Dataset Information

Spatial metagenomic characterization of microbial biogeography in the gut.

ABSTRACT: Spatial structuring is important for the maintenance of natural ecological systems1,2. Many microbial communities, including the gut microbiome, display intricate spatial organization3-9. Mapping the biogeography of bacteria can shed light on interactions that underlie community functions10-12, but existing methods cannot accommodate the hundreds of species that are found in natural microbiomes13-17. Here we describe metagenomic plot sampling by sequencing (MaPS-seq), a culture-independent method to characterize the spatial organization of a microbiome at micrometer-scale resolution. Intact microbiome samples are immobilized in a gel matrix and cryofractured into particles. Neighboring microbial taxa in the particles are then identified by droplet-based encapsulation, barcoded 16S rRNA amplification and deep sequencing. Analysis of three regions of the mouse intestine revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. We identified robust associations between Bacteroidales taxa in all gut compartments and showed that phylogenetically clustered local regions of bacteria were associated with a dietary perturbation. Spatial metagenomics could be used to study microbial biogeography in complex habitats.

SUBMITTER: Sheth RU

PROVIDER: S-EPMC6679743 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Spatial metagenomic characterization of microbial biogeography in the gut.

Sheth Ravi U RU Li Mingqiang M Jiang Weiqian W Sims Peter A PA Leong Kam W KW Wang Harris H HH

Nature biotechnology 20190722 8

Spatial structuring is important for the maintenance of natural ecological systems1,2. Many microbial communities, including the gut microbiome, display intricate spatial organization3-9. Mapping the biogeography of bacteria can shed light on interactions that underlie community functions10-12, but existing methods cannot accommodate the hundreds of species that are found in natural microbiomes13-17. Here we describe metagenomic plot sampling by sequen ...[more]

PMID: 31332325

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Project description:ObjectiveChanges in the gut microbiota are increasingly recognised to be involved in many diseases. This ecosystem is known to be shaped by many factors, including climate, geography, host nutrition, lifestyle and medication. Thus, knowledge of varying populations with different habits is important for a better understanding of the microbiome.DesignWe therefore conducted a metagenomic analysis of intestinal microbiota from Kazakh donors, recruiting 84 subjects, including male and female healthy subjects and metabolic syndrome (MetS) patients aged 25-75 years, from the Kazakh administrative centre, Astana. We characterise and describe these microbiomes, the first deep-sequencing cohort from Central Asia, in comparison with a global dataset (832 individuals from five countries on three continents), and explore correlations between microbiota, clinical and laboratory parameters as well as with nutritional data from Food Frequency Questionnaires.ResultsWe observe that Kazakh microbiomes are relatively different from both European and East Asian counterparts, though similar to other Central Asian microbiomes, with the most striking difference being significantly more samples falling within the Prevotella-rich enterotype, potentially reflecting regional diet and lifestyle. We show that this enterotype designation remains stable within an individual over time in 82% of cases. We further observe gut microbiome features that distinguish MetS patients from controls (eg, significantly reduced Firmicutes to Bacteroidetes ratio, Bifidobacteria and Subdoligranulum, alongside increased Prevotella), though these overlap little with previously published reports and thus may reflect idiosyncrasies of the present cohort.ConclusionTaken together, this exploratory study describes gut microbiome data from an understudied population, providing a starting point for further comparative work on biogeography and research on widespread diseases.Trial registration numberISRCTN37346212; Post-results.

Dataset Information

Spatial metagenomic characterization of microbial biogeography in the gut.

Publications

Spatial metagenomic characterization of microbial biogeography in the gut.

Similar Datasets

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