Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Youngblut, Nicholas D.; Reischer, Georg H.; Walters, William A.; Schuster, Nathalie; Walzer, Chris; Stalder, Gabrielle; Ley, Ruth E.; Farnleitner, Andreas H.

doi:10.1038/s41467-019-10191-3

Cited by 399 publications

(343 citation statements)

References 81 publications

Supporting

Mentioning

302

Contrasting

Order By: Relevance

“…Here, we developed an extensive metagenome assembly pipeline and applied it to a multi-species dataset of microbiome diversity across vertebrate species comprising 5 classes: Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii, with >80% of samples obtained from wild individuals 12 combined with data from 14 published animal gut metagenomes. Moreover, we also applied a recently developed gene-based metagenome assembly pipeline to the entire dataset in order to obtain gene-level diversity for rarer taxa that would otherwise be missed by genome-base assembly 13,14 .…”

Section: Introductionmentioning

confidence: 99%

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

Youngblut

Cuesta-Zuluaga

Reischer

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 4374 metagenome assembled genomes (MAGs) from gut samples of 180 predominantly wild animal species representing 5 classes. Combined with existing datasets, we produced 5596 non-redundant, quality MAGs and 1522 species-level genome bins (SGBs). Most SGBs were novel at the species, genus, or family levels, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1986 diverse and largely novel biosynthetic gene clusters. Gene-based assembly revealed tremendous gene diversity, much of it host or environment specific. Our MAG and gene datasets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to life within a living host.

show abstract

Section: Introductionmentioning

confidence: 99%

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

Youngblut

Cuesta-Zuluaga

Reischer

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Microbial communities differ between hosts that specialize on different substrates (Muegge et al , 2011) and changes in these communities and their functional capacity are integral to their hosts’ transition to utilizing novel substrates (Hammer and Bowers, 2015; Delsuc et al , 2013; Li et al , 2015; Kohl et al , 2014; 2016). This phenomenon is not isolated to herbivores – in many systems, gut microbial communities are influence by the inputs of their hosts (Goffredi et al , 2005; Roman et al , 2015; Muegge et al , 2011; Youngblut et al , 2019; Wang et al , 2011; Li et al , 2016).…”

Section: Introductionmentioning

confidence: 99%

Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass- and dicot-cutter ants

Khadempour

Fan

Keefover‐Ring

et al. 2018

Preprint

View full text Add to dashboard Cite

Leaf-cutter ants in the genus Atta are dominant herbivores in the Neotropics. While most species of Atta cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12 Atta fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. These differences in bacterial community composition and functional capacity show that different substrate inputs matter for fungus garden bacteria, and sheds light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.

show abstract

“…However, phylosymbiosis is agnostic to mechanism. Additional methods exist for determining the relationship between host phylogeny and the microbiome (e.g., using simulations in Mazel et al, 2018; Mantel tests in Pollock et al, 2018; multiple regression tests in Youngblut et al, 2019); however, the evolutionary processes that generate the microbiome have been relatively unexplored. Here, we proposed utilizing the microbiome as a trait of a host (Benson, 2016;Benson et al, 2010), and extrapolating that trait to host species.…”

mentioning

confidence: 99%

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

et al. 2020

View full text Add to dashboard Cite

How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining “microbiome traits”, we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein‐Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.

show abstract

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Cited by 399 publications

References 81 publications

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass- and dicot-cutter ants

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

Contact Info

Product

Resources

About