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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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2
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging. Microbiome 2024; 12:31. [PMID: 38383483 PMCID: PMC10882811 DOI: 10.1186/s40168-024-01758-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV - influenced by the infection itself, ART usage, sexual orientation, or other associated factors - affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. RESULTS PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. CONCLUSIONS We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract.
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Affiliation(s)
- Shalini Singh
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Leila B Giron
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Shivanjali Shankaran
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Zlata R Bogin
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Simona A Bambi
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Aaron R Goldman
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Joao L L C Azevedo
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | | | | | | | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Elena Sánchez-López
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Toshitha Kannan
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Ceylan E Tanes
- 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
| | - Alan L Landay
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
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3
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Rimal B, Collins SL, Tanes CE, Rocha ER, Granda MA, Solanki S, Hoque NJ, Gentry EC, Koo I, Reilly ER, Hao F, Paudel D, Singh V, Yan T, Kim MS, Bittinger K, Zackular JP, Krausz KW, Desai D, Amin S, Coleman JP, Shah YM, Bisanz JE, Gonzalez FJ, Vanden Heuvel JP, Wu GD, Zemel BS, Dorrestein PC, Weinert EE, Patterson AD. Bile salt hydrolase catalyses formation of amine-conjugated bile acids. Nature 2024; 626:859-863. [PMID: 38326609 PMCID: PMC10881385 DOI: 10.1038/s41586-023-06990-w] [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: 09/09/2022] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
Abstract
Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect host-mediated metabolic processes1-6; however, the bacterial gene(s) responsible for their production remain unknown. Herein, we report that bile salt hydrolase (BSH) possesses dual functions in bile acid metabolism. Specifically, we identified a previously unknown role for BSH as an amine N-acyltransferase that conjugates amines to bile acids, thus forming bacterial bile acid amidates (BBAAs). To characterize this amine N-acyltransferase BSH activity, we used pharmacological inhibition of BSH, heterologous expression of bsh and mutants in Escherichia coli and bsh knockout and complementation in Bacteroides fragilis to demonstrate that BSH generates BBAAs. We further show in a human infant cohort that BBAA production is positively correlated with the colonization of bsh-expressing bacteria. Lastly, we report that in cell culture models, BBAAs activate host ligand-activated transcription factors including the pregnane X receptor and the aryl hydrocarbon receptor. These findings enhance our understanding of how gut bacteria, through the promiscuous actions of BSH, have a significant role in regulating the bile acid metabolic network.
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Affiliation(s)
- Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Stephanie L Collins
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ceylan E Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edson R Rocha
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Megan A Granda
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Sumeet Solanki
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Nushrat J Hoque
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Imhoi Koo
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Erin R Reilly
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Fuhua Hao
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Devendra Paudel
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, USA
| | - Vishal Singh
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, USA
| | - Tingting Yan
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Min Soo Kim
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristopher W Krausz
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dhimant Desai
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - Shantu Amin
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA, USA
| | - James P Coleman
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Jordan E Bisanz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- One Health Microbiome Center, Huck Life Sciences Institute, University Park, PA, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John P Vanden Heuvel
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
- INDIGO Biosciences, Inc., State College, PA, USA
| | - Gary D Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Babette S Zemel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA.
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
- One Health Microbiome Center, Huck Life Sciences Institute, University Park, PA, USA.
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4
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Conrad MA, Bittinger K, Ren Y, Kachelries K, Vales J, Li H, Wu GD, Bushman FD, Devoto M, Baldassano RN, Kelsen JR. The intestinal microbiome of inflammatory bowel disease across the pediatric age range. Gut Microbes 2024; 16:2317932. [PMID: 38404111 PMCID: PMC10900269 DOI: 10.1080/19490976.2024.2317932] [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: 07/05/2023] [Accepted: 02/08/2024] [Indexed: 02/27/2024] Open
Abstract
Dysbiosis is associated with pediatric and adult-onset inflammatory bowel disease (IBD), but the role of dysbiosis and the microbiome in very early onset IBD (VEO-IBD) has not yet been described. Here, we aimed to demonstrate the impact of age and inflammation on microbial community structure using shotgun metagenomic sequencing in children with VEO-IBD, pediatric-onset IBD, and age-matched pediatric healthy controls (HC) observed longitudinally over the course of 8 weeks. We found disease-related differences in alpha and beta diversity between HC and children with IBD or VEO-IBD. Using a healthy microbial maturity index modeled from HC across the age range to characterize their gut microbiota, we found that children with pediatric-onset IBD and VEO-IBD had lower maturity than their age-matched HC groups, suggesting a disease effect on the microbial community. In addition, patients with pediatric IBD had significantly lower maturity than those with VEO-IBD, who had more heterogeneity at the youngest ages, highlighting differences in these two cohorts that were not captured in standard comparisons of alpha and beta diversity. These results demonstrate that young age and inflammation independently impact microbial community structure. However, the effect is not additive in the youngest patients, likely because of the heterogeneous and dynamic stool microbiome in this population.
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Affiliation(s)
- Máire A. Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, 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
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Ren
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jennifer Vales
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary D. Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcella Devoto
- Institute for Research in Genetics and Biomedicine, Consiglio Nazionale delle Ricerche, Monserrato, CA, Italy
- Department of Translational and Precision Medicine, Università Sapienza, Rome, Italy
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Judith R. Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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5
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Carr RM, Li Y, Chau L, Friedman ES, Lee JJ, Adorini L, Erickson M, Zaru L, Shringarpure R, MacConell L, Bittinger K, Li H, Wu GD. An integrated analysis of fecal microbiome and metabolomic features distinguish non-cirrhotic NASH from healthy control populations. Hepatology 2023; 78:1843-1857. [PMID: 37222264 PMCID: PMC10674038 DOI: 10.1097/hep.0000000000000474] [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: 11/10/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS There is great interest in identifying microbiome features as reliable noninvasive diagnostic and/or prognostic biomarkers for non-cirrhotic NASH fibrosis. Several cross-sectional studies have reported gut microbiome features associated with advanced NASH fibrosis and cirrhosis, where the most prominent features are associated with cirrhosis. However, no large, prospectively collected data exist establishing microbiome features that discern non-cirrhotic NASH fibrosis, integrate the fecal metabolome as disease biomarkers, and are unconfounded by BMI and age. APPROACH AND RESULTS Results from shotgun metagenomic sequencing performed on fecal samples prospectively collected from 279 US patients with biopsy-proven NASH (F1-F3 fibrosis) enrolled in the REGENERATE I303 study were compared to those from 3 healthy control cohorts and integrated with the absolute quantification of fecal bile acids. Microbiota beta-diversity was different, and BMI- and age-adjusted logistic regression identified 12 NASH-associated species. Random forest prediction models resulted in an AUC of 0.75-0.81 in a receiver operator characteristic analysis. In addition, specific fecal bile acids were significantly lower in NASH and correlated with plasma C4 levels. Microbial gene abundance analysis revealed 127 genes increased in controls, many involving protein synthesis, whereas 362 genes were increased in NASH many involving bacterial environmental responses (false discovery rate < 0.01). Finally, we provide evidence that fecal bile acid levels may be a better discriminator of non-cirrhotic NASH versus health than either plasma bile acids or gut microbiome features. CONCLUSIONS These results may have value as a set of baseline characteristics of non-cirrhotic NASH against which therapeutic interventions to prevent cirrhosis can be compared and microbiome-based diagnostic biomarkers identified.
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Affiliation(s)
- Rotonya M. Carr
- Division of Gastroenterology, University of Washington, Seattle, WA 981895
| | - Yun Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lillian Chau
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | | | - Luna Zaru
- Intercept Pharmaceuticals, San Diego, CA 92122
| | | | | | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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6
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Liu L, Mahalak KK, Bobokalonov JT, Narrowe AB, Firrman J, Lemons JMS, Bittinger K, Hu W, Jones SM, Moustafa AM. Impact of Ivermectin on the Gut Microbial Ecosystem. Int J Mol Sci 2023; 24:16125. [PMID: 38003317 PMCID: PMC10671733 DOI: 10.3390/ijms242216125] [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: 10/08/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME® (simulator of the human intestinal microbial ecosystem), using fecal material from three healthy adults. The microbial communities were grown using three different culture media: standard SHIME media and SHIME media with either soluble or insoluble fiber added (control, SF, ISF). IVM introduced minor and temporary changes to the gut microbial community in terms of composition and metabolite production, as revealed by 16S rRNA amplicon sequencing analysis, flow cytometry, and GC-MS. Thus, it was concluded that IVM is not expected to induce dysbiosis or yield adverse effects if administered to healthy adults. In addition, the donor's starting community influences the relationship between IVM and the gut microbiome, and the soluble fiber component in feed could protect the gut microbiota from IVM; an increase in short-chain fatty acid production was predicted by PICRUSt2 and detected with IVM treatment.
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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
| | - 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
| | - 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 Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - 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
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven M. Jones
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ahmed M. Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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7
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea IV, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV. Res Sq 2023:rs.3.rs-3492242. [PMID: 37961645 PMCID: PMC10635386 DOI: 10.21203/rs.3.rs-3492242/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background People with HIV (PWH), even with controlled viral replication through antiretroviral therapy (ART), experience persistent inflammation. This is partly due to intestinal microbial dysbiosis and translocation. Such ongoing inflammation may lead to the development of non-AIDS-related aging-associated comorbidities. However, there remains uncertainty regarding whether HIV affects the biological age of the intestines and whether microbial dysbiosis and translocation influence the biological aging process in PWH on ART. To fill this knowledge gap, we utilized a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PWH on ART and their matched HIV-negative counterparts. Results Despite having similar chronological ages, PWH on ART exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to HIV-negative controls. Investigating the relationship between microbial translocation and biological aging, PWH on ART had decreased levels of tight junction proteins in the colon and ileum, along with increased microbial translocation. This increased intestinal permeability correlated with faster intestinal and systemic biological aging, as well as increased systemic inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PWH on ART had higher abundance of specific pro-inflammatory bacterial genera, such as Catenibacterium and Prevotella. These bacteria significantly correlated with accelerated local and systemic biological aging. Conversely, the intestines of PWH on ART had lower abundance of bacterial genera known for producing short-chain fatty acids and exhibiting anti-inflammatory properties, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria taxa were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbial-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid and oleic acid. Conclusions We identified a specific microbial composition and microbiome-related metabolic pathways that are intertwined with both intestinal and systemic biological aging in PWH on ART. A deeper understanding of the mechanisms underlying these connections could potentially offer strategies to counteract premature aging and its associated health complications in PWH.
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8
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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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9
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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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10
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Fakharian F, Thirugnanam S, Welsh DA, Kim WK, Rappaport J, Bittinger K, Rout N. The Role of Gut Dysbiosis in the Loss of Intestinal Immune Cell Functions and Viral Pathogenesis. Microorganisms 2023; 11:1849. [PMID: 37513022 PMCID: PMC10384393 DOI: 10.3390/microorganisms11071849] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
The gut microbiome plays a critical role in maintaining overall health and immune function. However, dysbiosis, an imbalance in microbiome composition, can have profound effects on various aspects of human health, including susceptibility to viral infections. Despite numerous studies investigating the influence of viral infections on gut microbiome, the impact of gut dysbiosis on viral infection and pathogenesis remains relatively understudied. The clinical variability observed in SARS-CoV-2 and seasonal influenza infections, and the presence of natural HIV suppressors, suggests that host-intrinsic factors, including the gut microbiome, may contribute to viral pathogenesis. The gut microbiome has been shown to influence the host immune system by regulating intestinal homeostasis through interactions with immune cells. This review aims to enhance our understanding of how viral infections perturb the gut microbiome and mucosal immune cells, affecting host susceptibility and response to viral infections. Specifically, we focus on exploring the interactions between gamma delta (γδ) T cells and gut microbes in the context of inflammatory viral pathogenesis and examine studies highlighting the role of the gut microbiome in viral disease outcomes. Furthermore, we discuss emerging evidence and potential future directions for microbiome modulation therapy in the context of viral pathogenesis.
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Affiliation(s)
- Farzaneh Fakharian
- Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Siva Thirugnanam
- Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - David A. Welsh
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, LA 70806, USA
| | - Woong-Ki Kim
- Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jay Rappaport
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Namita Rout
- Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA
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11
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Hong G, Daniel SG, Lee JJ, Bittinger K, Glaser L, Mattei LM, Dorgan DJ, Hadjiliadis D, Kawut SM, Collman RG. Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis. J Cyst Fibros 2023; 22:636-643. [PMID: 36822979 PMCID: PMC10440372 DOI: 10.1016/j.jcf.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics. METHODS We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated. RESULTS Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences. CONCLUSION The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.
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Affiliation(s)
- Gina Hong
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of.
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Daniel J Dorgan
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Denis Hadjiliadis
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Steven M Kawut
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Ronald G Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
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12
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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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13
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Liu Y, Daniel SG, Kim HE, Koo H, Korostoff J, Teles F, Bittinger K, Hwang G. Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities. Microbiome 2023; 11:123. [PMID: 37264481 DOI: 10.1186/s40168-023-01561-7] [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] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by the synergistic polymicrobial interaction between the cariogenic bacterium, Streptococcus mutans, and an opportunistic fungal pathogen, Candida albicans. Although cross-sectional studies reveal their important roles in caries development, these exhibit limitations in determining the significance of these microbial interactions in the pathogenesis of the disease. Thus, it remains unclear the mechanism(s) through which the cross-kingdom interaction modulates the composition of the plaque microbiome. Here, we employed a novel ex vivo saliva-derived microcosm biofilm model to assess how exogenous pathogens could impact the structural and functional characteristics of the indigenous native oral microbiota. RESULTS Through shotgun whole metagenome sequencing, we observed that saliva-derived biofilm has decreased richness and diversity but increased sugar-related metabolism relative to the planktonic phase. Addition of S. mutans and/or C. albicans to the native microbiome drove significant changes in its bacterial composition. In addition, the effect of the exogenous pathogens on microbiome diversity and taxonomic abundances varied depending on the sugar type. While the addition of S. mutans induced a broader effect on Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog abundances with glucose/fructose, S. mutans-C. albicans combination under sucrose conditions triggered unique and specific changes in microbiota composition/diversity as well as specific effects on KEGG pathways. Finally, we observed the presence of human epithelial cells within the biofilms via confocal microscopy imaging. CONCLUSIONS Our data revealed that the presence of S. mutans and C. albicans, alone or in combination, as well as the addition of different sugars, induced unique alterations in both the composition and functional attributes of the biofilms. In particular, the combination of S. mutans and C. albicans seemed to drive the development (and perhaps the severity) of a dysbiotic/cariogenic oral microbiome. Our work provides a unique and pragmatic biofilm model for investigating the functional microbiome in health and disease as well as developing strategies to modulate the microbiome. Video Abstract.
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Affiliation(s)
- Yuan Liu
- Department of Preventive and Restorative Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Scott G Daniel
- Department of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hye-Eun Kim
- Department of Preventive and Restorative Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hyun Koo
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Innovation & Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jonathan Korostoff
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Flavia Teles
- Center for Innovation & Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Basic & Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kyle Bittinger
- Department of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
| | - Geelsu Hwang
- Department of Preventive and Restorative Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center for Innovation & Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
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14
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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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15
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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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Vizioli C, Jaime-Lara R, Daniel SG, Franks A, Diallo AF, Bittinger K, Tan TP, Merenstein DJ, Brooks B, Joseph PV, Maki KA. Administration of Bifidobacterium animalis subsp. lactis strain BB-12 ® in healthy children: characterization, functional composition, and metabolism of the gut microbiome. Front Microbiol 2023; 14:1165771. [PMID: 37333640 PMCID: PMC10275293 DOI: 10.3389/fmicb.2023.1165771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/17/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction The consumption of probiotics may influence children's gut microbiome and metabolome, which may reflect shifts in gut microbial diversity composition and metabolism. These potential changes might have a beneficial impact on health. However, there is a lack of evidence investigating the effect of probiotics on the gut microbiome and metabolome of children. We aimed to examine the potential impact of a two (Streptococcus thermophilus and Lactobacillus delbrueckii; S2) vs. three (S2 + Bifidobacterium animalis subsp. lactis strain BB-12) strain-supplemented yogurt. Methods Included in this study were 59 participants, aged one to five years old, recruited to phase I of a double-blinded, randomized controlled trial. Fecal samples were collected at baseline, after the intervention, and at twenty days post-intervention discontinuation, and untargeted metabolomics and shotgun metagenomics were performed. Results Shotgun metagenomics and metabolomic analyses showed no global changes in either intervention group's gut microbiome alpha or beta diversity indices, except for a lower microbial diversity in the S2 + BB12 group at Day 30. The relative abundance of the two and three intervention bacteria increased in the S2 and S2 + BB12 groups, respectively, from Day 0 to Day 10. In the S2 + BB12 group, the abundance of several fecal metabolites increased at Day 10, including alanine, glycine, lysine, phenylalanine, serine, and valine. These fecal metabolite changes did not occur in the S2 group. Discussion In conclusion, there were were no significant differences in the global metagenomic or metabolomic profiles between healthy children receiving two (S2) vs. three (S2 + BB12) probiotic strains for 10 days. Nevertheless, we observed a significant increase (Day 0 to Day 10) in the relative abundance of the two and three probiotics administered in the S2 and S2 + BB12 groups, respectively, indicating the intervention had a measurable impact on the bacteria of interest in the gut microbiome. Future research using longer probiotic intervention durations and in children at risk for gastrointestinal disorders may elucidate if functional metabolite changes confer a protective gastrointestinal effect.
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Affiliation(s)
- Carlotta Vizioli
- Department of Health and Human Services, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Department of Health and Human Services, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, United States
| | - Rosario Jaime-Lara
- Department of Health and Human Services, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, United States
- Department of Health and Human Services, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
- UCLA School of Nursing, University of California, Los Angeles, Los Angeles, CA, United States
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Alexis Franks
- Department of Health and Human Services, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| | - Ana F. Diallo
- Family and Community Health Nursing, School of Nursing, Institute of Inclusion, Inquiry and Innovation (iCubed), Virginia Commonwealth University, Richmond, VA, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Tina P. Tan
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC, United States
| | - Daniel J. Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC, United States
| | - Brianna Brooks
- Department of Health and Human Services, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| | - Paule V. Joseph
- Department of Health and Human Services, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, United States
- Department of Health and Human Services, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| | - Katherine A. Maki
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health, Clinical Center, Bethesda, MD, United States
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Williams PA, Naughton KE, Simon LA, Soto GE, Parham LR, Ma X, Danan CH, Hu W, Friedman ES, McMillan EA, Mehta H, Stoltz MA, Ocaña JS, Zackular JP, Bittinger K, Whelan KA, Karakasheva TA, Hamilton KE. Intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. Am J Physiol Gastrointest Liver Physiol 2023; 324:G354-G368. [PMID: 36852920 PMCID: PMC10069975 DOI: 10.1152/ajpgi.00248.2022] [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: 10/25/2022] [Revised: 01/30/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
Calorie restriction can enhance the regenerative capacity of the injured intestinal epithelium. Among other metabolic changes, calorie restriction can activate the autophagy pathway. Although independent studies have attributed the regenerative benefit of calorie restriction to downregulation of mTORC1, it is not known whether autophagy itself is required for the regenerative benefit of calorie restriction. We used mouse and organoid models with autophagy gene deletion to evaluate the contribution of autophagy to intestinal epithelial regeneration following calorie restriction. In the absence of injury, mice with intestinal epithelial-specific deletion of autophagy gene Atg7 (Atg7ΔIEC) exhibit weight loss and histological changes similar to wild-type mice following calorie restriction. Conversely, calorie-restricted Atg7ΔIEC mice displayed a significant reduction in regenerative crypt foci after irradiation compared with calorie-restricted wild-type mice. Targeted analyses of tissue metabolites in calorie-restricted mice revealed an association between calorie restriction and reduced glycocholic acid (GCA) in wild-type mice but not in Atg7ΔIEC mice. To evaluate whether GCA can directly modulate epithelial stem cell self-renewal, we performed enteroid formation assays with or without GCA. Wild-type enteroids exhibited reduced enteroid formation efficiency in response to GCA treatment, suggesting that reduced availability of GCA during calorie restriction may be one mechanism by which calorie restriction favors epithelial regeneration in a manner dependent upon epithelial autophagy. Taken together, our data support the premise that intestinal epithelial Atg7 is required for the regenerative benefit of calorie restriction, due in part to its role in modulating luminal GCA with direct effects on epithelial stem cell self-renewal.NEW & NOTEWORTHY Calorie restriction is associated with enhanced intestinal regeneration after irradiation, but the requirement of autophagy for this process is not known. Our data support the premise that intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. We also report that luminal levels of primary bile acid glycocholic acid are modulated by epithelial cell autophagy during calorie restriction with direct effects on epithelial stem cell function.
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Affiliation(s)
- Patrick A Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kaitlyn E Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Lauren A Simon
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Gloria E Soto
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Louis R Parham
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Charles H Danan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Elliot S Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Emily A McMillan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Hritik Mehta
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Madison A Stoltz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Joshua Soto Ocaña
- Division of Protective Immunity, Children's Hospital of Philadelphia, Pennsylvania United States
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Pennsylvania United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kelly A Whelan
- Department of Pathology & Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States
- Fels Institute for Cancer Research & Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States
| | - Tatiana A Karakasheva
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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Vizioli C, Jaime-Lara R, Daniel SG, Franks A, Diallo AF, Bittinger K, Tan TP, Merenstein DJ, Brooks B, Joseph PV, Maki KA. Administration of Bifidobacterium animalis subsp. lactis Strain BB-12 ® in Healthy Children: Characterization, Functional Composition, and Metabolism of the Gut Microbiome. medRxiv 2023:2023.02.02.23285145. [PMID: 36798243 PMCID: PMC9934720 DOI: 10.1101/2023.02.02.23285145] [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] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The consumption of probiotics may influence children's gut microbiome and metabolome, which may reflect shifts in gut microbial diversity composition and metabolism. These potential changes might have a beneficial impact on health. However, there is a lack of evidence investigating the effect of probiotics on the gut microbiome and metabolome of children. We aimed to examine the potential impact of a two ( Streptococcus thermophilus and Lactobacillus delbrueckii ; S2) vs . three (S2 + Bifidobacterium animalis subsp. lactis strain BB-12) strain-supplemented yogurt. Included in this study were 59 participants, aged one to five years old, recruited to phase I of a double-blinded, randomized controlled trial. Fecal samples were collected at baseline, after the intervention, and at twenty days post-intervention discontinuation, and untargeted metabolomics and shotgun metagenomics were performed. Shotgun metagenomics and metabolomic analyses showed no global changes in either intervention group's gut microbiome alpha or beta diversity indices. The relative abundance of the two and three intervention bacteria increased in the S2 and S2 + BB12 groups, respectively, from Day 0 to Day 10 . In the S2+BB12 group, the abundance of several fecal metabolites was reduced at Day 10 , including alanine, glycine, lysine, phenylalanine, serine, and valine. These fecal metabolite changes did not occur in the S2 group. Future research using longer probiotic intervention durations and in children at risk for gastrointestinal disorders may elucidate if functional metabolite changes confer a protective gastrointestinal effect.
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Affiliation(s)
- Carlotta Vizioli
- National Institute of Neurological Disease and Stroke, National Institutes of Health, Department of Health and Human Services, Bethesda, MD,National Institute on Alcohol Abuse and Alcoholism National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Rosario Jaime-Lara
- National Institute on Alcohol Abuse and Alcoholism National Institutes of Health, Department of Health and Human Services, Bethesda, MD,National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD,UCLA School of Nursing, University of California Los Angeles, Los Angeles, CA
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexis Franks
- National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Ana F. Diallo
- Institute of Inclusion, Inquiry & Innovation (iCubed), Family and Community Health Nursing, School of Nursing, Virginia Commonwealth University, Richmond, VA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Tina P. Tan
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC
| | - Daniel J. Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC
| | - Brianna Brooks
- National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Paule V. Joseph
- National Institute on Alcohol Abuse and Alcoholism National Institutes of Health, Department of Health and Human Services, Bethesda, MD,National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Katherine A. Maki
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health, Clinical Center, Bethesda, MD, 20814
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Firrman J, Liu L, Mahalak K, Hu W, Bittinger K, Moustafa A, Jones SM, Narrowe A, Tomasula P. An in vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner. Front Nutr 2023; 9:1040744. [PMID: 36778971 PMCID: PMC9908759 DOI: 10.3389/fnut.2022.1040744] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/14/2022] [Indexed: 01/27/2023] Open
Abstract
Introduction Following consumption of milk, lactose, a disaccharide of glucose and galactose, is hydrolyzed and absorbed in the upper gastrointestinal tract. However, hydrolysis and absorption are not always absolute, and some lactose will enter the colon where the gut microbiota is able to hydrolyze lactose and produce metabolic byproducts. Methods Here, the impact of lactose on the gut microbiota of healthy adults was examined, using a short-term, in vitro strategy where fecal samples harvested from 18 donors were cultured anaerobically with and without lactose. The data were compiled to identify donor-independent responses to lactose treatment. Results and discussion Metagenomic sequencing found that the addition of lactose decreased richness and evenness, while enhancing prevalence of the β-galactosidase gene. Taxonomically, lactose treatment decreased relative abundance of Bacteroidaceae and increased lactic acid bacteria, Lactobacillaceae, Enterococcaceae, and Streptococcaceae, and the probiotic Bifidobacterium. This corresponded with an increased abundance of the lactate utilizers, Veillonellaceae. These structural changes coincided with increased total short-chain fatty acids (SCFAs), specifically acetate, and lactate. These results demonstrated that lactose could mediate the gut microbiota of healthy adults in a donor-independent manner, consistent with other described prebiotics, and provided insight into how dietary milk consumption may promote human health through modifications of the gut microbiome.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States,*Correspondence: Jenni Firrman,
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
| | - Karley Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ahmed Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Steven M. Jones
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Adrienne Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
| | - Peggy Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, PA, United States
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Mahalak KK, Firrman J, Narrowe AB, Hu W, Jones SM, Bittinger K, Moustafa AM, Liu L. Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner. Front Nutr 2023; 9:1058910. [PMID: 36712525 PMCID: PMC9879625 DOI: 10.3389/fnut.2022.1058910] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction Fructooligosaccharides (FOS) are well-known carbohydrates that promote healthy gut microbiota and have been previously demonstrated to enhance levels of Bifidobacterium and Lactobacillus. Its bifidogenic properties are associated with positive health outcomes such as reduced obesity and anti-inflammatory properties, and, therefore, is in use as a prebiotic supplement to support healthy gut microbiota. However, the gut microbiota changes with age, which may lead to differential responses to treatments with prebiotics and other dietary supplements. Methods To address this concern, we implemented a 24-h in vitro culturing method to determine whether FOS treatment in three different adult age groups would have a differential effect. The age groups of interest ranged from 25 to 70 years and were split into young adults, adults, and older adults for the purposes of this analysis. Metagenomics and short-chain fatty acid analysis were performed to determine changes in the structure and function of the microbial communities. Results These analyses found that FOS created a bifidogenic response in all age groups, increased overall SCFA levels, decreased alpha diversity, and shifted the communities to be more similar in beta diversity metrics. However, the age groups differed in which taxa were most prevalent or most affected by FOS treatment. Discussion Overall, the results of this study demonstrate the positive effects of FOS on the gut microbiome, and importantly, how age may play a role in the effectiveness of this prebiotic.
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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, Wyndmoor, PA, United States,*Correspondence: Karley K. Mahalak,
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Steven M. Jones
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ahmed M. Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
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21
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Mukhopadhyay S, Lee JJ, Hartman E, Woodford E, Dhudasia MB, Mattei LM, Daniel SG, Wade KC, Underwood MA, Bittinger K. Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly. Gut Microbes 2022; 14:2154091. [PMID: 36474348 PMCID: PMC9733690 DOI: 10.1080/19490976.2022.2154091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are administered near-universally to very low birth weight (VLBW) infants after birth for suspected early-onset sepsis (EOS). We previously identified a phenotypic group of VLBW infants, referred to as low-risk for EOS (LRE), whose risk of EOS is low enough to avoid routine antibiotic initiation. In this cohort study, we compared 18 such infants with 30 infants categorized as non-LRE to determine if the lower risk of pathogen transmission at birth is accompanied by differences in microbiome acquisition and development. We did shotgun metagenomic sequencing of 361 fecal samples obtained serially. LRE infants had a higher human-to-bacterial DNA ratio than non-LRE infants in fecal samples on days 1-3 after birth, confirming lower bacterial acquisition among LRE infants. The microbial diversity and composition in samples from days 4-7 differed between the groups with a predominance of Staphylococcus epidermidis in LRE infants and Enterobacteriaceae sp. in non-LRE infants. Compositional differences were congruent with the distribution of virulence factors and antibiotic resistant genes. After the first week, the overall composition was similar, but changes in relative abundance for several taxa with increasing age differed between groups. Of the nine late-onset bacteremia episodes, eight occurred in non-LRE infants. Species isolated from the blood culture was detected in the pre-antibiotic fecal samples of the infant for all episodes, though these species were also found in infants without bacteremia. In conclusion, LRE infants present a distinct pattern of microbiome development that is aligned with their low risk for EOS. Further investigation to determine the impact of these differences on later outcomes such as late-onset bacteremia is warranted.
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Affiliation(s)
- Sagori Mukhopadhyay
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States,Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Sagori Mukhopadhyay Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Roberts Center for Pediatric Research, 2716 South Street, Office 19-322, Philadelphia, PA19146, United States
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Erica Hartman
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Emily Woodford
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Miren B. Dhudasia
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Kelly C. Wade
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States
| | - Mark A. Underwood
- Department of Pediatrics, University of California Davis, Sacramento, California, United States
| | - Kyle Bittinger
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States,Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,CONTACT Kyle Bittinger CHOP Microbiome Center, Children’s Hospital of Philadelphia, Roberts Center for Pediatric Research, 2716 South Street, Philadelphia, PA19146, United States
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22
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Nashed L, Mani J, Hazrati S, Stern DB, Subramanian P, Mattei L, Bittinger K, Hu W, Levy S, Maxwell GL, Hourigan SK. Gut microbiota changes are detected in asymptomatic very young children with SARS-CoV-2 infection. Gut 2022; 71:2371-2373. [PMID: 35135843 PMCID: PMC9357857 DOI: 10.1136/gutjnl-2021-326599] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Lydia Nashed
- Inova Children’s Hospital, Inova Health System, Falls Church, Virginia, USA
| | - Jyoti Mani
- Pediatric Gastroenterology, Children's National Health System, Washington, District of Columbia, USA
| | - Sahel Hazrati
- Women’s Service Line, Inova Health System, Falls Church, Virginia, USA
| | - David B Stern
- Bioinformatics and Computational Biosciences Branch, NIAID, Bethesda, Maryland, USA
| | - Poorani Subramanian
- Bioinformatics and Computational Biosciences Branch, NIAID, Bethesda, Maryland, USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia Pediatrics Residency Program, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia Pediatrics Residency Program, Philadelphia, Pennsylvania, USA
| | - Weiming Hu
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia Pediatrics Residency Program, Philadelphia, Pennsylvania, USA
| | - Shira Levy
- Inova Children’s Hospital, Inova Health System, Falls Church, Virginia, USA,Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - George L Maxwell
- Women’s Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Suchitra K Hourigan
- Inova Children's Hospital, Inova Health System, Falls Church, Virginia, USA .,Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
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23
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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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24
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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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25
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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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26
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Ricardo-Gonzalez RR, Kotas ME, O'Leary CE, Singh K, Damsky W, Liao C, Arouge E, Tenvooren I, Marquez DM, Schroeder AW, Cohen JN, Fassett MS, Lee J, Daniel SG, Bittinger K, Díaz RE, Fraser JS, Ali N, Ansel KM, Spitzer MH, Liang HE, Locksley RM. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. Immunity 2022; 55:1891-1908.e12. [PMID: 36044899 PMCID: PMC9561030 DOI: 10.1016/j.immuni.2022.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 01/05/2023]
Abstract
Demodex mites are commensal parasites of hair follicles (HFs). Normally asymptomatic, inflammatory outgrowth of mites can accompany malnutrition, immune dysfunction, and aging, but mechanisms restricting Demodex outgrowth are not defined. Here, we show that control of mite HF colonization in mice required group 2 innate lymphoid cells (ILC2s), interleukin-13 (IL-13), and its receptor, IL-4Ra-IL-13Ra1. HF-associated ILC2s elaborated IL-13 that attenuated HFs and epithelial proliferation at anagen onset; in their absence, Demodex colonization led to increased epithelial proliferation and replacement of gene programs for repair by aberrant inflammation, leading to the loss of barrier function and HF exhaustion. Humans with rhinophymatous acne rosacea, an inflammatory condition associated with Demodex, had increased HF inflammation with decreased type 2 cytokines, consistent with the inverse relationship seen in mice. Our studies uncover a key role for skin ILC2s and IL-13, which comprise an immune checkpoint that sustains cutaneous integrity and restricts pathologic infestation by colonizing HF mites.
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Affiliation(s)
- Roberto R Ricardo-Gonzalez
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Maya E Kotas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Claire E O'Leary
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Katelyn Singh
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - William Damsky
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Chang Liao
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Elizabeth Arouge
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Iliana Tenvooren
- Department of Otolaryngology and Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Diana M Marquez
- Department of Otolaryngology and Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Schroeder
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jarish N Cohen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Marlys S Fassett
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jinwoo Lee
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Niwa Ali
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew H Spitzer
- Department of Otolaryngology and Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hong-Erh Liang
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Richard M Locksley
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
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27
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Lee IK, Jacome DA, Cho JK, Tu V, Young AJ, Dominguez T, Northrup JD, Etersque JM, Lee HS, Ruff A, Aklilu O, Bittinger K, Glaser LJ, Dorgan D, Hadjiliadis D, Kohli RM, Mach RH, Mankoff DA, Doot RK, Sellmyer MA. Imaging sensitive and drug-resistant bacterial infection with [11C]-trimethoprim. J Clin Invest 2022; 132:156679. [PMID: 36106638 PMCID: PMC9479701 DOI: 10.1172/jci156679] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 07/19/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Several molecular imaging strategies can identify bacterial infections in humans. PET affords the potential for sensitive infection detection deep within the body. Among PET-based approaches, antibiotic-based radiotracers, which often target key bacterial-specific enzymes, have considerable promise. One question for antibiotic radiotracers is whether antimicrobial resistance (AMR) reduces specific accumulation within bacteria, diminishing the predictive value of the diagnostic test. METHODS Using a PET radiotracer based on the antibiotic trimethoprim (TMP), [11C]-TMP, we performed in vitro uptake studies in susceptible and drug-resistant bacterial strains and whole-genome sequencing (WGS) in selected strains to identify TMP resistance mechanisms. Next, we queried the NCBI database of annotated bacterial genomes for WT and resistant dihydrofolate reductase (DHFR) genes. Finally, we initiated a first-in-human protocol of [11C]-TMP in patients infected with both TMP-sensitive and TMP-resistant organisms to demonstrate the clinical feasibility of the tool. RESULTS We observed robust [11C]-TMP uptake in our panel of TMP-sensitive and -resistant bacteria, noting relatively variable and decreased uptake in a few strains of P. aeruginosa and E. coli. WGS showed that the vast majority of clinically relevant bacteria harbor a WT copy of DHFR, targetable by [11C]-TMP, and that despite the AMR, these strains should be “imageable.” Clinical imaging of patients with [11C]-TMP demonstrated focal radiotracer uptake in areas of infectious lesions. CONCLUSION This work highlights an approach to imaging bacterial infection in patients, which could affect our understanding of bacterial pathogenesis as well as our ability to better diagnose infections and monitor response to therapy. TRIAL REGISTRATION ClinicalTrials.gov NCT03424525. FUNDING Institute for Translational Medicine and Therapeutics, Burroughs Wellcome Fund, NIH Office of the Director Early Independence Award (DP5-OD26386), and University of Pennsylvania NIH T32 Radiology Research Training Grant (5T32EB004311-12).
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Affiliation(s)
- Iris K. Lee
- Department of Radiology and
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Vincent Tu
- Department of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Jean M. Etersque
- Department of Radiology and
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Kyle Bittinger
- Department of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laurel J. Glaser
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Dorgan
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care Medicine, and
| | - Denis Hadjiliadis
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care Medicine, and
| | - Rahul M. Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Division of Infectious Disease, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Mark A. Sellmyer
- Department of Radiology and
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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28
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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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29
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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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30
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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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31
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Ricardo-Gonzalez RR, Kotas ME, O’Leary C, Tenvooren I, Marquez D, Singh K, Damsky W, Liao C, Schroeder A, Cohen J, Fassett MS, Lee J, Daniel SG, Bittinger K, Diaz RE, Fraser J, Ansel KM, Spitzer M, Liang HE, Locksley RM. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.50.39] [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
Demodex mites are obligate commensal parasites of hair follicles (HF) in mammals. Normally asymptomatic, inflammatory outgrowth of mites can accompany malnutrition, immune dysfunction and aging, but mechanisms restricting Demodex outgrowth and pathogenesis are not defined. Here, we show that control over mite HF colonization of mice requires ILC2s, IL-13, and its receptor IL-4Ra, but not IL-4 or the adaptive immune system. Epithelial HF-associated ILC2s elaborate IL-13 that attenuates HF and epithelial cell proliferation at anagen onset; in their absence, Demodex colonization leads to increased epithelial proliferation and replacement of gene programs for repair by aberrant inflammatory programs leading to loss of barrier function and premature HF exhaustion over time. Humans with rhinophymatous acne rosacea, a nasal inflammatory condition associated with a high burden of Demodex, had increased HF inflammatory cells with decreased type 2 cytokines, consistent with the inverse relationship seen in mice. Our studies uncover a critical role for skin ILC2s and IL-13, which comprise an immune checkpoint necessary to sustain cutaneous integrity and restrict pathologic infestation by colonizing HF mites.
This work was supported by the National Institutes of Health (AR007175 to R.R.R.G. and M.S.F, AR075880 to R.R.R.G, HL140868 to M.E.K., DK121476 to C.E.O., AI159229 to W.D., AR074556 to M.S.F., AI026918 and HL107202 to R.M.L.), Dermatology Foundation (R.R.R.G., M.S.F.), A.P. Giannini Foundation (R.R.R.G, M.E.K.), Robert Wood Johnson Foundation (R.R.R.G.), Howard Hughes Medical Institute (R.M.L.), University of California Tobacco-Related Disease Research Program (T29IP0554 to J.S.F.), and the Sandler Asthma Basic Research Center at the University of California San Francisco. R.E. Díaz was supported by NSF GRFP (#1650113). R.E. Díaz is a Howard Hughes Medical Institute Gilliam Fellow (#GT11377).
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Affiliation(s)
| | | | | | | | | | | | | | - Chang Liao
- 1University of California, San Francisco
| | | | | | | | - Jinwoo Lee
- 1University of California, San Francisco
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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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Mennella JA, Li Y, Bittinger K, Friedman ES, Zhao C, Li H, Wu GD, Trabulsi JC. The Macronutrient Composition of Infant Formula Produces Differences in Gut Microbiota Maturation That Associate with Weight Gain Velocity and Weight Status. Nutrients 2022; 14:nu14061241. [PMID: 35334900 PMCID: PMC8951061 DOI: 10.3390/nu14061241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
This proof-of-principle study analyzed fecal samples from 30 infants who participated in a randomized controlled trial on the effects of the macronutrient composition of infant formula on growth and energy balance. In that study, infants randomized to be fed cow milk formula (CMF) had faster weight-gain velocity during the first 4 months and higher weight-for-length Z scores up to 11.5 months than those randomized to an isocaloric extensive protein hydrolysate formula (EHF). Here we examined associations among infant formula composition, gut microbial composition and maturation, and children’s weight status. Fecal samples collected before and monthly up to 4.5 months after randomization were analyzed by shotgun metagenomic sequencing and targeted metabolomics. The EHF group had faster maturation of gut microbiota than the CMF group, and increased alpha diversity driven by Clostridia taxa. Abundance of Ruminococcus gnavus distinguished the two groups after exclusive feeding of the assigned formula for 3 months. Abundance of Clostridia at 3–4 months negatively correlated with prior weight-gain velocity and body weight phenotypes when they became toddlers. Macronutrient differences between the formulas likely led to the observed divergence in gut microbiota composition that was associated with differences in transient rapid weight gain, a well-established predictor of childhood obesity and other comorbidities.
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Affiliation(s)
| | - Yun Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (Y.L.); (H.L.)
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (K.B.); (C.Z.)
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (E.S.F.); (G.D.W.)
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (K.B.); (C.Z.)
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (Y.L.); (H.L.)
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (E.S.F.); (G.D.W.)
| | - Jillian C. Trabulsi
- Department of Behavioral Health and Nutrition, University of Delaware, Newark, DE 19713, USA
- Correspondence: ; Tel.: +1-302-831-4991
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Shen TCD, Daniel SG, Patel S, Kaplan E, Phung L, Lemelle-Thomas K, Chau L, Herman L, Trisolini C, Stonelake A, Toal E, Khungar V, Bittinger K, Reddy KR, Wu GD. The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis. Gut Microbes 2022; 13:1987781. [PMID: 34747331 PMCID: PMC8583005 DOI: 10.1080/19490976.2021.1987781] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Most studies examining correlations between the gut microbiota and disease states focus on fecal samples due to ease of collection, yet there are distinct differences when compared to samples collected from the colonic mucosa. Although fecal microbiota has been reported to be altered in cirrhosis, correlation with mucosal microbiota characterized via rectal swab has not been previously described in this patient population. We conducted a cross-sectional analysis using 39 stool and 39 rectal swabs from adult patients with cirrhosis of different etiologies and performed shotgun metagenomic sequencing. Bacterial growth studies were performed with Escherichia coli. Two asaccharolytic bacterial taxa, Finegoldia magna and Porphyromonas asaccharolytica, were increased in rectal swabs relative to stool (FDR < 0.01). Genomic analysis of the microbiome revealed 58 genes and 16 pathways that differed between stool and rectal swabs (FDR < 0.05), where rectal swabs were enriched for pathways associated with protein synthesis and cellular proliferation but decreased in carbohydrate metabolism. Although no features in the fecal microbiome differentiated cirrhosis etiologies, the mucosal microbiome revealed decreased abundances of E. coli and Enterobacteriaceae in alcohol-related cirrhosis relative to non-alcohol related cirrhosis (FDR < 0.05). In vitro bacterial culture studies showed that physiological concentrations of ethanol and its oxidative metabolites inhibited E. coli growth in a pH- and concentration-dependent manner. Characterization of the mucosally associated gut microbiome via rectal swab revealed findings consistent with amino acid/nitrogen abundance versus carbohydrate limitation in the mucosal microenvironment as well as unique features of alcohol-related cirrhosis possibly consistent with the influence of host-derived metabolites on the composition of mucosally adherent microbiota.
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Affiliation(s)
- Ting-Chin David Shen
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,CONTACT Ting-Chin David Shen 906 BRB II/III, 421 Curie Blvd, Philadelphia, PA19104, USA
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shivali Patel
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emily Kaplan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lillian Phung
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kaylin Lemelle-Thomas
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lillian Chau
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lindsay Herman
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Calvin Trisolini
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aimee Stonelake
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emily Toal
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Vandana Khungar
- Division of Gastroenterology and Hepatology, Department of Medicine, 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
| | - K. Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Gary Wu 915 BRB II/III, 421 Curie Blvd, Philadelphia, PA19104, USA
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35
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Ferro LE, Crowley LN, Bittinger K, Friedman ES, Decker JE, Russel K, Katz S, Kim JK, Trabulsi J. Effects of prebiotics, probiotics, and synbiotics on the infant gut microbiota and other health outcomes: A systematic review. Crit Rev Food Sci Nutr 2022; 63:5620-5642. [PMID: 37667870 PMCID: PMC10480560 DOI: 10.1080/10408398.2021.2022595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The primary aim of this review was to systematically evaluate the literature regarding the effect of pre-, pro-, or synbiotic supplementation in infant formula on the gastrointestinal microbiota. The Cochrane methodology for systematic reviews of randomized controlled trials (RCTs) was employed. Five databases were searched and 32 RCTs (2010-2021) were identified for inclusion: 20 prebiotic, 6 probiotic, and 6 synbiotic. The methods utilized to evaluate gastrointestinal microbiota varied across studies and included colony plating, fluorescence in situ hybridization, quantitative real-time polymerase chain reaction, or tagged sequencing of the 16S rRNA gene. Fecal Bifidobacterium levels increased with supplementation of prebiotics and synbiotics but not with probiotics alone. Probiotic and synbiotic supplementation generally increased fecal levels of the bacterial strain supplemented in the formula. Across all pre-, pro-, and synbiotic-supplemented formulas, results were inconsistent regarding fecal Clostridium levels. Fecal pH was lower with some prebiotic and synbiotic supplementation; however, no difference was seen with probiotics. Softer stools were often reported in infants supplemented with pre- and synbiotics, yet results were inconsistent for probiotic-supplemented formula. Limited evidence demonstrates that pre- and synbiotic supplementation increases fecal Bifidobacterium levels. Future studies utilizing comprehensive methodologies and additional studies in probiotics and synbiotics are warranted.
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Affiliation(s)
- Lynn E. Ferro
- Department of Behavioral Health and Nutrition, University of Delaware, STAR Tower, 100 Discovery Blvd., Newark, DE 19713, USA
| | - Liana N. Crowley
- Department of Behavioral Health and Nutrition, University of Delaware, STAR Tower, 100 Discovery Blvd., Newark, DE 19713, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica E. Decker
- Department of Behavioral Health and Nutrition, University of Delaware, STAR Tower, 100 Discovery Blvd., Newark, DE 19713, USA
| | - Kathryn Russel
- Metropolitan Area Neighborhood Nutrition Alliance, 420 N 20 Street, Philadelphia, PA 19130, USA
| | - Sarah Katz
- Reference and Instructional Services Department, University of Delaware, 181 S. College Avenue, Newark, DE 19717, USA
| | - Jae Kyeom Kim
- Department of Behavioral Health and Nutrition, University of Delaware, STAR Tower, 100 Discovery Blvd., Newark, DE 19713, USA
| | - Jillian Trabulsi
- Department of Behavioral Health and Nutrition, University of Delaware, STAR Tower, 100 Discovery Blvd., Newark, DE 19713, USA
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36
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Rangu S, Lee JJ, Hu W, Bittinger K, Castelo-Soccio L. Understanding the Gut Microbiota in Pediatric Patients with Alopecia Areata and their Siblings: A Pilot Study. JID Innov 2021; 1:100051. [PMID: 34909748 PMCID: PMC8659389 DOI: 10.1016/j.xjidi.2021.100051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022] Open
Abstract
A cross-sectional study of 41 children aged 4–17 years with alopecia areata and 41 of their siblings without alopecia areata was conducted. A total of 51% had the Severity of Alopecia Tool scores in the range of 0–25%, 12% had scores between 26% and 49%, and 36% had scores between 75% and 100%. The fecal microbiome was characterized using shotgun metagenomic sequencing. A comparison of alpha and beta diversity yielded a small but statistically significant difference on the basis of Jaccard distance, which measures species presence and absence between samples. However, a follow-up analysis did not reveal the particular species that were present more often in one group. The relative abundance of one species, Ruminococcus bicirculans, was decreased in patients with alopecia areata relative to that in their sibling controls. An analysis of gene ortholog abundance identified 20 orthologs that were different between groups, including spore germination genes and genes for metal transportation. The associations reported in this study support a view of pediatric alopecia areata as a systemic disease that has effects on hair but also leads to internal changes, including differences in the gut microbiome.
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Affiliation(s)
- Sneha Rangu
- Section of Dermatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Leslie Castelo-Soccio
- Section of Dermatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Payne E, Harrington K, Richard P, Brackin R, Davis R, Couture S, Liff J, Asmus F, Mutina E, Fisher A, Giuvelis D, Sannajust S, Rostama B, King T, Mattei LM, Lee JJ, Friedman ES, Bittinger K, May M, Stevenson GW. Effects of Vancomycin on Persistent Pain-Stimulated and Pain-Depressed Behaviors in Female Fischer Rats With or Without Voluntary Access to Running Wheels. J Pain 2021; 22:1530-1544. [PMID: 34029686 PMCID: PMC8578155 DOI: 10.1016/j.jpain.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/02/2021] [Accepted: 05/15/2021] [Indexed: 10/21/2022]
Abstract
The present experiments determined the effects of the narrow-spectrum antibiotic vancomycin on inflammatory pain-stimulated and pain-depressed behaviors in rats. Persistent inflammatory pain was modeled using dilute formalin (0.5%). Two weeks of oral vancomycin administered in drinking water attenuated Phase II formalin pain-stimulated behavior, and prevented formalin pain-depressed wheel running. Fecal microbiota transplantation produced a non-significant trend toward reversal of the vancomycin effect on pain-stimulated behavior. Vancomycin depleted Firmicutes and Bacteroidetes populations in the gut while having a partial sparing effect on Lactobacillus species and Clostridiales. The vancomycin treatment effect was associated with an altered profile in amino acid concentrations in the gut with increases in arginine, glycine, alanine, proline, valine, leucine, and decreases in tyrosine and methionine. These results indicate that vancomycin may have therapeutic effects against persistent inflammatory pain conditions that are distal to the gut. PERSPECTIVE: The narrow-spectrum antibiotic vancomycin reduces pain-related behaviors in the formalin model of inflammatory pain. These data suggest that manipulation of the gut microbiome may be one method to attenuate inflammatory pain amplitude.
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Affiliation(s)
- Emily Payne
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Kylee Harrington
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Philomena Richard
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Rebecca Brackin
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Ravin Davis
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Sarah Couture
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Jacob Liff
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Francesca Asmus
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Elizabeth Mutina
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Anyssa Fisher
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Denise Giuvelis
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005
| | - Sebastien Sannajust
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005
| | - Bahman Rostama
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005
| | - Tamara King
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Elliot S Friedman
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Meghan May
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005
| | - Glenn W Stevenson
- Department of Psychology, University of New England, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005.
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Lewis JD, Sandler R, Brotherton C, Brensinger C, Li H, Kappelman MD, Daniel SG, Bittinger K, Albenberg L, Valentine JF, Hanson J, Suskind D, Meyer A, Compher CW, Bewtra M, Saxena A, Dobes A, Cohen B, Flynn AD, Fischer M, Saha S, Swaminath A, Yacyshyn B, Scherl E, Horst S, Curtis JR, Braly K, Nessel L, McCauley M, McKeever L, Herfarth H. A Randomized Trial Comparing the Specific Carbohydrate Diet to a Mediterranean Diet in Adults With Crohn's Disease. Gastroenterology 2021; 161:837-852.e9. [PMID: 34052278 PMCID: PMC8396394 DOI: 10.1053/j.gastro.2021.05.047] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [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: 02/28/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS This study compared the effectiveness of the Specific Carbohydrate Diet (SCD) to the Mediterranean diet (MD) as treatment for Crohn's disease (CD) with mild to moderate symptoms. METHODS Adult patients with CD and with mild-to-moderate symptoms were randomly assigned 1:1 to consume the MD or SCD for 12 weeks. For the first 6 weeks, participants received prepared meals and snacks according to their assigned diet. After 6 weeks, participants were instructed to follow the diet independently. The primary outcome was symptomatic remission at week 6. Key secondary outcomes at week 6 included fecal calprotectin (FC) response (FC <250 μg/g and reduction by >50% among those with baseline FC >250 μg/g) and C-reactive protein (CRP) response (high-sensitivity CRP <5 mg/L and >50% reduction from baseline among those with high-sensitivity CRP >5 mg/L). RESULTS The study randomized 194 patients, and 191 were included in the efficacy analyses. The percentage of participants who achieved symptomatic remission at week 6 was not superior with the SCD (SCD, 46.5%; MD, 43.5%; P = .77). FC response was achieved in 8 of 23 participants (34.8%) with the SCD and in 4 of 13 participants (30.8%) with the MD (P = .83). CRP response was achieved in 2 of 37 participants (5.4%) with the SCD and in 1 of 28 participants (3.6%) with the MD (P = .68). CONCLUSIONS The SCD was not superior to the MD to achieve symptomatic remission, FC response, and CRP response. CRP response was uncommon. Given these results, the greater ease of following the MD and other health benefits associated with the MD, the MD may be preferred to the SCD for most patients with CD with mild to moderate symptoms. ClinicalTrials.gov Identifier: NCT03058679.
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Affiliation(s)
- James D. Lewis
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania,Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania,Crohn’s & Colitis Foundation Clinical Research Alliance
| | - Robert Sandler
- Crohn’s & Colitis Foundation Clinical Research Alliance,Division of Gastroenterology and Hepatology, University of North Carolina
| | | | - Colleen Brensinger
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania
| | | | - Scott G. Daniel
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia
| | - Lindsey Albenberg
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia
| | - John F. Valentine
- Crohn’s & Colitis Foundation Clinical Research Alliance,Division of Gastroenterology, Hepatology and Nutrition, University of Utah Health
| | - John Hanson
- Crohn’s & Colitis Foundation Clinical Research Alliance,Atrium Health, Charlotte, NC, United States
| | - David Suskind
- Seattle Children’s Hospital,University of Washington
| | | | - Charlene W. Compher
- Department of Biobehavioral Health Science, University of Pennsylvania, School of Nursing, University of Pennsylvania
| | - Meenakshi Bewtra
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania,Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania,Crohn’s & Colitis Foundation Clinical Research Alliance
| | - Akriti Saxena
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania,Crohn’s & Colitis Foundation Clinical Research Alliance
| | | | - Benjamin Cohen
- Crohn’s & Colitis Foundation Clinical Research Alliance,Mount Sinai School of Medicine,Cleveland Clinic
| | - Ann D. Flynn
- Crohn’s & Colitis Foundation Clinical Research Alliance,Division of Gastroenterology, Hepatology and Nutrition, University of Utah Health
| | - Monika Fischer
- Crohn’s & Colitis Foundation Clinical Research Alliance,Division of Gastroenterology and Hepatology, Indiana University, Indianapolis, IN
| | - Sumona Saha
- Crohn’s & Colitis Foundation Clinical Research Alliance,Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health
| | - Arun Swaminath
- Crohn’s & Colitis Foundation Clinical Research Alliance,Lenox Hill Hospital
| | - Bruce Yacyshyn
- Crohn’s & Colitis Foundation Clinical Research Alliance,University of Cincinnati
| | - Ellen Scherl
- Crohn’s & Colitis Foundation Clinical Research Alliance,Cornell University
| | - Sara Horst
- Crohn’s & Colitis Foundation Clinical Research Alliance,Vanderbilt University
| | | | - Kimberly Braly
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania
| | - Lisa Nessel
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania
| | - Maureen McCauley
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania
| | - Liam McKeever
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania
| | - Hans Herfarth
- Crohn’s & Colitis Foundation Clinical Research Alliance,Division of Gastroenterology and Hepatology, University of North Carolina
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Byeon J, Blizinsky KD, Persaud A, Findley K, Lee J, Buscetta AJ, You S, Bittinger K, Minniti CP, Bonham VL, Grice EA. Insights into the skin microbiome of sickle cell disease leg ulcers. Wound Repair Regen 2021; 29:801-809. [PMID: 33964094 PMCID: PMC8410641 DOI: 10.1111/wrr.12924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/10/2021] [Accepted: 04/14/2021] [Indexed: 01/04/2023]
Abstract
Leg ulcers are estimated to occur in 1%-10% of North American patients with sickle cell disease (SCD). Their pathophysiology remains poorly defined, but as with other chronic wounds, it is hypothesised that the microbial milieu, or microbiome, contributes to their healing and clinical outcomes. This study utilises 16S ribosomal RNA (rRNA) gene sequencing to describe, for the first time, the microbiome of the SCD leg ulcer and its association with clinical factors. In a cross-sectional analysis of 42 ulcers, we recovered microbial profiles similar to other chronic wounds in the predominance of anaerobic bacteria and opportunistic pathogens including Staphylococcus, Corynebacterium, and Finegoldia. Ulcers separated into two clusters: one defined by predominance of Staphylococcus and smaller surface area, and the other displaying a greater diversity of taxa and larger surface area. We also find that the relative abundance of Porphyromonas is negatively associated with haemoglobin levels, a key clinical severity indicator for SCD, and that Finegoldia relative abundance is negatively associated with CD19+ B cell count. Finally, ratios of Corynebacterium:Lactobacillus and Staphylococcus:Lactobacillus are elevated in the intact skin of individuals with a history of SCD leg ulcers, while the ratio of Lactobacillus:Bacillus is elevated in that of individuals without a history of ulcers. Investigations of the skin microbiome in relation to SCD ulcer pathophysiology can inform clinical guidelines for this poorly understood chronic wound, as well as enhance broader understanding about the role of the skin microbiome in delayed wound healing.
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Affiliation(s)
- Julia Byeon
- Social and Behavioral Research BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Katherine D. Blizinsky
- All of Us Research ProgramNational Institutes of HealthBethesdaMarylandUSA
- NeurologyRush Alzheimer's Disease Center, Rush Medical CollegeChicagoIllinoisUSA
| | - Anitra Persaud
- Social and Behavioral Research BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Keisha Findley
- Social and Behavioral Research BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Jung‐Jin Lee
- The Children's Hospital of PhiladelphiaMicrobiome Center Roberts Center for Pediatric ResearchPhiladelphiaPennsylvaniaUSA
| | - Ashley J. Buscetta
- Social and Behavioral Research BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Shuo You
- Department of Medicine, Division of HematologyMontefiore Medical Center, Albert Einstein College of MedicineBronxNew YorkUSA
| | - Kyle Bittinger
- The Children's Hospital of PhiladelphiaMicrobiome Center Roberts Center for Pediatric ResearchPhiladelphiaPennsylvaniaUSA
| | - Caterina P. Minniti
- Albert Einstein College of Medicine, Center for Sickle Cell Disease ResearchMontefiore Medical CenterBronxNew YorkUSA
| | - Vence L. Bonham
- Social and Behavioral Research BranchNational Human Genome Research Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Elizabeth A. Grice
- Department of Dermatology and MicrobiologyUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
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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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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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42
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Tang SY, Meng H, Anderson ST, Sarantopoulou D, Ghosh S, Lahens NF, Theken KN, Ricciotti E, Hennessy EJ, Tu V, Bittinger K, Weiljie AM, Grant GR, FitzGerald GA. Sex-dependent compensatory mechanisms preserve blood pressure homeostasis in prostacyclin receptor-deficient mice. J Clin Invest 2021; 131:e136310. [PMID: 34101620 DOI: 10.1172/jci136310] [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] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/03/2021] [Indexed: 11/17/2022] Open
Abstract
Inhibitors of microsomal prostaglandin E synthase 1 (mPGES-1) are in the early phase of clinical development. Deletion of mPges-1 in mice confers analgesia, restrains atherogenesis, and fails to accelerate thrombogenesis, while suppressing prostaglandin E2 (PGE2), but increasing the biosynthesis of prostacyclin (PGI2). In low-density lipoprotein receptor-deficient (Ldlr-/-) mice, this last effect represents the dominant mechanism by which mPges-1 deletion restrains thrombogenesis, while suppression of PGE2 accounts for its antiatherogenic effect. However, the effect of mPges-1 depletion on blood pressure (BP) in this setting remains unknown. Here, we show that mPges-1 depletion significantly increased the BP response to salt loading in male Ldlr-/- mice, whereas, despite the direct vasodilator properties of PGI2, deletion of the I prostanoid receptor (Ipr) suppressed this response. Furthermore, combined deletion of the Ipr abrogated the exaggerated BP response in male mPges-1-/- mice. Interestingly, these unexpected BP phenotypes were not observed in female mice fed a high-salt diet (HSD). This is attributable to the protective effect of estrogen in Ldlr-/- mice and in Ipr-/- Ldlr-/- mice. Thus, estrogen compensates for a deficiency in PGI2 to maintain BP homeostasis in response to high salt in hyperlipidemic female mice. In male mice, by contrast, the augmented formation of atrial natriuretic peptide (ANP) plays a similar compensatory role, restraining hypertension and oxidant stress in the setting of Ipr depletion. Hence, men with hyperlipidemia on a HSD might be at risk of a hypertensive response to mPGES-1 inhibitors.
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Affiliation(s)
- Soon Y Tang
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hu Meng
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Seán T Anderson
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Soumita Ghosh
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine N Theken
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emanuela Ricciotti
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth J Hennessy
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Aalim M Weiljie
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Garret A FitzGerald
- Institute for Translational Medicine and Therapeutics, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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43
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Shirley M, Bittinger K, Li Y, Ford E, Friedman E, Gerber J, Elovitz M, Kelly A, DeRusso P, Albenberg L, Drigo D, Shults J, Walega R, Li H, Wu G, Zemel B. Dietary Patterns and Growth From 12 to 24 Months of Age in African American Infants. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab038_066] [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: 11/14/2022] Open
Abstract
Abstract
Objectives
To identify dietary patterns in 12-month-old African American infants and investigate their association with change in infant BMI z-score (BMIz) from 12 to 24 months.
Methods
The prospective longitudinal Infant Growth and Microbiome Study (IGram) enrolled African American women in their 3rd trimester of pregnancy who had a pre-pregnancy BMI >30 or <25 and followed them and their infants from birth to 24 months of age. At 12 months, mothers reported infant intake of 32 food items in the past 7 days using the CDC Infant Feeding Practices Study II questionnaire. With these data we employed principal component analysis to derive dietary patterns for infants aged 12 months. We used multiple regression to test associations of dietary pattern scores with change in infant BMIz between 12 and 24 months.
Results
IGram enrolled 368 infants at birth; 320 and 283 infants completed 12- and 24-month visits, respectively. The prevalence of BMIz > 2SD was 7.8% at 12 months and 6% at 24 months. We derived three dietary patterns which together explained 36% of the variation in the dataset. Based on the highest factor loadings for each pattern, they were named “Transitional/table food,” “Formula/baby cereal,” and “Fruit and vegetable/breast milk.” The former pattern included pancakes, pasta, rice, french fries, meat, eggs, and snack and sweet foods. Regression results suggested that, accounting for maternal pre-pregnancy obesity status, the “Fruit and vegetable/breast milk” pattern explained a small portion of the variance in BMIz increase from 12 to 24 months of age (β = 0.07, 95% CI = 0.01, 0.13, P = 0.03).
Conclusions
Preliminary findings of three distinct dietary patterns in African American infants at 12 months of age are an important first step in characterizing infant feeding patterns across the rich, longitudinal IGram dataset. A positive association of the “Fruit and vegetable/breast milk” pattern with change in infant BMIz from 12 to 24 months was unexpected and requires further investigation.
Funding Sources
An unrestricted donation from the American Beverage Foundation for a Healthy America to support the Children's Hospital of Philadelphia's Healthy Weight Program; the Research Institute of the Children's Hospital of Philadelphia; the National Center for Advancing Translational Sciences; the NIH NIDDK.
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Affiliation(s)
| | | | - Yun Li
- University of Pennsylvania Perelman School of Medicine
| | | | | | | | | | | | | | | | | | | | | | - Hongzhe Li
- University of Pennsylvania Perelman School of Medicine
| | - Gary Wu
- University of Pennsylvania Perelman School of Medicine
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44
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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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Abt MC, Alam Z, Littmann ER, Denny JE, Lee JJ, Bittinger K. CD4+ Foxp3+ T-regulatory cells support fecal microbiota transplantation engraftment and resolution of Clostridioides difficile infection. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.100.06] [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: 02/10/2023]
Abstract
Abstract
Clostridioides difficile is an opportunistic pathogen that infects the large intestine following perturbation of the intestinal microbiota causing epithelial damage and debilitating, potentially fatal, colitis. Fecal microbiota transplantation (FMT) is a successful therapeutic strategy for treating recurrent C. difficile infection. Despite remarkable efficacy, implementation of FMT therapy is limited and the mechanism of action remains poorly understood. Here, we demonstrate a critical role for Foxp3+ CD4+T-regulatory cells in supporting FMT therapy using a murine C. difficile infection system. Following FMT, chronically infected wild-type mice resolve C. difficile. In contrast, cohoused Rag1−/− or CD4+ T cell deficient mice fail to clear the infection. Genetic deletion of TH1 or TH17 effector cytokines does not impact efficacy of FMT, however, C. difficile infected Il10−/− mice are non-responsive to FMT therapy. Further, targeted ablation of CD4+ Foxp3+T-regulatory cells in C. difficile infected Foxp3-DTR mice prior to FMT reveal a necessary role for this CD4+T cell subset in FMT-mediated resolution of C. difficile infection. FMT non-responsive mice exhibit impaired engraftment of the FMT bacterial consortia and failed restoration of commensal bacteria-derived secondary bile acids in the large intestine, metabolites associated with limiting C. difficile disease in FMT recipient patients. These data demonstrate that the host’s inflammatory immune status can limit the efficacy of microbiota-based therapeutics to treat C. difficile infection.
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46
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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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Rhee RL, Lu J, Bittinger K, Lee JJ, Mattei LM, Sreih AG, Chou S, Miner JJ, Cohen NA, Kelly BJ, Lee H, Grayson PC, Collman RG, Merkel PA. Dynamic Changes in the Nasal Microbiome Associated With Disease Activity in Patients With Granulomatosis With Polyangiitis. Arthritis Rheumatol 2021; 73:1703-1712. [PMID: 33682371 DOI: 10.1002/art.41723] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/02/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Little is known about temporal changes in nasal bacteria in granulomatosis with polyangiitis (GPA). This study was undertaken to examine longitudinal changes in the nasal microbiome in association with relapse in GPA patients. METHODS Bacterial 16S ribosomal RNA gene sequencing was performed on nasal swabs from 19 patients with GPA who were followed up longitudinally for a total of 78 visits, including 9 patients who experienced a relapse and 10 patients who remained in remission. Relative abundance of bacteria and ratios between bacteria were examined. Generalized estimating equation models were used to evaluate the association between bacterial composition and 1) disease activity and 2) levels of antineutrophil cytoplasmic antibody (ANCA) with specificity for proteinase 3 (PR3), adjusted for medication. RESULTS Corynebacterium and Staphylococcus were the most abundant bacterial genera across all nasal samples. Patients with quiescent disease maintained a stable ratio of Corynebacterium to Staphylococcus across visits. In contrast, in patients who experienced a relapse, a significantly lower ratio was observed at the visit prior to relapse, followed by a higher ratio at the time of relapse (adjusted P < 0.01). Species-level analysis identified an association between a higher abundance of nasal Corynebacterium tuberculostearicum and 1) relapse (adjusted P = 0.04) and 2) higher PR3-ANCA levels (adjusted P = 0.02). CONCLUSION In GPA, significant changes occur in the nasal microbiome over time and are associated with disease activity. The occurrence of these changes months prior to the onset of relapse supports a pathogenic role of nasal bacteria in GPA. Our results uphold existing hypotheses implicating Staphylococcus as an instigator of disease and have generated a novel finding involving Corynebacterium as a potential mediator of disease in GPA.
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Affiliation(s)
| | - Jiarui Lu
- University of Pennsylvania, Philadelphia
| | - Kyle Bittinger
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jung-Jin Lee
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lisa M Mattei
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | | | | | | | | | - Peter C Grayson
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland
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48
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Roy Paladhi U, Harb AH, Daniel SG, Dawwas GK, Schnellinger EM, Wollack C, Aberra FN, Bewtra M, Green JA, Klaproth JMA, Lichtenstein GR, Saxena A, Berera S, Buchner A, Mehta SJ, Osterman MT, Rashid F, Tomov V, Caldera F, Sumona S, Mahadevan U, Roy A, Nessel L, Wu GD, Bittinger K, Lewis JD. The Impact of Introducing Patient-Reported Inflammatory Bowel Disease Symptoms via Electronic Survey on Clinic Visit Length, Patient and Provider Satisfaction, and the Environment Microbiome. Inflamm Bowel Dis 2021; 27:746-750. [PMID: 33452800 PMCID: PMC9115377 DOI: 10.1093/ibd/izaa356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 12/09/2022]
Affiliation(s)
- Unmesha Roy Paladhi
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,Address correspondence to: Unmesha Roy Paladhi, MPH, Department of Epidemiology, 1959 Pacific Street, Seattle, WA 98195 ()
| | - Ali H Harb
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ghadeer K Dawwas
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erin M Schnellinger
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Colin Wollack
- Corporate Information Services, Penn Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Faten N Aberra
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meenakshi Bewtra
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jesse A Green
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jan-Michael A Klaproth
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gary R Lichtenstein
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Akriti Saxena
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shivali Berera
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Buchner
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shivan J Mehta
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark T Osterman
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Farzana Rashid
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vesselin Tomov
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Freddy Caldera
- Division of Gastroenterology & Hepatology, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Saha Sumona
- Division of Gastroenterology & Hepatology, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Uma Mahadevan
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Abhik Roy
- Department of Gastroenterology, Kaiser Permanente, San Leandro, California, USA
| | - Lisa Nessel
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gary D Wu
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - James D Lewis
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Abstract
OBJECTIVES The objective of this study was to characterize gut microbiome profiles of infants with congenital hyperinsulinism (HI) who underwent near-total or partial pancreatectomy for hypoglycemia management, as compared with healthy controls. METHODS A prospective observational cohort study was performed. Subjects were infants (0-6 months) with HI who underwent removal of pancreatic tissue for management of intractable hypoglycemia from February 2017 to February 2018 at the Children's Hospital of Philadelphia. Fecal samples were collected postoperatively, on full enteral nutrition. The gut microbiome of HI subjects was analyzed and compared with age-matched samples from healthy infants. RESULTS Seven subjects with ≥50% pancreatectomy and 6 with <50% pancreatectomy were included. α (within-sample) diversity was lowest among infants with ≥50% pancreatectomy (richness: false discovery rate, 0.003; Shannon index: false discovery rate, 0.01). β (between-sample) diversity (Bray-Curtis dissimilarity, P = 0.02; Jaccard distance, P = 0.001) differed across groups (≥ or <50% pancreatectomy, controls). Bifidobacteria and Klebsiella species were least abundant among infants with ≥50% pancreatectomy but did not differ between infants with <50% pancreatectomy and historical controls. CONCLUSIONS Infants with HI who underwent ≥50% pancreatectomy differed from age-matched infants in gut microbiome profile, whereas those with <50% pancreatectomy more closely resembled control profiles. The durability of this difference should be investigated.
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Affiliation(s)
| | - Jung-Jin Lee
- Division of Gastoenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lauren Mitteer
- From the Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia
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50
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Mahalak KK, Firrman J, Tomasula PM, Nuñez A, Lee JJ, Bittinger K, Rinaldi W, Liu LS. Impact of Steviol Glycosides and Erythritol on the Human and Cebus apella Gut Microbiome. J Agric Food Chem 2020; 68:13093-13101. [PMID: 31869223 DOI: 10.1021/acs.jafc.9b06181] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Leaf extracts of Stevia rebaudiana, composed of more than 10 steviol glycosides (SGs), are used as non-nutritive, table sugar (sucrose) alternatives due to their high level of sweetness and low caloric impact. They are often combined with the sugar alcohol erythritol to increase volume and reduce aftertaste. Little is known of the impact of sugar alternatives on the human gut microbiota in terms of the diversity, composition, and metabolic products. Testing of SGs and erythritol using six representatives of the gut microbiota in vitro found no impact on bacterial growth, yet treatment with erythritol resulted in an enhancement of butyric and pentanoic acid production when tested using a human gut microbial community. Furthermore, administration of SGs and erythritol to a Cebus apella model resulted in changes to the gut microbial structure and diversity. Overall, the study did not find a negative impact of SGs and erythritol on the gut microbial community.
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Affiliation(s)
- Karley K Mahalak
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, 600E Mermaid Lane, Wyndmoor, Pennsylvania 19038, United States
| | - Jenni Firrman
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, 600E Mermaid Lane, Wyndmoor, Pennsylvania 19038, United States
| | - Peggy M Tomasula
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, 600E Mermaid Lane, Wyndmoor, Pennsylvania 19038, United States
| | - Alberto Nuñez
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600E Mermaid Lane, Wyndmoor, Pennsylvania 19038, United States
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - William Rinaldi
- Alpha Genesis Inc., 95 Castle Hall Road, Yemassee, South Carolina 29945, United States
| | - Lin Shu Liu
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, 600E Mermaid Lane, Wyndmoor, Pennsylvania 19038, United States
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