Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

ABSTRACT Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be...

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Autores principales:	Kasie Raymann, Andrew H. Moeller, Andrew L. Goodman, Howard Ochman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	archaea great apes gut microbiome microbial diversity species interactions Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/4b0fc2e0f9fc4c36afd549a226c39a39
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spelling	oai:doaj.org-article:4b0fc2e0f9fc4c36afd549a226c39a392021-11-15T15:22:03ZUnexplored Archaeal Diversity in the Great Ape Gut Microbiome10.1128/mSphere.00026-172379-5042https://doaj.org/article/4b0fc2e0f9fc4c36afd549a226c39a392017-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00026-17https://doaj.org/toc/2379-5042ABSTRACT Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.Kasie RaymannAndrew H. MoellerAndrew L. GoodmanHoward OchmanAmerican Society for Microbiologyarticlearchaeagreat apesgut microbiomemicrobial diversityspecies interactionsMicrobiologyQR1-502ENmSphere, Vol 2, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	archaea great apes gut microbiome microbial diversity species interactions Microbiology QR1-502
spellingShingle	archaea great apes gut microbiome microbial diversity species interactions Microbiology QR1-502 Kasie Raymann Andrew H. Moeller Andrew L. Goodman Howard Ochman Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
description	ABSTRACT Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.
format	article
author	Kasie Raymann Andrew H. Moeller Andrew L. Goodman Howard Ochman
author_facet	Kasie Raymann Andrew H. Moeller Andrew L. Goodman Howard Ochman
author_sort	Kasie Raymann
title	Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
title_short	Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
title_full	Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
title_fullStr	Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
title_full_unstemmed	Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
title_sort	unexplored archaeal diversity in the great ape gut microbiome
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/4b0fc2e0f9fc4c36afd549a226c39a39
work_keys_str_mv	AT kasieraymann unexploredarchaealdiversityinthegreatapegutmicrobiome AT andrewhmoeller unexploredarchaealdiversityinthegreatapegutmicrobiome AT andrewlgoodman unexploredarchaealdiversityinthegreatapegutmicrobiome AT howardochman unexploredarchaealdiversityinthegreatapegutmicrobiome
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Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

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