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Rahmanian M, Fathi M, Eftekhari M, Vakili K, Deravi N, Yaghoobpoor S, Sharifi H, Zeinodini R, Babajani A, Niknejad H. Developing a novel hypothesis to enhance mental resilience via targeting Faecalibacterium prausnitzii in gut-brain axis. Med Hypotheses 2024; 192:111468. [DOI: 10.1016/j.mehy.2024.111468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
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2
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Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. MICROBIOME 2024; 12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.
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Affiliation(s)
- Yingjian Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Na Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
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Barata T, Pereira V, Pires das Neves R, Rocha M. Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer. Comput Biol Med 2024; 170:108052. [PMID: 38308868 DOI: 10.1016/j.compbiomed.2024.108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The imbalance of epigenetic regulatory mechanisms such as DNA methylation, which can promote aberrant gene expression profiles without affecting the DNA sequence, may cause the deregulation of signaling, regulatory, and metabolic processes, contributing to a cancerous phenotype. Since some metabolites are substrates and cofactors of epigenetic regulators, their availability can be affected by characteristic cancer cell metabolic shifts, feeding cancer onset and progression through epigenetic deregulation. Hence, there is a need to study the influence of cancer metabolic reprogramming in DNA methylation to design new effective treatments. In this study, a generic Genome-Scale Metabolic Model (GSMM) of a human cell, integrating DNA methylation or demethylation reactions, was obtained and used for the reconstruction of Genome-Scale Metabolic Models enhanced with Enzymatic Constraints using Kinetic and Omics data (GECKOs) of 31 cancer cell lines. Furthermore, cell-line-specific DNA methylation levels were included in the models, as coefficients of a DNA composition pseudo-reaction, to depict the influence of metabolism over global DNA methylation in each of the cancer cell lines. Flux simulations demonstrated the ability of these models to provide simulated fluxes of exchange reactions similar to the equivalent experimentally measured uptake/secretion rates and to make good functional predictions. In addition, simulations found metabolic pathways, reactions and enzymes directly or inversely associated with the gene promoter methylation. Two potential candidates for targeted cancer epigenetic therapy were identified.
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Affiliation(s)
- Tânia Barata
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Vítor Pereira
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo Pires das Neves
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal; Department of Informatics, University of Minho, Portugal.
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Meng X, Shu Q. Novel primers to identify a wider diversity of butyrate-producing bacteria. World J Microbiol Biotechnol 2024; 40:76. [PMID: 38252387 DOI: 10.1007/s11274-023-03872-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024]
Abstract
Butyrate-producing bacteria are a functionally important part of the intestinal tract flora, and the resulting butyric acid is essential for maintaining host intestinal health, regulating the immune system, and influencing energy metabolism. However, butyrate-producing bacteria have not been defined as a coherent phylogenetic group. They are primarily identified using primers for key genes in the butyrate-producing pathway, and their use has been limited to the Bacillota and Bacteroidetes phyla. To overcome this limitation, we developed functional gene primers able to identify butyrate-producing bacteria through the butyrate kinase gene, which encodes the enzyme involved in the final step of the butyrate-producing pathway. Genomes extracted from human and rat feces were used to amplify the target genes through PCR. The obtained sequences were analyzed using BLASTX to construct a developmental tree using the MEGA software. The newly designed butyrate kinase gene primers allowed to recognize a wider diversity of butyrate-producing bacteria than that recognized using currently available primers. Specifically, butyrate-producing bacteria from the Synergistota and Spirochaetota phyla were identified for the first time using these primers. Thus, the developed primers provide a more accurate method for researchers and doctors to identify potential butyrate-producing bacteria and deepen our understanding of butyrate-producing bacterial species.
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Affiliation(s)
- Xianbin Meng
- College of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, China
| | - Qinglong Shu
- College of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, China.
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Kwao-Zigah G, Bediako-Bowan A, Boateng PA, Aryee GK, Abbang SM, Atampugbire G, Quaye O, Tagoe EA. Microbiome Dysbiosis, Dietary Intake and Lifestyle-Associated Factors Involve in Epigenetic Modulations in Colorectal Cancer: A Narrative Review. Cancer Control 2024; 31:10732748241263650. [PMID: 38889965 PMCID: PMC11186396 DOI: 10.1177/10732748241263650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/18/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Background: Colorectal cancer is the second cause of cancer mortality and the third most commonly diagnosed cancer worldwide. Current data available implicate epigenetic modulations in colorectal cancer development. The health of the large bowel is impacted by gut microbiome dysbiosis, which may lead to colon and rectum cancers. The release of microbial metabolites and toxins by these microbiotas has been shown to activate epigenetic processes leading to colorectal cancer development. Increased consumption of a 'Westernized diet' and certain lifestyle factors such as excessive consumption of alcohol have been associated with colorectal cancer.Purpose: In this review, we seek to examine current knowledge on the involvement of gut microbiota, dietary factors, and alcohol consumption in colorectal cancer development through epigenetic modulations.Methods: A review of several published articles focusing on the mechanism of how changes in the gut microbiome, diet, and excessive alcohol consumption contribute to colorectal cancer development and the potential of using these factors as biomarkers for colorectal cancer diagnosis.Conclusions: This review presents scientific findings that provide a hopeful future for manipulating gut microbiome, diet, and alcohol consumption in colorectal cancer patients' management and care.
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Affiliation(s)
- Genevieve Kwao-Zigah
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Antionette Bediako-Bowan
- Department of Surgery, University of Ghana Medical School, Accra, Ghana
- Department of Surgery, Korle Bu Teaching Hospital, Accra, Ghana
| | - Pius Agyenim Boateng
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Gloria Kezia Aryee
- Department of Medical Laboratory Sciences, University of Ghana, Accra, Ghana
| | - Stacy Magdalene Abbang
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Gabriel Atampugbire
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Emmanuel A. Tagoe
- Department of Medical Laboratory Sciences, University of Ghana, Accra, Ghana
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Zhang Y, Lin CL, Weber KM, Xing J, Peters BA, Sollecito CC, Grassi E, Wiek F, Xue X, Seaberg EC, Gustafson D, Anastos K, Sharma A, Burgess HJ, Burk RD, Qi Q, French AL. Association of Gut Microbiota With Objective Sleep Measures in Women With and Without Human Immunodeficiency Virus Infection: The IDOze Study. J Infect Dis 2023; 228:1456-1466. [PMID: 37650624 PMCID: PMC10640774 DOI: 10.1093/infdis/jiad371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Poor sleep health is an underrecognized health challenge, especially for people with human immunodeficiency virus (HIV). Gut microbiota related to sleep are underinvestigated. METHODS The IDOze microbiota substudy included 190 women (114 with HIV and 76 without HIV). Wrist actigraphy measured total sleep duration, sleep efficiency, number of wake bouts, wake after sleep onset, fragmentation index, and sleep timing. 16S rRNA gene sequencing identified gut microbial genera. Analysis of compositions of microbiomes with bias correction was used to investigate cross-sectional associations between gut microbiota and sleep. Abundances of sleep-related gut microbial genera were compared between women with and without HIV. RESULTS Enrichment of 7 short-chain fatty acid-producing genera (eg, Butyricimonas, Roseburia, and Blautia) was associated with lower fragmentation index. Enrichment of 9 genera (eg, Dorea) was associated with lower sleep efficiency and/or more wake after sleep onset. Enrichment of proinflammatory Acidaminococcus was associated with late sleep midpoint and offset time. These associations were largely consistent regardless of HIV status. The abundance of Butyricimonas was lower among women with HIV compared to those without HIV. CONCLUSIONS Seventeen genera were identified to be associated with sleep continuity or timing. Butyricimonas, a potentially beneficial genus associated with sleep continuity, was less abundant among women with HIV.
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Affiliation(s)
- Yanbo Zhang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Chin Lun Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Kathleen M Weber
- Hektoen Institute of Medicine/Cook County Health, Chicago, Illinois
| | - Jiaqian Xing
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | | | - Evan Grassi
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | - Fanua Wiek
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | - Xiaonan Xue
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Eric C Seaberg
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland
| | - Deborah Gustafson
- Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Helen J Burgess
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
- Department of Obstetrics, Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Audrey L French
- Department of Medicine, Stroger Hospital of Cook County Health, Chicago, Illinois
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7
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Chen HC, Liu YW, Chang KC, Wu YW, Chen YM, Chao YK, You MY, Lundy DJ, Lin CJ, Hsieh ML, Cheng YC, Prajnamitra RP, Lin PJ, Ruan SC, Chen DHK, Shih ESC, Chen KW, Chang SS, Chang CMC, Puntney R, Moy AW, Cheng YY, Chien HY, Lee JJ, Wu DC, Hwang MJ, Coonen J, Hacker TA, Yen CLE, Rey FE, Kamp TJ, Hsieh PCH. Gut butyrate-producers confer post-infarction cardiac protection. Nat Commun 2023; 14:7249. [PMID: 37945565 PMCID: PMC10636175 DOI: 10.1038/s41467-023-43167-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
The gut microbiome and its metabolites are increasingly implicated in several cardiovascular diseases, but their role in human myocardial infarction (MI) injury responses have yet to be established. To address this, we examined stool samples from 77 ST-elevation MI (STEMI) patients using 16 S V3-V4 next-generation sequencing, metagenomics and machine learning. Our analysis identified an enriched population of butyrate-producing bacteria. These findings were then validated using a controlled ischemia/reperfusion model using eight nonhuman primates. To elucidate mechanisms, we inoculated gnotobiotic mice with these bacteria and found that they can produce beta-hydroxybutyrate, supporting cardiac function post-MI. This was further confirmed using HMGCS2-deficient mice which lack endogenous ketogenesis and have poor outcomes after MI. Inoculation increased plasma ketone levels and provided significant improvements in cardiac function post-MI. Together, this demonstrates a previously unknown role of gut butyrate-producers in the post-MI response.
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Affiliation(s)
- Hung-Chih Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Yen-Wen Liu
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Kuan-Cheng Chang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
- School of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Yen-Wen Wu
- Cardiovascular Medical Center, Far Eastern Memorial Hospital, New Taipei City, 220, Taiwan
| | - Yi-Ming Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Yu-Kai Chao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Min-Yi You
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - David J Lundy
- Graduate Institute of Biomedical Materials and Tissue Engineering, Taipei Medical University, Taipei, 110, Taiwan
| | - Chen-Ju Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Marvin L Hsieh
- Model Organisms Research Core, Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yu-Che Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Ray P Prajnamitra
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Po-Ju Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Shu-Chian Ruan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | | | - Edward S C Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Ke-Wei Chen
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Shih-Sheng Chang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
- School of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Cindy M C Chang
- Model Organisms Research Core, Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Riley Puntney
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Amy Wu Moy
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Yuan-Yuan Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Hsin-Yuan Chien
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Jia-Jung Lee
- Division of Nephrology, Department of Medicine, Kaohsiung Medical University & Hospital, Kaohsiung, 807, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Medicine, Kaohsiung Medical University & Hospital, Kaohsiung, 807, Taiwan
| | - Ming-Jing Hwang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Jennifer Coonen
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Timothy A Hacker
- Model Organisms Research Core, Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - C-L Eric Yen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy J Kamp
- Department of Medicine and Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Patrick C H Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
- Department of Medicine and Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Institute of Medical Genomics and Proteomics and Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, 100, Taiwan.
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Modrego J, Ortega-Hernández A, Goirigolzarri J, Restrepo-Córdoba MA, Bäuerl C, Cortés-Macías E, Sánchez-González S, Esteban-Fernández A, Pérez-Villacastín J, Collado MC, Gómez-Garre D. Gut Microbiota and Derived Short-Chain Fatty Acids Are Linked to Evolution of Heart Failure Patients. Int J Mol Sci 2023; 24:13892. [PMID: 37762194 PMCID: PMC10530267 DOI: 10.3390/ijms241813892] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
There is a lack of direct evidence regarding gut microbiota dysbiosis and changes in short-chain fatty acids (SCFAs) in heart failure (HF) patients. We sought to assess any association between gut microbiota composition, SCFA production, clinical parameters, and the inflammatory profile in a cohort of newly diagnosed HF patients. In this longitudinal prospective study, we enrolled eighteen newly diagnosed HF patients. At admission and after 12 months, blood samples were collected for the assessment of proinflammatory cytokines, monocyte populations, and endothelial dysfunction, and stool samples were collected for analysis of gut microbiota composition and quantification of SCFAs. Twelve months after the initial HF episode, patients demonstrated improved clinical parameters and reduced inflammatory state and endothelial dysfunction. This favorable evolution was associated with a reversal of microbiota dysbiosis, consisting of the increment of health-related bacteria, such as genus Bifidobacterium, and levels of SCFAs, mainly butyrate. Furthermore, there was a decrease in the abundance of pathogenic bacteria. In vitro, fecal samples collected after 12 months of follow-up exhibited lower inflammation than samples collected at admission. In conclusion, the favorable progression of HF patients after the initial episode was linked to the reversal of gut microbiota dysbiosis and increased SCFA production, particularly butyrate. Whether restoring butyrate levels or promoting the growth of butyrate-producing bacteria could serve as a complementary treatment for these patients deserves further studies.
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Affiliation(s)
- Javier Modrego
- Laboratorio de Riesgo Cardiovascular y Microbiota, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (J.M.); (A.O.-H.); (S.S.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Adriana Ortega-Hernández
- Laboratorio de Riesgo Cardiovascular y Microbiota, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (J.M.); (A.O.-H.); (S.S.-G.)
| | - Josebe Goirigolzarri
- Servicio de Cardiología, Hospital Clínico de San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (J.G.); (M.A.R.-C.)
| | - María Alejandra Restrepo-Córdoba
- Servicio de Cardiología, Hospital Clínico de San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (J.G.); (M.A.R.-C.)
| | - Christine Bäuerl
- Instituto de Agroquímica y Tecnología de los Alimentos (IATA-CSIC), 46980 Paterna, Spain; (C.B.); (E.C.-M.); (M.C.C.)
| | - Erika Cortés-Macías
- Instituto de Agroquímica y Tecnología de los Alimentos (IATA-CSIC), 46980 Paterna, Spain; (C.B.); (E.C.-M.); (M.C.C.)
| | - Silvia Sánchez-González
- Laboratorio de Riesgo Cardiovascular y Microbiota, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (J.M.); (A.O.-H.); (S.S.-G.)
| | | | - Julián Pérez-Villacastín
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Servicio de Cardiología, Hospital Clínico de San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (J.G.); (M.A.R.-C.)
- Departamento de Medicina, Facultad de Medicina, Universidad Complutense, 28040 Madrid, Spain
- Fundación para la Investigación Interhospitalaria Cardiovascular, 28008 Madrid, Spain
| | - María Carmen Collado
- Instituto de Agroquímica y Tecnología de los Alimentos (IATA-CSIC), 46980 Paterna, Spain; (C.B.); (E.C.-M.); (M.C.C.)
| | - Dulcenombre Gómez-Garre
- Laboratorio de Riesgo Cardiovascular y Microbiota, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (J.M.); (A.O.-H.); (S.S.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Departamento de Fisiología, Facultad de Medicina, Universidad Complutense, 28040 Madrid, Spain
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Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J, Schülke O. The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels. MICROBIOME 2023; 11:165. [PMID: 37501202 PMCID: PMC10373267 DOI: 10.1186/s40168-023-01596-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/11/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored. RESULTS In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age. CONCLUSIONS In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract.
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Affiliation(s)
- Simone Anzà
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany.
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Michael Heistermann
- Endocrinology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Somboon Sangmaneedet
- Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Julia Ostner
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Oliver Schülke
- Behavioral Ecology Department, University of Goettingen, Goettingen, Germany
- Primate Social Evolution Group, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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10
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Moy M, Diakiw L, Amato KR. Human-influenced diets affect the gut microbiome of wild baboons. Sci Rep 2023; 13:11886. [PMID: 37482555 PMCID: PMC10363530 DOI: 10.1038/s41598-023-38895-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
Industrialized diets that incorporate processed foods and are often high in simple sugars and fats and low in fiber have myriad health impacts, many of which may operate via impacts on the gut microbiota. Examining how these diets affect the gut microbiota can be challenging given that lab animal models experience altered environmental contexts, and human studies include a suite of co-varying cultural and environmental factors that are likely to shape the gut microbiota alongside diet. To complement these approaches, we compare the microbiomes of wild populations of olive baboons (Papio anubis) with differential access to human trash high in processed foods, simple sugars, and fats in Rwanda's Akagera National Park. Baboons are a good model system since their microbiomes are compositionally similar to those of humans. Additionally, this population inhabits a common environment with different social groups consuming qualitatively different amounts of human trash, limiting variation in non-dietary factors. Using 16S rRNA gene amplicon sequencing we find that baboons with unlimited access to human trash have reduced microbial alpha diversity and reduced relative abundances of fiber-degrading taxa such as Ruminococcaceae, Prevotellaceae, and Lachnospiraceae. In contrast, baboons with limited access to human trash have a microbiome more similar to that of baboons with no access to human trash. Our results suggest that while a human-influenced diet high in processed foods, simple sugars, and fats is sufficient to alter the microbiome in wild baboons, there is a minimum threshold of dietary alteration that must occur before the microbiome is substantially altered. We recommend that data from wild primate populations such as these be used to complement ongoing research on diet-microbiome-health interactions in humans and lab animal models.
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Affiliation(s)
- Madelyn Moy
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura Diakiw
- Department of Ecology, University of Wyoming, Laramie, WY, 82071, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA.
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11
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Siptroth J, Moskalenko O, Krumbiegel C, Ackermann J, Koch I, Pospisil H. Variation of butyrate production in the gut microbiome in type 2 diabetes patients. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2023:10.1007/s10123-023-00324-6. [PMID: 36780038 PMCID: PMC10397123 DOI: 10.1007/s10123-023-00324-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 02/14/2023]
Abstract
BACKGROUND Diabetes mellitus type 2 is a common disease that poses a challenge to the healthcare system. The disease is very often diagnosed late. A better understanding of the relationship between the gut microbiome and type 2 diabetes can support early detection and form an approach for therapies. Microbiome analysis offers a potential opportunity to find markers for this disease. Next-generation sequencing methods can be used to identify the bacteria present in the stool sample and to generate a microbiome profile through an analysis pipeline. Statistical analysis, e.g., using Student's t-test, allows the identification of significant differences. The investigations are not only focused on single bacteria, but on the determination of a comprehensive profile. Also, the consideration of the functional microbiome is included in the analyses. The dataset is not from a clinical survey, but very extensive. RESULTS By examining 946 microbiome profiles of diabetes mellitus type 2 sufferers (272) and healthy control persons (674), a large number of significant genera (25) are revealed. It is possible to identify a large profile for type 2 diabetes disease. Furthermore, it is shown that the diversity of bacteria per taxonomic level in the group of persons with diabetes mellitus type 2 is significantly reduced compared to a healthy control group. In addition, six pathways are determined to be significant for type 2 diabetes describing the fermentation to butyrate. These parameters tend to have high potential for disease detection. CONCLUSIONS With this investigation of the gut microbiome of persons with diabetes type 2 disease, we present significant bacteria and pathways characteristic of this disease.
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Affiliation(s)
- Julienne Siptroth
- High Performance Computing in Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany.
| | - Olga Moskalenko
- BIOMES NGS GmbH, Schwartzkopffstraße 1, 15745, Wildau, Germany
| | | | - Jörg Ackermann
- Department of Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt, 60325, Frankfurt am Main, Germany
| | - Ina Koch
- Department of Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt, 60325, Frankfurt am Main, Germany
| | - Heike Pospisil
- High Performance Computing in Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
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12
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Singh V, Lee G, Son H, Koh H, Kim ES, Unno T, Shin JH. Butyrate producers, "The Sentinel of Gut": Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Front Microbiol 2023; 13:1103836. [PMID: 36713166 PMCID: PMC9877435 DOI: 10.3389/fmicb.2022.1103836] [Citation(s) in RCA: 98] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Gut-microbial butyrate is a short-chain fatty acid (SCFA) of significant physiological importance than the other major SCFAs (acetate and propionate). Most butyrate producers belong to the Clostridium cluster of the phylum Firmicutes, such as Faecalibacterium, Roseburia, Eubacterium, Anaerostipes, Coprococcus, Subdoligranulum, and Anaerobutyricum. They metabolize carbohydrates via the butyryl-CoA: acetate CoA-transferase pathway and butyrate kinase terminal enzymes to produce most of butyrate. Although, in minor fractions, amino acids can also be utilized to generate butyrate via glutamate and lysine pathways. Butyrogenic microbes play a vital role in various gut-associated metabolisms. Butyrate is used by colonocytes to generate energy, stabilizes hypoxia-inducible factor to maintain the anaerobic environment in the gut, maintains gut barrier integrity by regulating Claudin-1 and synaptopodin expression, limits pro-inflammatory cytokines (IL-6, IL-12), and inhibits oncogenic pathways (Akt/ERK, Wnt, and TGF-β signaling). Colonic butyrate producers shape the gut microbial community by secreting various anti-microbial substances, such as cathelicidins, reuterin, and β-defensin-1, and maintain gut homeostasis by releasing anti-inflammatory molecules, such as IgA, vitamin B, and microbial anti-inflammatory molecules. Additionally, butyrate producers, such as Roseburia, produce anti-carcinogenic metabolites, such as shikimic acid and a precursor of conjugated linoleic acid. In this review, we summarized the significance of butyrate, critically examined the role and relevance of butyrate producers, and contextualized their importance as microbial therapeutics.
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Affiliation(s)
- Vineet Singh
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - HyunWoo Son
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Hong Koh
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Tatsuya Unno
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biotechnology, Kyungpook National University, Daegu, Republic of Korea
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13
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Alam MZ, Maslanka JR, Abt MC. Immunological consequences of microbiome-based therapeutics. Front Immunol 2023; 13:1046472. [PMID: 36713364 PMCID: PMC9878555 DOI: 10.3389/fimmu.2022.1046472] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023] Open
Abstract
The complex network of microscopic organisms living on and within humans, collectively referred to as the microbiome, produce wide array of biologically active molecules that shape our health. Disruption of the microbiome is associated with susceptibility to a range of diseases such as cancer, diabetes, allergy, obesity, and infection. A new series of next-generation microbiome-based therapies are being developed to treat these diseases by transplanting bacteria or bacterial-derived byproducts into a diseased individual to reset the recipient's microbiome and restore health. Microbiome transplantation therapy is still in its early stages of being a routine treatment option and, with a few notable exceptions, has had limited success in clinical trials. In this review, we highlight the successes and challenges of implementing these therapies to treat disease with a focus on interactions between the immune system and microbiome-based therapeutics. The immune activation status of the microbiome transplant recipient prior to transplantation has an important role in supporting bacterial engraftment. Following engraftment, microbiome transplant derived signals can modulate immune function to ameliorate disease. As novel microbiome-based therapeutics are developed, consideration of how the transplants will interact with the immune system will be a key factor in determining whether the microbiome-based transplant elicits its intended therapeutic effect.
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Affiliation(s)
| | | | - Michael C. Abt
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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14
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Sang J, Zhuang D, Zhang T, Wu Q, Yu J, Zhang Z. Convergent and Divergent Age Patterning of Gut Microbiota Diversity in Humans and Nonhuman Primates. mSystems 2022; 7:e0151221. [PMID: 35758593 PMCID: PMC9426537 DOI: 10.1128/msystems.01512-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/08/2022] [Indexed: 12/24/2022] Open
Abstract
The gut microbiome has significant effects on healthy aging and aging-related diseases, whether in humans or nonhuman primates. However, little is known about the divergence and convergence of gut microbial diversity between humans and nonhuman primates during aging, which limits their applicability for studying the gut microbiome's role in human health and aging. Here, we performed 16S rRNA gene sequencing analysis for captive rhesus macaques (Macaca mulatta) and compared this data set with other freely available gut microbial data sets containing four human populations (Chinese, Japanese, Italian, and British) and two nonhuman primates (wild lemurs [Lemur catta] and wild chimpanzees [Pan troglodytes]). Based on the consistent V4 region of the 16S rRNA gene, beta diversity analysis suggested significantly separated gut microbial communities associated with host backgrounds of seven host groups, but within each group, significant gut microbial divergences were observed, and indicator bacterial genera were identified as associated with aging. We further discovered six common anti-inflammatory gut bacteria (Prevotellamassilia, Prevotella, Gemmiger, Coprococcus, Faecalibacterium, and Roseburia) that had butyrate-producing potentials suggested by pangenomic analysis and that showed similar dynamic changes in at least two selected host groups during aging, independent of distinct host backgrounds. Finally, we found striking age-related changes in 66 plasma metabolites in macaques. Two highly changed metabolites, hydroxyproline and leucine, enriched in adult macaques were significantly and positively correlated with Prevotella and Prevotellamassilia. Furthermore, genus-level pangenome analysis suggested that those six common indicator bacteria can synthesize leucine and arginine as hydroxyproline and proline precursors in both humans and macaques. IMPORTANCE This study provides the first comprehensive investigation of age patterning of gut microbiota of four human populations and three nonhuman primates and found that Prevotellamassilia, Prevotella, Gemmiger, Coprococcus, Faecalibacterium, and Roseburia may be common antiaging microbial markers in both humans and nonhuman primates due to their potential metabolic capabilities for host health benefits. Our results also provide key support for using macaques as animal models in studies of the gut microbiome's role during human aging.
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Affiliation(s)
- Jianan Sang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Daohua Zhuang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Tao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Qunfu Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary & Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jiangkun Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Zhigang Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary & Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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