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Boverhoff D, Kool J, Pijnacker R, Ducarmon QR, Zeller G, Shetty S, Sie S, Mulder AC, van der Klis F, Franz E, Mughini-Gras L, van Baarle D, Fuentes S. Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands. Cell Rep 2024; 43:114729. [PMID: 39264809 DOI: 10.1016/j.celrep.2024.114729] [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: 02/27/2024] [Revised: 05/23/2024] [Accepted: 08/22/2024] [Indexed: 09/14/2024] Open
Abstract
Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.
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Affiliation(s)
- David Boverhoff
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Roan Pijnacker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Quinten R Ducarmon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sudarshan Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephan Sie
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Annemieke Christine Mulder
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Fiona van der Klis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Debbie van Baarle
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands; Virology & Immunology Research, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
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Ryan MJ, Clemmer JS, Mathew RO, Faulkner JL, Taylor EB, Abais-Battad JM, Hollis F, Sullivan JC. Revisiting sex as a biological variable in hypertension research. J Clin Invest 2024; 134:e180078. [PMID: 39225093 PMCID: PMC11364402 DOI: 10.1172/jci180078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Half of adults in the United States have hypertension as defined by clinical practice guidelines. Interestingly, women are generally more likely to be aware of their hypertension and have their blood pressure controlled with treatment compared with men, yet hypertension-related mortality is greater in women. This may reflect the fact that the female sex remains underrepresented in clinical and basic science studies investigating the effectiveness of therapies and the mechanisms controlling blood pressure. This Review provides an overview of the impact of the way hypertension research has explored sex as a biological variable (SABV). Emphasis is placed on epidemiological studies, hypertension clinical trials, the genetics of hypertension, sex differences in immunology and gut microbiota in hypertension, and the effect of sex on the central control of blood pressure. The goal is to offer historical perspective on SABV in hypertension, highlight recent studies that include SABV, and identify key gaps in SABV inclusion and questions that remain in the field. Through continued awareness campaigns and engagement/education at the level of funding agencies, individual investigators, and in the editorial peer review system, investigation of SABV in the field of hypertension research will ultimately lead to improved clinical outcomes.
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Affiliation(s)
- Michael J. Ryan
- Columbia VA Health Care System, Columbia, South Carolina, USA
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - John S. Clemmer
- University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Roy O. Mathew
- Loma Linda VA Health Care System, Loma Linda, California, USA
| | | | - Erin B. Taylor
- University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Fiona Hollis
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
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3
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James D, Poveda C, Walton GE, Elmore JS, Linden B, Gibson J, Griffin BA, Robertson MD, Lewis MC. Do high-protein diets have the potential to reduce gut barrier function in a sex-dependent manner? Eur J Nutr 2024; 63:2035-2054. [PMID: 38662018 PMCID: PMC11377480 DOI: 10.1007/s00394-024-03407-w] [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: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
PURPOSE Impaired gut barrier function is associated with systemic inflammation and many chronic diseases. Undigested dietary proteins are fermented in the colon by the gut microbiota which produces nitrogenous metabolites shown to reduce barrier function in vitro. With growing evidence of sex-based differences in gut microbiotas, we determined whether there were sex by dietary protein interactions which could differentially impact barrier function via microbiota modification. METHODS Fermentation systems were inoculated with faeces from healthy males (n = 5) and females (n = 5) and supplemented with 0.9 g of non-hydrolysed proteins sourced from whey, fish, milk, soya, egg, pea, or mycoprotein. Microbial populations were quantified using fluorescence in situ hybridisation with flow cytometry. Metabolite concentrations were analysed using gas chromatography, solid phase microextraction coupled with gas chromatography-mass spectrometry and ELISA. RESULTS Increased protein availability resulted in increased proteolytic Bacteroides spp (p < 0.01) and Clostridium coccoides (p < 0.01), along with increased phenol (p < 0.01), p-cresol (p < 0.01), indole (p = 0.018) and ammonia (p < 0.01), varying by protein type. Counts of Clostridium cluster IX (p = 0.03) and concentration of p-cresol (p = 0.025) increased in males, while females produced more ammonia (p = 0.02), irrespective of protein type. Further, we observed significant sex-protein interactions affecting bacterial populations and metabolites (p < 0.005). CONCLUSIONS Our findings suggest that protein fermentation by the gut microbiota in vitro is influenced by both protein source and the donor's sex. Should these results be confirmed through human studies, they could have major implications for developing dietary recommendations tailored by sex to prevent chronic illnesses.
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Affiliation(s)
- Daniel James
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK.
| | - Carlos Poveda
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
| | - Gemma E Walton
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
| | - J Stephen Elmore
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
| | - Brandon Linden
- Department of Nutrition, Food & Exercise Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - John Gibson
- Food and Feed Innovations, Woodstock, Newcastle Rd, Woore, N Shropshire, CW3 95N, UK
| | - Bruce A Griffin
- Department of Nutrition, Food & Exercise Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - M Denise Robertson
- Department of Nutrition, Food & Exercise Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Marie C Lewis
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
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4
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Pérez-Prieto I, Plaza-Florido A, Ubago-Guisado E, Ortega FB, Altmäe S. Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis. J Sci Med Sport 2024:S1440-2440(24)00227-5. [PMID: 39048485 DOI: 10.1016/j.jsams.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/18/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND The effects of physical activity and sedentary behavior on human health are well known, however, the molecular mechanisms are poorly understood. Growing evidence points to physical activity as an important modulator of the composition and function of microbial communities, while evidence of sedentary behavior is scarce. We aimed to synthesize and meta-analyze the current evidence about the effects of physical activity and sedentary behavior on microbiome across different body sites and in different populations. METHODS A systematic search in PubMed, Web of Science, Scopus and Cochrane databases was conducted until September 2022. Random-effects meta-analyses including cross-sectional studies (active vs. inactive/athletes vs. non-athletes) or trials reporting the chronic effect of physical activity interventions on gut microbiome alpha-diversity in healthy individuals were performed. RESULTS Ninety-one studies were included in this systematic review. Our meta-analyses of 2632 participants indicated no consistent effect of physical activity on microbial alpha-diversity, although there seems to be a trend toward a higher microbial richness in athletes compared to non-athletes. Most of studies reported an increase in short-chain fatty acid-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella or Roseburia in active individuals and after physical activity interventions. CONCLUSIONS Physical activity levels were positively associated with the relative abundance of short-chain fatty acid-producing bacteria. Athletes seem to have a richer microbiome compared to non-athletes. However, high heterogeneity between studies avoids obtaining conclusive information on the role of physical activity in microbial composition. Future multi-omics studies would enhance our understanding of the molecular effects of physical activity and sedentary behavior on the microbiome.
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Affiliation(s)
- Inmaculada Pérez-Prieto
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Spain.
| | - Abel Plaza-Florido
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Spain; Pediatric Exercise and Genomics Research Center, UC Irvine School of Medicine, United States.
| | - Esther Ubago-Guisado
- Instituto de Investigación Biosanitaria ibs.GRANADA, Spain; Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Spain
| | - Francisco B Ortega
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Spain; CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Granada, Spain; Faculty of Sport and Health Sciences, University of Jyväskylä, Finland.
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Spain; Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Stockholm, Sweden.
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5
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Xu L, Li W, Ling L, Zhang Z, Cui Z, Ge J, Wang Y, Meng Q, Wang Y, Liu K, Zhou J, Zeng F, Wang J, Wu J. A Sedentary Lifestyle Changes the Composition and Predicted Functions of the Gut Bacterial and Fungal Microbiota of Subjects from the Same Company. Curr Microbiol 2023; 80:368. [PMID: 37831112 PMCID: PMC10575810 DOI: 10.1007/s00284-023-03480-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
A sedentary lifestyle affects the diversity and composition of the gut microbiota, but previous studies have mainly focused on bacteria instead of fungi. Here, we compared both the fecal bacterial and fungal microbiota compositions and functions in sedentary persons and controls. Subjects from the China Railway Corporation, including 99 inspectors and 88 officials, were enrolled in our study. Fecal microbiota communities were analyzed using 16S rRNA gene sequencing for bacteria and ITS sequencing for fungi. We found that the diversity of the gut microbiota of the sedentary group was significantly lower than that of the control group (P < 0.05). The sedentary group had a higher abundance of Firmicutes, a lower abundance of Actinobacteria and Proteobacteria and a higher abundance of Ascomycota, and a lower abundance of Basidiomycota. Furthermore, functional prediction analysis of the fungal microbiota revealed more L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde, more phospholipid remodeling (phosphatidylethanolamine, yeast), and more L-tyrosine degradation I, as well as less pentose phosphate pathway (non-oxidative branch), less adenosine nucleotide biosynthesis and less L-valine biosynthesis in the sedentary group (P < 0.05). Thus, a sedentary lifestyle changes the composition and function of the gut microbiota. It may change the pentose phosphate pathway (non-oxidative branch), nucleic acid and amino acid biosynthesis and phospholipid metabolism in fungi.
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Affiliation(s)
- Longwei Xu
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, School of Clinical Medicine, Peking University Ninth, Beijing, 100038, China
| | - Wenkun Li
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Lu Ling
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ziran Zhang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Zilu Cui
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Jiang Ge
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Yun Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Qianlong Meng
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yadan Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Kuiliang Liu
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Jun Zhou
- Department of Clinical Research Center, Dazhou Central Hospital, Sichuan, China
| | - Fanxin Zeng
- Department of Clinical Research Center, Dazhou Central Hospital, Sichuan, China.
| | - Jing Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.
| | - Jing Wu
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
- Department of Gastroenterology, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
- Department of Gastroenterology, School of Clinical Medicine, Peking University Ninth, Beijing, 100038, China.
- , No. 95, Yongan Road, Xicheng District, Beijing, 100050, China.
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6
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Politi C, Mobrici M, Parlongo RM, Spoto B, Tripepi G, Pizzini P, Cutrupi S, Franco D, Tino R, Farruggio G, Failla C, Marino F, Pioggia G, Testa A. Role of Gut Microbiota in Overweight Susceptibility in an Adult Population in Italy. Nutrients 2023; 15:2834. [PMID: 37447161 DOI: 10.3390/nu15132834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Although the gut microbiota is known to affect body weight, its relationship with overweight/obesity is unclear. Our aim was to characterize microbiota composition in a cohort from the southernmost area of Italy. We investigated whether an altered gut microbiota could play an etiological role in the pathogenesis of overweight/obesity. A total of 163 healthy adults were enrolled. Microbiome analysis was performed via 16S rRNA gene sequencing. We found significant phylum variations between overweight (N = 88) and normal-weight (N = 75) subjects. Bacteroidetes and Proteobacteria were higher in overweight participants (p = 0.004; p = 0.03), and Firmicutes and Verrucomicrobia were lower (p = 0.02; p = 0.008) compared to normal-weight participants. Additionally, Akkermansia and Bifidobacterium (genus level) were significantly lower in the overweight group, as well as Akkermansia muciniphila at the species level. The Firmicutes/Bacteroidetes ratio (F/B ratio), an index of dysbiosis, was found to be inversely associated with BMI in linear and logistic regression models (p = 0.001; p = 0.005). The association remained statistically significant after adjustment for potential confounders. This cross-sectional study contributes to defining the gut microbiota composition in an adult population living in southern Italy. It confirms the relationship between overweight susceptibility and the dysbiosis status, highlighting the possible etiological role of the F/B ratio in disease susceptibility.
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Affiliation(s)
- Cristina Politi
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
| | - Marco Mobrici
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
| | - Rosa Maria Parlongo
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
| | - Belinda Spoto
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
| | - Giovanni Tripepi
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
| | - Patrizia Pizzini
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
| | - Sebastiano Cutrupi
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
| | - Daniele Franco
- Medilink S.r.l., Via Parma 36/A, Città Giardino, 96010 Melilli, SR, Italy
| | - Renato Tino
- Medilink S.r.l., Via Parma 36/A, Città Giardino, 96010 Melilli, SR, Italy
| | - Giuseppe Farruggio
- SB SETEC S.p.A., Via Benedetto Croce 11, Città Giardino, 96010 Melilli, SR, Italy
| | - Chiara Failla
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, ME, Italy
- Classical Linguistic Studies and Education Department, Kore University of Enna, 94100 Enna, EN, Italy
| | - Flavia Marino
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, ME, Italy
| | - Giovanni Pioggia
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, ME, Italy
| | - Alessandra Testa
- Institute of Clinical Physiology (IFC), National Research Council of Italy (CNR), 89124 Reggio Calabria, RC, Italy
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7
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Henry Dasinger J, Joe B, Abais-Battad JM. Microbiota-associated mechanisms underlying sexual dimorphism in hypertension. MICROBIOTA AND HOST 2023; 1:e230016. [PMID: 38107627 PMCID: PMC10723812 DOI: 10.1530/mah-23-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Consistent research over the last 20 years has shown that there are clear sex differences in the pathogenesis of hypertension, the leading risk factor for the development of cardiovascular diseases. More recently, there is evidence in both humans and experimental animal models that causally implicates the gut microbiota in hypertension. It therefore follows that sex differences in the gut microbiota may mediate the extent of disease between sexes. This new field is rapidly changing and advancing, and the purpose of this review is to cover the most up-to-date evidence regarding the sexual dimorphism of the gut microbiota and its potential influence on the differential manifestation of hypertension in males versus females. Emphasis will be placed on the mechanisms thought to contribute to these sex differences in both the gut microbiota and hypertension, including sex steroid hormones, gut-derived metabolites, the immune system, and pregnancy.
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Affiliation(s)
| | - Bina Joe
- Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences
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8
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Yang Y, Lu W, Zhang X, Wu C. Gut fungi differentially response to the antipyretic (heat-clearing) and diaphoretic (exterior-releasing) traditional Chinese medicines in Coptis chinensis-conditioned gut microbiota. Front Pharmacol 2022; 13:1032919. [DOI: 10.3389/fphar.2022.1032919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Antipyretic (heat-clearing) and diaphoretic (exterior-releasing) drugs are two main groups of traditional Chinese medicines (TCMs) possessing anti-microbes and anti-inflammation effects, with the former mainly through clearing pyrogens while the latter through promoting diaphoresis. Although anti-microorganism is a common action of these two kinds of TCMs, their difference in antimicrobial spectrums and their interactions when combinedly used remain unclear. Herein, we prepared aqueous extracts from Coptis chinensis (HL) and other antipyretic or diaphoretic TCMs, orally administrated them to C57BL/6 mice at a clinical dose for fourteen days, and analyzed their impaction on both gut bacteria and fungi using full-length 16 S rRNA gene sequencing and internal transcribed spacer 1/2 (ITS1/2) gene sequencing, respectively. Oral administration of HL significantly changed the structure of gut bacteria but showed little influence on gut fungi. Co-treatment with antipyretic or diaphoretic TCMs alleviated the impact of HL on gut bacteria to a similar degree. However, combined with either heat-clearing or exterior-releasing TCMs significantly strengthened the influence of HL on gut fungi, with the latter superior to the former. The antipyretic TCMs enriched Penicillium spp. while diaphoretic TCMs promoted Fusarium spp. Further analysis revealed that the diaphoretic TCMs-enriched fungi Fusarium spp. were positively related to Akkermansia spp., a beneficial bacterium that interacts with Toll-like receptor 4 (TLR4) and regulates thermogenesis, thus providing a potential linkage with their pro-diaphoresis effect. Together, our results reveal that gut fungi differentially respond to the impact of heat-clearing and exterior-releasing TCMs on Coptis chinensis-conditioned gut microbiota, which provides insights into their functional characteristics.
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9
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Hu MY, Yu QZ, Lin JQ, Fang SG. Sexual Dimorphism of the Gut Microbiota in the Chinese Alligator and Its Convergence in the Wild Environment. Int J Mol Sci 2022; 23:12140. [PMID: 36292992 PMCID: PMC9603114 DOI: 10.3390/ijms232012140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 11/27/2022] Open
Abstract
The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. As a key intrinsic factor, sex has a persistent impact on the formation and development of gut microbiota. Few studies have analyzed sexual dimorphism of gut microbiota, particularly in wild animals. We used 16S rRNA gene sequencing to analyze the gut microbiota of juvenile and adult Chinese alligators, and untargeted metabolomics to study serum metabolomes of adult alligators. We observed significant sexual differences in the community diversity in juvenile, but not adult, alligators. In terms of taxonomic composition, the phylum Fusobacteriota and genus Cetobacterium were highly abundant in adult alligators, similar to those present in carnivorous fishes, whereas the gut microbiota composition in juvenile alligators resembled that in terrestrial reptiles, indicating that adults are affected by their wild aquatic environment and lack sex dimorphism in gut microbiota. The correlation analysis revealed that the gut microbiota of adults was also affected by cyanobacteria in the external environment, and this effect was sex-biased and mediated by sex hormones. Overall, this study reveals sexual differences in the gut microbiota of crocodilians and their convergence in the external environment, while also providing insights into host-microbiota interactions in wildlife.
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Affiliation(s)
- Meng-Yuan Hu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qin-Zhang Yu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jian-Qing Lin
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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10
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Syromyatnikov M, Nesterova E, Gladkikh M, Smirnova Y, Gryaznova M, Popov V. Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions. Microorganisms 2022; 10:microorganisms10091866. [PMID: 36144468 PMCID: PMC9501501 DOI: 10.3390/microorganisms10091866] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among the African population, the typical members of the microbiota are Bacteroides and Prevotella. The gut microbiome of Asians is very diverse and rich in members of the genera Prevotella, Bacteroides Lactobacillus, Faecalibacterium, Ruminococcus, Subdoligranulum, Coprococcus, Collinsella, Megasphaera, Bifidobacterium, and Phascolarctobacterium. Among Buddhists and Muslims, the Prevotella enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the Bacteroides enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn’s disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities.
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Affiliation(s)
- Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
- Correspondence:
| | - Ekaterina Nesterova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Maria Gladkikh
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Vasily Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
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11
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Nel Van Zyl K, Whitelaw AC, Hesseling AC, Seddon JA, Demers AM, Newton-Foot M. Fungal diversity in the gut microbiome of young South African children. BMC Microbiol 2022; 22:201. [PMID: 35978282 PMCID: PMC9387017 DOI: 10.1186/s12866-022-02615-w] [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: 03/07/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal microbiome, or mycobiome, is a poorly described component of the gut ecosystem and little is known about its structure and development in children. In South Africa, there have been no culture-independent evaluations of the child gut mycobiota. This study aimed to characterise the gut mycobiota and explore the relationships between fungi and bacteria in the gut microbiome of children from Cape Town communities. METHODS Stool samples were collected from children enrolled in the TB-CHAMP clinical trial. Internal transcribed spacer 1 (ITS1) gene sequencing was performed on a total of 115 stool samples using the Illumina MiSeq platform. Differences in fungal diversity and composition in relation to demographic, clinical, and environmental factors were investigated, and correlations between fungi and previously described bacterial populations in the same samples were described. RESULTS Taxa from the genera Candida and Saccharomyces were detected in all participants. Differential abundance analysis showed that Candida spp. were significantly more abundant in children younger than 2 years compared to older children. The gut mycobiota was less diverse than the bacterial microbiota of the same participants, consistent with the findings of other human microbiome studies. The variation in richness and evenness of fungi was substantial, even between individuals of the same age. There was significant association between vitamin A supplementation and higher fungal alpha diversity (p = 0.047), and girls were shown to have lower fungal alpha diversity (p = 0.003). Co-occurrence between several bacterial taxa and Candida albicans was observed. CONCLUSIONS The dominant fungal taxa in our study population were similar to those reported in other paediatric studies; however, it remains difficult to identify the true core gut mycobiota due to the challenges set by the low abundance of gut fungi and the lack of true gut colonising species. The connection between the microbiota, vitamin A supplementation, and growth and immunity warrants exploration, especially in populations at risk for micronutrient deficiencies. While we were able to provide insight into the gut mycobiota of young South African children, further functional studies are necessary to explain the role of the mycobiota and the correlations between bacteria and fungi in human health.
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Affiliation(s)
- K Nel Van Zyl
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa.
| | - A C Whitelaw
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- African Microbiome Institute, Stellenbosch University, Stellenbosch, South Africa
| | - A C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - J A Seddon
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
- Department of Infectious Diseases, Imperial College London, London, UK
| | - A-M Demers
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
- Service de Microbiologie, Département Clinique de Médecine de Laboratoire, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Canada
| | - M Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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12
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Xiong X, Rao Y, Tu X, Wang Z, Gong J, Yang Y, Wu H, Liu X. Gut archaea associated with bacteria colonization and succession during piglet weaning transitions. BMC Vet Res 2022; 18:243. [PMID: 35751084 PMCID: PMC9229118 DOI: 10.1186/s12917-022-03330-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods. Results We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3. Conclusion Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03330-4.
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Affiliation(s)
- Xinwei Xiong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China.
| | - Yousheng Rao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xutang Tu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Zhangfeng Wang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Jishang Gong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Yanbei Yang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Haobin Wu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xianxian Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, 330006, People's Republic of China.
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13
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Zeng S, Schnabl B. Roles for the mycobiome in liver disease. Liver Int 2022; 42:729-741. [PMID: 34995410 PMCID: PMC8930708 DOI: 10.1111/liv.15160] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022]
Abstract
Liver disease, a major cause of global mortality, has been associated with dysbiosis of the intestinal microbiota (bacteria, fungi, viruses, and other microbes). Studies have associated changes in gut bacteria with pathogenesis and severity of liver disease, but the contributions of the mycobiome (the fungal populations of the gut) to health and disease have not been well studied. We review recent findings of alterations in the composition of the mycobiota in patients with liver disease and discuss the mechanisms by which these might affect pathogenesis and disease progression. Strategies to manipulate the gut mycobiota might be developed to treat or prevent liver disease.
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Affiliation(s)
- Suling Zeng
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
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14
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Phuna ZX, Madhavan P. A CLOSER LOOK AT THE MYCOBIOME IN ALZHEIMER'S DISEASE: FUNGAL SPECIES, PATHOGENESIS AND TRANSMISSION. Eur J Neurosci 2022; 55:1291-1321. [DOI: 10.1111/ejn.15599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Zhi Xin Phuna
- School of Medicine, Faculty of Health & Medical Sciences, Taylor’s University Malaysia Subang Jaya Selangor
| | - Priya Madhavan
- School of Medicine, Faculty of Health & Medical Sciences, Taylor’s University Malaysia Subang Jaya Selangor
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15
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Comparison of Microbial Populations in Saliva and Feces from Healthy and Celiac Adolescents with Conventional and Molecular Approaches after Cultivation on Gluten-Containing Media: An Exploratory Study. Microorganisms 2021; 9:microorganisms9112375. [PMID: 34835500 PMCID: PMC8623131 DOI: 10.3390/microorganisms9112375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Microbes capable of metabolizing gluten are common in various parts of the intestinal tract. In this study, saliva and fecal samples were obtained from 10 adolescents (13–18 years of age), five of which had celiac disease (CD) and five of which were healthy volunteers (HV). Culture-enriched saliva and fecal samples were compared with molecular profiling, and microorganisms displaying lysis zones on gluten-containing media (i.e., gluten-degrading microorganisms; GDMs) were isolated. In total, 45 gluten-degrading strains were isolated, belonging to 13 genera and 15 species, including Candida albicans and Veillonella. GDMs were more common in HVs compared to CD patients and more diverse in saliva compared to feces. In saliva, GDMs showed partial overlap between HVs and CD patients. Bacterial communities in fecal samples determined with amplicon sequencing significantly differed between CD patients and HVs. Overall, 7–46 of all operational taxonomic units (OTUs) per sample were below the detection limit in the fecal samples but were present in the cultivated samples, and mainly included representatives from Lactobacillus and Enterococcus. Furthermore, differences in fecal short-chain fatty-acid concentrations between CD patients and HVs, as well as their correlations with bacterial taxa, were demonstrated.
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16
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Zhang L, Zhan H, Xu W, Yan S, Ng SC. The role of gut mycobiome in health and diseases. Therap Adv Gastroenterol 2021; 14:17562848211047130. [PMID: 34589139 PMCID: PMC8474302 DOI: 10.1177/17562848211047130] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.
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Affiliation(s)
| | | | - Wenye Xu
- Center for Gut Microbiota Research, Faculty of
Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China,Li Ka Shing Institute of Health Science, The
Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive disease,
Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin,
Hong Kong, China,Department of Medicine and Therapeutics,
Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China
| | - Shuai Yan
- Center for Gut Microbiota Research, Faculty of
Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China,Li Ka Shing Institute of Health Science, The
Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive disease,
Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin,
Hong Kong, China,Department of Anaesthesia and Intensive Care
and Peter Hung Pain Research Institute, The Chinese University of Hong Kong,
Shatin, Hong Kong, China
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17
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Phenotypic and Genotypic Characterization of Intestinal Candida spp. in Tunisia. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.113800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Yeasts naturally colonize the mammalian digestive tract and play an important role in health and disease. This community is composed of commensal yeasts, mostly Candida and Saccharomyces described as a part of the intestinal mycobiome and could be associated with resident or transient flora. Objectives: The aim of our study was to perform the phenotypic and genotypic characterization of culturable Candida isolates present in stool specimens of healthy Tunisian individuals and to evaluate their antifungal susceptibility. Methods: Yeasts were recovered from 46 stool samples cultured on Sabouraud dextrose agar at 37°C. Species were identified using conventional methods and ITS-PCR sequencing. Candida isolates were tested by exploring their tolerance to oxidative stress and extreme acidic conditions. In addition, their biofilm formation ability and in vitro resistance to antifungals was determined by the VITEK 2 system. Results: The identification by sequencing the ITS1-5.8S-ITS2 region of the 56 yeast strains isolated from 37 stool samples revealed that Candida was the dominant genus and was represented by Candida albicans (n = 21), C. parapsilosis (n = 10), C. glabrata (n = 9), and C. krusei (n = 9). In contrast, the other genera, including Trichosporon, Geotrichum, and Rhodotorula, were sporadically occurring. We found that most Candida isolates were able to form biofilms under oxidative stress and extreme pH conditions. Regarding antifungal susceptibility, a higher resistance rate to fluconazole was revealed in comparison to caspofungin and micafungin. However, no resistance was revealed against voriconazole, amphotericin B, and 5-flucytosine. Conclusions: This is the first work-generated data on cultivable yeasts from stool specimens of healthy individuals in Tunisia. Further metagenomic studies with a larger sample size are needed to better characterize the intestinal mycobiota.
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18
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Yoon K, Kim N. Roles of Sex Hormones and Gender in the Gut Microbiota. J Neurogastroenterol Motil 2021; 27:314-325. [PMID: 33762473 PMCID: PMC8266488 DOI: 10.5056/jnm20208] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/16/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
The distribution of gut microbiota varies according to age (childhood, puberty, pregnancy, menopause, and old age) and sex. Gut microbiota are known to contribute to gastrointestinal (GI) diseases such as irritable bowel syndrome, inflammatory bowel disease, and colon cancer; however, the exact etiology remains elusive. Recently, sex and gender differences in GI diseases and their relation to gut microbiota has been suggested. Furthermore, the metabolism of estrogen and androgen was reported to be related to the gut microbiome. As gut microbiome is involved in the excretion and circulation process of sex hormones, the concept of “microgenderome” indicating the role of sex hormone on the gut microbiota has been suggested. However, further research is needed for this concept to be universally accepted. In this review, we summarize sex- and gender-differences in gut microbiota and the interplay of microbiota and GI diseases, focusing on sex hormones. We also describe the metabolic role of the microbiota in this regard. Finally, current subjects, such as medication including probiotics, are briefly discussed.
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Affiliation(s)
- Kichul Yoon
- Department of Internal Medicine, Wonkwang University Sanbon Medical Center, Gunpo, Gyeonggi-do, Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
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19
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Huët MAL, Wong LW, Goh CBS, Hussain MH, Muzahid NH, Dwiyanto J, Lee SWH, Ayub Q, Reidpath D, Lee SM, Rahman S, Tan JBL. Investigation of culturable human gut mycobiota from the segamat community in Johor, Malaysia. World J Microbiol Biotechnol 2021; 37:113. [PMID: 34101035 DOI: 10.1007/s11274-021-03083-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
Although several studies have already been carried out in investigating the general profile of the gut mycobiome across several countries, there has yet to be an officially established baseline of a healthy human gut mycobiome, to the best of our knowledge. Microbial composition within the gastrointestinal tract differ across individuals worldwide, and most human gut fungi studies concentrate specifically on individuals from developed countries or diseased cohorts. The present study is the first culture-dependent community study assessing the prevalence and diversity of gut fungi among different ethnic groups from South East Asia. Samples were obtained from a multi-ethnic semi-rural community from Segamat in southern Malaysia. Faecal samples were screened for culturable fungi and questionnaire data analysis was performed. Culturable fungi were present in 45% of the participants' stool samples. Ethnicity had an impact on fungal prevalence and density in stool samples. The prevalence of resistance to fluconazole, itraconazole, voriconazole and 5-fluorocytosine, from the Segamat community, were 14%, 14%, 11% and 7% respectively. It was found that Jakun individuals had lower levels of antifungal resistance irrespective of the drug tested, and male participants had more fluconazole resistant yeast in their stool samples. Two novel point mutations were identified in the ERG11 gene from one azole resistant Candida glabrata, suggesting a possible cause of the occurrence of antifungal resistant isolates in the participant's faecal sample.
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Affiliation(s)
| | - Li Wen Wong
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | | | - Md Hamed Hussain
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | | | - Jacky Dwiyanto
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | | | - Qasim Ayub
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia.,Genomics Facility, Monash University Malaysia, Subang Jaya, Malaysia
| | - Daniel Reidpath
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia.,The South East Asia Community Observatory (SEACO), Segamat, Johor, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia.,Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Subang Jaya, Malaysia
| | - Joash Ban Lee Tan
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia. .,Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
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20
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Murovec B, Deutsch L, Stres B. General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways. Metabolites 2021; 11:336. [PMID: 34074026 PMCID: PMC8225202 DOI: 10.3390/metabo11060336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/14/2021] [Accepted: 05/23/2021] [Indexed: 11/23/2022] Open
Abstract
General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.
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Affiliation(s)
- Boštjan Murovec
- Faculty of Electrical Engineering, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia;
| | - Leon Deutsch
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Blaž Stres
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Jamova 2, SI-1000 Ljubljana, Slovenia
- Department of Automation, Jožef Stefan Institute, Biocybernetics and Robotics, Jamova 39, SI-1000 Ljubljana, Slovenia
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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21
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Risely A, Gillingham MAF, Béchet A, Brändel S, Heni AC, Heurich M, Menke S, Manser MB, Tschapka M, Wasimuddin, Sommer S. Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species. Front Microbiol 2021; 12:659918. [PMID: 34046023 PMCID: PMC8144293 DOI: 10.3389/fmicb.2021.659918] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
The filtering of gut microbial datasets to retain high prevalence taxa is often performed to identify a common core gut microbiome that may be important for host biological functions. However, prevalence thresholds used to identify a common core are highly variable, and it remains unclear how they affect diversity estimates and whether insights stemming from core microbiomes are comparable across studies. We hypothesized that if macroecological patterns in gut microbiome prevalence and abundance are similar across host species, then we would expect that increasing prevalence thresholds would yield similar changes to alpha diversity and beta dissimilarity scores across host species datasets. We analyzed eight gut microbiome datasets based on 16S rRNA gene amplicon sequencing and collected from different host species to (1) compare macroecological patterns across datasets, including amplicon sequence variant (ASV) detection rate with sequencing depth and sample size, occupancy-abundance curves, and rank-abundance curves; (2) test whether increasing prevalence thresholds generate universal or host-species specific effects on alpha and beta diversity scores; and (3) test whether diversity scores from prevalence-filtered core communities correlate with unfiltered data. We found that gut microbiomes collected from diverse hosts demonstrated similar ASV detection rates with sequencing depth, yet required different sample sizes to sufficiently capture rare ASVs across the host population. This suggests that sample size rather than sequencing depth tends to limit the ability of studies to detect rare ASVs across the host population. Despite differences in the distribution and detection of rare ASVs, microbiomes exhibited similar occupancy-abundance and rank-abundance curves. Consequently, increasing prevalence thresholds generated remarkably similar trends in standardized alpha diversity and beta dissimilarity across species datasets until high thresholds above 70%. At this point, diversity scores tended to become unpredictable for some diversity measures. Moreover, high prevalence thresholds tended to generate diversity scores that correlated poorly with the original unfiltered data. Overall, we recommend that high prevalence thresholds over 70% are avoided, and promote the use of diversity measures that account for phylogeny and abundance (Balance-weighted phylogenetic diversity and Weighted Unifrac for alpha and beta diversity, respectively), because we show that these measures are insensitive to prevalence filtering and therefore allow for the consistent comparison of core gut microbiomes across studies without the need for prevalence filtering.
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Affiliation(s)
- Alice Risely
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Mark A. F. Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Arnaud Béchet
- Institut de Recherche de la Tour du Valat, Le Sambuc, Arles, France
| | - Stefan Brändel
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Alexander C. Heni
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Marco Heurich
- Department of Visitor Management and National Park Monitoring, Bavarian Forest National Park, Grafenau, Germany
- Chair of Wildlife Ecology and Management, University of Freiburg, Freiburg, Germany
- Institute for Forest and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
| | - Sebastian Menke
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Marta B. Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Wasimuddin
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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22
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Hedžet S, Rupnik M, Accetto T. Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. Microorganisms 2021; 9:microorganisms9050892. [PMID: 33919474 PMCID: PMC8143477 DOI: 10.3390/microorganisms9050892] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroidesuniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.
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Affiliation(s)
- Stina Hedžet
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
| | - Maja Rupnik
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Tomaž Accetto
- Animal Science Department, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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Valeri F, Endres K. How biological sex of the host shapes its gut microbiota. Front Neuroendocrinol 2021; 61:100912. [PMID: 33713673 DOI: 10.1016/j.yfrne.2021.100912] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/10/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023]
Abstract
The gut microbiota is a complex system, consisting of a dynamic population of microorganisms, involved in the regulation of the host's homeostasis. A vast number of factors are driving the gut microbiota composition including diet, antibiotics, environment, and lifestyle. However, in the past decade, a growing number of studies also focused on the role of sex in relationship to changes in the gut microbiota composition in animal experiments as well as in human beings. Despite the progress in investigation techniques, still little is known about the mechanism behind the observed sex-related differences. In this review, we summarized current knowledge on the sex-dependent differences of the intestinal commensals and discuss the probable direct impact of sex hormones and more indirect effects such as dietary habits or antibiotics. While we have to conclude limited data on specific developmental stages, a clear role for sexual hormones and most probably for testosterone emerges.
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Affiliation(s)
- Francesco Valeri
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz 55131, Germany
| | - Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Center, Johannes Gutenberg-University Mainz, Mainz 55131, Germany.
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Fart F, Rajan SK, Wall R, Rangel I, Ganda-Mall JP, Tingö L, Brummer RJ, Repsilber D, Schoultz I, Lindqvist CM. Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults. Nutrients 2020; 12:nu12092610. [PMID: 32867153 PMCID: PMC7551621 DOI: 10.3390/nu12092610] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Gastrointestinal (GI) health is an important aspect of general health. Gastrointestinal symptoms are of specific importance for the elderly, an increasing group globally. Hence, promoting the elderly’s health and especially gastrointestinal health is important. Gut microbiota can influence gastrointestinal health by modulation of the immune system and the gut–brain axis. Diverse gut microbiota have been shown to be beneficial; however, for the elderly, the gut microbiota is often less diverse. Nutrition and physical activity, in particular, are two components that have been suggested to influence composition or diversity. Materials and Methods: In this study, we compared gut microbiota between two groups of elderly individuals: community-dwelling older adults and physically active senior orienteering athletes, where the latter group has less gastrointestinal symptoms and a reported better well-being. With this approach, we explored if certain gut microbiota were related to healthy ageing. The participant data and faecal samples were collected from these two groups and the microbiota was whole-genome sequenced and taxonomically classified with MetaPhlAn. Results: The physically active senior orienteers had a more homogeneous microbiota within the group and a higher abundance of Faecalibacterium prausnitzii compared to the community-dwelling older adults. Faecalibacterium prausnitzii has previously shown to have beneficial properties. Senior orienteers also had a lower abundance of Parasutterella excrementihominis and Bilophila unclassified, which have been associated with impaired GI health. We could not observe any difference between the groups in terms of Shannon diversity index. Interestingly, a subgroup of community-dwelling older adults showed an atypical microbiota profile as well as the parameters for gastrointestinal symptoms and well-being closer to senior orienteers. Conclusions: Our results suggest specific composition characteristics of healthy microbiota in the elderly, and show that certain components of nutrition as well as psychological distress are not as tightly connected with composition or diversity variation in faecal microbiota samples.
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Affiliation(s)
- Frida Fart
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Sukithar Kochappi Rajan
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Rebecca Wall
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Ignacio Rangel
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - John Peter Ganda-Mall
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
- Laboratory of Translational Mucosal Immunology, Digestive Diseases Research Unit, Vall d’Hebron Institut de Recerca, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Lina Tingö
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Robert J. Brummer
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Dirk Repsilber
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Ida Schoultz
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Carl Mårten Lindqvist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
- Correspondence:
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25
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Mitochondria, the gut microbiome and ROS. Cell Signal 2020; 75:109737. [PMID: 32810578 DOI: 10.1016/j.cellsig.2020.109737] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
In this review, we discuss the connections between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). We examine the mitochondrion as an endosymbiotic organelle that is a hub for energy production, signaling, and cell homeostasis. Maintaining a diverse gut microbiome is generally associated with organismal fitness, intestinal health and resistance to environmental stress. In contrast, gut microbiome imbalance, termed dysbiosis, is linked to a reduction in organismal well-being. ROS are essential signaling molecules but can be damaging when present in excess. Increasing ROS levels have been shown to influence human health, homeostasis of gut cells, and the gastrointestinal microbial community's biodiversity. Reciprocally, gut microbes can affect ROS levels, mitochondrial homeostasis, and host health. We propose that mechanistic understanding of the suite of bi-directional interactions between mitochondria and the gut microbiome will facilitate innovative interdisciplinary studies examining evolutionary divergence and provide novel treatments and therapeutics for disease. GLOSS: In this review, we focus on the nexus between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). Mitochondria are a cell organelle that is derived from an ancestral alpha-proteobacteria. They generate around 80% of the adenosine triphosphate that an organism needs to function and release a range of signaling molecules essential for cellular homeostasis. The gut microbiome is a suite of microorganisms that are commensal, symbiotic and pathogenic to their host. ROS are one predominant group of essential signaling molecules that can be harmful in excess. We suggest that the mitochondria- microbiome nexus is a frontier of research that has cross-disciplinary benefits in understanding genetic divergence and human well-being.
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Ruszkowski J, Kaźmierczak-Siedlecka K, Witkowski JM, Dębska-Ślizień A. Mycobiota of the human gastrointestinal tract. POSTEP HIG MED DOSW 2020. [DOI: 10.5604/01.3001.0014.3415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fungi (Mycota) that colonize the human digestive tract are collectively referred to as gastrointestinal
mycobiota. The most common method of fungi identification is based on the culture
of a clinical sample with subsequent classic phenotypic identification detailed by biochemical
and/or molecular (e.g. sequencing of ITS regions of rDNA) tests in some cases. Additionally,
the culture-independent identification is gaining popularity, especially in scientific research.
The composition of the human mycobiota significantly differs across the digestive tract. In the oral cavity of healthy people, <i>Candida</i>, <i>Cladosporium</i>, <i>Auerobasidium</i>, and <i>Aspergillus</i> are
most often identified fungi genera; however, in recent studies the presence of Malassezia spp.
has been also emphasized. In the case of the lower gastrointestinal tract, <i>Candida</i>, <i>Saccharomyces</i>,
<i>Penicillium</i>, <i>Aspergillus</i>, <i>Cryptococcus</i>, <i>Malassezia</i>, <i>Cladosporium</i>, <i>Galactomyces</i>, <i>Debaryomyces</i>, and
<i>Trichosporon</i> genera are most often reported. This paper summarizes the factors that are associated with the composition of mycobiota in both children (age, type of delivery, breastfeeding) and adults (age, gender, diet, saliva flow rate and composition). Changes in the composition
of mycobiota also occur in pathological conditions, including both gastrointestinal diseases
(Crohn’s disease, oral lichen planus) and metabolic diseases (diabetes, obesity). Additionally,
this paper summarizes the already known, putative interactions between fungi and bacteria
colonizing the human digestive tract.
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Affiliation(s)
- Jakub Ruszkowski
- Katedra i Zakład Fizjopatologii, Wydział Lekarski, Gdański Uniwersytet Medyczny
| | | | - Jacek M. Witkowski
- Katedra i Zakład Fizjopatologii, Wydział Lekarski, Gdański Uniwersytet Medyczny
| | - Alicja Dębska-Ślizień
- Katedra i Klinika Nefrologii, Transplantologii i Chorób Wewnętrznych, Wydział Lekarski, Gdański Uniwersytet Medyczny
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Gallè F, Valeriani F, Cattaruzza MS, Gianfranceschi G, Liguori R, Antinozzi M, Mederer B, Liguori G, Romano Spica V. Mediterranean Diet, Physical Activity and Gut Microbiome Composition: A Cross-Sectional Study among Healthy Young Italian Adults. Nutrients 2020; 12:nu12072164. [PMID: 32708278 PMCID: PMC7401267 DOI: 10.3390/nu12072164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 02/06/2023] Open
Abstract
Background. This cross-sectional study aimed to explore the microbial composition of the gut and its possible association with the Mediterranean diet (MD) after adjusting for demographic and anthropometric characteristics in a sample of healthy young Italian adults. Methods. Gut microbiota, demographic information, and data on adherence to MD and physical activity (PA) habits were collected in a sample of 140 university students (48.6% males, mean age 22.5 ± 2.9) with a mean body mass index (BMI) of 22.4 ± 2.8 kg/m2 (15.2–33.8) and a mean PA level of 3006.2 ± 2973.6 metabolic equivalent (MET)-minutes/week (148–21,090). Results. A high prevalence of Firmicutes and Bacteroidetes was found in all the fecal samples. Significant dissimilarities in the microbiota composition were found on the basis of MD adherence and PA levels (p = 0.001). At the genus level, Streptococcus and Dorea were highly abundant in overweight/obese individuals, Ruminococcus and Oscillospira in participants with lower adherence to MD, and Lachnobacterium in subjects with low levels of PA (p = 0.001). A significantly higher abundance of Paraprevotella was shown by individuals with lower BMI, lower MD adherence, and lower PA levels (p = 0.001). Conclusions. This study contributes to the characterization of the gut microbiome of healthy humans. The findings suggest the role of diet and PA in determining gut microbiota variability.
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Affiliation(s)
- Francesca Gallè
- Department of Movement Sciences and Wellbeing, University of Naples “Parthenope”, 80133 Naples, Italy; (F.G.); (G.L.)
| | - Federica Valeriani
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, 00135 Rome, Italy; (F.V.); (G.G.)
| | - Maria Sofia Cattaruzza
- Department of Public Health and Infectious Diseases, Sapienza University, 00185 Rome, Italy; (M.S.C.); (M.A.)
| | - Gianluca Gianfranceschi
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, 00135 Rome, Italy; (F.V.); (G.G.)
| | - Renato Liguori
- Department of Sciences and Technologies, University of Naples “Parthenope”, 80143 Naples, Italy;
| | - Martina Antinozzi
- Department of Public Health and Infectious Diseases, Sapienza University, 00185 Rome, Italy; (M.S.C.); (M.A.)
| | - Beatriz Mederer
- Department of Didactics of Language and Literatura, University of Granada, 18150 Granada, Spain;
| | - Giorgio Liguori
- Department of Movement Sciences and Wellbeing, University of Naples “Parthenope”, 80133 Naples, Italy; (F.G.); (G.L.)
| | - Vincenzo Romano Spica
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, 00135 Rome, Italy; (F.V.); (G.G.)
- Correspondence:
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28
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Taylor KJM, Ngunjiri JM, Abundo MC, Jang H, Elaish M, Ghorbani A, Kc M, Weber BP, Johnson TJ, Lee CW. Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics. Appl Environ Microbiol 2020; 86:e00431-20. [PMID: 32276973 PMCID: PMC7267191 DOI: 10.1128/aem.00431-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus, that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome.IMPORTANCE Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The microorganisms present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys is entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments influence respiratory communities; consequently, they induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities.
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Affiliation(s)
- Kara J M Taylor
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - John M Ngunjiri
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Michael C Abundo
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Hyesun Jang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Mohamed Elaish
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Amir Ghorbani
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Mahesh Kc
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Bonnie P Weber
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
| | - Chang-Won Lee
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
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Kaźmierczak-Siedlecka K, Dvořák A, Folwarski M, Daca A, Przewłócka K, Makarewicz W. Fungal Gut Microbiota Dysbiosis and Its Role in Colorectal, Oral, and Pancreatic Carcinogenesis. Cancers (Basel) 2020; 12:E1326. [PMID: 32455985 PMCID: PMC7281455 DOI: 10.3390/cancers12051326] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The association between bacterial as well as viral gut microbiota imbalance and carcinogenesis has been intensively analysed in many studies; nevertheless, the role of fungal gut microbiota (mycobiota) in colorectal, oral, and pancreatic cancer development is relatively new and undiscovered field due to low abundance of intestinal fungi as well as lack of well-characterized reference genomes. Several specific fungi amounts are increased in colorectal cancer patients; moreover, it was observed that the disease stage is strongly related to the fungal microbiota profile; thus, it may be used as a potential diagnostic biomarker for adenomas. Candida albicans, which is the major microbe contributing to oral cancer development, may promote carcinogenesis via several mechanisms, mainly triggering inflammation. Early detection of pancreatic cancer provides the opportunity to improve survival rate, therefore, there is a need to conduct further studies regarding the role of fungal microbiota as a potential prognostic tool to diagnose this cancer at early stage. Additionally, growing attention towards the characterization of mycobiota may contribute to improve the efficiency of therapeutic methods used to alter the composition and activity of gut microbiota. The administration of Saccharomyces boulardii in oncology, mainly in immunocompromised and/or critically ill patients, is still controversial.
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Affiliation(s)
| | - Aleš Dvořák
- Institute of Medical Biochemistry and Laboratory Diagnostics, Faculty General Hospital and 1st Faculty of Medicine, Charles University, 12108 Prague, Czech Republic;
| | - Marcin Folwarski
- Department of Clinical Nutrition and Dietetics, Medical University of Gdansk, 80-211 Gdańsk, Poland;
| | - Agnieszka Daca
- Department of Pathology and Experimental Rheumatology, Medical University of Gdansk, 80-211 Gdańsk, Poland;
| | - Katarzyna Przewłócka
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdansk, 80-210 Gdańsk, Poland;
| | - Wojciech Makarewicz
- Department of Surgical Oncology, Medical University of Gdansk, 80-214 Gdańsk, Poland;
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Barcik W, Boutin RCT, Sokolowska M, Finlay BB. The Role of Lung and Gut Microbiota in the Pathology of Asthma. Immunity 2020; 52:241-255. [PMID: 32075727 PMCID: PMC7128389 DOI: 10.1016/j.immuni.2020.01.007] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/30/2019] [Accepted: 01/20/2020] [Indexed: 02/08/2023]
Abstract
Asthma is a common chronic respiratory disease affecting more than 300 million people worldwide. Clinical features of asthma and its immunological and molecular etiology vary significantly among patients. An understanding of the complexities of asthma has evolved to the point where precision medicine approaches, including microbiome analysis, are being increasingly recognized as an important part of disease management. Lung and gut microbiota play several important roles in the development, regulation, and maintenance of healthy immune responses. Dysbiosis and subsequent dysregulation of microbiota-related immunological processes affect the onset of the disease, its clinical characteristics, and responses to treatment. Bacteria and viruses are the most extensively studied microorganisms relating to asthma pathogenesis, but other microbes, including fungi and even archaea, can potently influence airway inflammation. This review focuses on recently discovered connections between lung and gut microbiota, including bacteria, fungi, viruses, and archaea, and their influence on asthma.
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Affiliation(s)
- Weronika Barcik
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Rozlyn C T Boutin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research, University of Zurich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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Mahnic A, Breskvar M, Dzeroski S, Skok P, Pintar S, Rupnik M. Distinct Types of Gut Microbiota Dysbiosis in Hospitalized Gastroenterological Patients Are Disease Non-related and Characterized With the Predominance of Either Enterobacteriaceae or Enterococcus. Front Microbiol 2020; 11:120. [PMID: 32117143 PMCID: PMC7026674 DOI: 10.3389/fmicb.2020.00120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/20/2020] [Indexed: 12/30/2022] Open
Abstract
Typical disease-associated microbiota changes are widely studied as potential diagnostic or therapeutic targets. Our aim was to analyze a hospitalized cohort including various gastroenterological pathologies in order to fine-map the gut microbiota dysbiosis. Bacterial (V3 V4) and fungal (ITS2) communities were determined in 121 hospitalized gastrointestinal patients from a single ward and compared to 162 healthy controls. Random Forest models implemented in this study indicated that the gut community structure is in most cases not sufficient to differentiate the subjects based on their underlying disease. Instead, hospitalized patients in our study formed three distinct disease non-related clusters (C1, C2, and C3), partially explained by antibiotic use. Majority of the subjects (cluster C1) closely resembled healthy controls, showing only mild signs of community disruption; most significantly decreased in this cluster were Faecalibacterium and Roseburia. The remaining two clusters (C2 and C3) were characterized by severe signs of dysbiosis; cluster C2 was associated with an increase in Enterobacteriaceae and cluster C3 by an increase in Enterococcus. According to the cluster affiliation, subjects also showed different degrees of inflammation, most prominent was the positive correlation between levels of C-reactive protein and the abundance of Enterococcus.
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Affiliation(s)
- Aleksander Mahnic
- National Laboratory for Health, Environment and Food, Department for Microbiological Research, Maribor, Slovenia
| | - Martin Breskvar
- Department of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Saso Dzeroski
- Department of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
| | - Pavel Skok
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Department of Gastroenterology, University Clinical Centre Maribor, Maribor, Slovenia
| | - Spela Pintar
- Department of Gastroenterology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Department for Microbiological Research, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
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Morita E, Yokoyama H, Imai D, Takeda R, Ota A, Kawai E, Hisada T, Emoto M, Suzuki Y, Okazaki K. Aerobic Exercise Training with Brisk Walking Increases Intestinal Bacteroides in Healthy Elderly Women. Nutrients 2019; 11:E868. [PMID: 30999699 PMCID: PMC6520866 DOI: 10.3390/nu11040868] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022] Open
Abstract
This study examined the effect of an exercise intervention on the composition of the intestinal microbiota in healthy elderly women. Thirty-two sedentary women that were aged 65 years and older participated in a 12-week, non-randomized comparative trial. The subjects were allocated to two groups receiving different exercise interventions, trunk muscle training (TM), or aerobic exercise training (AE). AE included brisk walking, i.e., at an intensity of ≥ 3 metabolic equivalents (METs). The composition of the intestinal microbiota in fecal samples was determined before and after the training period. We also assessed the daily physical activity using an accelerometer, trunk muscle strength by the modified Kraus-Weber (K-W) test, and cardiorespiratory fitness by a 6-min. walk test (6MWT). K-W test scores and distance achieved during the 6MWT (6MWD) improved in both groups. The relative abundance of intestinal Bacteroides only significantly increased in the AE group, particularly in subjects showing increases in the time spent in brisk walking. Overall, the increases in intestinal Bacteroides following the exercise intervention were associated with increases in 6MWD. In conclusion, aerobic exercise training that targets an increase of the time spent in brisk walking may increase intestinal Bacteroides in association with improved cardiorespiratory fitness in healthy elderly women.
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Affiliation(s)
- Emiko Morita
- Department of Environmental Physiology for Exercise, Osaka City University Graduate School of Medicine, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
- Department of Physical Therapy Faculty of Health Science, Aino University, 4-5-4 Higashiohda, Ibaraki-shi, Osaka 567-0012, Japan.
| | - Hisayo Yokoyama
- Department of Environmental Physiology for Exercise, Osaka City University Graduate School of Medicine, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
- Research Center for Urban Health and Sports, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
| | - Daiki Imai
- Department of Environmental Physiology for Exercise, Osaka City University Graduate School of Medicine, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
- Research Center for Urban Health and Sports, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
| | - Ryosuke Takeda
- Research Center for Urban Health and Sports, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
| | - Akemi Ota
- Department of Health and Sports Science, Osaka Electro-communication University, 1130-70 Kiyotaki, Shijonawate-shi, Osaka 575-0063, Japan.
| | - Eriko Kawai
- Department of Environmental Physiology for Exercise, Osaka City University Graduate School of Medicine, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
| | - Takayoshi Hisada
- TechnoSuruga Laboratory Company, Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan.
| | - Masanori Emoto
- Metabolism, Endocrinology and Molecular Medicine, Osaka City University Graduate School of Medicine, 1-4-3, Asahi-Machi, Abeno-ku, Osaka-shi, Osaka 545-8586, Japan.
| | - Yuta Suzuki
- Department of Environmental Physiology for Exercise, Osaka City University Graduate School of Medicine, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
- Research Center for Urban Health and Sports, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
| | - Kazunobu Okazaki
- Department of Environmental Physiology for Exercise, Osaka City University Graduate School of Medicine, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
- Research Center for Urban Health and Sports, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka-shi, Osaka 558-8585, Japan.
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