Review Article | Published:

A great-ape view of the gut microbiome

Nature Reviews Genetics (2019) | Download Citation


Humans assemble a specialized microbiome from a world teeming with diverse microorganisms. Comparison to the microbiomes of great apes provides a dimension that is indispensable to understanding how these microbial communities form, function and change. This evolutionary perspective exposes not only how human gut microbiomes have been shaped by our great-ape heritage but also the features that make humans unique, as exemplified by an expansive loss of bacterial and archaeal diversity and the identification of microbial lineages that have co-diversified with their hosts.

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The authors thank K. Hammond for assistance with preparation of the figures. This work was supported by grants from the US National Institutes of Health (R35 GM118038 to H.O.) and the US National Science Foundation (Graduate Research Fellowship 2016226761 to A.H.N.).

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  1. Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA

    • Alex H. Nishida
    •  & Howard Ochman


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The authors contributed equally to all aspects of this manuscript.

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The authors declare no competing interests.

Corresponding author

Correspondence to Howard Ochman.



The community of microorganisms in an organism or specified environment. The term is often used synonymously with ‘microbiota’ to refer to the taxonomic identity and genomic repertoire of human-associated microbial communities.


A change or perturbation in microbiome composition that differs considerably from that of a control or healthy cohort. The term is frequently used to describe the altered microbiome compositions observed in association with disorders or disease.

Great apes

Members of eight extant species within four genera — Pongo, Gorilla, Pan and Homo — that belong to the family Hominidae. Humans (Homo), gorillas (Gorilla), chimpanzees (Pan) and bonobos (Pan) constitute the African great apes, and orangutans (Pongo) are Asian great apes.


A taxonomic term used to describe unique lineages that are represented by a distinct branch in a phylogenetic tree. In the context of microbiome studies, a phylotype is any sequence that differs by a selected sequence identity threshold, or even a single site, from other sequences.


Characteristic microbial community structures defined by the over-representation of distinct sets of resident bacterial taxa. Originally, the variation in human gut microbiomes appeared to stratify into three enterotypes on the basis of microbial community compositions, although subsequent studies have reported different numbers of gut enterotypes.

Tree topology

The branching order and relationships depicted by a phylogenetic tree.

Vertical inheritance

With regard to microbiomes, the transfer of microorganisms over generations within a host lineage. In human microbiome studies, this describes the transfer of microorganisms from parents and community members to offspring after birth.

Phylogenetic congruency

The matching tree topologies for two different groups of organisms.


Reciprocal changes in organisms of different species that arise owing to their association or interaction, such that each species reciprocally affects the evolution of the other species.


Concurrent diversification of associated or interacting organisms. Cases of co-speciation are usually uncovered by the concordance of the branching orders of the species’ phylogenies. Note that co-evolution may result in co-speciation, but co-speciation can occur in the absence of co-evolution, as would be the case when the co-diversified species are not reciprocally evolving in response to one another.


One species living off the metabolic by-product of another species.

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