Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions

Sharma, Ashok; Petrželková, Klára J.; Pafčo, Barbora; Robinson, Carolyn A. Jost; Fuh, Terence; Wilson, Brenda A.; Stumpf, Rebecca M.; Torralba, Manolito; Blekhman, Ran; White, Bryan A.; Nelson, Karen E.; Leigh, Steven R.; Gómez, Andrés

doi:10.1128/msystems.00815-20

Cited by 19 publications

(18 citation statements)

References 99 publications

(141 reference statements)

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“…Likewise, Faecalibacterium is a good example of inhibition by metabolites considering that Faecalibacterium prausnitzii has been considered a major producer of butyrate in the gut, a substance involved in regulating the immune system [119] . By contrast, the presence of Collinsella could have a dietary basis, since it has been associated with low fiber intake [122] , [123] .…”

Section: Resultsmentioning

confidence: 99%

Exploring the universal healthy human gut microbiota around the World

Piquer-Esteban

Ruiz-Ruiz

Arnau

et al. 2022

Computational and Structural Biotechnology Journal

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Section: Resultsmentioning

confidence: 99%

Exploring the universal healthy human gut microbiota around the World

Piquer-Esteban

Ruiz-Ruiz

Arnau

et al. 2022

Computational and Structural Biotechnology Journal

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“…This suggests a level of functional redundancy in the gut microbial taxa of wood mice that respond seasonally to the same stimuli, at broad geographical scales. Convergence of gut microbiota composition or functional capability linked to environmental conditions has been shown in primates and humans ( Gomez et al, 2019 ; Sharma et al, 2020 ), myrmecophagous mammals ( Delsuc et al, 2014 ) and in yaks and Tibetan sheep ( Zhang et al, 2016 ; Guo et al, 2021 ). Further functional studies, for example, using metagenomic or metatranscriptomic approaches, would be valuable to illuminate what seasonal functions these microbes might perform for the wood mouse host, and the potential significance of such microbiome shifts in providing hosts living in variable environments with adaptive seasonal plasticity.…”

Section: Discussionmentioning

confidence: 99%

Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations

et al. 2022

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The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.

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“…To illustrate the challenges in defining the core microbiome, we consider the community and functional profiling of a relatively small dataset composed of 370 human and 277 animal samples from nine cohorts of fecal samples. These include healthy Westerners from the US (HMP phases 1, 2, and 3) [ 9 , 37 ] and Denmark (MetaHIT), individuals with IBD from Spain (MetaHIT) [ 28 ], and a group of hunter-gatherers and traditional Bantu agriculturalists from the Central Africa Republic [ 38 ]. As controls, we consider fecal samples from gorillas [ 38 ], mice [ 39 ], and chickens [ 40 ].…”

Section: Defining the Core Microbiomementioning

confidence: 99%

“…These include healthy Westerners from the US (HMP phases 1, 2, and 3) [ 9 , 37 ] and Denmark (MetaHIT), individuals with IBD from Spain (MetaHIT) [ 28 ], and a group of hunter-gatherers and traditional Bantu agriculturalists from the Central Africa Republic [ 38 ]. As controls, we consider fecal samples from gorillas [ 38 ], mice [ 39 ], and chickens [ 40 ]. Community composition was evaluated using MetaPhlan3, and functional profiles were generated using HUMAnN3 [ 41 ] (see Supplementary Information for more details).…”

Section: Defining the Core Microbiomementioning

confidence: 99%

The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

et al. 2022

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The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.

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Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions

Abstract: The results of this study highlight parallel gut microbiome traits in human and nonhuman primates, depending on subsistence strategy. Although these similarities have been reported before, the functional and ecological bases of this convergence are not fully understood.

Cited by 19 publications

References 99 publications

Exploring the universal healthy human gut microbiota around the World

Exploring the universal healthy human gut microbiota around the World

Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations

The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

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