Worlds within worlds: evolution of the vertebrate gut microbiota

By Ruth E. Ley, Catherine A. Lozupone, Micah Hamady, Rob Knight, Jeffrey I. Gordon. Nature Reviews Microbiology, 2008

1,583 citations recorded by the source corpus.

In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a74139799e9001d043990d6176cd951069d8d2a7

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Citations in the corpus

The seed microbiome: Origins, interactions, and impacts (2017, background): “An increasing literature on environmental microbiology and microbial ecology coupled with contemporary studies on vertebrate and invertebrate gut microbiomes of nondomesticated animals (Ley et al. 2008; Muegge et al. 2011) is providing a means to generate strong hypotheses about the type, magnitude,”
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. (2009, methodology): “…of many improved computational methods for comparing large numbers of microbial communities including UniFrac (Lozupone and Knight 2005; Lozupone et al. 2006), SONS (Schloss and Handelsman 2006), and network-based comparisons (Ley et al. 2008a) will allow very rapid progress to be made.”
Probiotics and prebiotics in animal feeding for safe food production. (2010, background): “Studies on the survey of the gut bacterial communities in 60 species of mammals based on 16S rRNAanalysis showed that diet, host phylogeny and gut morphology influence the microbial ecology of the gastrointestinal tract (Ley et al., 2008, 2009).”
Holobionts as Units of Selection and a Model of Their Population Dynamics and Evolution (2018, background): “In vertebrates, the development of the immune and digestive systems is not completed without gut bacteria (Ley et al. 2008; Lee and Mazmanian 2010).”
Intestinal microbiota in human health and disease: the impact of probiotics (2011, background): “The intestinal microbiota and the host have coevolved (Ley et al. 2008).”
Composition, Diversity, and Origin of the Bacterial Community in Grass Carp Intestine (2012, background): “[2] that intestinal bacteria play important roles”
Animal behaviour meets microbial ecology (2011, background): “For instance, animals’ bacterial communities help them extract energy and nutrients from food (Nalepa 1994; Ley et al. 2008), produce vitamins (Hill 1997), fight pathogens (Fons et al. 2000; Dillon et al. 2005; Ruiz-Rodríguez et al. 2009) and train the immune system (Umesaki et al. 1999; Macpherson…”
Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysis (2012, methodology): “Proteobacterial species comprised <30% of the OTUs from their gut communities, which were instead unique in their combined enrichment of species from the Bacteroidetes and Firmicutes (>50% of the OTUs in each; Fig.”
Interactions between gut microbiota and host metabolism predisposing to obesity and diabetes. (2011, background): “The collective genome of these microorganisms (the “microbiome”) exceeds the size of the human nuclear genome by two orders of magnitude, contributing a broad range of biochemical and metabolic functions that the host could not otherwise perform (1).”