Assembly of the human intestinal microbiota

Dethlefsen, Les; Eckburg, Paul B.; Bik, Elisabeth M.; Relman, David A.

doi:10.1016/j.tree.2006.06.013

Cited by 451 publications

(321 citation statements)

References 64 publications

Supporting

Mentioning

300

Contrasting

Unclassified

Order By: Relevance

“…In many species the gut microbiota varies along the length of the digestive tract (Dethlefsen et al, 2006); we averaged across such variation by using the entire intestine because the spatial structure of stickleback gut microbiota is unknown. Also, by sampling the entire intestine we include bacteria in the gut lumen, as well as those associated with mucosal surfaces.…”

Section: Sample Acquisitionmentioning

confidence: 99%

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

et al. 2015

View full text Add to dashboard Cite

To explain differences in gut microbial communities we must determine how processes regulating microbial community assembly (colonization, persistence) differ among hosts and affect microbiota composition. We surveyed the gut microbiota of threespine stickleback (Gasterosteus aculeatus) from 10 geographically clustered populations and sequenced environmental samples to track potential colonizing microbes and quantify the effects of host environment and genotype. Gut microbiota composition and diversity varied among populations. These among-population differences were associated with multiple covarying ecological variables: habitat type (lake, stream, estuary), lake geomorphology and food-(but not water-) associated microbiota. Fish genotype also covaried with gut microbiota composition; more genetically divergent populations exhibited more divergent gut microbiota. Our results suggest that population level differences in stickleback gut microbiota may depend more on internal sorting processes (host genotype) than on colonization processes (transient environmental effects).

show abstract

Section: Sample Acquisitionmentioning

confidence: 99%

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Recent advances in sequencing allow us to observe and describe microbial communities with unprecedented depth and accuracy, but using these data to make inferences about how they assemble remains challenging. One approach to addressing this issue is to adopt a conceptual framework where animal hosts are viewed as ecosystems and their associated microbiota are treated as ecological communities (Dethlefsen et al, 2006;Robinson et al, 2010;Costello et al, 2012). This approach is attractive because it allows researchers to borrow concepts and tools developed over decades of research in ecology.…”

Section: Introductionmentioning

confidence: 99%

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

et al. 2015

View full text Add to dashboard Cite

Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct subgroups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.

show abstract

“…Distinct community structure and composition characterizes different vertebrate and invertebrate species in their natural environments, global microbiota and interspecies relatedness, reflecting host phylogeny and incorporating elements of developmental and nutritional specialization (Ley et al, 2008a, b;Ochman et al, 2010;Yidirim et al, 2010). Such complex interactions between deterministic (genetic and developmental), environmental and stochastic factors in the assembly and dynamics of vertebrate gut microbiota are being studied intensely, from fundamental ecological perspectives to its impact on host health and disease (Dethlefsen et al, 2006;Ley et al, 2006;Dethlefsen et al, 2007;Palmer et al, 2007;Ley et al, 2008a;Turnbaugh et al, 2009;Reid et al, 2011;Spor et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Host genetic and environmental effects on mouse intestinal microbiota

et al. 2012

View full text Add to dashboard Cite

The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strainspecific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.

show abstract

Assembly of the human intestinal microbiota

Cited by 451 publications

References 64 publications

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

Host genetic and environmental effects on mouse intestinal microbiota

Contact Info

Product

Resources

About