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      Links between environment, diet, and the hunter-gatherer microbiome

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          Abstract

          The study of traditional populations provides a view of human-associated microbes unperturbed by industrialization, as well as a window into the microbiota that co-evolved with humans. Here we discuss our recent work characterizing the microbiota from the Hadza hunter-gatherers of Tanzania. We found seasonal shifts in bacterial taxa, diversity, and carbohydrate utilization by the microbiota. When compared to the microbiota composition from other populations around the world, the Hadza microbiota shares bacterial families with other traditional societies that are rare or absent from microbiotas of industrialized nations. We present additional observations from the Hadza microbiota and their lifestyle and environment, including microbes detected on hands, water, and animal sources, how the microbiota varies with sex and age, and the short-term effects of introducing agricultural products into the diet. In the context of our previously published findings and of these additional observations, we discuss a path forward for future work.

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          Most cited references 9

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          Is Open Access

          The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes.

          Although recent research revealed an impact of westernization on diversity and composition of the human gut microbiota, the exact consequences on metacommunity characteristics are insufficiently understood, and the underlying ecological mechanisms have not been elucidated. Here, we have compared the fecal microbiota of adults from two non-industrialized regions in Papua New Guinea (PNG) with that of United States (US) residents. Papua New Guineans harbor communities with greater bacterial diversity, lower inter-individual variation, vastly different abundance profiles, and bacterial lineages undetectable in US residents. A quantification of the ecological processes that govern community assembly identified bacterial dispersal as the dominant process that shapes the microbiome in PNG but not in the US. These findings suggest that the microbiome alterations detected in industrialized societies might arise from modern lifestyle factors limiting bacterial dispersal, which has implications for human health and the development of strategies aimed to redress the impact of westernization.
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            Quantitative Imaging of Gut Microbiota Spatial Organization.

            Genomic technologies have significantly advanced our understanding of the composition and diversity of host-associated microbial populations. However, their spatial organization and functional interactions relative to the host have been more challenging to study. Here we present a pipeline for the assessment of intestinal microbiota localization within immunofluorescence images of fixed gut cross-sections that includes a flexible software package, BacSpace, for high-throughput quantification of microbial organization. Applying this pipeline to gnotobiotic and human microbiota-colonized mice, we demonstrate that elimination of microbiota-accessible carbohydrates (MACs) from the diet results in thinner mucus in the distal colon, increased proximity of microbes to the epithelium, and heightened expression of the inflammatory marker REG3β. Measurements of microbe-microbe proximity reveal that a MAC-deficient diet alters monophyletic spatial clustering. Furthermore, we quantify the invasion of Helicobacter pylori into the glands of the mouse stomach relative to host mitotic progenitor cells, illustrating the generalizability of this approach.
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              Geographical variation of human gut microbial composition.

              Although we know there is considerable variation in gut microbial composition within host species, little is known about how this variation is shaped and why such variation exists. In humans, obesity is associated with the relative abundance of two dominant bacterial phyla: an increase in the proportion of Firmicutes and a decrease in the proportion of Bacteroidetes. As there is evidence that humans have adapted to colder climates by increasing their body mass (e.g. Bergmann's rule), we tested whether Firmicutes increase and Bacteroidetes decrease with latitude, using 1020 healthy individuals drawn from 23 populations and six published studies. We found a positive correlation between Firmicutes and latitude and a negative correlation between Bacteroidetes and latitude. The overall pattern appears robust to sex, age and bacterial detection methods. Comparisons between African Americans and native Africans and between European Americans and native Europeans suggest no evidence of host genotype explaining the observed patterns. The variation of gut microbial composition described here is consistent with the pattern expected by Bergmann's rule. This surprising link between large-scale geography and human gut microbial composition merits further investigation.
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                Author and article information

                Journal
                Gut Microbes
                Gut Microbes
                Informa UK Limited
                1949-0976
                1949-0984
                August 17 2018
                August 17 2018
                : 1-12
                Affiliations
                [1 ] Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
                [2 ] Department of Microbiology & Immunology, Department of Surgery, Western University, Lawson Health Research Institute, London, Ontario, Canada
                [3 ] Departments of Pediatrics and Computer Science & Engineering and Center for Microbiome Innovation, University of California, San Diego, CA, USA
                [4 ] Parasitic Diseases Programme and Laboratory Sciences Programme, National Institute for Medical Research, Mwanza Centre, Mwanza, Tanzania
                [5 ] Sexual and Reproductive Health Programme and Laboratory Sciences Programme, National Institute for Medical Research, Mwanza Centre, Mwanza, Tanzania
                [6 ] Department of Biochemistry and Microbiology, Department of AnthropologyRutgers, The State University of New Jersey, New Brunswick, NJUSA
                [7 ] Human Food Project, Terlingua, Texas, USA
                [8 ] The Department of Twin Research and Genetic EpidemiologyKing’s College London, St Thomas’ Hospital, London, UK
                [9 ] Chan Zuckerberg Biohub, San Francisco, CA, USA
                Article
                10.1080/19490976.2018.1494103
                6546328
                30118385
                © 2018

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