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      Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome

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          ABSTRACT

          The approximately 10 11 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.

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          The core gut microbiome, energy balance and obesity.

          Peter J. Turnbaugh, Jeffrey Gordon (2009)
          Metagenomics is an emerging field focused on characterizing the structures, functions and dynamic operations of microbial communities sampled in their native habitats without the need for culture. Here, we present findings from a 16S rRNA gene sequence- and whole community DNA shotgun sequencing-based analysis of the adult human gut microbiomes of lean and obese mono- and dizygotic twins. Our findings indicate that a core microbiome can be found at the gene level, despite large variation in community membership, and that variations from the core are associated with obesity. These findings have implications for ongoing Human Microbiome Project(s), and highlight important challenges to the field of metagenomics.
          Article 0 comments Cited 360 times – based on 0 reviews     Review now
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            PHAST: A Fast Phage Search Tool

            YOU-XING ZHOU, Yongjie Liang, Karlene H Lynch … (2011)
            PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage ‘cornerstone’ feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage ‘quality’ and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at (http://phast.wishartlab.com).
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              Understanding the effects of diet on bacterial metabolism in the large intestine.

              P Louis, K. Scott, S. Duncan … (2007)
              Recent analyses of ribosomal RNA sequence diversity have demonstrated the extent of bacterial diversity in the human colon, and have provided new tools for monitoring changes in the composition of the gut microbial community. There is now an excellent opportunity to correlate ecological niches and metabolic activities with particular phylogenetic groups among the microbiota of the human gut. Bacteria that associate closely with particulate material and surfaces in the gut include specialized primary degraders of insoluble substrates, including resistant starch, plant structural polysaccharides and mucin. Butyrate-producing bacteria found in human faeces belong mainly to the clostridial clusters IV and XIVa. In vitro and in vivo evidence indicates that a group related to Roseburia and Eubacterium rectale plays a major role in mediating the butyrogenic effect of fermentable dietary carbohydrates. Additional cluster XIVa species can convert lactate to butyrate, while some members of the clostridial cluster IX convert lactate to propionate. The metabolic outputs of the gut microbial community depend not only on available substrate, but also on the gut environment, with pH playing a major role. Better understanding of the colonic microbial ecosystem will help to explain and predict the effects of dietary additives, including nondigestible carbohydrates, probiotics and prebiotics.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Gut Microbes
                Journal ID (iso-abbrev): Gut Microbes
                Title: Gut Microbes
                Publisher: Taylor & Francis
                ISSN (Print): 1949-0976
                ISSN (Electronic): 1949-0984
                Publication date (Electronic, pub): 13 January 2020
                Publication date (Electronic, collection): 2020
                Publication date PMC-release: 13 January 2020
                Volume: 11
                Issue: 4
                Pages: 721-734
                Affiliations
                [a ]Department of Biology, San Diego State University; , San Diego, CA, USA
                [b ]Computational Sciences Research Center, San Diego State University; , San Diego, CA, USA
                [c ]Department of Computer Science, San Diego State University; , San Diego, CA, USA
                [d ]Ronin Institute; , Montclair, NJ, USA
                Author notes
                CONTACT Lance Boling liquidgrey@ 123456gmail.com Department of Biology, San Diego State University; , LS301, 5500 Campanile Dr, San Diego, CA92182USA
                [*]

                Current address: University of California, Merced, Merced, CA 95343

                [#]

                Current address: School of Molecular BioSciences and Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA 99164

                [&]

                Current address: Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901

                Author information
                https://orcid.org/0000-0002-3945-0135
                https://orcid.org/0000-0002-5611-0685
                https://orcid.org/0000-0002-9421-8689
                https://orcid.org/0000-0001-9036-3259
                Article
                Publisher ID: 1701353
                DOI: 10.1080/19490976.2019.1701353
                PMC ID: 7524278
                PubMed ID: 31931655
                SO-VID: d89d8a7c-aaa3-4a08-bae9-2b1f0f134f1b
                Copyright © © 2020 The Author(s). Published with license by Taylor & Francis Group, LLC.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License ( http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.

                History
                Page count
                Figures: 3, Tables: 1, References: 74, Pages: 14
                Categories
                Subject: Research Article
                Subject: Research Paper/Report

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: bacteriophage,gut microbiome,diet,antimicrobials,bactericidal,prophage induction,flow cytometry,bacteroidetes,firmicutes,stevia
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: bacteriophage, gut microbiome, diet, antimicrobials, bactericidal, prophage induction, flow cytometry, bacteroidetes, firmicutes, stevia

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