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      Factors affecting the composition of the gut microbiota, and its modulation

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      Author(s): 1 , 2 , 1 ,
      Editor(s):
      Publication date (Electronic):
      Journal: PeerJ
      Publisher: PeerJ Inc.
      Keywords: Antibiotics, miRNA, Diet, Probiotics, Gut microbiota, Prebiotics, AMPs, FMT

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          Abstract

          Gut microbiota have important functions in the body, and imbalances in the composition and diversity of those microbiota can cause several diseases. The host fosters favorable microbiota by releasing specific factors, such as microRNAs, and nonspecific factors, such as antimicrobial peptides, mucus and immunoglobulin A that encourage the growth of specific types of bacteria and inhibit the growth of others. Diet, antibiotics, and age can change gut microbiota, and many studies have shown the relationship between disorders of the microbiota and several diseases and reported some ways to modulate that balance. In this review, we highlight how the host shapes its gut microbiota via specific and nonspecific factors, how environmental and nutritional factors affect it, and how to modulate it using prebiotics, probiotics, and fecal microbiota transplantation.

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          Diet rapidly and reproducibly alters the human gut microbiome

          Lawrence A David, Corinne F. Maurice, Rachel Carmody … (2013)
          Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut 1–5 , but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals 2 , reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease 6 . In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
          Article 0 comments Cited 2126 times – based on 0 reviews     Review now
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            A human gut microbial gene catalogue established by metagenomic sequencing.

            Junjie Qin, Ruiqiang Li, Jeroen Raes … (2010)
            To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
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              Human gut microbiome viewed across age and geography

              Tanya Yatsunenko, Federico E Rey, Mark Manary … (2012)
              Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ between human populations when viewed from the perspective of component microbial lineages, encoded metabolic functions, stage of postnatal development, and environmental exposures, we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the representation of genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial species assemblages and functional gene repertoires were noted between individuals residing in the USA compared to the other two countries. These distinctive features are evident in early infancy as well as adulthood. In addition, the similarity of fecal microbiomes among family members extends across cultures. These findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations, and the impact of Westernization.
              Article 0 comments Cited 1480 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Hongyi Yang
                Journal
                Journal ID (nlm-ta): PeerJ
                Journal ID (iso-abbrev): PeerJ
                Journal ID (pmc): PeerJ
                Journal ID (publisher-id): PeerJ
                Title: PeerJ
                Publisher: PeerJ Inc. (San Diego, USA )
                ISSN (Electronic): 2167-8359
                Publication date (Electronic): 16 August 2019
                Publication date Collection: 2019
                Volume: 7
                Electronic Location Identifier: e7502
                Affiliations
                [1 ]Department of Microbiology, Northeast Forestry University , Harbin, Heilongjiang, China
                [2 ]Faculty of Health Science, Al-Baath University , Homs, Syria
                Article
                Publisher ID: 7502
                DOI: 10.7717/peerj.7502
                PMC ID: 6699480
                PubMed ID: 31440436
                SO-VID: 48163498-82ae-481c-a7a9-5aff87e9af51
                Copyright © © 2019 Hasan and Yang
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                Date received : 1 May 2019
                Date accepted : 17 July 2019
                Funding
                Funded by: Fundamental Research Funds for the Central universities
                Award ID: 2572017DA07
                Funded by: Natural Science Foundation of Heilongjiang Province, China
                Award ID: LC2016005
                The study was supported by the Fundamental Research Funds for the Central universities (2572017DA07), and the Natural Science Foundation of Heilongjiang Province, China (LC2016005). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Microbiology

                Keywords: antibiotics,mirna,diet,probiotics,gut microbiota,prebiotics,amps,fmt
                Data availability:
                Keywords: antibiotics, mirna, diet, probiotics, gut microbiota, prebiotics, amps, fmt

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