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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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2017-02-01
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| Series: | mSphere |
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| Online Access: | https://journals.asm.org/doi/10.1128/mSphere.00026-17 |
| _version_ | 1818567651914416128 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T06:26:07Z |
| format | Article |
| id | doaj.art-4b0fc2e0f9fc4c36afd549a226c39a39 |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-12-14T06:26:07Z |
| publishDate | 2017-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj.art-4b0fc2e0f9fc4c36afd549a226c39a392022-12-21T23:13:41ZengAmerican Society for MicrobiologymSphere2379-50422017-02-012110.1128/mSphere.00026-17Unexplored Archaeal Diversity in the Great Ape Gut MicrobiomeKasie Raymann0Andrew H. Moeller1Andrew L. Goodman2Howard Ochman3Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USADepartment of Integrative Biology, University of Texas at Austin, Austin, Texas, USADepartment of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, Connecticut, USADepartment of Integrative Biology, University of Texas at Austin, Austin, Texas, USAABSTRACT 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.https://journals.asm.org/doi/10.1128/mSphere.00026-17archaeagreat apesgut microbiomemicrobial diversityspecies interactions |
| spellingShingle | Kasie Raymann Andrew H. Moeller Andrew L. Goodman Howard Ochman Unexplored Archaeal Diversity in the Great Ape Gut Microbiome mSphere archaea great apes gut microbiome microbial diversity species interactions |
| title | 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_short | Unexplored Archaeal Diversity in the Great Ape Gut Microbiome |
| title_sort | unexplored archaeal diversity in the great ape gut microbiome |
| topic | archaea great apes gut microbiome microbial diversity species interactions |
| url | https://journals.asm.org/doi/10.1128/mSphere.00026-17 |
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