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      Human gut microbiota community structures in urban and rural populations in Russia

      a , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 2 , 2 , 2 , 3 , 4 , 4 , 4 , 5 , 6 , 7 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 1 , 1 , 14 , 1 , 14 , 15

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          Abstract

          The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status.

          Abstract

          The structure of the human gut microbiota has been shown to vary between populations. Tyakht et al. analyse the gut microbiota assembly from Russian individuals living in urban and rural areas, and compare these with previously studied populations.

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          Most cited references 10

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          Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota.

          Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.
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            Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.

            The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial-microbial and microbial-host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.
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              Country-specific antibiotic use practices impact the human gut resistome.

              Despite increasing concerns over inappropriate use of antibiotics in medicine and food production, population-level resistance transfer into the human gut microbiota has not been demonstrated beyond individual case studies. To determine the "antibiotic resistance potential" for entire microbial communities, we employ metagenomic data and quantify the totality of known resistance genes in each community (its resistome) for 68 classes and subclasses of antibiotics. In 252 fecal metagenomes from three countries, we show that the most abundant resistance determinants are those for antibiotics also used in animals and for antibiotics that have been available longer. Resistance genes are also more abundant in samples from Spain, Italy, and France than from Denmark, the United States, or Japan. Where comparable country-level data on antibiotic use in both humans and animals are available, differences in these statistics match the observed resistance potential differences. The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                16 September 2013
                : 4
                Affiliations
                [1 ]Research Institute of Physico-Chemical Medicine , Malaya Pirogovskaya 1a, Moscow 119435, Russia
                [2 ]Moscow State University of Medicine and Dentistry, Department of Internal Diseases Propedeutics and Gastroenterology , Delegatskaya 20-1, Moscow 127473, Russia
                [3 ]Central Scientific Institute of Gastroenterology , Shosse Entuziastov 86, Moscow 111123, Russia
                [4 ]Kirov Military Medical Academy , Lebedeva 6, Saint Petersburg 194175, Russia
                [5 ]Kazan’ State Medical University, Department of Hospital Therapy , Butlerova 49, Kazan’ 420012, Russia
                [6 ]Kazan' (Volga Region) Federal University, Department of Human Anatomy , Kremlyovskaya 18, Kazan' 420008, Russia
                [7 ]Omsk State Medical Academy , Lenina 12, Omsk 644043, Russia
                [8 ]Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences , Prospekt Akademika Lavrent'eva 8, Novosibirsk 630090, Russia
                [9 ]International Tomography Center of the Siberian Branch of the Russian Academy of Sciences , Institutskaya 3A, Novosibirsk 630090, Russia
                [10 ]Scientific Research Institute of Medical Problems of the North , Partizana Zhelezniaka 3G, Krasnoyarsk 660022, Russia
                [11 ]Novosibirsk State Medical University, Department of Internal Diseases Propedeutics , Krasny Prospect 52, Novosibirsk 630091, Russia
                [12 ]Saratov State Medical University, Department of Therapy , Bolshaya Kazachia 112, Saratov 410012, Russia
                [13 ]Rostov State Medical University, Department of Internal Diseases Propedeutics , Suvorova 118/50, Rostov-on-Don 344022, Russia
                [14 ]Moscow Institute of Physics and Technology , Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia
                [15 ]Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences , GSP-7, Miklukho-Maklaya 16/10, Moscow 117997, Russia
                Author notes
                Article
                ncomms3469
                10.1038/ncomms3469
                3778515
                24036685
                Copyright © 2013, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/

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