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Li C, Stražar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ. Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria. Cell 2024; 187:1834-1852.e19. [PMID: 38569543 PMCID: PMC11071153 DOI: 10.1016/j.cell.2024.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.
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Affiliation(s)
- Chenhao Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ahmed M T Mohamed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Tina Lebar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Shijie Zhao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Lockart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrea Dame
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qi Yan Ang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Dallis Sergio
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachele Invernizzi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonio Tinoco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Ramachandran S Vasan
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA; Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA; University of Texas School of Public Health, San Antonio, TX, USA
| | - Emily Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stanley Y Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Bu S, Kar W, Tucker RM, Comstock SS. Minimal Influence of Cayenne Pepper on the Human Gastrointestinal Microbiota and Intestinal Inflammation in Healthy Adult Humans-A Pilot Study. Life (Basel) 2022; 12:life12111849. [PMID: 36430985 PMCID: PMC9695709 DOI: 10.3390/life12111849] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Diet impacts human gut microbial composition. Phytochemicals in cayenne pepper (CP), such as capsaicin, have anti-inflammatory properties and alter bacterial growth in vitro. However, the evidence that CP impacts the human microbiota and intestinal inflammation in free-living adults is lacking. Thus, the objective of this randomized cross-over study was to determine the influence of CP on human gut microbiota and intestinal inflammation in vivo. A total of 29 participants were randomly allocated to consume two 250 mL servings of tomato juice plus 1.8 g of CP each day or juice only for 5 days before crossing over to the other study arm. Fecal samples were analyzed. CP reduced Oscillibacter and Phascolarctobacterium but enriched Bifidobacterium and Gp6. When stratified by BMI (body mass index), only the increase in Gp6 was observed in all BMI groups during CP treatment. Stool concentrations of lipocalin-2 and calprotectin were similar regardless of CP treatment. However, lipocalin-2 and calprotectin levels were positively correlated in samples taken after CP consumption. Neither lipocalin-2 nor calprotectin levels were related to gut microbial composition. In conclusion, in healthy adult humans under typical living conditions, consumption of CP minimally influenced the gut microbiota and had little impact on intestinal inflammation.
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Kitahara M, Shigeno Y, Shime M, Matsumoto Y, Nakamura S, Motooka D, Fukuoka S, Nishikawa H, Benno Y. Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 34726590 DOI: 10.1099/ijsem.0.005066] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Six strains of Gram-stain-negative, obligately anaerobic, non-spore-forming, non-motile rods were isolated from human faeces. Based on phylogenetic characteristics, the six isolates were included in the family Ruminococcaceae, and divided into three groups. The six isolates showed 16S rRNA gene sequence similarity values lower than 96.2 % to the closely related species, Oscillibacter ruminantium GH1T, Oscillibacter valericigenes Sjm18-20T and Dysosmobacter welbiomis J115T. Coherently with the 16S rRNA gene sequence results, the in silico DNA-DNA hybridization and average nucleotide identity values clearly indicated that strains MM35T, MM50T and MM59T belong to different species from the closely related three species. Based on phenotypic features and phylogenetic positions, three novel species, Vescimonas coprocola gen. nov., sp. nov., Vescimonas fastidiosa gen. nov., sp. nov. and Pusillimonas faecalis gen. nov., sp. nov. are proposed. The type strain of V. coprocola is strain MM50T (=JCM 34012T=DSM 111893T). The type strain of V. fastidiosa is strain MM35T (=JCM 34016T=DSM 111899T). The type strain of P. faecalis is strain MM59T (=JCM 34011T=DSM 111669T). The DNA G+C contents estimated according to the whole genomes of strains MM35T, MM50T and MM59T were 56.4, 58.2 and 55.2 mol%, respectively.
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Affiliation(s)
- Maki Kitahara
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
| | - Yuko Shigeno
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
| | - Mari Shime
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
| | - Yuki Matsumoto
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Fukuoka
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
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Broutin L, Deroche L, Michaud A, Le Moal G, Burucoa C, Gayet LE, Plouzeau C, Pichon M. First description of bacteremia caused by Oscillibacter valericigenes in a patient hospitalized for leg amputation. Anaerobe 2020; 64:102244. [PMID: 32712374 DOI: 10.1016/j.anaerobe.2020.102244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/13/2020] [Revised: 07/07/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
Initially isolated from the alimentary canal of a Japanese corbicula clam, Oscillibacter valericigenes is a Gram-negative rod, of which culture remains very difficult. Herein we present the first case of bacteremia due to Oscillibacter valericigenes, in humans. A 55-year-old man was hospitalized for clinical management of multiple neglected leg wounds (colonized with maggots) that had occurred during a motorcycle accident. Following radiological confirmation of the bone infection, a transfemoral amputation was performed to limit the risk of extended infection. During hospitalization, before the amputation, the patient experienced fever, biological inflammation justifying the sampling of multiple blood cultures. Anaerobic blood culture was positive after 34 hours, without identification by routine procedure (MALDI-TOF), justifying identification by 16S DNA sequencing. In the absence of possible subculture, antibiotic sensitivity testing could not be performed. A pre-emptive treatment by piperacillin-tazobactam was introduced for 14 days. The evolution was good, except for a local disunion. Complete phylogenic analysis of the clinical strain showed that it significantly differed from the reference strain, which is distantly related to the Clostridia cluster IV. Due to the culture conditions and specialized identification method by sequencing, prevalence of O. valericigenes may be underestimated. Optimization of blood culture procedures and utilization of 16S rRNA gene sequencing are tools needed for identification of rare pathogens that could help to optimize clinical management of infected patients.
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Affiliation(s)
- Lauranne Broutin
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Luc Deroche
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Anthony Michaud
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Gwenaël Le Moal
- University Hospital of Poitiers, Department of Infectious Diseases, CHU, Poitiers, France
| | - Christophe Burucoa
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Louis-Etienne Gayet
- University Hospital of Poitiers, Department of Orthopedic Surgery and Traumatology, CHU, Poitiers, France
| | - Chloé Plouzeau
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Maxime Pichon
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France.
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Kim JE, Kim HE, Park JI, Cho H, Kwak MJ, Kim BY, Yang SH, Lee JP, Kim DK, Joo KW, Kim YS, Kim BS, Lee H. The Association between Gut Microbiota and Uremia of Chronic Kidney Disease. Microorganisms 2020; 8:E907. [PMID: 32560104 DOI: 10.3390/microorganisms8060907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/13/2020] [Accepted: 06/14/2020] [Indexed: 12/16/2022] Open
Abstract
Chronic kidney disease (CKD)-associated uremia aggravates-and is aggravated by-gut dysbiosis. However, the correlation between CKD severity and gut microbiota and/or their uremic metabolites is unclear. We enrolled 103 CKD patients with stage 1 to 5 and 46 healthy controls. We analyzed patients' gut microbiota by MiSeq system and measured the serum concentrations of four uremic metabolites (p-cresyl sulfate, indoxyl sulfate, p-cresyl glucuronide, and trimethylamine N-oxide) by liquid chromatography-tandem mass spectrometry. Serum concentrations of the uremic metabolites increased with kidney function deterioration. Gut microbial diversity did not differ among the examined patient and control groups. In moderate or higher stage CKD groups, Oscillibacter showed positive interactions with other microbiota, and the proportions of Oscillibacter were positively correlated with those of the uremic metabolites. The gut microbiota, particularly Oscillibacter, was predicted to contribute to pyruvate metabolism which increased with CKD progression. Relative abundance of Oscillibacter was significantly associated with both serum uremic metabolite levels and kidney function. Predicted functional analysis suggested that kidney-function-associated changes in the contribution of Oscillibacter to pyruvate metabolism in CKD may greatly affect the gut environment according to kidney function, resulting in dysbiosis concomitant with uremic toxin production. The gut microbiota could be associated with uremia progression in CKD. These results may provide basis for further metagenomics analysis of kidney diseases.
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Vermeire S, Joossens M, Verbeke K, Wang J, Machiels K, Sabino J, Ferrante M, Van Assche G, Rutgeerts P, Raes J. Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease. J Crohns Colitis 2016; 10:387-94. [PMID: 26519463 PMCID: PMC4946755 DOI: 10.1093/ecco-jcc/jjv203] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [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: 08/02/2015] [Accepted: 10/25/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Faecal microbiota transplantation is a successful therapy for patients with refractory Clostridium difficile infections. It has also been suggested as a treatment option for inflammatory bowel disease, given the role of the intestinal microbiota in this disease. We assessed the impact of faecal microbiota transplantation in patients with inflammatory bowel disease and studied predictors of clinical (non-)response in microbial profiles of donors and patients. METHODS Fourteen refractory patients (8 with ulcerative colitis and 6 with Crohn's disease) underwent ileocolonoscopy with faecal microbiota transplantation through a nasojejunal (n = 9) or rectal (n = 5) tube. Efficacy was assessed by endoscopic healing at week 8, clinical activity scores and C-reactive protein measurement. Faecal microbiota was analysed by 16S rDNA pyrosequencing. RESULTS There was no significant improvement among the 6 patients with Crohn's disease at week 8 following faecal microbiota transplantation. One patient experienced temporary clinical remission for 6 weeks. In contrast, 2/8 patients with ulcerative colitis had endoscopic remission at week 8, and of the 6 remaining patients with ulcerative colitis, 1 reported temporary remission for 6 weeks. The donor microbiota richness and the number of transferred phylotypes were associated with treatment success. Persistent increased C-reactive protein 2 weeks after transplantation was predictive of failure of response. CONCLUSION Faecal microbiota transplantation led to endoscopic and long-term (>2 years) remission in 2 out of 8 ulcerative colitis patients. Higher donor richness was associated with successful transplant. Therefore, faecal microbiota transplantation with donor prescreening could be a treatment option for selected refractory ulcerative colitis patients.
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Affiliation(s)
- Severine Vermeire
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | | | - Kristin Verbeke
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jun Wang
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium,VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Kathleen Machiels
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - João Sabino
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Marc Ferrante
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Gert Van Assche
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Paul Rutgeerts
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium,VIB, Center for the Biology of Disease, Leuven, Belgium
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