α, CXC motif ligand 1, and S100 calcium-binding protein A8. Finally, we discovered that postburn alterations in the microbiome correlated with measures of strength in all treatment groups, and those that performed better on the rotarod and hanging wire tests had higher abundance of Akkermansia than those that performed worse. Taken together, these findings indicate that loss of protective bacteria after burn injury in aged mice contributes to alterations in the colon, gut leakiness, neuroinflammation, and strength. Therefore, supplementation of protective bacteria, such as Akkermansia , after burn injury in aged patients may have therapeutic benefit.
Collapse
Affiliation(s)
- Travis Walrath
- Department of Surgery, Burn Research and Alcohol Research Programs, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Kevin M. Najarro
- Department of Surgery, Burn Research and Alcohol Research Programs, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Lauren E. Giesy
- Department of Surgery, Burn Research and Alcohol Research Programs, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Shanawaj Khair
- Department of Surgery, Burn Research and Alcohol Research Programs, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Molecular Biology Graduate Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Medical Scientist Training Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Daniel N. Frank
- Department of Medicine, Division of Infectious Disease, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Charles E. Robertson
- Department of Medicine, Division of Infectious Disease, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - David J. Orlicky
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Nidia Quillinan
- Department of Anesthesiology, Neuronal Injury Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Juan-Pablo Idrovo
- Department of Surgery, Burn Research and Alcohol Research Programs, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Rachel H. McMahan
- Department of Surgery, Burn Research and Alcohol Research Programs, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Elizabeth J. Kovacs
- Department of Surgery, Burn Research and Alcohol Research Programs, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Department of Surgery, Division of GI, Trauma, and Endocrine Surgery, and Burn Research Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| |
Collapse
|
7
|
Fechtner S, Allen BE, Chriswell ME, Jubair WK, Robertson CE, Kofonow JN, Frank DN, Holers VM, Kuhn KA. 3,3-dimethyl-1-butanol and its metabolite 3,3-dimethylbutyrate ameliorate collagen-induced arthritis independent of choline trimethylamine lyase activity. Res Sq 2023:rs.3.rs-3297018. [PMID: 37720032 PMCID: PMC10503834 DOI: 10.21203/rs.3.rs-3297018/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Previous studies have identified significant alterations in intestinal carnitine metabolism in mice with collagen-induced arthritis (CIA), potentially linking bacterial dysbiosis with autoimmunity. Bacterial trimethylamine (TMA) lyases metabolize dietary carnitine to TMA, which is oxidized in the liver to trimethylamine-N-oxide (TMAO). TMAO is associated with inflammatory diseases, such as atherosclerosis, whose immunologic processes mirror that of rheumatoid arthritis (RA). Therefore, we investigated the possibility of ameliorating CIA by inhibiting TMA lyase activity using 3,3-dimethyl-1-butanol (DMB) or fluoromethylcholine (FMC). During CIA, mice were treated with 1% vol/vol DMB, 100mg/kg FMC, or vehicle. DMB-treated mice demonstrated significant (>50%) reduction in arthritis severity compared to FMC and vehicle-treated mice. However, in contrast to FMC, DMB treatment did not reduce cecal TMA nor circulating TMAO concentrations. Using gas chromatography, we confirmed the effect of DMB is independent of TMA lyase inhibition. Further, we identified a novel host-derived metabolite of DMB, 3,3-dimethyl-1-butyric acid (DMBut), which also significantly reduced disease and proinflammatory cytokines in CIA mice. Altogether, our study suggests that DMB the immunomodulatory activity of DMB and/or its metabolites are protective in CIA. Elucidating its target and mechanism of action may provide new directions for RA therapeutic development.
Collapse
|
8
|
Odiase E, Frank DN, Young BE, Robertson CE, Kofonow JM, Davis KN, Berman LM, Krebs NF, Tang M. The Gut Microbiota Differ in Exclusively Breastfed and Formula-Fed United States Infants and are Associated with Growth Status. J Nutr 2023; 153:2612-2621. [PMID: 37506974 PMCID: PMC10517231 DOI: 10.1016/j.tjnut.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Evidence regarding the effects of infant feeding type (exclusive breastfeeding compared with exclusive formula feeding) on the gut microbiota and how it impacts infant growth status is limited. OBJECTIVES The primary objective was to compare gut microbiota by feeding type and characterize the associations between gut microbiota and infant growth status. METHODS Stool samples from healthy, full-term infants (4-5 mo-old) who were either exclusively breastfed (BF) or exclusively formula-fed (FF) in Denver, CO, United States were collected, and fecal 16S ribosomal ribonucleic acid gene-based profiling was conducted. Length and weight were measured at the time of stool collection. Length-for-age z-score, weight-for-age z-scores (WAZ), and weight-for-length z-scores were calculated based on the World Health Organization standards. Associations between gut microbial taxa and anthropometric z-scores were assessed by Spearman's rank correlation test. RESULTS A total of 115 infants (BF n = 54; FF n = 61) were included in this study. Feeding type (BF compared with FF) was the most significant tested variable on gut microbiota composition (P < 1 × 10-⁶), followed by mode of delivery and race. Significant differences were observed in α-diversity, β-diversity, and relative abundances of individual taxa between BF and FF. BF infants had lower α-diversity than FF infants. Abundances of Bifidobacterium and Lactobacillus were greater in the breastfeeding group. FF infants had a higher relative abundance of unclassified Ruminococcaceae (P < 0.001), which was associated with a higher WAZ (P < 0.001) and length-for-age z-score (P < 0.01). Lactobacillus was inversely associated with WAZ (P < 0.05). CONCLUSIONS Feeding type is the main driver of gut microbiota differences in young infants. The gut microbiota differences based on feeding type (exclusive breast- or formula feeding) were associated with observed differences in growth status. This trial was registered at clinicaltrials.gov as NCT02142647, NCT01693406, and NCT04137445.
Collapse
Affiliation(s)
- Eunice Odiase
- Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, University of Virginia, Charlottesville, VA, 22904, USA
| | - Daniel N Frank
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bridget E Young
- University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Charles E Robertson
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jennifer M Kofonow
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kathryn N Davis
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lillian M Berman
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nancy F Krebs
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Minghua Tang
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| |
Collapse
|
9
|
Leroue MK, Williamson KM, Curtin PC, Sontag MK, Wagner BD, Ambroggio L, Bixby M, Busgang SA, Murphy SE, Peterson LA, Vevang KR, Sipe CJ, Kirk Harris J, Reeder RW, Locandro C, Carpenter TC, Maddux AB, Simões EAF, Osborne CM, Robertson CE, Langelier C, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Mourani PM. Tobacco smoke exposure, the lower airways microbiome and outcomes of ventilated children. Pediatr Res 2023; 94:660-667. [PMID: 36750739 PMCID: PMC9903281 DOI: 10.1038/s41390-023-02502-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/18/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND Tobacco smoke exposure increases the risk and severity of lower respiratory tract infections in children, yet the mechanisms remain unclear. We hypothesized that tobacco smoke exposure would modify the lower airway microbiome. METHODS Secondary analysis of a multicenter cohort of 362 children between ages 31 days and 18 years mechanically ventilated for >72 h. Tracheal aspirates from 298 patients, collected within 24 h of intubation, were evaluated via 16 S ribosomal RNA sequencing. Smoke exposure was determined by creatinine corrected urine cotinine levels ≥30 µg/g. RESULTS Patients had a median age of 16 (IQR 568) months. The most common admission diagnosis was lower respiratory tract infection (53%). Seventy-four (20%) patients were smoke exposed and exhibited decreased richness and Shannon diversity. Smoke exposed children had higher relative abundances of Serratia spp., Moraxella spp., Haemophilus spp., and Staphylococcus aureus. Differences were most notable in patients with bacterial and viral respiratory infections. There were no differences in development of acute respiratory distress syndrome, days of mechanical ventilation, ventilator free days at 28 days, length of stay, or mortality. CONCLUSION Among critically ill children requiring prolonged mechanical ventilation, tobacco smoke exposure is associated with decreased richness and Shannon diversity and change in microbial communities. IMPACT Tobacco smoke exposure is associated with changes in the lower airways microbiome but is not associated with clinical outcomes among critically ill pediatric patients requiring prolonged mechanical ventilation. This study is among the first to evaluate the impact of tobacco smoke exposure on the lower airway microbiome in children. This research helps elucidate the relationship between tobacco smoke exposure and the lower airway microbiome and may provide a possible mechanism by which tobacco smoke exposure increases the risk for poor outcomes in children.
Collapse
Affiliation(s)
- Matthew K Leroue
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA.
| | - Kayla M Williamson
- Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Paul C Curtin
- CHEAR Data Center, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marci K Sontag
- Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Brandie D Wagner
- Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Lilliam Ambroggio
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Moira Bixby
- CHEAR Data Center, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stefanie A Busgang
- CHEAR Data Center, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharon E Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lisa A Peterson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Karin R Vevang
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | | | - J Kirk Harris
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Ron W Reeder
- Pediatrics, University of Utah, Salt Lake City, UT, USA
| | | | - Todd C Carpenter
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Aline B Maddux
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Eric A F Simões
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
- Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Christina M Osborne
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Charles E Robertson
- Medicine, Division of Infectious Diseases, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Charles Langelier
- Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Kathleen L Meert
- Pediatrics, Children's Hospital of Michigan, Central Michigan University, Detroit, MI, USA
| | | | | | - Peter M Mourani
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
- Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| |
Collapse
|
10
|
Elling CL, Goff SH, Hirsch SD, Tholen K, Kofonow JM, Curtis D, Robertson CE, Prager JD, Yoon PJ, Wine TM, Chan KH, Scholes MA, Friedman NR, Frank DN, Herrmann BW, Santos-Cortez RLP. Otitis Media in Children with Down Syndrome Is Associated with Shifts in the Nasopharyngeal and Middle Ear Microbiotas. Genet Test Mol Biomarkers 2023; 27:221-228. [PMID: 37522794 PMCID: PMC10494904 DOI: 10.1089/gtmb.2023.0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Background: Otitis media (OM) is defined as middle ear (ME) inflammation that is usually due to infection. Globally, OM is a leading cause of hearing loss and is the most frequently diagnosed disease in young children. For OM, pediatric patients with Down syndrome (DS) demonstrate higher incidence rates, greater severity, and poorer outcomes. However, to date, no studies have investigated the bacterial profiles of children with DS and OM. Method: We aimed to determine if there are differences in composition of bacterial profiles or the relative abundance of individual taxa within the ME and nasopharyngeal (NP) microbiotas of pediatric OM patients with DS (n = 11) compared with those without DS (n = 84). We sequenced the 16S rRNA genes and analyzed the sequence data for diversity indices and relative abundance of individual taxa. Results: Individuals with DS demonstrated increased biodiversity in their ME and NP microbiotas. In children with OM, DS was associated with increased biodiversity and higher relative abundance of specific taxa in the ME. Conclusion: Our findings suggest that dysbioses in the NP of DS children contributes to their increased susceptibility to OM compared with controls. These findings suggest that DS influences regulation of the mucosal microbiota and contributes to OM pathology.
Collapse
Affiliation(s)
- Christina L. Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Salina H. Goff
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Scott D. Hirsch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kaitlyn Tholen
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Danielle Curtis
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jeremy D. Prager
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Patricia J. Yoon
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Todd M. Wine
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Kenny H. Chan
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Melissa A. Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Norman R. Friedman
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Brian W. Herrmann
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Center for Children's Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
| |
Collapse
|
11
|
Harris JK, Wagner BD, Robertson CE, Stevens MJ, Lingard C, Borowitz D, Leung DH, Heltshe SL, Ramsey BW, Zemanick ET. Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen. J Cyst Fibros 2023; 22:644-651. [PMID: 37137746 PMCID: PMC10524365 DOI: 10.1016/j.jcf.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023]
Abstract
BACKGROUND Changes in upper airway microbiota may impact early disease manifestations in infants with cystic fibrosis (CF). To investigate early airway microbiota, the microbiota present in the oropharynx of CF infants over the first year of life was assessed along with the relationships between microbiota and growth, antibiotic use and other clinical variables. METHODS Oropharyngeal (OP) swabs were collected longitudinally between 1 and 12 months of age from infants diagnosed with CF by newborn screen and enrolled in the Baby Observational and Nutrition Study (BONUS). DNA extraction was performed after enzymatic digestion of OP swabs. Total bacterial load was determined by qPCR and community composition assessed using 16S rRNA gene analysis (V1/V2 region). Changes in diversity with age were evaluated using mixed models with cubic B-splines. Associations between clinical variables and bacterial taxa were determined using a canonical correlation analysis. RESULTS 1,052 OP swabs collected from 205 infants with CF were analyzed. Most infants (77%) received at least one course of antibiotics during the study and 131 OP swabs were collected while the infant was prescribed an antibiotic. Alpha diversity increased with age and was only marginally impacted by antibiotic use. Community composition was most highly correlated with age and was only moderately correlated with antibiotic exposure, feeding method and weight z-scores. Relative abundance of Streptococcus decreased while Neisseria and other taxa increased over the first year. CONCLUSIONS Age was more influential on the oropharyngeal microbiota of infants with CF than clinical variables including antibiotics in the first year of life.
Collapse
Affiliation(s)
- J Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA.
| | - Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mark J Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| | - Conor Lingard
- Spartanburg Regional Healthcare Systems, Spartanburg, SC, USA
| | - Drucy Borowitz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Bonnie W Ramsey
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| |
Collapse
|
12
|
Robertson CE, Weaver FE, Nurse CA. "Turning up the heat": Role of neurotrophic batokines in the postnatal maturation and remodelling of brown adipose tissue in deer mice. Am J Physiol Endocrinol Metab 2023. [PMID: 37224469 DOI: 10.1152/ajpendo.00331.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
Activation of brown adipose tissue (BAT) thermogenesis impacts energy balance and must be tightly regulated. Several neurotrophic factors, expressed in BAT of adult laboratory rodents, have been implicated in remodelling the sympathetic neural network to enhance thermogenesis (e.g., NGF, NRG4 and S100b). Here, we compare for the first time the relative roles of three neurotropic 'batokines' in establishing/remodelling innervation during postnatal development and adult cold stress. We used lab-reared P. maniculatus, which rely heavily on BAT-based thermogenesis for survival in the wild, beginning between postnatal days (P) 8 and 10. BAT sympathetic innervation was enhanced from P6-10, and exogenous NGF, NRG4, and S100b stimulated neurite outgrowth from P6 sympathetic neurons. Endogenous BAT protein stores and/or gene expression of NRG4, S100b, and calsyntenin-3ß (which regulates S100b secretion), remained high and constant during development. However, endogenous NGF was low and ngf mRNA was undetectable. Conditioned media (CM) from cultured P10 BAT slices stimulated neurite outgrowth from sympathetic neurons in vitro that was inhibited by antibodies against all three growth factors. P10 CM had significant amounts of secreted NRG4 and S100b protein, but not NGF. By contrast, BAT slices from cold-acclimated adults released significant amounts of all three factors relative to thermoneutral controls. These data suggest that while neurotrophic batokines regulate sympathetic innervation in vivo, their relative contributions differ depending on life stage. They also provide novel insight into the regulation of BAT remodelling and BAT's secretory role, which are both critical to our understanding of mammalian energy homeostasis.
Collapse
Affiliation(s)
- C E Robertson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - F E Weaver
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - C A Nurse
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
13
|
Taylor JZ, Fong DL, Habenicht LM, Fink MK, Leszczynski JK, Frank DN, Kofonow JM, Robertson CE, Nicklawsky AG, Schurr MJ, Manuel CA. Effects of Extended Cage Component Sanitation Interval on the Microenvironment, Health, and Gastrointestinal Microbiome of Rats ( Rattus norvegicus). J Am Assoc Lab Anim Sci 2023; 62:212-221. [PMID: 37072181 PMCID: PMC10230543 DOI: 10.30802/aalas-jaalas-22-000113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 04/20/2023]
Abstract
Washing and sanitizing rodent cage components requires costly equipment, significant personnel effort, and use of natural resources. The benchmark frequency for sanitation of individually ventilated caging (IVC) has traditionally been every 2 wk. In this study, we investigated the effects of extending this interval on the cage microenvironment, basic markers of health, and the gastrointestinal microbiota of rats. We compared our institutional standard of changing the sanitation interval for rat cage lids, box feeders, and enrichment devices from every 4 wk to an interval of 12 wk. The cage bottom and bedding continued to be changed every 2 wk for both groups. We hypothesized that we would find no significant difference between our current practice of 4 wks and continuous use for 12 wk. Our data showed that intracage ammonia levels remained below 5 ppm for most cages in both groups, with the exception of cages that experienced a cage flood. We found no significant difference between groups in bacterial colony forming units (CFU) on cage components. We used 3 novel methods of assessing cleanliness of enrichment devices and found no significant effect of continuous use for 12 wk on the number of CFU. In addition, we found no significant differences between groups for animal weight, routine blood work, or fecal and cecal microbiomes. These data indicate that a sanitation interval of up to 12 wk for components of rat IVC caging has no significant effects on the microenvironment or health of rats. Using the longer interval will improve efficiency, reduce the use of natural resources, and decrease costs while maintaining high-quality animal care.
Collapse
Affiliation(s)
- Jazmyne Z Taylor
- Office of Laboratory Animal Resources, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Derek L Fong
- Office of Laboratory Animal Resources, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Lauren M Habenicht
- Office of Laboratory Animal Resources, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Michael K Fink
- Office of Laboratory Animal Resources, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Jori K Leszczynski
- Office of Laboratory Animal Resources, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jennifer M Kofonow
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Andrew G Nicklawsky
- University of Colorado Cancer Center Biostatistics Core, Aurora, Colorado; and
| | - Michael J Schurr
- Department of Immunology and Microbiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| | - Christopher A Manuel
- Office of Laboratory Animal Resources, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado
| |
Collapse
|
14
|
Colbert JF, Kirsch JM, Erzen CL, Langouët-Astrié CJ, Thompson GE, McMurtry SA, Kofonow JM, Robertson CE, Kovacs EJ, Sullivan RC, Hippensteel JA, Sawant NV, De Nisco NJ, McCollister BD, Schwartz RS, Horswill AR, Frank DN, Duerkop BA, Schmidt EP. Aging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity. mBio 2023:e0005223. [PMID: 37102874 DOI: 10.1128/mbio.00052-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition but also an overabundance of genomic virulence factors that have functional consequence on host immune evasion. IMPORTANCE Older adults suffer more frequent and worse outcomes from sepsis, a critical illness secondary to infection. The reasons underlying this unique susceptibility are incompletely understood. Prior work in this area has focused on how the immune response changes with age. The current study, however, focuses instead on alterations in the community of bacteria that humans live with within their gut (i.e., the gut microbiome). The central concept of this paper is that the bacteria in our gut evolve along with the host and "age," making them more efficient at causing sepsis.
Collapse
Affiliation(s)
- James F Colbert
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA
| | - Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Christopher L Erzen
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | | | - Sarah A McMurtry
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jennifer M Kofonow
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Elizabeth J Kovacs
- Department of Surgery, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Ryan C Sullivan
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Joseph A Hippensteel
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Namrata V Sawant
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce D McCollister
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Robert S Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eric P Schmidt
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
15
|
Furuta GT, Fillon SA, Williamson KM, Robertson CE, Stevens MJ, Aceves SS, Arva NC, Chehade M, Collins MH, Davis CM, Dellon ES, Falk GW, Gonsalves N, Gupta SK, Hirano I, Khoury P, Leung J, Martin LJ, Menard-Katcher P, Mukkada VA, Peterson K, Spergel JM, Wechsler JB, Yang GY, Rothenberg ME, Harris JK. Mucosal Microbiota Associated With Eosinophilic Esophagitis and Eosinophilic Gastritis. J Pediatr Gastroenterol Nutr 2023; 76:347-354. [PMID: 36525669 PMCID: PMC10201396 DOI: 10.1097/mpg.0000000000003685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
OBJECTIVE The aim of the study was to determine the mucosal microbiota associated with eosinophilic esophagitis (EoE) and eosinophilic gastritis (EoG) in a geographically diverse cohort of patients compared to controls. METHODS We conducted a prospective study of individuals with eosinophilic gastrointestinal disease (EGID) in the Consortium of Eosinophilic Gastrointestinal Disease Researchers, including pediatric and adult tertiary care centers. Eligible individuals had clinical data, mucosal biopsies, and stool collected. Total bacterial load was determined from mucosal biopsy samples by quantitative polymerase chain reaction (PCR). Community composition was determined by small subunit rRNA gene amplicons. RESULTS One hundred thirty-nine mucosal biopsies were evaluated corresponding to 93 EoE, 17 EoG, and 29 control specimens (18 esophageal) from 10 sites across the United States. Dominant community members across disease activity differed significantly. When comparing EoE and EoG with controls, the dominant taxa in individuals with EGIDs was increased ( Streptococcus in esophagus; Prevotella in stomach). Specific taxa were associated with active disease for both EoE ( Streptococcus , Gemella ) and EoG ( Leptotrichia ), although highly individualized communities likely impacted statistical testing. Alpha diversity metrics were similar across groups, but with high variability among individuals. Stool analyses did not correlate with bacterial communities found in mucosal biopsy samples and was similar in patients and controls. CONCLUSIONS Dominant community members ( Streptococcus for EoE, Prevotella for EoG) were different in the mucosal biopsies but not stool of individuals with EGIDs compared to controls; taxa associated with EGIDs were highly variable across individuals. Further study is needed to determine if therapeutic interventions contribute to the observed community differences.
Collapse
Affiliation(s)
- Glenn T. Furuta
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Digestive Health Institute, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Disease Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO
| | - Sophie A. Fillon
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Digestive Health Institute, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Disease Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO
| | - Kayla M. Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, Aurora, CO
| | - Charles E. Robertson
- Division of Infectious Disease, University of Colorado School of Medicine, Aurora, CO
| | - Mark J. Stevens
- Division of Infectious Disease, University of Colorado School of Medicine, Aurora, CO
| | - Seema S. Aceves
- Division of Allergy/Immunology, Department of Pediatrics, University of California, San Diego, Rady Children’s Hospital, San Diego, CA
| | - Nicoleta C. Arva
- Department of Pathology, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Mirna Chehade
- Departments of Pediatrics and Medicine, Mount Sinai Center for Eosinophilic Disorders, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Margaret H. Collins
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH
| | - Carla M. Davis
- Division of Immunology, Allergy and Retrovirology, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Evan S. Dellon
- Center for Esophageal Diseases and Swallowing and Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Gary W. Falk
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nirmala Gonsalves
- Division of Gastroenterology and Hepatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Sandeep K. Gupta
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Riley Hospital for Children/Indiana University School of Medicine, and Community Health Network, Indianapolis, IN
| | - Ikuo Hirano
- Division of Gastroenterology and Hepatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Paneez Khoury
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Human Eosinophil Section, NIAID, Bethesda, MD
| | - John Leung
- Divisions of Allergy/Immunology and Gastroenterology, Tuft’s Medical Center, Boston, MA
| | - Lisa J. Martin
- Department of Pediatrics, Cincinnati Children’s Hospital and the University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH
| | | | - Vincent A. Mukkada
- Division of Gastroenterology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH
| | - Kathryn Peterson
- Division of Gastroenterology, University of Utah, Salt Lake City, UT
| | - Jonathan M. Spergel
- Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine of University of Pennsylvania, Philadelphia, PA
| | - Joshua B. Wechsler
- Division of Gastroenterology, Hepatology, and Nutrition, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Guang-Yu Yang
- Division of Gastrointestinal Pathology, Department of Pathology, Fineberg School of Medicine, Northwestern University, Chicago, IL
| | - Marc E. Rothenberg
- Division of Allergy/Immunology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH
| | - J. Kirk Harris
- Breathing Institute, Section of Pediatric Pulmonology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO
| |
Collapse
|
16
|
Tang M, Ma C, Weinheimer-Haus EM, Robertson CE, Kofonow JM, Berman LM, Waljee A, Zhu J, Frank DN, Krebs NF. Different gut microbiota in U.S. formula-fed infants consuming a meat vs. dairy-based complementary foods: A randomized controlled trial. Front Nutr 2023; 9:1063518. [PMID: 36778973 PMCID: PMC9909089 DOI: 10.3389/fnut.2022.1063518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/29/2022] [Indexed: 01/27/2023] Open
Abstract
Objective This project aimed to evaluate the impact of meat- vs. dairy-based complementary foods on gut microbiota and whether it relates to growth. Design Full-term, formula-fed infants were recruited from the metro Denver area (Colorado, US) and randomized to a meat- or dairy-based complementary diet from 5 to 12 months of age. Infant's length and weight were measured, and stool samples were collected at 5, 10, and 12 months for 16S rRNA gene sequencing and short-chain fatty acids (SCFAs) quantification. Results Sixty-four infants completed the dietary intervention (n = 32/group). Weight-for-age Z (WAZ) scores increased in both groups and length-for-age Z scores (LAZ) increased in the meat group only, which led to a significant group-by-time interaction (P = 0.02) of weight-for-length Z (WLZ) score. Microbiota composition (Beta-diversity) differed between groups at 12 months (weighted PERMANOVA P = 0.01) and had a group-by-time interaction of P = 0.09. Microbial community richness (Chao1) increased in the meat group only. Genus Akkermansia had a significant group-by-time interaction and increased in the dairy group and decreased in the meat group. A significant fold change of butyric acid from 5 to 12 months was found in the meat group (+1.75, P = 0.011) but not in the dairy group. Regression analysis showed that Chao1 had a negative association with WLZ and WAZ. Several genera also had significant associations with all growth Z scores. Conclusion Complementary feeding not only impacts infant growth but also affects gut microbiota maturation. Complementary food choices can affect both the gut microbiota diversity and structures and these changes in gut microbiota are associated with infant growth.
Collapse
Affiliation(s)
- Minghua Tang
- Section of Nutrition, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Cheng Ma
- Department of Statistics, University of Michigan, Ann Arbor, MI, United States
| | - Eileen M. Weinheimer-Haus
- Division of Gastroenterology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, United States
| | - Charles E. Robertson
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jennifer M. Kofonow
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lillian M. Berman
- Section of Nutrition, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Akbar Waljee
- Division of Gastroenterology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, United States
- Center for Clinical Management Research, VA Ann Arbor Healthcare System, Ann Arbor, MI, United States
| | - Ji Zhu
- Department of Statistics, University of Michigan, Ann Arbor, MI, United States
| | - Daniel N. Frank
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nancy F. Krebs
- Section of Nutrition, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| |
Collapse
|
17
|
Colbert JF, Kirsch JM, Erzen CL, Langouët-Astrié CJ, Thompson GE, McMurtry SA, Kofonow JM, Robertson CE, Kovacs EJ, Sullivan RC, Hippensteel JA, Sawant NV, De Nisco NJ, McCollister BD, Schwartz RS, Horswill AR, Frank DN, Duerkop BA, Schmidt EP. Aging-associated augmentation of gut microbiome virulence capability drives sepsis severity. bioRxiv 2023:2023.01.10.523523. [PMID: 36711447 PMCID: PMC9882086 DOI: 10.1101/2023.01.10.523523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host, but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition, but an overabundance of genomic virulence factors that have functional consequence on host immune evasion. One Sentence Summary The severity of sepsis in the aged host is in part mediated by longevity-associated increases in gut microbial virulence.
Collapse
|
18
|
Wang XX, Xie C, Libby AE, Ranjit S, Levi J, Myakala K, Bhasin K, Jones BA, Orlicky DJ, Takahashi S, Dvornikov A, Kleiner DE, Hewitt SM, Adorini L, Kopp JB, Krausz KW, Rosenberg A, McManaman JL, Robertson CE, Ir D, Frank DN, Luo Y, Gonzalez FJ, Gratton E, Levi M. The role of FXR and TGR5 in reversing and preventing progression of Western diet-induced hepatic steatosis, inflammation, and fibrosis in mice. J Biol Chem 2022; 298:102530. [PMID: 36209823 PMCID: PMC9638804 DOI: 10.1016/j.jbc.2022.102530] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/06/2022] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is the most common chronic liver disease in the US, partly due to the increasing incidence of metabolic syndrome, obesity, and type 2 diabetes. The roles of bile acids and their receptors, such as the nuclear receptor farnesoid X receptor (FXR) and the G protein-coupled receptor TGR5, on the development of NASH are not fully clear. C57BL/6J male mice fed a Western diet (WD) develop characteristics of NASH, allowing determination of the effects of FXR and TGR5 agonists on this disease. Here we show that the FXR-TGR5 dual agonist INT-767 prevents progression of WD-induced hepatic steatosis, inflammation, and fibrosis, as determined by histological and biochemical assays and novel label-free microscopy imaging techniques, including third harmonic generation, second harmonic generation, and fluorescence lifetime imaging microscopy. Furthermore, we show INT-767 decreases liver fatty acid synthesis and fatty acid and cholesterol uptake, as well as liver inflammation. INT-767 markedly changed bile acid composition in the liver and intestine, leading to notable decreases in the hydrophobicity index of bile acids, known to limit cholesterol and lipid absorption. In addition, INT-767 upregulated expression of liver p-AMPK, SIRT1, PGC-1α, and SIRT3, which are master regulators of mitochondrial function. Finally, we found INT-767 treatment reduced WD-induced dysbiosis of gut microbiota. Interestingly, the effects of INT-767 in attenuating NASH were absent in FXR-null mice, but still present in TGR5-null mice. Our findings support treatment and prevention protocols with the dual FXR-TGR5 agonist INT-767 arrest progression of WD-induced NASH in mice mediated by FXR-dependent, TGR5-independent mechanisms.
Collapse
Affiliation(s)
- Xiaoxin X Wang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA.
| | - Cen Xie
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Jonathan Levi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Komuraiah Myakala
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Kanchan Bhasin
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Bryce A Jones
- Department of Pharmacology and Physiology, Georgetown University, Washington, District of Columbia, USA
| | - David J Orlicky
- Department of Pathology, University of Colorado AMC, Aurora, Colorado, USA
| | - Shogo Takahashi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Alexander Dvornikov
- Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California, USA
| | - David E Kleiner
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen M Hewitt
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Jeffrey B Kopp
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristopher W Krausz
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Avi Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - James L McManaman
- The Integrated Physiology Program, University of Colorado AMC, Aurora, Colorado, USA
| | | | - Diana Ir
- Department of Medicine, University of Colorado AMC, Aurora, Colorado, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado AMC, Aurora, Colorado, USA
| | - Yuhuan Luo
- Department of Medicine, University of Colorado AMC, Aurora, Colorado, USA
| | - Frank J Gonzalez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California, USA
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA.
| |
Collapse
|
19
|
Ramos RJ, Zhu C, Joseph DF, Thaker S, Lacomb JF, Markarian K, Lee HJ, Petrov JC, Monzur F, Buscaglia JM, Chawla A, Small-Harary L, Gathungu G, Morganstern JA, Yang J, Li J, Pamer EG, Robertson CE, Frank DN, Cross JR, Li E. Metagenomic and bile acid metabolomic analysis of fecal microbiota transplantation for recurrent Clostridiodes difficile and/or inflammatory bowel diseases. Med Res Arch 2022; 10:10.18103/mra.v10i10.3318. [PMID: 36618438 PMCID: PMC9817289 DOI: 10.18103/mra.v10i10.3318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI), but has more limited efficacy in treating either ulcerative colitis (UC) or Crohn's disease (CD), two major forms of inflammatory bowel diseases (IBD). We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that differ significantly from that of their healthy donors and that FMT will normalize the BA compositions. AIM To study the effect of single colonoscopic FMT on microbial composition and function in four recipient groups: 1.) rCDI patients without IBD (rCDI-IBD); 2.) rCDI with IBD (rCDI+IBD); 3.) UC patients without rCDI (UC-rCDI); 4.) CD patients without rCDI (CD-rCDI). METHODS We performed 16S rRNA gene sequence, shotgun DNA sequence and quantitative bile acid metabolomic analyses on stools collected from 55 pairs of subjects and donors enrolled in two prospective single arm FMT clinical trials (Clinical Trials.gov ID NCT03268213, 479696, UC no rCDI ≥ 2x IND 1564 and NCT03267238, IND 16795). Fitted linear mixed models were used to examine the effects of four recipient groups, FMT status (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on microbial diversity and composition, bile acid metabolites and bile acid metabolizing enzyme gene abundance. RESULTS The pre-FMT stools collected from rCDI ± IBD recipients had reduced α-diversity compared to the healthy donor stools and was restored post-FMT. The α-diversity in the pre-FMT stools collected from UC-rCDI or CD-rCDI recipients did not differ significantly from donor stools. FMT normalized some recipient/donor ratios of genus level taxa abundance in the four groups. Fecal secondary BA levels, including some of the secondary BA epimers that exhibit in vitro immunomodulatory activities, were lower in rCDI±IBD and CD-rCDI but not UC-rCDI recipients compared to donors. FMT restored secondary BA levels. Metagenomic baiE gene and some of the eight bile salt hydrolase (BSH) phylotype abundances were significantly correlated with fecal BA levels. CONCLUSION Restoration of multiple secondary BA levels, including BA epimers implicated in immunoregulation, are associated with restoration of fecal baiE gene counts, suggesting that the 7-α-dehydroxylation step is rate-limiting.
Collapse
|
20
|
Tang M, Weaver NE, Frank DN, Ir D, Robertson CE, Kemp JF, Westcott J, Shankar K, Garces AL, Figueroa L, Tshefu AK, Lokangaka AL, Goudar SS, Somannavar M, Aziz S, Saleem S, McClure EM, Hambidge KM, Hendricks AE, Krebs NF. Longitudinal Reduction in Diversity of Maternal Gut Microbiota During Pregnancy Is Observed in Multiple Low-Resource Settings: Results From the Women First Trial. Front Microbiol 2022; 13:823757. [PMID: 35979501 PMCID: PMC9376441 DOI: 10.3389/fmicb.2022.823757] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Objective To characterize the changes in gut microbiota during pregnancy and determine the effects of nutritional intervention on gut microbiota in women from sub-Saharan Africa (the Democratic Republic of the Congo, DRC), South Asia (India and Pakistan), and Central America (Guatemala). Methods Pregnant women in the Women First (WF) Preconception Maternal Nutrition Trial were included in this analysis. Participants were randomized to receive a lipid-based micronutrient supplement either ≥3 months before pregnancy (Arm 1); started the same intervention late in the first trimester (Arm 2); or received no nutrition supplements besides those self-administered or prescribed through local health services (Arm 3). Stool and blood samples were collected during the first and third trimesters. Findings presented here include fecal 16S rRNA gene-based profiling and systemic and intestinal inflammatory biomarkers, including alpha (1)-acid glycoprotein (AGP), C-reactive protein (CRP), fecal myeloperoxidase (MPO), and calprotectin. Results Stool samples were collected from 640 women (DRC, n = 157; India, n = 102; Guatemala, n = 276; and Pakistan, n = 105). Gut microbial community structure did not differ by intervention arm but changed significantly during pregnancy. Richness, a measure of alpha-diversity, decreased over pregnancy. Community composition (beta-diversity) also showed a significant change from first to third trimester in all four sites. Of the top 10 most abundant genera, unclassified Lachnospiraceae significantly decreased in Guatemala and unclassified Ruminococcaceae significantly decreased in Guatemala and DRC. The change in the overall community structure at the genus level was associated with a decrease in the abundances of certain genera with low heterogeneity among the four sites. Intervention arms were not significantly associated with inflammatory biomarkers at 12 or 34 weeks. AGP significantly decreased from 12 to 34 weeks of pregnancy, whereas CRP, MPO, and calprotectin did not significantly change over time. None of these biomarkers were significantly associated with the gut microbiota diversity. Conclusion The longitudinal reduction of individual genera (both commensals and potential pathogens) and alpha-diversity among all sites were consistent and suggested that the effect of pregnancy on the maternal microbiota overrides other influencing factors, such as nutrition intervention, geographical location, diet, race, and other demographical variables.
Collapse
Affiliation(s)
- Minghua Tang
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nicholas E. Weaver
- Department of Mathematical and Statistical Sciences, University of Colorado, Denver, Denver, CO, United States
| | - Daniel N. Frank
- Department of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Diana Ir
- Department of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles E. Robertson
- Department of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jennifer F. Kemp
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jamie Westcott
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kartik Shankar
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ana L. Garces
- Institute of Nutrition in Central America and Panama (INCAP), Guatemala City, Guatemala
| | - Lester Figueroa
- Institute of Nutrition in Central America and Panama (INCAP), Guatemala City, Guatemala
| | - Antoinette K. Tshefu
- Institute of Nutrition in Central America and Panama (INCAP), Guatemala City, Guatemala
| | - Adrien L. Lokangaka
- Institute of Nutrition in Central America and Panama (INCAP), Guatemala City, Guatemala
| | - Shivaprasad S. Goudar
- KLE Academy of Higher Education and Research (Deemed-to-be-University), Jawaharlal Nehru Medical College, Belagavi, India
| | - Manjunath Somannavar
- KLE Academy of Higher Education and Research (Deemed-to-be-University), Jawaharlal Nehru Medical College, Belagavi, India
| | - Sumera Aziz
- Department of Community Health Sciences, Aga Khan University, Karachi, Pakistan
| | - Sarah Saleem
- Department of Community Health Sciences, Aga Khan University, Karachi, Pakistan
| | | | - K. Michael Hambidge
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Audrey E. Hendricks
- Department of Mathematical and Statistical Sciences, University of Colorado, Denver, Denver, CO, United States
| | - Nancy F. Krebs
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| |
Collapse
|
21
|
Tayachew B, Vanden Brink H, Garcia-Reyes Y, Rahat H, D'Alessandro A, Frank DN, Robertson CE, Silveira L, Kelsey M, Pyle L, Cree-Green M. Combined Oral Contraceptive Treatment Does Not Alter the Gut Microbiome but Affects Amino Acid Metabolism in Sera of Obese Girls With Polycystic Ovary Syndrome. Front Physiol 2022; 13:887077. [PMID: 35800349 PMCID: PMC9255376 DOI: 10.3389/fphys.2022.887077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/16/2022] [Indexed: 12/30/2022] Open
Abstract
Background: The gut microbiome is altered in obese adolescents with polycystic ovary syndrome (PCOS), and is associated with free testosterone, metabolic markers, and insulin resistance. Combined oral contraceptives (OCP) are a primary treatment for PCOS and decrease testosterone, but the effect on the serum metabolome or gut microbiome in obese adolescents with PCOS is unknown. Objective: Contrast gut microbiome profiles, targeted serum metabolomics, hormone levels, and metabolic measures in adolescents with PCOS and obesity with and without OCP treatment. Methods: Adolescent girls with obesity and PCOS underwent stool and fasting blood collection and MRI for hepatic fat fraction. Fecal bacteria were profiled by high-throughput 16S rRNA gene sequencing and fasting serum metabolomics performed with high resolution mass spectrometry. Groups were contrasted using t-tests and principle least squares discrimination analysis (PLS-DA). Associations between bacterial taxa, baseline metabolic measures, hormone levels and the metabolome were conducted using Spearman analysis. Analyses were adjusted for false discovery rate. Results: 29 adolescents with obesity [Untreated N = 21, 16 ± 1.2 years, BMI%ile 36.5 ± 3.0; OCP N = 8, 15.5 ± 0.9 years, BMI%ile 32.5 ± 3.9] participated. Of the untreated adolescents, N = 14 contributed serum for metabolomic analysis. Participants on OCP therapy had lower free testosterone and free androgen index (p < 0.001) and higher sex hormone binding globulin. There was no difference in measures of fasting glucose, insulin, lipids or HOMA-IR between groups. PLS-DA of serum metabolomics showed discrimination between the groups, secondary amino acid changes. Untreated and OCP had similar stool microbiome α-diversity based on evenness (p = 0.28), richness (p = 0.39), and Shannon diversity (p = 0.24) and global microbial composition (β-diversity, p = 0.56). There were no differences in % relative abundance at any level. Bacterial α-diversity was negatively associated with serum long chain fatty acids and branched chain amino acids. A higher %relative abundance of family Ruminococcaceae was significantly associated with serum bile acids and HOMA-IR. Conclusion: Despite hormone and serum amino acid differences, girls treated with OCP had similar metabolic and gut microbiome profiles compared to the untreated PCOS group. The association between bacterial α-diversity, Ruminococcaceae, clinical markers and long chain fatty acids suggests a potential role of the gut microbiome in the pathogenesis of the metabolic comorbidities in PCOS.
Collapse
Affiliation(s)
- Beza Tayachew
- Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Heidi Vanden Brink
- Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Yesenia Garcia-Reyes
- Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Haseeb Rahat
- Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Angelo D'Alessandro
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N. Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles E. Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lori Silveira
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, United States
| | - Megan Kelsey
- Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Laura Pyle
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, United States
| | - Melanie Cree-Green
- Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,*Correspondence: Melanie Cree-Green,
| |
Collapse
|
22
|
Frank DN, Magno JPM, Velasco KJS, Bootpetch TC, Salud JED, David KJV, Miller AL, Yee EC, Dulnuan HP, Pyles RB, Lacuata JAC, Arbizo JL, Kofonow JM, Guce B, Mendoza KMD, Robertson CE, Ilustre GMS, Chiong ANE, Lu SL, Tongol EA, Sacayan ND, Yarza TKL, Chiong CM, Santos-Cortez RLP. Microbiota Associated With Cholesteatoma Tissue in Chronic Suppurative Otitis Media. Front Cell Infect Microbiol 2022; 12:746428. [PMID: 35521215 PMCID: PMC9063009 DOI: 10.3389/fcimb.2022.746428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Otitis media (OM), defined as infection or inflammation of the middle ear (ME), remains a major public health problem worldwide. Cholesteatoma is a non-cancerous, cyst-like lesion in the ME that may be acquired due to chronic OM and cause disabling complications. Surgery is required for treatment, with high rates of recurrence. Current antibiotic treatments have been largely targeted to previous culturable bacteria, which may lead to antibiotic resistance or treatment failures. For this study, our goal was to determine the microbiota of cholesteatoma tissue in comparison with other ME tissues in patients with long-standing chronic OM. ME samples including cholesteatoma, granulation tissue, ME mucosa and discharge were collected from patients undergoing tympanomastoidectomy surgery for chronic OM. Bacteria were profiled by 16S rRNA gene sequencing in 103 ME samples from 53 patients. Respiratory viruses were also screened in 115 specimens from 45 patients. Differences in bacterial profiles (beta-diversity) and the relative abundances of individual taxa were observed between cholesteatoma and ME sample-types. Additionally, patient age was associated with differences in overall microbiota composition while numerous individual taxa were differentially abundant across age quartiles. No viruses were identified in screened ME samples. Biodiversity was moderately lower in cholesteatoma and ME discharge compared to ME mucosal tissues. We also present overall bacterial profiles of ME tissues by sample-type, age, cholesteatoma diagnosis and quinolone use, including prevalent bacterial taxa. Our findings will be useful for fine-tuning treatment protocols for cholesteatoma and chronic OM in settings with limited health care resources.
Collapse
Affiliation(s)
- Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jose Pedrito M. Magno
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Karen Joyce S. Velasco
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Tori C. Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jacob Ephraim D. Salud
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Kevin Jer V. David
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Aaron L. Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States
| | - Eljohn C. Yee
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Heather P. Dulnuan
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Richard B. Pyles
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States
| | - Jan Alexeis C. Lacuata
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Jeric L. Arbizo
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Beatrice Guce
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Kevin Michael D. Mendoza
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Gabriel Martin S. Ilustre
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Alessandra Nadine E. Chiong
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Shi-Long Lu
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Erik A. Tongol
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Nicole D. Sacayan
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Talitha Karisse L. Yarza
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Newborn Hearing Screening Reference Center, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
| | - Charlotte M. Chiong
- Department of Otolaryngology - Head and Neck Surgery, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Newborn Hearing Screening Reference Center, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Center for Children’s Surgery, Children’s Hospital Colorado, Aurora, CO, United States
- *Correspondence: Regie Lyn P. Santos-Cortez,
| |
Collapse
|
23
|
Frank DN, Qiu Y, Cao Y, Zhang S, Lu L, Kofonow JM, Robertson CE, Liu Y, Wang H, Levens CL, Kuhn KA, Song J, Ramakrishnan VR, Lu SL. A dysbiotic microbiome promotes head and neck squamous cell carcinoma. Oncogene 2022; 41:1269-1280. [PMID: 35087236 PMCID: PMC8882136 DOI: 10.1038/s41388-021-02137-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/10/2021] [Accepted: 11/24/2021] [Indexed: 12/14/2022]
Abstract
Recent studies have reported dysbiotic oral microbiota and tumor-resident bacteria in human head and neck squamous cell carcinoma (HNSCC). We aimed to identify and validate oral microbial signatures in treatment-naïve HNSCC patients compared with healthy control subjects. We confirm earlier reports that the relative abundances of Lactobacillus spp. and Neisseria spp. are elevated and diminished, respectively, in human HNSCC. In parallel, we examined the disease-modifying effects of microbiota in HNSCC, through both antibiotic depletion of microbiota in an induced HNSCC mouse model (4-Nitroquinoline 1-oxide, 4NQO) and reconstitution of tumor-associated microbiota in a germ-free orthotopic mouse model. We demonstrate that depletion of microbiota delays oral tumorigenesis, while microbiota transfer from mice with oral cancer accelerates tumorigenesis. Enrichment of Lactobacillus spp. was also observed in murine HNSCC, and activation of the aryl-hydrocarbon receptor was documented in both murine and human tumors. Together, our findings support the hypothesis that dysbiosis promotes HNSCC development.
Collapse
Affiliation(s)
- Daniel N Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA.
| | - Yue Qiu
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA.,Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, China
| | - Yu Cao
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA.,Department of Surgical Oncology, The First University Hospital, China Medical University, Shenyang, 110122, China
| | - Shuguang Zhang
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Ling Lu
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Jennifer M Kofonow
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Charles E Robertson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Yanqiu Liu
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Haibo Wang
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Cassandra L Levens
- Division of Rheumatology and the Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Kristine A Kuhn
- Division of Rheumatology and the Mucosal Inflammation Program, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - John Song
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Vijay R Ramakrishnan
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Shi-Long Lu
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Center, Aurora, CO, USA.
| |
Collapse
|
24
|
Elling CL, Scholes MA, Streubel SO, Larson ED, Wine TM, Bootpetch TC, Yoon PJ, Kofonow JM, Gubbels SP, Cass SP, Robertson CE, Jenkins HA, Prager JD, Frank DN, Chan KH, Friedman NR, Ryan AF, Santos-Cortez RLP. The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media. Front Cell Infect Microbiol 2022; 11:798246. [PMID: 35096646 PMCID: PMC8798324 DOI: 10.3389/fcimb.2021.798246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/20/2021] [Indexed: 12/30/2022] Open
Abstract
Otitis media (OM) is a leading cause of childhood hearing loss. Variants in FUT2, which encodes alpha-(1,2)-fucosyltransferase, were identified to increase susceptibility to OM, potentially through shifts in the middle ear (ME) or nasopharyngeal (NP) microbiotas as mediated by transcriptional changes. Greater knowledge of differences in relative abundance of otopathogens in carriers of pathogenic variants can help determine risk for OM in patients. In order to determine the downstream effects of FUT2 variation, we examined gene expression in relation to carriage of a common pathogenic FUT2 c.461G>A (p.Trp154*) variant using RNA-sequence data from saliva samples from 28 patients with OM. Differential gene expression was also examined in bulk mRNA and single-cell RNA-sequence data from wildtype mouse ME mucosa after inoculation with non-typeable Haemophilus influenzae (NTHi). In addition, microbiotas were profiled from ME and NP samples of 65 OM patients using 16S rRNA gene sequencing. In human carriers of the FUT2 variant, FN1, KMT2D, MUC16 and NBPF20 were downregulated while MTAP was upregulated. Post-infectious expression in the mouse ME recapitulated these transcriptional differences, with the exception of Fn1 upregulation after NTHi-inoculation. In the NP, Candidate Division TM7 was associated with wildtype genotype (FDR-adj-p=0.009). Overall, the FUT2 c.461G>A variant was associated with transcriptional changes in processes related to response to infection and with increased load of potential otopathogens in the ME and decreased commensals in the NP. These findings provide increased understanding of how FUT2 variants influence gene transcription and the mucosal microbiota, and thus contribute to the pathology of OM.
Collapse
Affiliation(s)
- Christina L. Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A. Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Sven-Olrik Streubel
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Eric D. Larson
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Todd M. Wine
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Tori C. Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J. Yoon
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Samuel P. Gubbels
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Stephen P. Cass
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A. Jenkins
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jeremy D. Prager
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kenny H. Chan
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Norman R. Friedman
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Allen F. Ryan
- Division of Otolaryngology, Department of Surgery, San Diego School of Medicine and Veterans Affairs Medical Center, University of California, La Jolla, CA, United States
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Center for Children’s Surgery, Children’s Hospital Colorado, Aurora, CO, United States
| |
Collapse
|
25
|
O’Connor JB, Mottlowitz MM, Wagner BD, Boyne KL, Stevens MJ, Robertson CE, Harris JK, Laguna TA. Divergence of bacterial communities in the lower airways of CF patients in early childhood. PLoS One 2021; 16:e0257838. [PMID: 34613995 PMCID: PMC8494354 DOI: 10.1371/journal.pone.0257838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
Rationale Chronic airway infection and inflammation resulting in progressive, obstructive lung disease is the leading cause of morbidity and mortality in cystic fibrosis. Understanding the lower airway microbiota across the ages can provide valuable insight and potential therapeutic targets. Objectives To characterize and compare the lower airway microbiota in cystic fibrosis and disease control subjects across the pediatric age spectrum. Methods Bronchoalveolar lavage fluid samples from 191 subjects (63 with cystic fibrosis) aged 0 to 21 years were collected along with relevant clinical data. We measured total bacterial load using quantitative polymerase chain reaction and performed 16S rRNA gene sequencing to characterize bacterial communities with species-level sensitivity for select genera. Clinical comparisons were investigated. Measurements and main results Cystic fibrosis samples had higher total bacterial load and lower microbial diversity, with a divergence from disease controls around 2–5 years of age, as well as higher neutrophilic inflammation relative to bacterial burden. Cystic fibrosis samples had increased abundance of traditional cystic fibrosis pathogens and decreased abundance of the Streptococcus mitis species group in older subjects. Interestingly, increased diversity in the heterogeneous disease controls was independent of diagnosis and indication. Sequencing was more sensitive than culture, and antibiotic exposure was more common in disease controls, which showed a negative relationship with load and neutrophilic inflammation. Conclusions Analysis of lower airway samples from people with cystic fibrosis and disease controls across the ages revealed key differences in airway microbiota and inflammation. The divergence in subjects during early childhood may represent a window of opportunity for intervention and additional study.
Collapse
Affiliation(s)
- John B. O’Connor
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Madison M. Mottlowitz
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
| | - Brandie D. Wagner
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kathleen L. Boyne
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Mark J. Stevens
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jonathan K. Harris
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Theresa A. Laguna
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| |
Collapse
|
26
|
Dillon SM, Abdo MH, Wilson MP, Liu J, Jankowski CM, Robertson CE, Tuncil Y, Hamaker B, Frank DN, MaWhinney S, Wilson CC, Erlandson KM. A Unique Gut Microbiome-Physical Function Axis Exists in Older People with HIV: An Exploratory Study. AIDS Res Hum Retroviruses 2021; 37:542-550. [PMID: 33787299 PMCID: PMC8260890 DOI: 10.1089/aid.2020.0283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Impairments in physical function and increased systemic levels of inflammation have been observed in middle-aged and older persons with HIV (PWH). We previously demonstrated that in older persons, associations between gut microbiota and inflammation differed by HIV serostatus. To determine whether relationships between the gut microbiome and physical function measurements would also be distinct between older persons with and without HIV, we reanalyzed existing gut microbiome and short chain fatty acid (SCFA) data in conjunction with previously collected measurements of physical function and body composition from the same cohorts of older (51-74 years), nonfrail PWH receiving effective antiretroviral therapy (N = 14) and age-balanced uninfected controls (N = 22). Associations between relative abundance (RA) of the most abundant bacterial taxa or stool SCFA levels with physical function and body composition were tested using HIV-adjusted linear regression models. In older PWH, but not in controls, greater RA of Alistipes, Escherichia, Prevotella, Megasphaera, and Subdoligranulum were associated with reduced lower extremity muscle function, decreased lean mass, or lower Short Physical Performance Battery (SPPB) scores. Conversely, greater RA of Dorea, Coprococcus, and Phascolarctobacterium in older PWH were associated with better muscle function, lean mass, and SPPB scores. Higher levels of the SCFA butyrate associated with increased grip strength in both PWH and controls. Our findings indicate that in older PWH, both negative and positive associations exist between stool microbiota abundance and physical function. Different relationships were observed in older uninfected persons, suggesting features of a unique gut-physical function axis in PWH.
Collapse
Affiliation(s)
- Stephanie M. Dillon
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mona H. Abdo
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Melissa P. Wilson
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Jay Liu
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Catherine M. Jankowski
- College of Nursing, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yunus Tuncil
- Department of Food Science, Purdue University, West Lafayette, Indiana, USA
| | - Bruce Hamaker
- Department of Food Science, Purdue University, West Lafayette, Indiana, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Samantha MaWhinney
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Cara C. Wilson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kristine M. Erlandson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| |
Collapse
|
27
|
Jobira B, Frank DN, Silveira LJ, Garcia-Reyes Y, Robertson CE, Ir D, Alexander KL, D’Alessandro A, Nadeau K, Cree-Green M. Combined Oral Contraceptive Treatment Does Not Alter the Gut Microbiome or Serum Metabolomic Profile in Obese Girls with Polycystic Ovary Syndrome. J Endocr Soc 2021. [DOI: 10.1210/jendso/bvab048.1448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Abstract
Title: Combined Oral Contraceptive Treatment Does Not Alter the Gut Microbiome or Serum Metabolomic Profile in Obese Girls with Polycystic Ovary Syndrome
Background: The gut microbiome is altered in obese adolescents with polycystic ovary syndrome (PCOS), and is associated with free testosterone, metabolic markers and insulin resistance. Combined oral contraceptives (OCP) are a primary treatment for PCOS and lower testosterone, but it was unknown if they changed the gut microbiome in obese adolescents with PCOS.
Objective: Assess the gut microbiome profile, targeted serum metabolomics, hormonal and metabolic measures in adolescents with PCOS and obesity with and without OCP treatment.
Methods: Adolescent girls with PCOS and obesity with and without PCOS were recruited from a tertiary referral hospital and underwent stool and fasting blood collection, an oral glucose tolerance test and MRI for hepatic fat fraction. Fecal bacterial were profiled by high throughput 16S rRNA gene sequencing and fasting serum metabolomics performed with mass spectroscopy. Groups were compared with t-tests and correlations performed. Results: Twenty-nine obese adolescents with PCOS [Untreated N=21, 16±1.2 years, BMI%ile 36.5± 3.0; OCP N=8, 15.5±0.9, BMI%ile 32.5±3.9] participated. OCP therapy had lower free testosterone and higher SHBG (p<0.001). Platelets were significantly higher (p=0.01), along with a trend in elevated CRP (p=0.09) in the OCP group. There was no difference in measures of fasting glucose, insulin or lipids. Measures of insulin resistance including HOMA-IR and Matsuda were also similar. Principle components analysis of the serum metabolome was not different between the groups. Girls treated with OCP had similar stool microbiome α-diversity measures of bacterial evenness (p=0.28), bacterial diversity (p=0.15), and global microbial composition (β-diversity, p=0.56). Further, the percent relative abundance (%RA) of the Firmicutes: Bacteroidetes ratio was similar, as well as the %RA at the phyla, family and genus level. Bacterial α-diversity was negatively associated with serum bile acids and branched chain amino acids. A higher %RA of family Ruminococcaceae was significantly associated with serum conjugated bile acids and HOMA-IR.
Conclusion: Despite changes in free testosterone and SHBG, adolescent girls with PCOS treated with OCP had similar clinical and gut microbiome profile compared to the untreated PCOS group. The significant association between bacterial α-diversity, Ruminococcaceae, clinical markers and bile acids suggests a potential role of the gut microbiome in the pathogenesis of metabolic syndrome and PCOS.
Collapse
Affiliation(s)
- Beza Jobira
- University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, USA
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, Aurora, CO, USA
| | - Lori J Silveira
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, Aurora, CO, USA
| | - Yesenia Garcia-Reyes
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, Aurora, CO, USA
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, Aurora, CO, USA
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, Aurora, CO, USA
| | - Keisha L Alexander
- University of Colorado Anschutz Medical Campus Pharmaceutical Science, Aurora, CO, USA
| | - Angelo D’Alessandro
- University of Colorado Anschutz Medical Campus School of Medicine, Biochemistry and Molecular Genetics, Aurora, CO, USA
| | - Kristen Nadeau
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, Aurora, CO, USA
| | - Melanie Cree-Green
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, Aurora, CO, USA
| |
Collapse
|
28
|
Malik SA, Zhu C, Li J, LaComb JF, Denoya PI, Kravets I, Miller JD, Yang J, Kramer M, McCombie WR, Robertson CE, Frank DN, Li E. Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections. World J Gastroenterol 2021; 27:1465-1482. [PMID: 33911468 PMCID: PMC8047535 DOI: 10.3748/wjg.v27.i14.1465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/03/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases. Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer (CRC) resections. We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors. AIM To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection samples. METHODS Genomic DNA (gDNA) and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from 2010-2020. The 16S rRNA gene sequencing (V3V4 region, paired end, 300 bp) and confirmatory quantitative polymerase chain reaction (qPCR) assays were conducted on gDNA. RNA sequencing (IPE, 125 bp) was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores ≥ 6. RESULTS PERMANOVA detected significant effects of tumor vs nontumor histology (P = 0.002) and antibiotics (P = 0.001) on microbial β-diversity, but CRC tumor location (left vs right), diabetes mellitus vs not diabetic and Black/African Ancestry (AA) vs not Black/AA, did not reach significance. Linear mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level taxa. QPCR confirmed increased Fusobacterium abundance in tumor vs nontumor groups, and detected significantly reduced bacterial load in the (+)antibiotics group. Principal coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor samples. Differentially expressed genes obtained from separate analyses of tumor and nontumor samples, are presented for the antibiotics, CRC location, diabetes and Black/AA race groups. CONCLUSION Recent adoption of additional preoperative antibiotics as standard of care, has a measurable impact on -omics analysis of resected specimens. This study still confirmed increased Fusobacterium nucleatum in tumor.
Collapse
Affiliation(s)
- Sarah A Malik
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Chencan Zhu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, United States
| | - Jinyu Li
- Stony Brook Cancer Center Biostatistics and Bioinformatics Shared Resource, Stony Brook University, Stony Brook, NY 11794, United States
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Joseph F LaComb
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Paula I Denoya
- Department of Surgery, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Igor Kravets
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Joshua D Miller
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Jie Yang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, United States
- Stony Brook Cancer Center Biostatistics and Bioinformatics Shared Resource, Stony Brook University, Stony Brook, NY 11794, United States
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Melissa Kramer
- Cold Spring Harbor Laboratory Cancer Center Sequencing Technologies and Analysis Shared Resource, Cold Spring Harbor, NY 11724, United States
| | - W Richard McCombie
- Cold Spring Harbor Laboratory Cancer Center Sequencing Technologies and Analysis Shared Resource, Cold Spring Harbor, NY 11724, United States
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Ellen Li
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| |
Collapse
|
29
|
Williamson KM, Wagner BD, Robertson CE, Stevens MJ, Sontag MK, Mourani PM, Harris JK. Modified PCR protocol to increase sensitivity for determination of bacterial community composition. Microbiome 2021; 9:90. [PMID: 33849648 PMCID: PMC8045227 DOI: 10.1186/s40168-020-00958-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing. Two PCR protocols (standard and modified) were examined in airway samples where we observed a large range in bacterial load (3.1-6.2 log10 16S rRNA gene copies/reaction). Tracheal aspirate (TA) samples (n = 99) were collected from sixteen children requiring mechanical ventilation at a single center. DNA was extracted, and total bacterial load (TBL) was assessed using qPCR. Amplification of 16S rRNA was attempted with both protocols in all samples. RESULTS PCR product was observed using both protocols in 52 samples and in 24 additional samples only with the modified protocol. TBL, diversity metrics, and prominent taxa were compared for samples in three groups based on success of the two protocols (successful with both, success with modified only, unsuccessful for both). TBL differed significantly across the three groups (p<0.001). Specifically, the modified protocol allowed amplification from samples with intermediate TBL. Shannon diversity was similar between the two protocols, and Morisita-Horn beta diversity index showed high agreement between the two protocols within samples (median value 0.9997, range 0.9947 to 1). We show that both protocols identify similar communities, and the technical variability of both protocols was very low. The use of limited PCR cycles was a key feature to limit impact of background by exclusion of 24% of samples with no evidence of bacterial DNA present in the sample. CONCLUSION The modified amplification protocol represents a viable approach that increased sensitivity of bacterial community analysis, which is important for study of the human airway microbiome where bacterial load is highly variable. Video abstract.
Collapse
Affiliation(s)
- Kayla M. Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - Charles E. Robertson
- Division of Infectious Diseases, School of Medicine, University of Colorado, 12700 East 19th Avenue, Mail Stop B168, Aurora, CO 80045 USA
| | - Mark J. Stevens
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - Marci K. Sontag
- Department of Epidemiology, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
| | - Peter M. Mourani
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - J. Kirk Harris
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| |
Collapse
|
30
|
Khalaf RT, Furuta GT, Wagner BD, Robertson CE, Andrews R, Stevens MJ, Fillon SA, Zemanick ET, Harris JK. Influence of Acid Blockade on the Aerodigestive Tract Microbiome in Children With Cystic Fibrosis. J Pediatr Gastroenterol Nutr 2021; 72:520-527. [PMID: 33394582 PMCID: PMC8315410 DOI: 10.1097/mpg.0000000000003010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Acid blockade is commonly prescribed in patients with cystic fibrosis (CF). Growing concerns, however, exist about its possible role in the pathophysiology of pulmonary infections. We aimed to investigate if acid blockade alters esophageal and respiratory microbiota leading to dysbiosis and inflammation. METHODS We performed a cross sectional study of children with CF who were either prescribed acid blockade or not. Samples from the gastrointestinal and respiratory tracts were obtained and microbiome analyzed. Mixed effect models were used to compare outcomes between cohorts and across sampling sites. A random subject intercept was included to account for the multiple sampling sites per individual. RESULTS A cohort of 25 individuals, 44% girls with median age of 13.8 years [IQR 11.2--14.8] were enrolled. Alpha diversity, total bacterial load, and beta diversity were similar across anatomic compartments, across the upper gastrointestinal tract, and in respiratory samples. Similar alpha diversity, total bacterial load, and beta diversity results were also observed when comparing individuals on versus those off acid blockade. IL-8 was elevated in the distal versus proximal esophagus in the whole cohort (P < 0.01). IL-8 concentrations were similar in the distal esophagus in patients on and off acid blockade, but significantly greater in the proximal esophagus of subjects on treatment (P < 0.01). CONCLUSIONS On the basis of these data, acid blockade use does not appear to influence the microbiome of the aerodigestive tract in children with cystic fibrosis suggesting a complex interplay between these medications and the bacterial composition of the esophagus and lung.
Collapse
Affiliation(s)
- Racha T. Khalaf
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Glenn T. Furuta
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora
| | - Charles E. Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rachel Andrews
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
| | - Mark J. Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Sophie A. Fillon
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Mucosal Inflammation Program, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
31
|
Vickery TW, Armstrong M, Kofonow JM, Robertson CE, Kroehl ME, Reisdorph NA, Ramakrishnan VR, Frank DN. Specialized pro-resolving mediator lipidome and 16S rRNA bacterial microbiome data associated with human chronic rhinosinusitis. Data Brief 2021; 36:107023. [PMID: 33937456 PMCID: PMC8076692 DOI: 10.1016/j.dib.2021.107023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 03/29/2021] [Indexed: 02/03/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a clinical syndrome defined by symptoms including nasal congestion, facial pain and pressure, anosmia, and rhinorrhea lasting more than 12 weeks. Several mechanistically distinct processes lead to the development of clinical symptoms in CRS including innate immune dysfunction, dysregulated eicosanoid metabolism and perturbations in host-microbiome interactions [1]. We developed a database comprised of patient demographic information, lipid mediator metabolomic profiles, and 16S bacterial rRNA gene sequence data from 66 patients undergoing endoscopic sinus surgery. Briefly, ethmoid sinus tissue and middle meatal swabs were collected from patients, including non-CRS controls, CRS with polyps (CRSwNP), and CRS without polyps (CRSsNP). Lipid mediator pathways from arachidonic acid (AA) and docosahexanoic acid (DHA) were analyzed by liquid chromatography/tandem mass spectrometry. Bacterial taxa were profiled in parallel by 16S rRNA gene sequencing. This database provides a useful compendium of AA/DHA metabolomic profiles and associated bacterial microbiota in patients with varying disease subtypes, demographics, and risk factors/comorbidities.
Collapse
Affiliation(s)
- Thad W Vickery
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Head and Neck Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Michael Armstrong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jennifer M Kofonow
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Miranda E Kroehl
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, United States
| | - Nichole A Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vijay R Ramakrishnan
- Department of Otolaryngology-Head & Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| |
Collapse
|
32
|
Mourani PM, Sontag MK, Williamson KM, Harris JK, Reeder R, Locandro C, Carpenter TC, Maddux AB, Ziegler K, Simões EAF, Osborne CM, Ambroggio L, Leroue MK, Robertson CE, Langelier C, DeRisi JL, Kamm J, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Dean JM, Wagner BD. Temporal airway microbiome changes related to ventilator-associated pneumonia in children. Eur Respir J 2021; 57:13993003.01829-2020. [PMID: 33008935 DOI: 10.1183/13993003.01829-2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/02/2020] [Indexed: 12/27/2022]
Abstract
We sought to determine whether temporal changes in the lower airway microbiome are associated with ventilator-associated pneumonia (VAP) in children.Using a multicentre prospective study of children aged 31 days to 18 years requiring mechanical ventilation support for >72 h, daily tracheal aspirates were collected and analysed by sequencing of the 16S rRNA gene. VAP was assessed using 2008 Centers for Disease Control and Prevention paediatric criteria. The association between microbial factors and VAP was evaluated using joint longitudinal time-to-event modelling, matched case-control comparisons and unsupervised clustering.Out of 366 eligible subjects, 66 (15%) developed VAP at a median of 5 (interquartile range 3-5) days post intubation. At intubation, there was no difference in total bacterial load (TBL), but Shannon diversity and the relative abundance of Streptococcus, Lactobacillales and Prevotella were lower for VAP subjects versus non-VAP subjects. However, higher TBL on each sequential day was associated with a lower hazard (hazard ratio 0.39, 95% CI 0.23-0.64) for developing VAP, but sequential values of diversity were not associated with VAP. Similar findings were observed from the matched analysis and unsupervised clustering. The most common dominant VAP pathogens included Prevotella species (19%), Pseudomonas aeruginosa (14%) and Streptococcus mitis/pneumoniae (10%). Mycoplasma and Ureaplasma were also identified as dominant organisms in several subjects.In mechanically ventilated children, changes over time in microbial factors were marginally associated with VAP risk, although these changes were not suitable for predicting VAP in individual patients. These findings suggest that focusing exclusively on pathogen burden may not adequately inform VAP diagnosis.
Collapse
Affiliation(s)
- Peter M Mourani
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Marci K Sontag
- Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Kayla M Williamson
- Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - J Kirk Harris
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Ron Reeder
- Pediatrics, University of Utah, Salt Lake City, UT, USA
| | | | - Todd C Carpenter
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Aline B Maddux
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Katherine Ziegler
- Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Eric A F Simões
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA.,Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Christina M Osborne
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Lilliam Ambroggio
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA.,Epidemiology, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | - Matthew K Leroue
- Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Charles E Robertson
- Medicine, Division of Infectious Diseases, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Charles Langelier
- Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Dept of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark W Hall
- Dept of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Athena F Zuppa
- Anesthesiology and Critical Care Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Kathleen Meert
- Pediatrics, Children's Hospital of Michigan, Detroit, MI, USA
| | - Anil Sapru
- Pediatrics, University of California Los Angeles, Los Angeles, CA, USA
| | - Murray M Pollack
- Pediatrics, Children's National Medical Center and George Washington School of Medicine and Health Sciences, Washington, DC, USA
| | - Patrick McQuillen
- Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Brandie D Wagner
- Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO, USA
| | | | | |
Collapse
|
33
|
Jobira B, Frank DN, Silveira LJ, Pyle L, Kelsey MM, Garcia-Reyes Y, Robertson CE, Ir D, Nadeau KJ, Cree-Green M. Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome. PLoS One 2021; 16:e0245219. [PMID: 33465100 PMCID: PMC7815089 DOI: 10.1371/journal.pone.0245219] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
Objective Hepatic steatosis (HS) is common in adolescents with obesity and polycystic ovary syndrome (PCOS). Gut microbiota are altered in adults with obesity, HS, and PCOS, which may worsen metabolic outcomes, but similar data is lacking in youth. Methods Thirty-four adolescents with PCOS and obesity underwent stool and fasting blood collection, oral glucose tolerance testing, and MRI for hepatic fat fraction (HFF). Fecal bacteria were profiled by high-throughput 16S rRNA gene sequencing. Results 50% had HS (N = 17, age 16.2±1.5 years, BMI 38±7 kg/m2, HFF 9.8[6.5, 20.7]%) and 50% did not (N = 17, age 15.8±2.2 years, BMI 35±4 kg/m2, HFF 3.8[2.6, 4.4]%). The groups showed no difference in bacterial α-diversity (richness p = 0.202; evenness p = 0.087; and diversity p = 0.069) or global difference in microbiota (β-diversity). Those with HS had lower % relative abundance (%RA) of Bacteroidetes (p = 0.013), Bacteroidaceae (p = 0.009), Porphyromonadaceae (p = 0.011), and Ruminococcaceae (p = 0.008), and higher Firmicutes:Bacteroidetes (F:B) ratio (47.8% vs. 4.3%, p = 0.018) and Streptococcaceae (p = 0.034). Bacterial taxa including phyla F:B ratio, Bacteroidetes, and family Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae correlated with metabolic markers. Conclusions Obese adolescents with PCOS and HS have differences in composition of gut microbiota, which correlate with metabolic markers, suggesting a modifying role of gut microbiota in HS and PCOS.
Collapse
Affiliation(s)
- Beza Jobira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Daniel N. Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Lori J. Silveira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Laura Pyle
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Megan M. Kelsey
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Yesenia Garcia-Reyes
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kristen J. Nadeau
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Melanie Cree-Green
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Center for Women’s Health Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- * E-mail:
| |
Collapse
|
34
|
Stanish LF, Sherwood OA, Lackey G, Osborn S, Robertson CE, Harris JK, Pace N, Ryan JN. Microbial and Biogeochemical Indicators of Methane in Groundwater Aquifers of the Denver Basin, Colorado. Environ Sci Technol 2021; 55:292-303. [PMID: 33296185 DOI: 10.1021/acs.est.0c04228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The presence of methane and other hydrocarbons in domestic-use groundwater aquifers poses significant environmental and human health concerns. Isotopic measurements are often relied upon as indicators of groundwater aquifer contamination with methane. While these parameters are used to infer microbial metabolisms, there is growing evidence that isotopes present an incomplete picture of subsurface microbial processes. This study examined the relationships between microbiology and chemistry in groundwater wells located in the Denver-Julesburg Basin of Colorado, a rapidly urbanizing area with active oil and gas development. A primary goal was to determine if microbial data can reliably indicate the quantities and sources of groundwater methane. Comprehensive chemical and molecular analyses were performed on 39 groundwater well samples from five aquifers. Elevated methane concentrations were found in only one aquifer, and both isotopic and microbial data support a microbial origin. Microbial parameters had similar explanatory power as chemical parameters for predicting sample methane concentrations. Furthermore, a subset of samples with unique microbiology corresponded with unique chemical signatures that may be useful indicators of methane gas migration, potentially from nearby coal seams interacting with the aquifer. Microbial data may allow for more accurate determination of groundwater contamination and improved long-term water quality monitoring compared solely to isotopic and chemical data in areas with microbial methane.
Collapse
Affiliation(s)
- Lee F Stanish
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Owen A Sherwood
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Greg Lackey
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Stephen Osborn
- Department of Geological Sciences, California State Polytechnic University, Pomona, California 91768, United States
| | | | | | - Norman Pace
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Joseph N Ryan
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
35
|
Erlandson KM, Liu J, Johnson R, Dillon S, Jankowski CM, Kroehl M, Robertson CE, Frank DN, Tuncil Y, Higgins J, Hamaker B, Wilson CC. An exercise intervention alters stool microbiota and metabolites among older, sedentary adults. Ther Adv Infect Dis 2021; 8:20499361211027067. [PMID: 34262758 PMCID: PMC8246564 DOI: 10.1177/20499361211027067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/03/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Physiologic aging has been associated with gut dysbiosis. Although short exercise interventions have been linked to beneficial changes in gut microbiota in younger adults, limited data are available from older populations. We hypothesized that exercise would produce beneficial shifts in microbiota and short-chain fatty acid (SCFA) levels in older persons. METHODS Stool samples were collected before and at completion of a supervised 24-week cardiovascular and resistance exercise intervention among 50-75-year-old participants. SCFA levels were analyzed by gas chromatography and microbiome by 16S rRNA gene sequencing. Negative binomial regression models compared pre- and post-differences using false discovery rates for multiple comparison. RESULTS A total of 22 participants provided pre-intervention samples; 15 provided samples at study completion. At baseline, the majority of participants were men (95%), mean age 58.0 (8.8) years, mean body mass index 27.4 (6.4) kg/m2. After 24 weeks of exercise, at the genus level, exercise was associated with significant increases in Bifidobacterium (and other unidentified genera within Bifidobacteriaceae), Oscillospira, Anaerostipes, and decreased Prevotella and Oribacterium (p < 0.001). Stool butyrate increased with exercise [5.44 (95% confidence interval 1.54, 9.24) mmol/g, p = 0.02], though no significant differences in acetate or propionate (p ⩾ 0.09) were seen. CONCLUSION Our pilot study suggested that an exercise intervention is associated with changes in the microbiome of older adults and a key bacterial metabolite, butyrate. Although some of these changes could potentially reverse age-related dysbiosis, future studies are required to determine the contribution of changes to the microbiome in the beneficial effect of exercise on overall health of older adults. Clinical Trials NCT02404792.
Collapse
Affiliation(s)
- Kristine M. Erlandson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, 12700 E. 19th Avenue, Mail Stop B168, Aurora, CO 80045, USA
| | - Jay Liu
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rachel Johnson
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Stephanie Dillon
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Miranda Kroehl
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Charles E. Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Daniel N. Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yunus Tuncil
- Food Engineering Department, Ordu University, Ordu, Turkey
| | - Janine Higgins
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bruce Hamaker
- Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Cara C. Wilson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
36
|
Vickery TW, Armstrong M, Kofonow JM, Robertson CE, Kroehl ME, Reisdorph NA, Ramakrishnan VR, Frank DN. Altered tissue specialized pro-resolving mediators in chronic rhinosinusitis. Prostaglandins Leukot Essent Fatty Acids 2021; 164:102218. [PMID: 33338738 PMCID: PMC7855833 DOI: 10.1016/j.plefa.2020.102218] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
Current literature implicates arachidonic acid-derived leukotrienes and prostaglandins in the pathogenesis of chronic rhinosinusitis. However, other omega-3 and omega-6 derived lipid mediators, such as specialized pro-resolving mediators (SPMs), may also be important in chronic inflammatory disorders of the upper airway. We hypothesize that SPMs differ among CRS subtypes compared to controls and in relation to sinonasal microbiota. Ethmoid sinus tissue and middle meatal swabs were collected from a convenience sample of 66 subjects, including non-CRS controls, CRS with polyps (CRSwNP), and CRS without polyps (CRSsNP). Lipid mediator pathways were analyzed by liquid chromatography/tandem mass spectrometry. Bacterial taxa were profiled in parallel by 16S rRNA gene sequencing. Resolvin D2 was elevated in both CRSwNP (p = 0.00076) and CRSsNP (p = 0.030) compared with non-CRS controls. Lipoxin A4 was significantly increased in CRSwNP compared with CRSsNP (p = 0.000033) and controls (p = 0.044). Cigarette smoking was associated with significantly lower concentrations of several 15-lipoxygenase metabolites including resolvin D1 (p = 0.0091) and resolvin D2 (p = 0.0097), compared with never-smokers. Several of the lipid compounds also correlated with components of the sinonasal mucosal microbiota, including bacterial pathogens such as Pseudomonas aeruginosa. These data suggest that dysfunctional lipid mediator pathways in CRS extend beyond the traditional descriptions of leukotrienes and prostaglandins and include SPMs. Furthermore, dysregulated SPM signaling may contribute to persistent inflammation and bacterial colonization in CRS.
Collapse
Affiliation(s)
- Thad W Vickery
- Department of Otolaryngology - Head & Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Head and Neck Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Armstrong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jennifer M Kofonow
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Miranda E Kroehl
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Nichole A Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Vijay R Ramakrishnan
- Department of Otolaryngology - Head & Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| |
Collapse
|
37
|
Soderborg TK, Carpenter CM, Janssen RC, Weir TL, Robertson CE, Ir D, Young BE, Krebs NF, Hernandez TL, Barbour LA, Frank DN, Kroehl M, Friedman JE. Gestational Diabetes Is Uniquely Associated With Altered Early Seeding of the Infant Gut Microbiota. Front Endocrinol (Lausanne) 2020; 11:603021. [PMID: 33329403 PMCID: PMC7729132 DOI: 10.3389/fendo.2020.603021] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is a worldwide public health problem affecting up to 27% of pregnancies with high predictive values for childhood obesity and inflammatory diseases. Compromised seeding of the infant gut microbiota is a risk factor for immunologic and metabolic diseases in the offspring; however, how GDM along with maternal obesity interact to alter colonization remains unknown. We hypothesized that GDM individually and in combination with maternal overweight/obesity would alter gut microbial composition, diversity, and short-chain fatty acid (SCFA) levels in neonates. We investigated 46 full-term neonates born to normal-weight or overweight/obese mothers with and without GDM, accounting for confounders including cesarean delivery, lack of breastfeeding, and exposure to antibiotics. Gut microbiota in 2-week-old neonates born to mothers with GDM exhibited differences in abundance of 26 microbial taxa; 14 of which showed persistent differential abundance after adjusting for pre-pregnancy BMI. Key pioneering gut taxa, including potentially important taxa for establishing neonatal immunity, were reduced. Lactobacillus, Flavonifractor, Erysipelotrichaceae, and unspecified families in Gammaproteobacteria were significantly reduced in neonates from mothers with GDM. GDM was associated with an increase in microbes involved in suppressing early immune cell function (Phascolarctobacterium). No differences in infant stool SCFA levels by maternal phenotype were noted; however, significant correlations were found between microbial abundances and SCFA levels in neonates. Our results suggest that GDM alone and together with maternal overweight/obesity uniquely influences seeding of specific infant microbiota in patterns that set the stage for future risk of inflammatory and metabolic disease.
Collapse
Affiliation(s)
- Taylor K. Soderborg
- Department of Pediatrics, Section of Neonatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles M. Carpenter
- Division of Biostatistics and Epidemiology, University of Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Rachel C. Janssen
- Department of Pediatrics, Section of Neonatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Tiffany L. Weir
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, United States
| | - Charles E. Robertson
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Diana Ir
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Bridget E. Young
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nancy F. Krebs
- Department of Pediatrics, Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Teri L. Hernandez
- Department of Medicine, Division of Endocrinology, Metabolism & Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- College of Nursing, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Linda A. Barbour
- Department of Medicine, Division of Endocrinology, Metabolism & Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N. Frank
- Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Miranda Kroehl
- Division of Biostatistics and Epidemiology, University of Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jacob E. Friedman
- Department of Pediatrics, Section of Neonatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Medicine, Division of Endocrinology, Metabolism & Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| |
Collapse
|
38
|
Kimber C, Zhang S, Johnson C, West RE, Prokopienko AJ, Mahnken JD, Yu AS, Hoofnagle AN, Ir D, Robertson CE, Miyazaki M, Chonchol M, Jovanovich A, Kestenbaum B, Frank DN, Nolin TD, Stubbs JR. Randomized, Placebo-Controlled Trial of Rifaximin Therapy for Lowering Gut-Derived Cardiovascular Toxins and Inflammation in CKD. ACTA ACUST UNITED AC 2020; 1:1206-1216. [PMID: 34322673 PMCID: PMC8315698 DOI: 10.34067/kid.0003942020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background Recent evidence suggests the systemic accumulation of by-products of gut microbes contributes to cardiovascular morbidity in patients with CKD. Limiting the generation of toxic bacterial by-products by manipulating the intestinal microbiota may be a novel strategy for reducing cardiovascular disease in CKD. Rifaximin is a minimally absorbed, oral antibiotic that targets intestinal pathogens and is commonly used as chronic therapy for the prevention of encephalopathy in patients with cirrhosis. Methods We conducted a randomized, double-blinded, placebo-controlled trial to determine the effect of a 10-day course of oral rifaximin 550 mg BID versus placebo on circulating concentrations of gut-derived cardiovascular toxins and proinflammatory cytokines in patients with stage 3-5 CKD (n=38). The primary clinical outcome was change in serum trimethylamine N-oxide (TMAO) concentrations from baseline to study end. Secondary outcomes included change in serum concentrations of p-cresol sulfate, indoxyl sulfate, kynurenic acid, deoxycholic acid, and inflammatory cytokines (C-reactive protein, IL-6, IL-1β), and change in composition and diversity of fecal microbiota. Results A total of 19 patients were randomized to each of the rifaximin and placebo arms, with n=17 and n=14 completing both study visits in these respective groups. We observed no difference in serum TMAO change (post-therapy minus baseline TMAO) between the rifaximin and placebo groups (mean TMAO change -3.9±15.4 for rifaximin versus 0.5±9.5 for placebo, P=0.49). Similarly, we found no significant change in serum concentrations for p-cresol sulfate, indoxyl sulfate, kynurenic acid, deoxycholic acid, and inflammatory cytokines. We did observe differences in colonic bacterial communities, with the rifaximin group exhibiting significant decreases in bacterial richness (Chao1, P=0.02) and diversity (Shannon H, P=0.05), along with altered abundance of several bacterial genera. Conclusions Short-term rifaximin treatment failed to reduce gut-derived cardiovascular toxins and inflammatory cytokines in patients with CKD. Clinical Trial registry name and registration number Rifaximin Therapy in Chronic Kidney Disease, NCT02342639.
Collapse
Affiliation(s)
- Cassandra Kimber
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas.,Division of Nephrology and Hypertension, Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Shiqin Zhang
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas.,Division of Nephrology and Hypertension, Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Cassandra Johnson
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas
| | - Raymond E West
- Department of Pharmacy and Therapeutics, Center for Clinical Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alexander J Prokopienko
- Department of Pharmacy and Therapeutics, Center for Clinical Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jonathan D Mahnken
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas.,Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas
| | - Alan S Yu
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas.,Division of Nephrology and Hypertension, Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Diana Ir
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Denver, Colorado
| | - Charles E Robertson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Denver, Colorado
| | - Makoto Miyazaki
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Michel Chonchol
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Anna Jovanovich
- Division of Renal Diseases and Hypertension, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado
| | - Bryan Kestenbaum
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington.,Kidney Research Institute, Seattle, Washington
| | - Daniel N Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Denver, Colorado
| | - Thomas D Nolin
- Department of Pharmacy and Therapeutics, Center for Clinical Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jason R Stubbs
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas.,Division of Nephrology and Hypertension, Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas
| |
Collapse
|
39
|
Olli KE, Rapp C, O’Connell L, Collins CB, McNamee EN, Jensen O, Jedlicka P, Allison KC, Goldberg MS, Gerich ME, Frank DN, Ir D, Robertson CE, Evans CM, Aherne CM. Muc5ac Expression Protects the Colonic Barrier in Experimental Colitis. Inflamm Bowel Dis 2020; 26:1353-1367. [PMID: 32385500 PMCID: PMC7441107 DOI: 10.1093/ibd/izaa064] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The mucus gel layer (MGL) lining the colon is integral to exclusion of bacteria and maintaining intestinal homeostasis in health and disease. Some MGL defects allowing bacteria to directly contact the colonic surface are commonly observed in ulcerative colitis (UC). The major macromolecular component of the colonic MGL is the secreted gel-forming mucin MUC2, whose expression is essential for homeostasis in health. In UC, another gel-forming mucin, MUC5AC, is induced. In mice, Muc5ac is protective during intestinal helminth infection. Here we tested the expression and functional role of MUC5AC/Muc5ac in UC biopsies and murine colitis. METHODS We measured MUC5AC/Muc5ac expression in UC biopsies and in dextran sulfate sodium (DSS) colitis. We performed DSS colitis in mice deficient in Muc5ac (Muc5ac-/-) to model the potential functional role of Muc5ac in colitis. To assess MGL integrity, we quantified bacterial-epithelial interaction and translocation to mesenteric lymph nodes. Antibiotic treatment and 16S rRNA gene sequencing were performed to directly investigate the role of bacteria in murine colitis. RESULTS Colonic MUC5AC/Muc5ac mRNA expression increased significantly in active UC and murine colitis. Muc5ac-/- mice experienced worsened injury and inflammation in DSS colitis compared with control mice. This result was associated with increased bacterial-epithelial contact and translocation to the mesenteric lymph nodes. However, no change in microbial abundance or community composition was noted. Antibiotic treatment normalized colitis severity in Muc5ac-/- mice to that of antibiotic-treated control mice. CONCLUSIONS MUC5AC/Muc5ac induction in the acutely inflamed colon controls injury by reducing bacterial breach of the MGL.
Collapse
Affiliation(s)
- Kristine E Olli
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Caroline Rapp
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Lauren O’Connell
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Colm B Collins
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Digestive Health Institute, Children’s Hospital Colorado, Aurora, Colorado, USA
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Eoin N McNamee
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- Kathleen Lonsdale Institute for Human Health Research, Department of Biology, Maynooth University, County Kildare, Ireland
| | - Owen Jensen
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Paul Jedlicka
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kristen C Allison
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Matthew S Goldberg
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Mark E Gerich
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Christopher M Evans
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Carol M Aherne
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| |
Collapse
|
40
|
Frank DN, Giese APJ, Hafren L, Bootpetch TC, Yarza TKL, Steritz MJ, Pedro M, Labra PJ, Daly KA, Tantoco MLC, Szeremeta W, Reyes-Quintos MRT, Ahankoob N, Llanes EGDV, Pine HS, Yousaf S, Ir D, Einarsdottir E, de la Cruz RAR, Lee NR, Nonato RMA, Robertson CE, Ong KMC, Magno JPM, Chiong ANE, Espiritu-Chiong MC, San Agustin ML, Cruz TLG, Abes GT, Bamshad MJ, Cutiongco-de la Paz EM, Kere J, Nickerson DA, Mohlke KL, Riazuddin S, Chan A, Mattila PS, Leal SM, Ryan AF, Ahmed ZM, Chonmaitree T, Sale MM, Chiong CM, Santos-Cortez RLP. Otitis media susceptibility and shifts in the head and neck microbiome due to SPINK5 variants. J Med Genet 2020; 58:442-452. [PMID: 32709676 DOI: 10.1136/jmedgenet-2020-106844] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/06/2020] [Accepted: 05/24/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Otitis media (OM) susceptibility has significant heritability; however, the role of rare variants in OM is mostly unknown. Our goal is to identify novel rare variants that confer OM susceptibility. METHODS We performed exome and Sanger sequencing of >1000 DNA samples from 551 multiethnic families with OM and unrelated individuals, RNA-sequencing and microbiome sequencing and analyses of swabs from the outer ear, middle ear, nasopharynx and oral cavity. We also examined protein localisation and gene expression in infected and healthy middle ear tissues. RESULTS A large, intermarried pedigree that includes 81 OM-affected and 53 unaffected individuals cosegregates two known rare A2ML1 variants, a common FUT2 variant and a rare, novel pathogenic variant c.1682A>G (p.Glu561Gly) within SPINK5 (LOD=4.09). Carriage of the SPINK5 missense variant resulted in increased relative abundance of Microbacteriaceae in the middle ear, along with occurrence of Microbacteriaceae in the outer ear and oral cavity but not the nasopharynx. Eight additional novel SPINK5 variants were identified in 12 families and individuals with OM. A role for SPINK5 in OM susceptibility is further supported by lower RNA counts in variant carriers, strong SPINK5 localisation in outer ear skin, faint localisation to middle ear mucosa and eardrum and increased SPINK5 expression in human cholesteatoma. CONCLUSION SPINK5 variants confer susceptibility to non-syndromic OM. These variants potentially contribute to middle ear pathology through breakdown of mucosal and epithelial barriers, immunodeficiency such as poor vaccination response, alteration of head and neck microbiota and facilitation of entry of opportunistic pathogens into the middle ear.
Collapse
Affiliation(s)
- Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Arnaud P J Giese
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Lena Hafren
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tori C Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Talitha Karisse L Yarza
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Matthew J Steritz
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Melquiadesa Pedro
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Patrick John Labra
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines
| | - Kathleen A Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ma Leah C Tantoco
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Wasyl Szeremeta
- Department of Otolaryngology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Maria Rina T Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines.,National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Niaz Ahankoob
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Erasmo Gonzalo D V Llanes
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Harold S Pine
- Department of Otolaryngology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Sairah Yousaf
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Nanette R Lee
- Department of Anthropology, Sociology and History, University of San Carlos, Cebu City, Philippines
| | | | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kimberly Mae C Ong
- Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Jose Pedrito M Magno
- Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Alessandra Nadine E Chiong
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | | | - Maria Luz San Agustin
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Teresa Luisa G Cruz
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Generoso T Abes
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Eva Maria Cutiongco-de la Paz
- National Institutes of Health, University of the Philippines Manila, Manila, Philippines.,Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Abner Chan
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Petri S Mattila
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, USA
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, University of California San Diego School of Medicine and Veterans Affairs Medical Center, La Jolla, California, USA
| | - Zubair M Ahmed
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Tasnee Chonmaitree
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Michele M Sale
- Center for Public Health Genomics, School of Medicine, Department of Biochemistry and Molecular Genetics, and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Charlotte M Chiong
- Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Newborn Hearing Screening Reference Center, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Department of Otorhinolaryngology, Philippine General Hospital, Manila, Philippines
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA .,Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health, Manila, Philippines.,Center for Children's Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
| |
Collapse
|
41
|
Jobira B, Frank DN, Pyle L, Silveira LJ, Kelsey MM, Garcia-Reyes Y, Robertson CE, Ir D, Nadeau KJ, Cree-Green M. Obese Adolescents With PCOS Have Altered Biodiversity and Relative Abundance in Gastrointestinal Microbiota. J Clin Endocrinol Metab 2020; 105:5709658. [PMID: 31970418 PMCID: PMC7147870 DOI: 10.1210/clinem/dgz263] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/11/2019] [Indexed: 12/31/2022]
Abstract
CONTEXT Alterations in gut microbiota relate to the metabolic syndrome, but have not been examined in at-risk obese youth with polycystic ovary syndrome (PCOS). OBJECTIVE Compare the composition and diversity of the gut microbiota and associations with metabolic and hormonal measures between 2 groups of female adolescents with equal obesity with or without PCOS. DESIGN Prospective, case-control cross-sectional study. SETTING Tertiary-care center. PARTICIPANTS A total of 58 obese female adolescents (n = 37 with PCOS; 16.1 ± 0.3 years of age; body mass index [BMI] 98.5th percentile) and (n = 21 without PCOS; 14.5 ± 0.4 years of age; BMI 98.7th percentile). OUTCOMES Bacterial diversity, percent relative abundance (%RA), and correlations with hormonal and metabolic measures. RESULTS Participants with PCOS had decreased α-diversity compared with the non-PCOS group (Shannon diversity P = 0.045 and evenness P = 0.0052). β-diversity, reflecting overall microbial composition, differed between groups (P < 0.001). PCOS had higher %RA of phyla Actinobacteria (P = 0.027), lower Bacteroidetes (P = 0.004), and similar Firmicutes and Proteobacteria. PCOS had lower %RA of families Bacteroidaceae (P < 0.001) and Porphyromonadaceae (P = 0.024) and higher Streptococcaceae (P = 0.047). Lower bacterial α-diversity was strongly associated with higher testosterone concentrations. Several individual taxa correlated with testosterone and metabolic measures within PCOS and across the entire cohort. Receiver operative curve analysis showed 6 taxa for which the %RA related to PCOS status and lower Bacteroidaceae conferred a 4.4-fold likelihood ratio for PCOS. CONCLUSION Alterations in the gut microbiota exist in obese adolescents with PCOS versus obese adolescents without PCOS and these changes relate to markers of metabolic disease and testosterone. Further work is needed to determine if microbiota changes are reflective of, or influencing, hormonal metabolism.
Collapse
Affiliation(s)
- Beza Jobira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Laura Pyle
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado
| | - Lori J Silveira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado
| | - Megan M Kelsey
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Center for Women’s Health Research; University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Yesenia Garcia-Reyes
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kristen J Nadeau
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Center for Women’s Health Research; University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Melanie Cree-Green
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Center for Women’s Health Research; University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Correspondence: Melanie Cree-Green, MD, PhD, Children’s Hospital Colorado, University of Colorado Anschutz Medical Campus, PO Box 265, 13123 E 16th Ave, Aurora, Colorado 80045.
| |
Collapse
|
42
|
Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ, Furey TS. Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis 2020; 26:1843-1855. [PMID: 32469069 PMCID: PMC7676424 DOI: 10.1093/ibd/izaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen have been proposed as a contributor to CD dybiosis. METHODS The authors generated 16S rRNA data using colonic and ileal mucosal bacteria from patients with CD and without inflammatory bowel disease. We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes. RESULTS Bacterial diversity decreased in CD in both the ileum and the colon. Aerotolerance profiles significantly differed between intestinal segments in patients without inflammatory bowel disease, although both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundances of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, although specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected tissues of patients who developed postoperative disease recurrence across 2 independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera. CONCLUSIONS Mucosally adherent bacteria in the colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.
Collapse
Affiliation(s)
- Nur M Shahir
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy R Wang
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E Ashley Wolber
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew S Schaner
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Diana Ir
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nicole Chaumont
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy S Sadiq
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J Koruda
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Reza Rahbar
- Department of Surgery, REX Healthcare of Wakefield, Wakefield, North Carolina, USA
| | - B Darren Nix
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Rodney D Newberry
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shehzad Z Sheikh
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Terrence S Furey
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Biology, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Address correspondence to: Terrence S. Furey, PhD, Departments of Genetics and Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC 27599 ()
| |
Collapse
|
43
|
Takahashi S, Luo Y, Ranjit S, Xie C, Libby AE, Orlicky DJ, Dvornikov A, Wang XX, Myakala K, Jones BA, Bhasin K, Wang D, McManaman JL, Krausz KW, Gratton E, Ir D, Robertson CE, Frank DN, Gonzalez FJ, Levi M. Bile acid sequestration reverses liver injury and prevents progression of nonalcoholic steatohepatitis in Western diet-fed mice. J Biol Chem 2020; 295:4733-4747. [PMID: 32075905 DOI: 10.1074/jbc.ra119.011913] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease is a rapidly rising problem in the 21st century and is a leading cause of chronic liver disease that can lead to end-stage liver diseases, including cirrhosis and hepatocellular cancer. Despite this rising epidemic, no pharmacological treatment has yet been established to treat this disease. The rapidly increasing prevalence of nonalcoholic fatty liver disease and its aggressive form, nonalcoholic steatohepatitis (NASH), requires novel therapeutic approaches to prevent disease progression. Alterations in microbiome dynamics and dysbiosis play an important role in liver disease and may represent targetable pathways to treat liver disorders. Improving microbiome properties or restoring normal bile acid metabolism may prevent or slow the progression of liver diseases such as NASH. Importantly, aberrant systemic circulation of bile acids can greatly disrupt metabolic homeostasis. Bile acid sequestrants are orally administered polymers that bind bile acids in the intestine, forming nonabsorbable complexes. Bile acid sequestrants interrupt intestinal reabsorption of bile acids, decreasing their circulating levels. We determined that treatment with the bile acid sequestrant sevelamer reversed the liver injury and prevented the progression of NASH, including steatosis, inflammation, and fibrosis in a Western diet-induced NASH mouse model. Metabolomics and microbiome analysis revealed that this beneficial effect is associated with changes in the microbiota population and bile acid composition, including reversing microbiota complexity in cecum by increasing Lactobacillus and decreased Desulfovibrio The net effect of these changes was improvement in liver function and markers of liver injury and the positive effects of reversal of insulin resistance.
Collapse
Affiliation(s)
- Shogo Takahashi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057.,National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhuan Luo
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057.,Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California 92697
| | - Cen Xie
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - David J Orlicky
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Alexander Dvornikov
- Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California 92697
| | - Xiaoxin X Wang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - Komuraiah Myakala
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - Bryce A Jones
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057.,Department of Pharmacology and Physiology, Georgetown University, Washington, D.C., 20057
| | - Kanchan Bhasin
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - Dong Wang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - James L McManaman
- Division of Reproductive Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045.,Graduate Program in Integrated Physiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Kristopher W Krausz
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Enrico Gratton
- Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California 92697
| | - Diana Ir
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Frank J Gonzalez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| |
Collapse
|
44
|
Tang M, Frank DN, Tshefu A, Lokangaka A, Goudar SS, Dhaded SM, Somannavar MS, Hendricks AE, Ir D, Robertson CE, Kemp JF, Lander RL, Westcott JE, Hambidge KM, Krebs NF. Different Gut Microbial Profiles in Sub-Saharan African and South Asian Women of Childbearing Age Are Primarily Associated With Dietary Intakes. Front Microbiol 2019; 10:1848. [PMID: 31474951 PMCID: PMC6702451 DOI: 10.3389/fmicb.2019.01848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/26/2019] [Indexed: 01/20/2023] Open
Abstract
Background To compare and characterize the gut microbiota in women of childbearing age from sub-Saharan Africa (the Democratic Republic of the Congo, DRC) and South Asia (India), in relation to dietary intakes. Methods Women of childbearing age were recruited from rural DRC and India as part of the Women First (WF) preconception maternal nutrition trial. Findings presented include fecal 16S rRNA gene-based profiling of women in the WF trial from samples obtained at the time of randomization, prior to initiation of nutrition intervention and to conception. Results Stool samples were collected from 217 women (DRC n = 117; India n = 100). Alpha diversity of the gut microbiota was higher in DRC than in India (Chao1: 91 ± 11 vs. 82 ± 12, P = 6.58E-07). The gut microbial community structure was not significantly affected by any demographical or environmental variables, such as maternal BMI, education, and water source. Prevotella, Succinivibrio, and Roseburia were at relatively high abundance without differences between sites. Bifidobacterium was higher in India (4.95 ± 1.0%) than DRC (0.3 ± 0.1%; P = 2.71E-27), as was Lactobacillus (DRC: 0.2 ± 0.0%; India: 1.2 ± 0.1%; P = 2.39E-13) and Faecalibacterium (DRC: 6.0 ± 1.7%; India: 8.4 ± 2.9%; P = 6.51E-7). Ruminococcus was higher in DRC (2.3 ± 0.7%) than in India (1.8 ± 0.4%; P = 3.24E-5) and was positively associated with consumption of flesh foods. Succinivibrio was positively associated with dairy intake in India and fish/insects in DRC. Faecalibacterium was positively associated with vitamin A-rich fruits and vegetables. Overall, these observations were consistent with India being primarily vegetarian with regular fermented dairy consumption and DRC regularly consuming animal-flesh foods. Conclusion Consumption of animal-flesh foods and fermented dairy foods were independently associated with the gut microbiota while demographic variables were not, suggesting that diet may have a stronger association with microbiota than demographic characteristics.
Collapse
Affiliation(s)
- Minghua Tang
- Section of Nutrition, Department of Pediatrics, University of Colorado Denver, Aurora, CO, United States
| | - Daniel N Frank
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Antoinette Tshefu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Adrien Lokangaka
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Shivaprasad S Goudar
- KLE Academy of Higher Education and Research's Jawaharlal Nehru Medical College, Belagavi, India
| | - Sangappa M Dhaded
- KLE Academy of Higher Education and Research's Jawaharlal Nehru Medical College, Belagavi, India
| | - Manjunath S Somannavar
- KLE Academy of Higher Education and Research's Jawaharlal Nehru Medical College, Belagavi, India
| | - Audrey E Hendricks
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Aurora, CO, United States
| | - Diana Ir
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Charles E Robertson
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Jennifer F Kemp
- Section of Nutrition, Department of Pediatrics, University of Colorado Denver, Aurora, CO, United States
| | - Rebecca L Lander
- Section of Nutrition, Department of Pediatrics, University of Colorado Denver, Aurora, CO, United States
| | - Jamie E Westcott
- Section of Nutrition, Department of Pediatrics, University of Colorado Denver, Aurora, CO, United States
| | - K Michael Hambidge
- Section of Nutrition, Department of Pediatrics, University of Colorado Denver, Aurora, CO, United States
| | - Nancy F Krebs
- Section of Nutrition, Department of Pediatrics, University of Colorado Denver, Aurora, CO, United States
| |
Collapse
|
45
|
Kelly CJ, Alexeev EE, Farb L, Vickery TW, Zheng L, Eric L C, Kitzenberg DA, Battista KD, Kominsky DJ, Robertson CE, Frank DN, Stabler SP, Colgan SP. Oral vitamin B 12 supplement is delivered to the distal gut, altering the corrinoid profile and selectively depleting Bacteroides in C57BL/6 mice. Gut Microbes 2019; 10:654-662. [PMID: 31062653 PMCID: PMC6866687 DOI: 10.1080/19490976.2019.1597667] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Vitamin B12 is a critical nutrient for humans as well as microbes. Due to saturable uptake, high dose oral B12 supplements are largely unabsorbed and reach the distal gut where they are available to interact with the microbiota. The aim of this study was to determine if oral B12 supplementation in mice alters 1) the concentration of B12 and related corrinoids in the distal gut, 2) the fecal microbiome, 3) short chain fatty acids (SCFA), and 4) susceptibility to experimental colitis. C57BL/6 mice (up to 24 animals/group) were supplemented with oral 3.94 µg/ml cyanocobalamin (B12), a dose selected to approximate a single 5 mg supplement for a human. Active vitamin B12 (cobalamin), and four B12-analogues ([ADE]CN-Cba, [2Me-ADE]CN-Cba, [2MeS-ADE]CN-Cba, CN-Cbi) were analyzed in cecal and fecal contents using liquid chromatography/mass spectrometry (LC/MS), in parallel with evaluation of fecal microbiota, cecal SCFA, and susceptibility to dextran sodium sulfate (DSS) colitis. At baseline, active B12 was a minor constituent of overall cecal (0.86%) and fecal (0.44%) corrinoid. Oral B12 supplementation increased active B12 at distal sites by >130-fold (cecal B12 increased from 0.08 to 10.60 ng/mg, fecal B12 increased from 0.06 to 7.81 ng/ml) and reduced microbe-derived fecal corrinoid analogues ([ADE]CN-Cba, [2Me-ADE]CN-Cba, [2MeS-ADE]CN-Cba). Oral B12 had no effect on cecal SCFA. Microbial diversity was unaffected by this intervention, however a selective decrease in Bacteroides was observed with B12 treatment. Lastly, no difference in markers of DSS-induced colitis were detected with B12 treatment.
Collapse
Affiliation(s)
- Caleb J Kelly
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA,CONTACT Sean P. Colgan Mucosal Inflammation Program, University of Colorado, 12700 East 19th Ave. MS B-146, Aurora, CO 80045, USA
| | - Erica E Alexeev
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Linda Farb
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Thad W Vickery
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Leon Zheng
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Campbell Eric L
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA,Centre for Experimental Medicine, Queens University, Belfast, UK
| | - David A Kitzenberg
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Kayla D Battista
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Douglas J Kominsky
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Centre for Experimental Medicine, Queens University, Belfast, UK,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Sally P Stabler
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Sean P Colgan
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| |
Collapse
|
46
|
Wagner BD, Sontag MK, Harris JK, Miller JI, Morrow L, Robertson CE, Stephens MJ, Poindexter BB, Abman SH, Mourani PM. Prenatal complications are associated with the postnatal airway host response and microbiota in intubated preterm infants. J Matern Fetal Neonatal Med 2019; 32:1499-1506. [PMID: 29157044 PMCID: PMC6212338 DOI: 10.1080/14767058.2017.1407310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/06/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
PURPOSE To prospectively examine the relationship between prenatal events, postnatal airway host response and microbiota, and clinical outcomes. MATERIALS AND METHODS Tracheal aspirates collected at seven days of age from 71 mechanically ventilated infants (median gestational age (GA), 25 weeks [range 23-28]) were simultaneously processed for a 12-plex protein assay and bacterial identification by 16S rRNA sequencing. Phenotypes were determined by unsupervised clustering of the protein analytes. Subject characteristics, microbial communities and clinical factors and outcomes were compared across the phenotype groups. RESULTS Three clusters were identified: 1 (high protein levels), 2 (high proinflammatory proteins and low anti-inflammatory proteins), and 3 (low protein levels), respectively. Antenatal hemorrhage was most common in cluster 1, while chorioamnionitis characterized cluster 2 and preeclampsia was most prevalent in cluster 3, which was characterized by a predominance of Staphylococcus and relative absence of Ureaplasma. There were higher rates of adverse clinical outcomes in cluster 1. CONCLUSIONS Airway protein profiles in seven days old mechanically ventilated preterm infants are associated with important antenatal events and unique airway microbial communities. These relationships may reveal new mechanisms by which antenatal events impact the course and outcomes of preterm infants.
Collapse
Affiliation(s)
- Brandie D Wagner
- a Department of Biostatistics, Colorado School of Public Health , University of Colorado , Aurora , CO , USA
| | - Marci K Sontag
- b Department of Epidemiology, Colorado School of Public Health , University of Colorado , Aurora , CO , USA
| | - J Kirk Harris
- c Department of Pediatrics, Section of Pulmonary Medicine , University of Colorado , Aurora , CO , USA
| | - Joshua I Miller
- b Department of Epidemiology, Colorado School of Public Health , University of Colorado , Aurora , CO , USA
| | - Lindsey Morrow
- a Department of Biostatistics, Colorado School of Public Health , University of Colorado , Aurora , CO , USA
| | - Charles E Robertson
- d Department of Medicine, Section of Infectious Disease , University of Colorado , Aurora , CO , USA
| | - Mark J Stephens
- c Department of Pediatrics, Section of Pulmonary Medicine , University of Colorado , Aurora , CO , USA
| | - Brenda B Poindexter
- e Perinatal Institute, Cincinnati Children's Hospital Medical Center , Cincinnati , OH , USA
| | - Steven H Abman
- c Department of Pediatrics, Section of Pulmonary Medicine , University of Colorado , Aurora , CO , USA
- f Pediatric Heart-Lung Center, Department of Pediatrics , University of Colorado , Aurora , CO , USA
| | - Peter M Mourani
- f Pediatric Heart-Lung Center, Department of Pediatrics , University of Colorado , Aurora , CO , USA
- g Department of Pediatrics, Section of Critical Care Medicine , University of Colorado , Aurora , CO , USA
| |
Collapse
|
47
|
Li E, Zhang Y, Tian X, Wang X, Gathungu G, Wolber A, Shiekh SS, Sartor RB, Davidson NO, Ciorba MA, Zhu W, Nelson LM, Robertson CE, Frank DN. Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome. PLoS One 2019; 14:e0213108. [PMID: 30818349 PMCID: PMC6395037 DOI: 10.1371/journal.pone.0213108] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/14/2019] [Indexed: 12/13/2022] Open
Abstract
We have previously identified NOD2 genotype and inflammatory bowel diseases (IBD) phenotype, as associated with shifts in the ileal microbiome ("dysbiosis") in a patient cohort. Here we report an integrative analysis of an expanded number of Crohn's disease (CD) related genetic defects in innate immune function (NOD2, ATG16L1, IRGM, CARD9, XBP1, ORMDL3) and composition of the ileal microbiome by combining the initial patient cohort (Batch 1, 2005-2010, n = 165) with a second consecutive patient cohort (Batch 2, 2010-2012, n = 118). These combined patient cohorts were composed of three non-overlapping phenotypes: 1.) 106 ileal CD subjects undergoing initial ileocolic resection for diseased ileum, 2.) 88 IBD colitis subjects without ileal disease (predominantly ulcerative colitis but also Crohn's colitis and indeterminate colitis, and 3.) 89 non-IBD subjects. Significant differences (FDR < 0.05) in microbiota were observed between macroscopically disease unaffected and affected regions of resected ileum in ileal CD patients. Accordingly, analysis of the effects of genetic and clinical factors were restricted to disease unaffected regions of the ileum. Beta-diversity differed across the three disease categories by PERMANOVA (p < 0.001), whereas no significant differences in alpha diversity were noted. Using negative binomial models, we confirmed significant effects of IBD phenotype, C. difficile infection, and NOD2 genotype on ileal dysbiosis in the expanded analysis. The relative abundance of the Proteobacteria phylum was positively associated with ileal CD and colitis phenotypes, but negatively associated with NOD2R genotype. Additional associations with ORMDL3 and XBP1 were detected at the phylum/subphylum level. IBD medications, such as immunomodulators and anti-TNFα agents, may have a beneficial effect on reversing dysbiosis associated with the IBD phenotype. Exploratory analysis comparing microbial composition of the disease unaffected region of the resected ileum between 27 ileal CD patients who subsequently developed endoscopic recurrence within 6-12 months versus 34 patients who did not, suggested that microbial biomarkers in the resected specimen helped stratify patients with respect to risk of post-surgical recurrence.
Collapse
Affiliation(s)
- Ellen Li
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Yuanhao Zhang
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Xinyu Tian
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States of America
| | - Grace Gathungu
- Department of Pediatrics, Stony Brook University, Stony Brook, NY, United States of America
| | - Ashley Wolber
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Shehzad S. Shiekh
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - R. Balfour Sartor
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Nicholas O. Davidson
- Department of Medicine, Washington University St. Louis, St. Louis, MO, United States of America
| | - Matthew A. Ciorba
- Department of Medicine, Washington University St. Louis, St. Louis, MO, United States of America
| | - Wei Zhu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States of America
| | - Leah M. Nelson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Charles E. Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Daniel N. Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| |
Collapse
|
48
|
Liu J, Johnson R, Dillon S, Kroehl M, Frank DN, Tuncil YE, Zhang X, Ir D, Robertson CE, Seifert S, Higgins J, Hamaker B, Wilson CC, Erlandson KM. Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus. EBioMedicine 2019; 40:583-594. [PMID: 30685386 PMCID: PMC6413415 DOI: 10.1016/j.ebiom.2019.01.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 12/18/2022] Open
Abstract
Background HIV-1 infection and physiological aging are independently linked to elevated systemic inflammation and changes in enteric microbial communities (dysbiosis). However, knowledge of the direct effect of HIV infection on the aging microbiome and potential links to systemic inflammation is lacking. Methods In a cross-sectional study of older people living with HIV (PLWH) (median age 61.5 years, N = 14) and uninfected controls (median 58 years, n = 22) we compared stool microbiota, levels of microbial metabolites (short-chain fatty acid levels, SCFA) and systemic inflammatory biomarkers by HIV serostatus and age. Findings HIV and age were independently associated with distinct changes in the stool microbiome. For example, abundances of Enterobacter and Paraprevotella were higher and Eggerthella and Roseburia lower among PLWH compared to uninfected controls. Age-related microbiome changes also differed by HIV serostatus. Some bacteria with inflammatory potential (e.g. Escherichia) increased with age among PLWH, but not controls. Stool SCFA levels were similar between the two groups yet patterns of associations between individual microbial taxa and SCFA levels differed. Abundance of various genera including Escherichia and Bifidobacterium positively associated with inflammatory biomarkers (e.g. soluble Tumor Necrosis Factor Receptors) among PLWH, but not among controls. Interpretation The age effect on the gut microbiome and associations between microbiota and microbial metabolites or systemic inflammation differed based on HIV serostatus, raising important implications for the impact of therapeutic interventions, dependent on HIV serostatus or age.
Collapse
Affiliation(s)
- Jay Liu
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rachel Johnson
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Stephanie Dillon
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Miranda Kroehl
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yunus E Tuncil
- Food Engineering Department, Ordu University, Ordu, Turkey; Department of Food Science, Purdue University, Lafayette, IN, USA
| | - Xiaowei Zhang
- Department of Food Science, Purdue University, Lafayette, IN, USA
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sharon Seifert
- Department of Pharmacology, Children's Hospital Colorado, Aurora, CO, USA
| | - Janine Higgins
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bruce Hamaker
- Department of Food Science, Purdue University, Lafayette, IN, USA
| | - Cara C Wilson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Kristine M Erlandson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| |
Collapse
|
49
|
Hull NM, Rosenblum JS, Robertson CE, Harris JK, Linden KG. Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver-Julesburg Basin. Sci Total Environ 2018; 644:183-192. [PMID: 29981518 DOI: 10.1016/j.scitotenv.2018.06.067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 05/25/2023]
Abstract
Hydraulic fracturing flowback and produced water (FPW) samples were analyzed for toxicity and microbiome characterization over 220 days for a horizontally drilled well in the Denver-Julesberg (DJ) Basin in Colorado. Cytotoxicity, mutagenicity, and estrogenicity of FPW were measured via the BioLuminescence Inhibition Assay (BLIA), Ames II mutagenicity assay (AMES), and Yeast Estrogen Screen (YES). Raw FPW stimulated bacteria in BLIA, but were cytotoxic to yeast in YES. Filtered FPW stimulated cell growth in both BLIA and YES. Concentrating 25× by solid phase extraction (SPE) revealed significant toxicity throughout well production by BLIA, toxicity during the first 55 days of flowback by YES, and mutagenicity by AMES. The selective pressures of fracturing conditions (including toxicity) affected bacterial and archaeal communities, which were characterized by 16S rRNA gene V4V5 region sequencing. Conditions selected for thermophilic, anaerobic, halophilic bacteria and methanogenic archaea from the groundwater used for fracturing fluid, and from the native shale community. Trends in toxicity echoed the microbial community, which indicated distinct stages of early flowback water, a transition stage, and produced water. Biota in another sampled DJ Basin horizontal well resembled similarly aged samples from this well. However, microbial signatures were unique compared to samples from DJ Basin vertical wells, and wells from other basins. These data can inform treatability, reuse, and management decisions specific to the DJ Basin to minimize adverse environmental health and well production outcomes.
Collapse
Affiliation(s)
- Natalie M Hull
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, Boulder, CO 80303, USA.
| | - James S Rosenblum
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, Boulder, CO 80303, USA.
| | - Charles E Robertson
- University of Colorado School of Medicine, Anschutz Campus, Division of Infectious Disease, Aurora, CO 80405, USA.
| | - J Kirk Harris
- University of Colorado School of Medicine, Anschutz Campus, Department of Pediatrics, Aurora, CO 80405, USA.
| | - Karl G Linden
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, Boulder, CO 80303, USA.
| |
Collapse
|
50
|
Santos-Cortez RLP, Chiong CM, Frank DN, Ryan AF, Giese APJ, Bootpetch Roberts T, Daly KA, Steritz MJ, Szeremeta W, Pedro M, Pine H, Yarza TKL, Scholes MA, Llanes EGDV, Yousaf S, Friedman N, Tantoco MLC, Wine TM, Labra PJ, Benoit J, Ruiz AG, de la Cruz RAR, Greenlee C, Yousaf A, Cardwell J, Nonato RMA, Ray D, Ong KMC, So E, Robertson CE, Dinwiddie J, Lagrana-Villagracia SM, Gubbels SP, Shaikh RS, Cass SP, Einarsdottir E, Lee NR, Schwartz DA, Gloria-Cruz TLI, Bamshad MJ, Yang IV, Kere J, Abes GT, Prager JD, Riazuddin S, Chan AL, Yoon PJ, Nickerson DA, Cutiongco-de la Paz EM, Streubel SO, Reyes-Quintos MRT, Jenkins HA, Mattila P, Chan KH, Mohlke KL, Leal SM, Hafrén L, Chonmaitree T, Sale MM, Ahmed ZM. FUT2 Variants Confer Susceptibility to Familial Otitis Media. Am J Hum Genet 2018; 103:679-690. [PMID: 30401457 PMCID: PMC6217759 DOI: 10.1016/j.ajhg.2018.09.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/19/2018] [Indexed: 01/30/2023] Open
Abstract
Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154∗) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202∗) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2 × 10-5) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154∗) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10-7) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants-namely p.Ala104Val, p.Arg138Cys, p.Trp154∗, and p.Arg202∗-reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.
Collapse
Affiliation(s)
- Regie Lyn P Santos-Cortez
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Center for Children's Surgery, Children's Hospital Colorado (CHCO), Aurora, CO 80045, USA; Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines.
| | - Charlotte M Chiong
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; National Hearing Screening Reference Center, UP Manila-NIH, Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Daniel N Frank
- Division of Infectious Diseases, Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Arnaud P J Giese
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Tori Bootpetch Roberts
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Kathleen A Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew J Steritz
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Wasyl Szeremeta
- Department of Otolaryngology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Melquiadesa Pedro
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines
| | - Harold Pine
- Department of Otolaryngology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Talitha Karisse L Yarza
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; National Hearing Screening Reference Center, UP Manila-NIH, Manila 1000, Philippines
| | - Melissa A Scholes
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Erasmo Gonzalo D V Llanes
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Saira Yousaf
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Norman Friedman
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Ma Leah C Tantoco
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Todd M Wine
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Patrick John Labra
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Jeanne Benoit
- Division of Infectious Diseases, Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Amanda G Ruiz
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Rhodieleen Anne R de la Cruz
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Christopher Greenlee
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Ayesha Yousaf
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | | | - Rachelle Marie A Nonato
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Dylan Ray
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Kimberly Mae C Ong
- Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Edward So
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Charles E Robertson
- Division of Infectious Diseases, Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Jordyn Dinwiddie
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Sheryl Mae Lagrana-Villagracia
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines
| | - Samuel P Gubbels
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Rehan S Shaikh
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Stephen P Cass
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki 00014, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden
| | - Nanette R Lee
- USC-Office of Population Studies Foundation and Department of Anthropology, Sociology and History, University of San Carlos, Cebu City 6000, Philippines
| | | | - Teresa Luisa I Gloria-Cruz
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ivana V Yang
- Department of Medicine, CUSOM, Aurora, CO 80045, USA
| | - Juha Kere
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki 00014, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden; Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Generoso T Abes
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Jeremy D Prager
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Abner L Chan
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines
| | - Patricia J Yoon
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Sven-Olrik Streubel
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Maria Rina T Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines (UP) Manila - National Institutes of Health (NIH), Manila 1000, Philippines; National Hearing Screening Reference Center, UP Manila-NIH, Manila 1000, Philippines; Department of Otorhinolaryngology, UP Manila College of Medicine - Philippine General Hospital, Manila 1000, Philippines; UP Manila - NIH, Manila 1000, Philippines
| | - Herman A Jenkins
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA
| | - Petri Mattila
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, 00029 HUS, Finland
| | - Kenny H Chan
- Department of Otolaryngology, University of Colorado School of Medicine (CUSOM), Aurora, CO 80045, USA; Department of Pediatric Otolaryngology, CHCO, Aurora, CO 80045, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, 00029 HUS, Finland
| | - Tasnee Chonmaitree
- Department of Pediatrics, Division of Infectious Diseases, UTMB, Galveston, TX 77555, USA
| | - Michele M Sale
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Zubair M Ahmed
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| |
Collapse
|