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Hecht AL, Harling LC, Friedman ES, Tanes C, Lee J, Firrman J, Hao F, Tu V, Liu L, Patterson AD, Bittinger K, Goulian M, Wu GD. Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae. J Clin Invest 2024; 134:e174726. [PMID: 38512401 PMCID: PMC11060737 DOI: 10.1172/jci174726] [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: 08/11/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024] Open
Abstract
Bacterial translocation from the gut microbiota is a source of sepsis in susceptible patients. Previous work suggests that overgrowth of gut pathobionts, including Klebsiella pneumoniae, increases the risk of disseminated infection. Our data from a human dietary intervention study found that, in the absence of fiber, K. pneumoniae bloomed during microbiota recovery from antibiotic treatment. We thus hypothesized that dietary nutrients directly support or suppress colonization of this gut pathobiont in the microbiota. Consistent with our study in humans, complex carbohydrates in dietary fiber suppressed the colonization of K. pneumoniae and allowed for recovery of competing commensals in mouse models. In contrast, through ex vivo and in vivo modeling, we identified simple carbohydrates as a limiting resource for K. pneumoniae in the gut. As proof of principle, supplementation with lactulose, a nonabsorbed simple carbohydrate and an FDA-approved therapy, increased colonization of K. pneumoniae. Disruption of the intestinal epithelium led to dissemination of K. pneumoniae into the bloodstream and liver, which was prevented by dietary fiber. Our results show that dietary simple and complex carbohydrates were critical not only in the regulation of pathobiont colonization but also disseminated infection, suggesting that targeted dietary interventions may offer a preventative strategy in high-risk patients.
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Affiliation(s)
- Aaron L. Hecht
- Division of Gastroenterology and Hepatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lisa C. Harling
- Division of Gastroenterology and Hepatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Junhee Lee
- Division of Gastroenterology and Hepatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Fuhua Hao
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Bass R, Tanes C, Bittinger K, Li Y, Lee H, Friedman ES, Koo I, Patterson AD, Liu Q, Wu GD, Stallings VA. Changes in fecal lipidome after treatment with ivacaftor without changes in microbiome or bile acids. J Cyst Fibros 2023:S1569-1993(23)00915-3. [PMID: 37813785 PMCID: PMC10998923 DOI: 10.1016/j.jcf.2023.09.010] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/28/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Alterations in gastrointestinal health are prominent manifestations of cystic fibrosis (CF) and can independently impact pulmonary function. Ivacaftor has been associated with robust improvements in pulmonary function and weight gain, but less is known about the impact of ivacaftor on the fecal microbiome, lipidome, and bile acids. METHODS Stool samples from 18 patients with CF and gating mutations (ages 6-61 years, 13 pancreatic insufficient) were analyzed for fecal microbiome and lipidome composition as well as bile acid concentrations at baseline and after 3 months of treatment with ivacaftor. Microbiome composition was also assessed in a healthy reference cohort. RESULTS Alpha and beta diversity of the microbiome were different between CF and reference cohort at baseline, but no treatment effect was seen in the CF cohort between baseline and 3 months. Seven lipids increased with treatment. No differences were seen in bile acid concentrations after treatment in CF. At baseline, 403 lipids and unconjugated bile acids were different between pancreatic insufficient (PI-CF) and sufficient (PS-CF) groups and 107 lipids were different between PI-CF and PS-CF after 3 months of treatment. CONCLUSIONS The composition and diversity of the fecal microbiome were different in CF as compared to a healthy reference, and did not change after 3 months of ivacaftor. We detected modest differences in the fecal lipidome with treatment. Differences in lipid and bile acid profiles between PS-CF and PI-CF were attenuated after 3 months of treatment.
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Affiliation(s)
- Rosara Bass
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA; Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Ceylan Tanes
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Kyle Bittinger
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Yun Li
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr., Philadelphia, PA 19104, USA
| | - Hongzhe Lee
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr., Philadelphia, PA 19104, USA
| | - Elliot S Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 322 Life Sciences Building, University Park, PA 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 322 Life Sciences Building, University Park, PA 16802, USA
| | - Qing Liu
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Gary D Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Virginia A Stallings
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA; Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
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3
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Lemons JMS, Conrad M, Tanes C, Chen J, Friedman ES, Roggiani M, Curry D, Chau L, Hecht AL, Harling L, Vales J, Kachelries KE, Baldassano RN, Goulian M, Bittinger K, Master SR, Liu L, Wu GD. Enterobacteriaceae Growth Promotion by Intestinal Acylcarnitines, a Biomarker of Dysbiosis in Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 17:131-148. [PMID: 37739064 PMCID: PMC10694575 DOI: 10.1016/j.jcmgh.2023.09.005] [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] [Received: 05/02/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND & AIMS Altered plasma acylcarnitine levels are well-known biomarkers for a variety of mitochondrial fatty acid oxidation disorders and can be used as an alternative energy source for the intestinal epithelium when short-chain fatty acids are low. These membrane-permeable fatty acid intermediates are excreted into the gut lumen via bile and are increased in the feces of patients with inflammatory bowel disease (IBD). METHODS Herein, based on studies in human subjects, animal models, and bacterial cultures, we show a strong positive correlation between fecal carnitine and acylcarnitines and the abundance of Enterobacteriaceae in IBD where they can be consumed by bacteria both in vitro and in vivo. RESULTS Carnitine metabolism promotes the growth of Escherichia coli via anaerobic respiration dependent on the cai operon, and acetylcarnitine dietary supplementation increases fecal carnitine levels with enhanced intestinal colonization of the enteric pathogen Citrobacter rodentium. CONCLUSIONS In total, these results indicate that the increased luminal concentrations of carnitine and acylcarnitines in patients with IBD may promote the expansion of pathobionts belonging to the Enterobacteriaceae family, thereby contributing to disease pathogenesis.
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Affiliation(s)
- Johanna M S Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania
| | - Maire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jie Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elliot S Friedman
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Manuela Roggiani
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dylan Curry
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lillian Chau
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aaron L Hecht
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lisa Harling
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer Vales
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly E Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stephen R Master
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania.
| | - Gary D Wu
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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4
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Hecht AL, Harling LC, Friedman ES, Tanes C, Lee J, Firrman J, Tu V, Liu L, Bittinger K, Goulian M, Wu GD. Colonization and Dissemination of Klebsiella pneumoniae is Dependent on Dietary Carbohydrates. bioRxiv 2023:2023.05.25.542283. [PMID: 37292978 PMCID: PMC10245944 DOI: 10.1101/2023.05.25.542283] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dysbiosis of the gut microbiota is increasingly appreciated as both a consequence and precipitant of human disease. The outgrowth of the bacterial family Enterobacteriaceae is a common feature of dysbiosis, including the human pathogen Klebsiella pneumoniae . Dietary interventions have proven efficacious in the resolution of dysbiosis, though the specific dietary components involved remain poorly defined. Based on a previous human diet study, we hypothesized that dietary nutrients serve as a key resource for the growth of bacteria found in dysbiosis. Through human sample testing, and ex-vivo , and in vivo modeling, we find that nitrogen is not a limiting resource for the growth of Enterobacteriaceae in the gut, contrary to previous studies. Instead, we identify dietary simple carbohydrates as critical in colonization of K. pneumoniae . We additionally find that dietary fiber is necessary for colonization resistance against K. pneumoniae , mediated by recovery of the commensal microbiota, and protecting the host against dissemination from the gut microbiota during colitis. Targeted dietary therapies based on these findings may offer a therapeutic strategy in susceptible patients with dysbiosis.
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Conrey PE, Denu L, O'Boyle KC, Rozich I, Green J, Maslanka J, Lubin JB, Duranova T, Haltzman BL, Gianchetti L, Oldridge DA, De Luna N, Vella LA, Allman D, Spergel JM, Tanes C, Bittinger K, Henrickson SE, Silverman MA. IgA deficiency destabilizes homeostasis toward intestinal microbes and increases systemic immune dysregulation. Sci Immunol 2023; 8:eade2335. [PMID: 37235682 DOI: 10.1126/sciimmunol.ade2335] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
The ability of most patients with selective immunoglobulin A (IgA) deficiency (SIgAD) to remain apparently healthy has been a persistent clinical conundrum. Compensatory mechanisms, including IgM, have been proposed, yet it remains unclear how secretory IgA and IgM work together in the mucosal system and, on a larger scale, whether the systemic and mucosal anti-commensal responses are redundant or have unique features. To address this gap in knowledge, we developed an integrated host-commensal approach combining microbial flow cytometry and metagenomic sequencing (mFLOW-Seq) to comprehensively define which microbes induce mucosal and systemic antibodies. We coupled this approach with high-dimensional immune profiling to study a cohort of pediatric patients with SIgAD and household control siblings. We found that mucosal and systemic antibody networks cooperate to maintain homeostasis by targeting a common subset of commensal microbes. In IgA-deficiency, we find increased translocation of specific bacterial taxa associated with elevated levels of systemic IgG targeting fecal microbiota. Associated features of immune system dysregulation in IgA-deficient mice and humans included elevated levels of inflammatory cytokines, enhanced follicular CD4 T helper cell frequency and activation, and an altered CD8 T cell activation state. Although SIgAD is clinically defined by the absence of serum IgA, the symptomatology and immune dysregulation were concentrated in the SIgAD participants who were also fecal IgA deficient. These findings reveal that mucosal IgA deficiency leads to aberrant systemic exposures and immune responses to commensal microbes, which increase the likelihood of humoral and cellular immune dysregulation and symptomatic disease in patients with IgA deficiency.
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Affiliation(s)
- Peyton E Conrey
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lidiya Denu
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kaitlin C O'Boyle
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Isaiah Rozich
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamal Green
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffrey Maslanka
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jean-Bernard Lubin
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Tereza Duranova
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Lauren Gianchetti
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Derek A Oldridge
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nina De Luna
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura A Vella
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan M Spergel
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyle Bittinger
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah E Henrickson
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A Silverman
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Liu L, Narrowe AB, Firrman JA, Mahalak KK, Bobokalonov JT, Lemons JMS, Bittinger K, Daniel S, Tanes C, Mattei L, Friedman ES, Soares JW, Kobori M, Zeng WB, Tomasula PM. Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME). Foods 2023; 12:2105. [PMID: 37297350 PMCID: PMC10252382 DOI: 10.3390/foods12112105] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/13/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
In the present research, we investigated changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). The probiotics were added to the ascending colon region of mature microbial communities established in a human intestinal microbial ecosystem simulator. Shotgun metagenomic sequencing and metabolome analysis suggested that the changes in microbial community composition corresponded with changes to metabolic output, and we can infer linkages between some metabolites and microorganisms. The in vitro method permits a spatially-resolved view of metabolic transformations under human physiological conditions. By this method, we found that tryptophan and tyrosine were mainly produced in the ascending colon region, while their derivatives were detected in the transverse and descending regions, revealing sequential amino acid metabolic pathways along with the colonic tract. The addition of LGG appeared to promote the production of indole propionic acid, which is positively associated with human health. Furthermore, the microbial community responsible for the production of indole propionic acid may be broader than is currently known.
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Affiliation(s)
- LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Jenni A. Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Jamshed T. Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
- V.I. Nikitin Chemistry Institute of Tajikistan Academy of Sciences, Dushanbe 734063, Tajikistan
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elliot S. Friedman
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason W. Soares
- Bioprocessing and Bioengineering Group, US Army Combat Capabilities Development Command Soldier Center (CCDC-SC), Natick, MA 01760, USA
| | - Masuko Kobori
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Ibaraki, Japan
| | - Wei-Bin Zeng
- Department of Mathematics, University of Louisville, Louisville, KY 40292, USA
| | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
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7
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Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Correction for Merenstein et al., "Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome". mBio 2022; 13:e0229322. [PMID: 36043873 PMCID: PMC9601094 DOI: 10.1128/mbio.02293-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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8
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Mahalak KK, Firrman J, Bobokalonov J, Narrowe AB, Bittinger K, Daniel S, Tanes C, Mattei LM, Zeng WB, Soares JW, Kobori M, Lemons JMS, Tomasula PM, Liu L. Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome. Int J Mol Sci 2022; 23:12973. [PMID: 36361763 PMCID: PMC9657340 DOI: 10.3390/ijms232112973] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2023] Open
Abstract
The consumption of probiotics is widely encouraged due to reports of their positive effects on human health. In particular, Lacticaseibacillus rhamnosus strain GG (LGG) is an approved probiotic that has been reported to improve health outcomes, especially for gastrointestinal disorders. However, how LGG cooperates with the gut microbiome has not been fully explored. To understand the interaction between LGG and its ability to survive and grow within the gut microbiome, this study introduced LGG into established microbial communities using an in vitro model of the colon. LGG was inoculated into the simulated ascending colon and its persistence in, and transit through the subsequent transverse and descending colon regions was monitored over two weeks. The impact of LGG on the existing bacterial communities was investigated using 16S rRNA sequencing and short-chain fatty acid analysis. LGG was able to engraft and proliferate in the ascending region for at least 10 days but was diminished in the transverse and descending colon regions with little effect on short-chain fatty acid abundance. These data suggest that the health benefits of the probiotic LGG rely on its ability to transiently engraft and modulate the host microbial community.
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Affiliation(s)
- Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Jamshed Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Wei-Bin Zeng
- Department of Mathematics, University of Louisville, Louisville, KY 40292, USA
| | - Jason W. Soares
- Bioprocessing and Bioengineering Group, US Army Combat Capabilities Development Command Soldier Center (CCDC-SC), Natick, MA 01760, USA
| | - Masuko Kobori
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba 305-8642, Ibaraki, Japan
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
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9
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Bartolo L, Afroz S, Pan YG, Xu R, Williams L, Lin CF, Tanes C, Bittinger K, Friedman ES, Gimotty PA, Wu GD, Su LF. SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens. Sci Immunol 2022; 7:eabn3127. [PMID: 35857619 PMCID: PMC9348748 DOI: 10.1126/sciimmunol.abn3127] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 11/19/2021] [Accepted: 06/30/2022] [Indexed: 01/18/2023]
Abstract
The baseline composition of T cells directly affects later response to pathogens, but the complexity of precursor states remains poorly defined. Here, we examined the baseline state of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells in unexposed individuals. SARS-CoV-2-specific CD4+ T cells were identified in prepandemic blood samples by major histocompatibility complex (MHC) class II tetramer staining and enrichment. Our data revealed a substantial number of SARS-CoV-2-specific T cells that expressed memory phenotype markers. Integrated phenotypic analyses demonstrated diverse preexisting memory states that included cells with distinct polarization features and trafficking potential to barrier tissues. T cell clones generated from tetramer-labeled cells cross-reacted with antigens from commensal bacteria in the skin and gastrointestinal tract. Direct ex vivo tetramer staining for one spike-specific population showed a similar level of cross-reactivity to sequences from endemic coronavirus and commensal bacteria. These data highlight the complexity of precursor T cell repertoire and implicate noninfectious exposures to common microbes as a key factor that shapes human preexisting immunity to SARS-CoV-2.
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Affiliation(s)
- Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sumbul Afroz
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruozhang Xu
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Lea Williams
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Chin-Fang Lin
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura F. Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
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10
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Breton J, Tanes C, Tu V, Albenberg L, Rowley S, Devas N, Hwang R, Kachelries K, Wu GD, Baldassano RN, Bittinger K, Mattei P. A Microbial Signature for Paediatric Perianal Crohn's Disease. J Crohns Colitis 2022; 16:1281-1292. [PMID: 35211723 DOI: 10.1093/ecco-jcc/jjac032] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/09/2021] [Accepted: 02/23/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Perianal fistulising disease can affect up to 25% of patients with Crohn's disease [CD] and lead to significant morbidity. Although the role of the gut microbiota in inflammatory bowel disease [IBD] has been increasingly recognised, its role in fistula development has scarcely been studied. Here, we aimed to define the microbial signature associated with perianal fistulising CD in children. METHODS A prospective observational study including children age 6-18 years with a diagnosis of perianal fistulising CD was conducted. Stool samples and rectal and perianal fistula swabs were collected. Stool samples and rectal swabs from children with CD without perianal disease and healthy children were included as comparison. Whole shotgun metagenomic sequencing was performed. RESULTS A total of 31 children [mean age 15.5 ± 3.5 years] with perianal CD were prospectively enrolled. The fistula-associated microbiome showed an increase in alpha diversity and alteration in the abundance of several taxa compared with the rectal- and faecal-associated microbiome with key taxa belonging to the Proteobacteria phylum. Genes conferring resistance to the clinically used antibiotic regimen ciprofloxacin and metronidazole were found in the three sample types. In comparison with children without the perianal phenotype [N = 36] and healthy controls [N = 41], the mucosally-associated microbiome of children with perianal CD harboured a reduced butyrogenic potential. Linear discriminant analysis identified key taxa distinguishing the rectal mucosally-associated microbiome of children with perianal CD from children without this phenotype. CONCLUSIONS The microbial community within CD-related anorectal fistula is compositionally and functionally unique. Taken together, these findings emphasise the need to better understand the ecosystem of the fistula milieu to guide development of novel microbiome-based strategies in this CD phenotype.
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Affiliation(s)
- Jessica Breton
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lindsey Albenberg
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Rowley
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nina Devas
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rosa Hwang
- Division of General Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelly Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gary D Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter Mattei
- Division of General Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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11
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Kastl A, Zong W, Gershuni VM, Friedman ES, Tanes C, Boateng A, Mitchell WJ, O’Connor K, Bittinger K, Terry NA, Bales C, Albenberg L, Wu GD. Dietary fiber-based regulation of bile salt hydrolase activity in the gut microbiota and its relevance to human disease. Gut Microbes 2022; 14:2083417. [PMID: 35658830 PMCID: PMC9176262 DOI: 10.1080/19490976.2022.2083417] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Complications of short bowel syndrome (SBS) include malabsorption and bacterial overgrowth, requiring prolonged dependence on parenteral nutrition (PN). We hypothesized that the intolerance of whole food in some SBS patients might be due to the effect of dietary fiber on the gut microbiome. Shotgun metagenomic sequencing and targeted metabolomics were performed using biospecimens collected from 55 children with SBS and a murine dietary fiber model. Bioinformatic analyses were performed on these datasets as well as from a healthy human dietary intervention study. Compared to healthy controls, the gut microbiota in SBS had lower diversity and increased Proteobacteria, a pattern most pronounced in children on PN and inversely correlated with whole food consumption. Whole food intake correlated with increased glycoside hydrolases (GH) and bile salt hydrolases (BSH) with reduced fecal conjugated bile acids suggesting that dietary fiber regulates BSH activity via GHs. Mechanistic evidence supporting this notion was generated via fecal and plasma bile acid profiling in a healthy human fiber-free dietary intervention study as well as in a dietary fiber mouse experiment. Gaussian mixture modeling of fecal bile acids was used to identify three clinically relevant SBS phenotypes. Dietary fiber is associated with bile acid deconjugation likely via an interaction between gut microbiota BSHs and GHs in the small intestine, which may lead to whole food intolerance in patients with SBS. This mechanism not only has potential utility in clinical phenotyping and targeted therapeutics in SBS based on bile acid metabolism but may have relevance to other intestinal disease states.
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Affiliation(s)
- Arthur Kastl
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wenjing Zong
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Victoria M. Gershuni
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adoma Boateng
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - William J. Mitchell
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kathleen O’Connor
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Natalie A. Terry
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christina Bales
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lindsey Albenberg
- Division of Gastroenterology, Hepatology, and Nutrition, the Children’s Hospital of Philadelphia, Philadelphia, PA, USA,CONTACT Lindsey Albenberg Children’s Hospital of Philadelphia, 2716 South Street, 14-140, Philadelphia, PA, 19146, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Gary D. Wu Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, 915 BRB II/III, 421 Curie Blvd., Philadelphia, PA, 19104, USA
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12
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Silverman MA, Conrey PE, Denu L, O’Boyle KC, Tanes C, Green J, Bittinger K, Allman D, Lubin JB, Duranova T, Oldridge D, Henrickson S. IgA deficiency destabilizes immunological homeostasis towards intestinal microbiota and increases the risk of systemic immune dysregulation. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.160.06] [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] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Mammals produce large quantities of mucosal and systemic antibodies that maintain the intestinal barrier, shape the intestinal microbiome and promote lifelong mutualism with commensal microbes. Here, we developed an integrated host-commensal approach combining microbial flow cytometry and 16S rRNA gene sequencing to define the population of microbes that induce mucosal and systemic antibodies with CyTOF analysis in pediatric selective Immunoglobulin A (IgA) deficient and household control siblings to determine the impacts of IgA deficiency on host cellular immune phenotype. In healthy controls, mucosal secretory IgA and IgM antibodies coat an overlapping subset of microbes, predominantly Firmicutes and Proteobacteria. Serum IgG antibodies target a similar consortium of fecal microbes, revealing connections between mucosal and systemic antibody networks. Furthermore, we find broad systemic immune dysregulation in a subset of children and mice lacking IgA, including enhanced IgG targeting of fecal microbiota, elevated levels of inflammatory and allergic cytokines and alterations in T cell activation state. Thus, IgA tunes systemic interactions between the host and commensal microbiota. Understanding how IgA affects baseline immune tone has implications for predicting and preventing autoimmune, inflammatory and allergic diseases, as well as providing improved prognostic guidance to patients with IgA deficiency.
Supported by CHOP Microbiome Pilot Grant K08AI135091 Burroughs Wellcome Fund, the American Academy of Allergy, Asthma, and Immunology, the Immune Deficiency Foundation, the Primary Immune Deficiency Treatment Consortium and Chan Zuckerberg Initiative
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Affiliation(s)
| | | | | | | | - Ceylan Tanes
- 4Gastroenterology, Children’s Hospital of Philadelphia
| | - Jamal Green
- 5Perelman Sch. of Med., Univ. of Pennsylvania
| | | | - David Allman
- 6Pathology, Perelman School of Medicine, University of Pennsylvania
| | | | | | | | - Sarah Henrickson
- 9Pediatrics, Perelman School of Medicine, University of Pennsylvania
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13
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Firrman J, Liu L, Mahalak K, Tanes C, Bittinger K, Tu V, Bobokalonov J, Mattei L, Zhang H, Van den Abbeele P. The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production. FEMS Microbiol Ecol 2022; 98:6564177. [PMID: 35383853 DOI: 10.1093/femsec/fiac038] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 11/02/2021] [Revised: 02/17/2022] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Abstract
Environmental pH is a critical parameter for maintenance of the gut microbiota. Here, the impact of pH on the gut microbiota luminal and mucosal community structure and short chain fatty acid (SCFA) production was evaluated in vitro, and data compiled to reveal a donor-independent response to an increase or decrease in environmental pH. The results found that raising environmental pH significantly increased luminal community richness and decreased mucosal community evenness. This corresponded with an increased abundance of Ruminococcaceae Ruminococcus, and Erysipelotrichaceae Erysipelatoclostridium, and a decreased abundance of Coriobacteriaceae Collinsella, and Enterobacteriaceae Shigella for both the luminal and mucosal communities. Total SCFA levels were significantly higher, primarily due to an increase in acetic and 2-methylbutanoic acids. Lowering pH decreased luminal community evenness and decreased mucosal community evenness and richness. This corresponded with an increased abundance of Lachnospiraceae Enterocloster, Veillonellaceae Megasphaera, Veillonellaceae Sporomusa, Erysipelotrichaceae Eubacterium, and Alcaligenaceae Sutterella, and decreased abundance of Odoribacteraceae Butyricimonas, Fusobacteriaceae Fusobacterium, Veillonellaceae Phascolarctobacterium, and multiple Enterobacteriaceae species for both the luminal and mucosal communities. Total SCFA levels were significantly lower, with an observed drop in acetic and propionic acids, and increased butyric and valeric acids. Taken together, these results indicate that alterations to environmental pH can modulate the gut microbiota community structure and function, and some changes may occur in a donor-independent manner.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - Karley Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Jamshed Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
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14
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Elgarten CW, Tanes C, Lee JJ, Danziger-Isakov LA, Grimley MS, Green M, Michaels MG, Barnum JL, Ardura MI, Auletta JJ, Blumenstock J, Seif AE, Bittinger KL, Fisher BT. Early stool microbiome and metabolome signatures in pediatric patients undergoing allogeneic hematopoietic cell transplantation. Pediatr Blood Cancer 2022; 69:e29384. [PMID: 34709713 PMCID: PMC8629955 DOI: 10.1002/pbc.29384] [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] [Received: 06/10/2021] [Revised: 08/25/2021] [Accepted: 09/16/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND The contribution of the gastrointestinal tract microbiome to outcomes after allogeneic hematopoietic cell transplantation (HCT) is increasingly recognized. Investigations of larger pediatric cohorts aimed at defining the microbiome state and associated metabolic patterns pretransplant are needed. METHODS We sought to describe the pretransplant stool microbiome in pediatric allogenic HCT patients at four centers. We performed shotgun metagenomic sequencing and untargeted metabolic profiling on pretransplant stool samples. Samples were compared with normal age-matched controls and by clinical characteristics. We then explored associations between stool microbiome measurements and metabolite concentrations. RESULTS We profiled stool samples from 88 pediatric allogeneic HCT patients, a median of 4 days before transplant. Pretransplant stool samples differed from healthy controls based on indices of alpha diversity and in the proportional abundance of specific taxa and bacterial genes. Relative to stool from healthy patients, samples from HCT patients had decreased proportion of Bacteroides, Ruminococcaeae, and genes involved in butyrate production, but were enriched for gammaproteobacterial species. No systematic differences in stool microbiome or metabolomic profiles by age, transplant indication, or hospital were noted. Stool metabolites demonstrated strong correlations with microbiome composition. DISCUSSION Stool samples from pediatric allogeneic HCT patients demonstrate substantial dysbiosis early in the transplant course. As microbiome disruptions associate with adverse transplant outcomes, pediatric-specific analyses examining longitudinal microbiome and metabolome changes are imperative to identify causal associations and to inform rational design of interventions.
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Affiliation(s)
- Caitlin W. Elgarten
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia,Center for Pediatric Clinical Effectiveness Research, Children’s Hospital of Philadelphia
| | - Ceylan Tanes
- PennCHOP Microbiome Program, Children’s Hospital of Philadelphia Research Institute
| | - Jung-jin Lee
- PennCHOP Microbiome Program, Children’s Hospital of Philadelphia Research Institute
| | - Lara A. Danziger-Isakov
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children’s Hospital, Medical Center and University of Cincinnati
| | - Michael S. Grimley
- Division of Bone Marrow Transplantation and Immune Deficiency, Department of Pediatrics, Cincinnati Children’s Hospital
| | - Michael Green
- Division of Infectious Diseases, UPMC Children’s Hospital of Pittsburgh
| | | | - Jessie L. Barnum
- Division of Blood and Marrow Transplantation, UPMC Children’s Hospital of Pittsburgh
| | | | - Jeffery J. Auletta
- Division of Infectious Diseases, Nationwide Children’s Hospital,Division of Hematology/Oncology/BMT, Nationwide Children’s Hospital,National Marrow Donor Program/Be The Match
| | - Jesse Blumenstock
- Center for Pediatric Clinical Effectiveness Research, Children’s Hospital of Philadelphia
| | - Alix E. Seif
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia,Center for Pediatric Clinical Effectiveness Research, Children’s Hospital of Philadelphia
| | - Kyle L. Bittinger
- PennCHOP Microbiome Program, Children’s Hospital of Philadelphia Research Institute,Division of Gastroenterology, Department of Pediatrics, Children’s Hospital of Philadelphia
| | - Brian T. Fisher
- Center for Pediatric Clinical Effectiveness Research, Children’s Hospital of Philadelphia,Division of Infectious Diseases, Department of Pediatrics, Children’s Hospital of Philadelphia
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15
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Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome. mBio 2021; 12:e0177721. [PMID: 34399607 PMCID: PMC8406335 DOI: 10.1128/mbio.01777-21] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [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] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/14/2021] [Indexed: 01/12/2023] Open
Abstract
Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated the respiratory tract microbiome in coronavirus disease 2019 (COVID-19) and its relationship to disease severity, systemic immunologic features, and outcomes. We examined 507 oropharyngeal, nasopharyngeal, and endotracheal samples from 83 hospitalized COVID-19 patients as well as non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, and the commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR. We found that COVID-19 patients had upper respiratory microbiome dysbiosis and greater change over time than critically ill patients without COVID-19. Oropharyngeal microbiome diversity at the first time point correlated inversely with disease severity during hospitalization. Microbiome composition was also associated with systemic immune parameters in blood, as measured by lymphocyte/neutrophil ratios and immune profiling of peripheral blood mononuclear cells. Intubated patients showed patient-specific lung microbiome communities that were frequently highly dynamic, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Thus, the respiratory tract microbiome and commensal viruses are disturbed in COVID-19 and correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, its possible use as biomarkers, and the role of bacterial and viral taxa identified here in COVID-19 pathogenesis. IMPORTANCE COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, results in highly variable outcomes ranging from minimal illness to death, but the reasons for this are not well understood. We investigated the respiratory tract bacterial microbiome and small commensal DNA viruses in hospitalized COVID-19 patients and found that each was markedly abnormal compared to that in healthy people and differed from that in critically ill patients without COVID-19. Early airway samples tracked with the level of COVID-19 illness reached during hospitalization, and the airway microbiome also correlated with immune parameters in blood. These findings raise questions about the mechanisms linking SARS-CoV-2 infection and other microbial inhabitants of the airway, including whether the microbiome might regulate severity of COVID-19 disease and/or whether early microbiome features might serve as biomarkers to discriminate disease severity.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Samantha A. Whiteside
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ana G. Cobián-Güemes
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Madeline S. Merlino
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Louis J. Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Abigail Glascock
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Layla A. Khatib
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ayannah S. Fitzgerald
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amy E. Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Josephine R. Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Derek A. Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nuala J. Meyer
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John E. McGinniss
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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16
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Tanes C, Walker EM, Slisarenko N, Gerrets GL, Grasperge BF, Qin X, Jazwinski SM, Bushman FD, Bittinger K, Rout N. Gut Microbiome Changes Associated with Epithelial Barrier Damage and Systemic Inflammation during Antiretroviral Therapy of Chronic SIV Infection. Viruses 2021; 13:1567. [PMID: 34452432 PMCID: PMC8402875 DOI: 10.3390/v13081567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
Gut dysbiosis is a common feature associated with the chronic inflammation of HIV infection. Toward understanding the interplay of chronic treated HIV infection, dysbiosis, and systemic inflammation, we investigated longitudinal fecal microbiome changes and plasma inflammatory markers in the nonhuman primate model. Following simian immunodeficiency virus (SIV) infection in rhesus macaques, significant changes were observed in several members of the phylum Firmicutes along with an increase in Bacteroidetes. Viral suppression with antiretroviral therapy (ART) resulted in an early but partial recovery of compositional changes and butyrate producing genes in the gut microbiome. Over the course of chronic SIV infection and long-term ART, however, the specific loss of Faecalibacterium prausnitzii and Treponema succinifaciens significantly correlated with an increase in plasma inflammatory cytokines including IL-6, G-CSF, I-TAC, and MIG. Further, the loss of T. succinifaciens correlated with an increase in circulating biomarkers of gut epithelial barrier damage (IFABP) and microbial translocation (LBP and sCD14). As F. prausnitzii and T. succinifaciens are major short-chain fatty acid producing bacteria, their sustained loss during chronic SV-ART may contribute to gut inflammation and metabolic alterations despite effective long-term control of viremia. A better understanding of the correlations between the anti-inflammatory bacterial community and healthy gut barrier functions in the setting of long-term ART may have a major impact on the clinical management of inflammatory comorbidities in HIV-infected individuals.
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Affiliation(s)
- Ceylan Tanes
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (C.T.); (K.B.)
| | - Edith M. Walker
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Nadia Slisarenko
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Giovanni L. Gerrets
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
| | - Brooke F. Grasperge
- Division of Veterinary Medicine, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA;
| | - Xuebin Qin
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA;
| | - S. Michal Jazwinski
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA;
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (C.T.); (K.B.)
| | - Namita Rout
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA 70433, USA; (E.M.W.); (N.S.); (G.L.G.)
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA;
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Benitez AJ, Tanes C, Mattei L, Hofstaedter CE, Kim DK, Gross J, Ruffner MA, Albenberg L, Spergel J, Bittinger K, Muir AB. Effect of topical swallowed steroids on the bacterial and fungal esophageal microbiota in eosinophilic esophagitis. Allergy 2021; 76:1549-1552. [PMID: 32990947 DOI: 10.1111/all.14602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/02/2020] [Accepted: 09/15/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Alain J. Benitez
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
- Department of Pediatrics Perelman School of Medicine at the University of Pennsylvania Philadelphia PA USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
| | - Casey E. Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
| | - Dorothy K. Kim
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
| | - Jonathan Gross
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
| | - Melanie A. Ruffner
- Department of Pediatrics Perelman School of Medicine at the University of Pennsylvania Philadelphia PA USA
- Division of Allergy and Immunology Children’s Hospital of Philadelphia Philadelphia PA USA
| | - Lindsey Albenberg
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
- Department of Pediatrics Perelman School of Medicine at the University of Pennsylvania Philadelphia PA USA
| | - Jonathan Spergel
- Department of Pediatrics Perelman School of Medicine at the University of Pennsylvania Philadelphia PA USA
- Division of Allergy and Immunology Children’s Hospital of Philadelphia Philadelphia PA USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
- Department of Pediatrics Perelman School of Medicine at the University of Pennsylvania Philadelphia PA USA
| | - Amanda B. Muir
- Division of Gastroenterology, Hepatology, and Nutrition Children's Hospital of Philadelphia Philadelphia PA USA
- Department of Pediatrics Perelman School of Medicine at the University of Pennsylvania Philadelphia PA USA
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18
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Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Signatures of COVID-19 severity and immune response in the respiratory tract microbiome. medRxiv 2021:2021.04.02.21254514. [PMID: 33851179 PMCID: PMC8043476 DOI: 10.1101/2021.04.02.21254514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rationale Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Objective To define the respiratory tract microbiome in COVID-19 and relationship disease severity, systemic immunologic features, and outcomes. Methods and Measurements We examined 507 oropharyngeal, nasopharyngeal and endotracheal samples from 83 hospitalized COVID-19 patients, along with non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR, and immune features were characterized by lymphocyte/neutrophil (L/N) ratios and deep immune profiling of peripheral blood mononuclear cells (PBMC). Main Results COVID-19 patients had upper respiratory microbiome dysbiosis, and greater change over time than critically ill patients without COVID-19. Diversity at the first time point correlated inversely with disease severity during hospitalization, and microbiome composition was associated with L/N ratios and PBMC profiles in blood. Intubated patients showed patient-specific and dynamic lung microbiome communities, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Conclusions The respiratory tract microbiome and commensal virome are disturbed in COVID-19, correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, possible use as biomarkers, and role of bacterial and viral taxa identified here in COVID-19 pathogenesis.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Samantha A Whiteside
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Ana G Cobián-Güemes
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Madeline S Merlino
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Louis J Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Abigail Glascock
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Layla A Khatib
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Ayannah S Fitzgerald
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Derek A Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Nuala J Meyer
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - John E McGinniss
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Ronald G Collman
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
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19
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Firrman J, Liu L, Tanes C, Friedman ES, Bittinger K, Daniel S, van den Abbeele P, Evans B. Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an In Vitro Platform. J Agric Food Chem 2020; 68:13056-13067. [PMID: 31690071 DOI: 10.1021/acs.jafc.9b05202] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The colon gut microbiota is responsible for complex chemical conversions of nutrients and subsequent release of metabolites that have diverse biological consequences. However, information on the metabolic dynamics that occur longitudinally through the colon is limited. Here, gas and liquid chromatographies coupled with mass spectrometry were applied to generate metabolic profiles of the region-specific microbial communities cultured using an in vitro platform simulating the ascending (AC), transverse (TC), and descending (DC) colon regions. Comparative analysis revealed a large divergence between metabolic profiles of the AC and the TC and DC regions in terms of short-chain fatty acid production, metabolic spectrum, and conversion of bile acids. Metagenomic evaluation revealed that the regionally derived metabolic profiles had strong correlation to community composition and genetic potential. Together, the results provide key insights regarding the metabolic divergence of the regional communities that are integral to understand the structure-function relationship of the gut microbiota.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wyndmoor, Pennsylvania 19038, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wyndmoor, Pennsylvania 19038, United States
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Elliot S Friedman
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | | | - Bradley Evans
- Proteomics & Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, Missouri 63132, United States
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20
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Polster SP, Sharma A, Tanes C, Tang AT, Mericko P, Cao Y, Carrión-Penagos J, Girard R, Koskimäki J, Zhang D, Stadnik A, Romanos SG, Lyne SB, Shenkar R, Yan K, Lee C, Akers A, Morrison L, Robinson M, Zafar A, Bittinger K, Kim H, Gilbert JA, Kahn ML, Shen L, Awad IA. Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma. Nat Commun 2020; 11:2659. [PMID: 32461638 PMCID: PMC7253448 DOI: 10.1038/s41467-020-16436-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/03/2019] [Accepted: 05/04/2020] [Indexed: 11/09/2022] Open
Abstract
Cavernous angiomas (CA) are common vascular anomalies causing brain hemorrhage. Based on mouse studies, roles of gram-negative bacteria and altered intestinal homeostasis have been implicated in CA pathogenesis, and pilot study had suggested potential microbiome differences between non-CA and CA individuals based on 16S rRNA gene sequencing. We here assess microbiome differences in a larger cohort of human subjects with and without CA, and among subjects with different clinical features, and conduct more definitive microbial analyses using metagenomic shotgun sequencing. Relative abundance of distinct bacterial species in CA patients is shown, consistent with postulated permissive microbiome driving CA lesion genesis via lipopolysaccharide signaling, in humans as in mice. Other microbiome differences are related to CA clinical behavior. Weighted combinations of microbiome signatures and plasma inflammatory biomarkers enhance associations with disease severity and hemorrhage. This is the first demonstration of a sensitive and specific diagnostic microbiome in a human neurovascular disease.
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Affiliation(s)
- Sean P Polster
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Anukriti Sharma
- Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of California San Diego and Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA, 19146, USA
| | - Alan T Tang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Patricia Mericko
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Ying Cao
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Julián Carrión-Penagos
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Romuald Girard
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Janne Koskimäki
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Dongdong Zhang
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Agnieszka Stadnik
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Sharbel G Romanos
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Seán B Lyne
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Robert Shenkar
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Kimberly Yan
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Cornelia Lee
- Angioma Alliance, 520W 21st Street, Norfolk, VA, 23517, USA
| | - Amy Akers
- Angioma Alliance, 520W 21st Street, Norfolk, VA, 23517, USA
| | - Leslie Morrison
- Department of Neurology, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Myranda Robinson
- Department of Neurology, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Atif Zafar
- Department of Neurology, University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA, 19146, USA
| | - Helen Kim
- Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Jack A Gilbert
- Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of California San Diego and Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Le Shen
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA.
- Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA.
| | - Issam A Awad
- Section of Neurosurgery, Department of Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA.
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21
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Rubel MA, Abbas A, Taylor LJ, Connell A, Tanes C, Bittinger K, Ndze VN, Fonsah JY, Ngwang E, Essiane A, Fokunang C, Njamnshi AK, Bushman FD, Tishkoff SA. Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. Genome Biol 2020; 21:122. [PMID: 32450885 PMCID: PMC7249393 DOI: 10.1186/s13059-020-02020-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 09/19/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia. RESULTS We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids. CONCLUSIONS These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.
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Affiliation(s)
- Meagan A. Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Present Address: Department of Radiology, Center for Translational Imaging and Precision Medicine, UC San Diego, San Diego, CA USA
| | - Arwa Abbas
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Present Address: Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Louis J. Taylor
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Andrew Connell
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Valantine N. Ndze
- Johns Hopkins Cameroon Program, Yaoundé, Cameroon
- Department of Microbiology, Hematology, Parasitology and Infectious Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Julius Y. Fonsah
- Department of Neurology, Faculty of Medicine and Biomedical Sciences, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Eric Ngwang
- Department of Anthropology, Faculty of Arts, Letters and Social Sciences, University of Yaoundé I, PO Box 755, Yaoundé, Cameroon
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K. Njamnshi
- Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sarah A. Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
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22
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Hribe-Herranz M, Bittinger K, Tanes C, Rafail S, Pierini S, Ben-Joseph E, Tanyi J, Facciabene A. Abstract IA25: Tumors alter gut microbiota to suppress immunity and foster progression. Cancer Res 2020. [DOI: 10.1158/1538-7445.mvc2020-ia25] [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] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immune dysfunction is commonly observed in patients with cancer contributing to tumor progression. While previous work established a connection between the gut microbiota and the immune system, the mechanisms by which microbiotas contribute to cancer-associated immune dysfunction are not well understood. Using multiple mouse cancer models, we demonstrated robust alterations of gut microbiota in tumor-bearing mice and a substantial change in antimicrobial peptides produced by the gut epithelium. We identified an overall reduction in IFN-γ T cells in tumor-bearing mice, which was rescued with antibiotics treatment or by co-housing tumor-bearing mice with healthy mice. Similar to mouse, we observed changes in gut microbiota and antimicrobial peptides levels of patients diagnosed with ovarian or lung cancer. We identify Firmicutes Ruminococcus members as key promoters of immune dysfunctions and tumor development. These findings identify a new mechanism of immune modulation utilized by tumors to undermine the immune responses and promote tumor progression.
Citation Format: Mireia Hribe-Herranz, Kyle Bittinger, Ceylan Tanes, Stavros Rafail, Stefano Pierini, Edgar Ben-Joseph, Janos Tanyi, Andrea Facciabene. Tumors alter gut microbiota to suppress immunity and foster progression [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA25.
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Affiliation(s)
| | | | | | | | | | | | - Janos Tanyi
- University of Pennsylvania, Philadelphia, PA
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23
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Tang AT, Sullivan KR, Hong CC, Goddard LM, Mahadevan A, Ren A, Pardo H, Peiper A, Griffin E, Tanes C, Mattei LM, Yang J, Li L, Mericko-Ishizuka P, Shen L, Hobson N, Girard R, Lightle R, Moore T, Shenkar R, Polster SP, Rödel CJ, Li N, Zhu Q, Whitehead KJ, Zheng X, Akers A, Morrison L, Kim H, Bittinger K, Lengner CJ, Schwaninger M, Velcich A, Augenlicht L, Abdelilah-Seyfried S, Min W, Marchuk DA, Awad IA, Kahn ML. Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation. Sci Transl Med 2019; 11:eaaw3521. [PMID: 31776290 PMCID: PMC6937779 DOI: 10.1126/scitranslmed.aaw3521] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/17/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022]
Abstract
Cerebral cavernous malformation (CCM) is a genetic, cerebrovascular disease. Familial CCM is caused by genetic mutations in KRIT1, CCM2, or PDCD10 Disease onset is earlier and more severe in individuals with PDCD10 mutations. Recent studies have shown that lesions arise from excess mitogen-activated protein kinase kinase kinase 3 (MEKK3) signaling downstream of Toll-like receptor 4 (TLR4) stimulation by lipopolysaccharide derived from the gut microbiome. These findings suggest a gut-brain CCM disease axis but fail to define it or explain the poor prognosis of patients with PDCD10 mutations. Here, we demonstrate that the gut barrier is a primary determinant of CCM disease course, independent of microbiome configuration, that explains the increased severity of CCM disease associated with PDCD10 deficiency. Chemical disruption of the gut barrier with dextran sulfate sodium augments CCM formation in a mouse model, as does genetic loss of Pdcd10, but not Krit1, in gut epithelial cells. Loss of gut epithelial Pdcd10 results in disruption of the colonic mucosal barrier. Accordingly, loss of Mucin-2 or exposure to dietary emulsifiers that reduce the mucus barrier increases CCM burden analogous to loss of Pdcd10 in the gut epithelium. Last, we show that treatment with dexamethasone potently inhibits CCM formation in mice because of the combined effect of action at both brain endothelial cells and gut epithelial cells. These studies define a gut-brain disease axis in an experimental model of CCM in which a single gene is required for two critical components: gut epithelial function and brain endothelial signaling.
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Affiliation(s)
- Alan T Tang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Katie R Sullivan
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Courtney C Hong
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Lauren M Goddard
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Aparna Mahadevan
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Aileen Ren
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Heidy Pardo
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amy Peiper
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Erin Griffin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jisheng Yang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Li Li
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Patricia Mericko-Ishizuka
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Le Shen
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Nicholas Hobson
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Thomas Moore
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Robert Shenkar
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Sean P Polster
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Claudia J Rödel
- Institute for Biochemistry and Biology, Department of Animal Physiology, Potsdam University, Karl-Liebknecht-Str. 24-25, Haus 26, 14476 Potsdam, Germany
| | - Ning Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qin Zhu
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin J Whitehead
- Division of Cardiovascular Medicine and the Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Xiangjian Zheng
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
- Centenary Institute, Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
| | - Amy Akers
- Angioma Alliance, Norfolk, VA 23517, USA
| | - Leslie Morrison
- Department of Neurology and Pediatrics, University of New Mexico, Albuquerque, NM 87106, USA
| | - Helen Kim
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Markus Schwaninger
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, 23562 Lübeck, Germany
| | - Anna Velcich
- Department of Cell Biology, Albert Einstein College of Medicine/Albert Einstein Cancer Center, NY 10461, USA
| | - Leonard Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine/Albert Einstein Cancer Center, NY 10461, USA
| | - Salim Abdelilah-Seyfried
- Institute for Biochemistry and Biology, Department of Animal Physiology, Potsdam University, Karl-Liebknecht-Str. 24-25, Haus 26, 14476 Potsdam, Germany
- Institute of Molecular Biology, Hannover Medical School, Carl-Neuberg Str. 1, D-30625 Hannover, Germany
| | - Wang Min
- Department of Pathology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA.
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Firrman J, Liu L, Tanes C, Bittinger K, Mahalak K, Rinaldi W. Metagenomic assessment of the Cebus apella gut microbiota. Am J Primatol 2019; 81:e23023. [PMID: 31240754 DOI: 10.1002/ajp.23023] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 05/13/2019] [Accepted: 05/27/2019] [Indexed: 12/19/2022]
Abstract
Cebus Apella (C. apella) is a species of Nonhuman Primate (NHP) used for biomedical research because it is phylogenetically similar and shares anatomical commonalities with humans. Here, the gut microbiota of three C. apella were examined in the different regions of the intestinal tract. Using metagenomics, the gut microbiota associated with the luminal content and mucus layer for each intestinal region was identified, and functionality was investigated by quantifying the levels of short chain fatty acids (SCFAs) produced. The results of this study show a high degree of similarity in the intestinal communities among C. apella subjects, with multiple shared characteristics. First, the communities in the lumen were more phylogenetically diverse and rich compared to the mucus layer communities throughout the entire intestinal tract. The small intestine communities in the lumen displayed a higher Shannon diversity index compared to the colon communities. Second, all the communities were dominated by aero-tolerant taxa such as Streptococcus, Enterococcus, Abiotrophia, and Lactobacillus, although there was preferential colonization of specific taxa observed. Finally, the primary SCFA produced throughout the intestinal tract was acetic acid, with some propionic acid and butyric acid detected in the colon regions. The small intestine microbiota produced significantly less SCFAs compared to the communities in the colon. Collectively, these data provide an in-depth report on the composition, distribution, and SCFA production of the gut microbiota along the intestinal tract of the C. apella NHP animal model.
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Affiliation(s)
- Jenni Firrman
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, Pennsylvania
| | - LinShu Liu
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, Pennsylvania
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Karley Mahalak
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, Pennsylvania
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25
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Melo-Gonzalez F, Kammoun H, Evren E, Dutton EE, Papadopoulou M, Bradford BM, Tanes C, Fardus-Reid F, Swann JR, Bittinger K, Mabbott NA, Vallance BA, Willinger T, Withers DR, Hepworth MR. Antigen-presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria. J Exp Med 2019; 216:728-742. [PMID: 30814299 PMCID: PMC6446868 DOI: 10.1084/jem.20180871] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [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: 05/10/2018] [Revised: 12/12/2018] [Accepted: 02/08/2019] [Indexed: 01/05/2023] Open
Abstract
Intestinal immune homeostasis is dependent upon tightly regulated and dynamic host interactions with the commensal microbiota. Immunoglobulin A (IgA) produced by mucosal B cells dictates the composition of commensal bacteria residing within the intestine. While emerging evidence suggests the majority of IgA is produced innately and may be polyreactive, mucosal-dwelling species can also elicit IgA via T cell-dependent mechanisms. However, the mechanisms that modulate the magnitude and quality of T cell-dependent IgA responses remain incompletely understood. Here we demonstrate that group 3 innate lymphoid cells (ILC3) regulate steady state interactions between T follicular helper cells (TfH) and B cells to limit mucosal IgA responses. ILC3 used conserved migratory cues to establish residence within the interfollicular regions of the intestinal draining lymph nodes, where they act to limit TfH responses and B cell class switching through antigen presentation. The absence of ILC3-intrinsic antigen presentation resulted in increased and selective IgA coating of bacteria residing within the colonic mucosa. Together these findings implicate lymph node resident, antigen-presenting ILC3 as a critical regulatory checkpoint in the generation of T cell-dependent colonic IgA and suggest ILC3 act to maintain tissue homeostasis and mutualism with the mucosal-dwelling commensal microbiota.
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Affiliation(s)
- Felipe Melo-Gonzalez
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Hana Kammoun
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Elza Evren
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Emma E Dutton
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Markella Papadopoulou
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Barry M Bradford
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Easter Bush, UK
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Fahmina Fardus-Reid
- Division of Integrative Systems Medicine and Digestive Diseases, Imperial College London, South Kensington, UK
| | - Jonathan R Swann
- Division of Integrative Systems Medicine and Digestive Diseases, Imperial College London, South Kensington, UK
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Neil A Mabbott
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Easter Bush, UK
| | - Bruce A Vallance
- Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Tim Willinger
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David R Withers
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Matthew R Hepworth
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK .,Manchester Collaborative Centre for Inflammation Research, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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26
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Firrman J, Liu L, Van den Abbeele P, Tanes C, Bittinger K, Tomasula P. Applying Advanced In Vitro Culturing Technology to Study the Human Gut Microbiota. J Vis Exp 2019. [PMID: 30829328 DOI: 10.3791/59054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The human gut microbiota plays a vital role in both human health and disease. Studying the gut microbiota using an in vivo model, is difficult due to its complex nature, and its diverse association with mammalian components. The goal of this protocol is to culture the gut microbiota in vitro, which allows for the study of the gut microbiota dynamics, without having to consider the contribution of the mammalian milieu. Using in vitro culturing technology, the physiological conditions of the gastro intestinal tract are simulated, including parameters such as pH, temperature, anaerobiosis, and transit time. The intestinal surface of the colon is simulated by adding mucin-coated carriers, creating a mucosal phase, and adding further dimension. The gut microbiota is introduced by inoculating with the human fecal material. Upon inoculation with this complex mixture of bacteria, specific microbes are enriched in the different longitudinal (ascending, transverse and descending colons) and transversal (luminal and mucosal) environments of the in vitro model. It is crucial to allow the system to reach a steady state, in which the community and the metabolites produced remain stable. The experimental results in this manuscript demonstrate how the inoculated gut microbiota community develops into a stable community over time. Once steady state is achieved, the system can be used to analyze bacterial interactions and community functions or to test the effects of any additives on the gut microbiota, such as food, food components, or pharmaceuticals.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture;
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture
| | | | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia
| | - Peggy Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture
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Hantsoo L, Jašarević E, Criniti S, McGeehan B, Tanes C, Sammel MD, Elovitz MA, Compher C, Wu G, Epperson CN. Childhood adversity impact on gut microbiota and inflammatory response to stress during pregnancy. Brain Behav Immun 2019; 75:240-250. [PMID: 30399404 PMCID: PMC6349044 DOI: 10.1016/j.bbi.2018.11.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [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: 07/06/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Adverse childhood experiences (ACEs), such as abuse or chronic stress, program an exaggerated adult inflammatory response to stress. Emerging rodent research suggests that the gut microbiome may be a key mediator in the association between early life stress and dysregulated glucocorticoid-immune response. However, ACE impact on inflammatory response to stress, or on the gut microbiome, have not been studied in human pregnancy, when inflammation increases risk of poor outcomes. The aim of this study was to assess the relationships among ACE, the gut microbiome, and cytokine response to stress in pregnant women. METHODS Physically and psychiatrically healthy adult pregnant women completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and gave a single stool sample between 20 and 26 weeks gestation. Stool DNA was isolated and 16S sequencing was performed. Three 24-hour food recalls were administered to assess dietary nutrient intake. A subset of women completed the Trier Social Stress Test (TSST) at 22-34 weeks gestation; plasma interleukin-6 (IL-6), interleukin-1β (IL-1β), high sensitivity C-reactive protein (hsCRP), tumor necrosis factor α (TNF-α), and cortisol were measured at four timepoints pre and post stressor, and area under the curve (AUC) was calculated. RESULTS Forty-eight women completed the ACE-Q and provided stool; 19 women completed the TSST. Women reporting 2 or more ACEs (high ACE) had greater differential abundance of gut Prevotella than low ACE participants (q = 5.7 × 10^-13). Abundance of several gut taxa were significantly associated with cortisol, IL-6, TNF-α and CRP AUCs regardless of ACE status. IL-6 response to stress was buffered among high ACE women with high intake of docosahexaenoic acid (DHA) (p = 0.03) and eicosapentaenoic acid (EPA) (p = 0.05). DISCUSSION Our findings suggest that multiple childhood adversities are associated with changes in gut microbiota composition during pregnancy, and such changes may contribute to altered inflammatory and glucocorticoid response to stress. While preliminary, this is the first study to demonstrate an association between gut microbiota and acute glucocorticoid-immune response to stress in a clinical sample. Finally, exploratory analyses suggested that high ACE women with high dietary intake of ω-3 polyunsaturated fatty acids (PUFAs) had a dampened inflammatory response to acute stress, suggesting potentially protective effects of ω-3s in this high-risk population. Given the adverse effects of inflammation on pregnancy and the developing fetus, mechanisms by which childhood adversity influence the gut-brain axis and potential protective factors such as diet should be further explored.
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Affiliation(s)
- Liisa Hantsoo
- Department of Psychiatry, The University of Pennsylvania Perelman School of Medicine, 3535 Market St., Philadelphia, PA 19104, United States.
| | - Eldin Jašarević
- Department of Pharmacology, Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, 670 W Baltimore St. HSF3, 9-173, Baltimore, MD 21201
| | - Stephanie Criniti
- Department of Psychiatry, The University of Pennsylvania Perelman School of Medicine, 3535 Market St., Philadelphia, PA 19104
| | - Brendan McGeehan
- Department of Psychiatry, The University of Pennsylvania Perelman School of Medicine, 3535 Market St., Philadelphia, PA 19104
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104
| | - Mary D. Sammel
- Department of Biostatistics, Epidemiology and Informatics, The University of Pennsylvania Perelman School of Medicine, 423 Guardian Drive, 605 Blockley Hall, Philadelphia, PA 19104
| | - Michal A. Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, The University of Pennsylvania Perelman School of Medicine, 421 Curie Blvd., 1354 BRB II/III Philadelphia, PA 19104
| | - Charlene Compher
- Department of Biobehavioral Health Sciences, The University of Pennsylvania School of Nursing, 137 Claire Fagin Hall, Philadelphia, PA 19104
| | - Gary Wu
- Department of Gastroenterology, The University of Pennsylvania Perelman School of Medicine, 915 BRB II/III, 421 Curie Blvd, Philadelphia, PA 19104
| | - C. Neill Epperson
- Department of Psychiatry, The University of Pennsylvania Perelman School of Medicine, 3535 Market St., Philadelphia, PA 19104
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Liu L, Firrman J, Tanes C, Bittinger K, Thomas-Gahring A, Wu GD, Van den Abbeele P, Tomasula PM. Establishing a mucosal gut microbial community in vitro using an artificial simulator. PLoS One 2018; 13:e0197692. [PMID: 30016326 PMCID: PMC6050037 DOI: 10.1371/journal.pone.0197692] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/07/2018] [Indexed: 11/19/2022] Open
Abstract
The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10–20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion.
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Affiliation(s)
- LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
- * E-mail:
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Audrey Thomas-Gahring
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Gary D. Wu
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
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Uribe-Herranz M, Bittinger K, Rafail S, Guedan S, Pierini S, Tanes C, Gill SA, Tany J, Morgan MA, Bushman FD, June CH, Facciabene A. Abstract 3798: Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3798] [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] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Adoptive T-Cell therapy (ACT) is a promising new modality for malignancies. Here, we report that adoptive T-cell efficacy in tumor-bearing mice is significantly affected by differences in the native composition of the gut microbiome, treatment with antibiotics or by heterologous fecal transfer. Depletion of bacteria with vancomycin, decreased the rate of tumor growth in mice receiving ACT, whereas treatment with neomycin and metronidazole had no effect, indicating the role of specific bacteria in host response. Vancomycin treatment induced an increase in systemic CD8α+ dendritic cells, which mediated a sustained systemic expansion of adoptively transferred antitumor T cells in an IL-12-dependent manner. In subjects undergoing allogeneic hematopoietic cell transplantation, we found that oral vancomycin also increased IL-12 levels. Collectively, our findings demonstrate an important role played by the gut microbiota in the antitumor effectiveness of ACT and suggest new avenues to improve response to ACT by altering the gut microbiota.
Citation Format: Mireia Uribe-Herranz, Kyle Bittinger, Stavros Rafail, Sonia Guedan, Stefano Pierini, Ceylan Tanes, Saar A. Gill, Janos Tany, Mark A. Morgan, Frederic D. Bushman, Carl H. June, Andrea Facciabene. Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3798.
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Affiliation(s)
| | | | | | | | | | - Ceylan Tanes
- 2Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Janos Tany
- 1University of Pennsylvania, Philadelphia, PA
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30
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Uribe-Herranz M, Bittinger K, Rafail S, Guedan S, Pierini S, Tanes C, Ganetsky A, Morgan MA, Gill S, Tanyi JL, Bushman FD, June CH, Facciabene A. Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. JCI Insight 2018; 3:94952. [PMID: 29467322 DOI: 10.1172/jci.insight.94952] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [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: 05/12/2017] [Accepted: 01/18/2018] [Indexed: 12/30/2022] Open
Abstract
Adoptive T cell therapy (ACT) is a promising new modality for malignancies. Here, we report that adoptive T cell efficacy in tumor-bearing mice is significantly affected by differences in the native composition of the gut microbiome or treatment with antibiotics, or by heterologous fecal transfer. Depletion of bacteria with vancomycin decreased the rate of tumor growth in mice from The Jackson Laboratory receiving ACT, whereas treatment with neomycin and metronidazole had no effect, indicating the role of specific bacteria in host response. Vancomycin treatment induced an increase in systemic CD8α+ DCs, which sustained systemic adoptively transferred antitumor T cells in an IL-12-dependent manner. In subjects undergoing allogeneic hematopoietic cell transplantation, we found that oral vancomycin also increased IL-12 levels. Collectively, our findings demonstrate an important role played by the gut microbiota in the antitumor effectiveness of ACT and suggest potentially new avenues to improve response to ACT by altering the gut microbiota.
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Affiliation(s)
- Mireia Uribe-Herranz
- Ovarian Cancer Research Center, and.,Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Sonia Guedan
- Abramson Cancer Center and the Department of Pathology and Laboratory Medicine, Perelman School of Medicine
| | - Stefano Pierini
- Ovarian Cancer Research Center, and.,Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | - Saar Gill
- Division of Hematology Oncology, Department of Medicine, and
| | | | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carl H June
- Abramson Cancer Center and the Department of Pathology and Laboratory Medicine, Perelman School of Medicine
| | - Andrea Facciabene
- Ovarian Cancer Research Center, and.,Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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31
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Tang AT, Choi JP, Kotzin JJ, Yang Y, Hong CC, Hobson N, Girard R, Zeineddine HA, Lightle R, Moore T, Cao Y, Shenkar R, Chen M, Mericko P, Yang J, Li L, Tanes C, Kobuley D, Võsa U, Whitehead KJ, Li DY, Franke L, Hart B, Schwaninger M, Henao-Mejia J, Morrison L, Kim H, Awad IA, Zheng X, Kahn ML. Endothelial TLR4 and the microbiome drive cerebral cavernous malformations. Nature 2017; 545:305-310. [PMID: 28489816 PMCID: PMC5757866 DOI: 10.1038/nature22075] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [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: 07/13/2016] [Accepted: 03/20/2017] [Indexed: 12/22/2022]
Abstract
Cerebral cavernous malformations (CCMs) are a cause of stroke and seizure for which no effective medical therapies yet exist. CCMs arise from the loss of an adaptor complex that negatively regulates MEKK3-KLF2/4 signalling in brain endothelial cells, but upstream activators of this disease pathway have yet to be identified. Here we identify endothelial Toll-like receptor 4 (TLR4) and the gut microbiome as critical stimulants of CCM formation. Activation of TLR4 by Gram-negative bacteria or lipopolysaccharide accelerates CCM formation, and genetic or pharmacologic blockade of TLR4 signalling prevents CCM formation in mice. Polymorphisms that increase expression of the TLR4 gene or the gene encoding its co-receptor CD14 are associated with higher CCM lesion burden in humans. Germ-free mice are protected from CCM formation, and a single course of antibiotics permanently alters CCM susceptibility in mice. These studies identify unexpected roles for the microbiome and innate immune signalling in the pathogenesis of a cerebrovascular disease, as well as strategies for its treatment.
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Affiliation(s)
- Alan T Tang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Jaesung P Choi
- Laboratory of Cardiovascular Signaling, Centenary Institute, Sydney, New South Wales 2050, Australia
| | - Jonathan J Kotzin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yiqing Yang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Courtney C Hong
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Nicholas Hobson
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Hussein A Zeineddine
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Thomas Moore
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Ying Cao
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Robert Shenkar
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Mei Chen
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Patricia Mericko
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Jisheng Yang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Li Li
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Ceylan Tanes
- CHOP Microbiome Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Dmytro Kobuley
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Urmo Võsa
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Kevin J Whitehead
- Division of Cardiovascular Medicine and the Program in Molecular Medicine, University of Utah, Salt Lake City, Utah 84112, USA
| | - Dean Y Li
- Division of Cardiovascular Medicine and the Program in Molecular Medicine, University of Utah, Salt Lake City, Utah 84112, USA
| | - Lude Franke
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Blaine Hart
- Department of Neurology and Pediatrics, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Markus Schwaninger
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, 23562 Lübeck, Germany
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Leslie Morrison
- Department of Neurology and Pediatrics, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Helen Kim
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California 94143, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago School of Medicine and Biological Sciences, Chicago, Illinois 60637, USA
| | - Xiangjian Zheng
- Laboratory of Cardiovascular Signaling, Centenary Institute, Sydney, New South Wales 2050, Australia
- Faculty of Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales 2050, Australia
- Department of Pharmacology, School of Basic Medical Sciences, Tianjian Medical University, Tianjin, China
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
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32
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Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K. Optimizing methods and dodging pitfalls in microbiome research. Microbiome 2017; 5:52. [PMID: 28476139 PMCID: PMC5420141 DOI: 10.1186/s40168-017-0267-5] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [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: 12/24/2016] [Accepted: 04/21/2017] [Indexed: 05/09/2023]
Abstract
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.
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Affiliation(s)
- Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Casey E. Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Erik Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Abigail Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Christel Chehoud
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Máire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
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33
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Chen K, Wu K, Cai S, Zhang W, Zhou J, Wang J, Ertel A, Li Z, Rui H, Quong A, Lisanti MP, Tozeren A, Tanes C, Addya S, Gormley M, Wang C, McMahon SB, Pestell RG. Dachshund binds p53 to block the growth of lung adenocarcinoma cells. Cancer Res 2013; 73:3262-74. [PMID: 23492369 DOI: 10.1158/0008-5472.can-12-3191] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hyperactive EGF receptor (EGFR) and mutant p53 are common genetic abnormalities driving the progression of non-small cell lung cancer (NSCLC), the leading cause of cancer deaths in the world. The Drosophila gene Dachshund (Dac) was originally cloned as an inhibitor of hyperactive EGFR alleles. Given the importance of EGFR signaling in lung cancer etiology, we examined the role of DACH1 expression in lung cancer development. DACH1 protein and mRNA expression was reduced in human NSCLC. Reexpression of DACH1 reduced NSCLC colony formation and tumor growth in vivo via p53. Endogenous DACH1 colocalized with p53 in a nuclear, extranucleolar location, and shared occupancy of -15% of p53-bound genes in ChIP sequencing. The C-terminus of DACH1 was necessary for direct p53 binding, contributing to the inhibition of colony formation and cell-cycle arrest. Expression of the stem cell factor SOX2 was repressed by DACH1, and SOX2 expression was inversely correlated with DACH1 in NSCLC. We conclude that DACH1 binds p53 to inhibit NSCLC cellular growth.
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Affiliation(s)
- Ke Chen
- Departments of Cancer Biology, Stem Cell Biology and Regenerative Medicine, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia,PA 19107, USA
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