The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.

<h4>Background</h4>The human gastrointestinal tract contains a complex community of microbes, fulfilling important health-promoting functions. However, this vast complexity of species hampers the assignment of responsible organisms to these functions. Recently, Akkermansia muciniphila, a...

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Autores principales:	Mark W J van Passel, Ravi Kant, Erwin G Zoetendal, Caroline M Plugge, Muriel Derrien, Stephanie A Malfatti, Patrick S G Chain, Tanja Woyke, Airi Palva, Willem M de Vos, Hauke Smidt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/215154250c80462eb04e498316e186fa
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spelling	oai:doaj.org-article:215154250c80462eb04e498316e186fa2021-11-18T06:57:50ZThe genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.1932-620310.1371/journal.pone.0016876https://doaj.org/article/215154250c80462eb04e498316e186fa2011-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21390229/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The human gastrointestinal tract contains a complex community of microbes, fulfilling important health-promoting functions. However, this vast complexity of species hampers the assignment of responsible organisms to these functions. Recently, Akkermansia muciniphila, a new species from the deeply branched phylum Verrucomicrobia, was isolated from the human intestinal tract based on its capacity to efficiently use mucus as a carbon and nitrogen source. This anaerobic resident is associated with the protective mucus lining of the intestines.<h4>Methodology/principal findings</h4>In order to uncover the functional potential of A. muciniphila, its genome was sequenced and annotated. It was found to contain numerous candidate mucinase-encoding genes, but lacking genes encoding canonical mucus-binding domains. Numerous phage-associated sequences found throughout the genome indicate that viruses have played an important part in the evolution of this species. Furthermore, we mined 37 GI tract metagenomes for the presence, and genetic diversity of Akkermansia sequences. Out of 37, eleven contained 16S ribosomal RNA gene sequences that are >95% identical to that of A. muciniphila. In addition, these libraries were found to contain large amounts of Akkermansia DNA based on average nucleotide identity scores, which indicated in one subject co-colonization by different Akkermansia phylotypes. An additional 12 libraries also contained Akkermansia sequences, making a total of ∼16 Mbp of new Akkermansia pangenomic DNA. The relative abundance of Akkermansia DNA varied between <0.01% to nearly 4% of the assembled metagenomic reads. Finally, by testing a large collection of full length 16S sequences, we find at least eight different representative species in the genus Akkermansia.<h4>Conclusions/significance</h4>These large repositories allow us to further mine for genetic heterogeneity and species diversity in the genus Akkermansia, providing novel insight towards the functionality of this abundant inhabitant of the human intestinal tract.Mark W J van PasselRavi KantErwin G ZoetendalCaroline M PluggeMuriel DerrienStephanie A MalfattiPatrick S G ChainTanja WoykeAiri PalvaWillem M de VosHauke SmidtPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 3, p e16876 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mark W J van Passel Ravi Kant Erwin G Zoetendal Caroline M Plugge Muriel Derrien Stephanie A Malfatti Patrick S G Chain Tanja Woyke Airi Palva Willem M de Vos Hauke Smidt The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
description	<h4>Background</h4>The human gastrointestinal tract contains a complex community of microbes, fulfilling important health-promoting functions. However, this vast complexity of species hampers the assignment of responsible organisms to these functions. Recently, Akkermansia muciniphila, a new species from the deeply branched phylum Verrucomicrobia, was isolated from the human intestinal tract based on its capacity to efficiently use mucus as a carbon and nitrogen source. This anaerobic resident is associated with the protective mucus lining of the intestines.<h4>Methodology/principal findings</h4>In order to uncover the functional potential of A. muciniphila, its genome was sequenced and annotated. It was found to contain numerous candidate mucinase-encoding genes, but lacking genes encoding canonical mucus-binding domains. Numerous phage-associated sequences found throughout the genome indicate that viruses have played an important part in the evolution of this species. Furthermore, we mined 37 GI tract metagenomes for the presence, and genetic diversity of Akkermansia sequences. Out of 37, eleven contained 16S ribosomal RNA gene sequences that are >95% identical to that of A. muciniphila. In addition, these libraries were found to contain large amounts of Akkermansia DNA based on average nucleotide identity scores, which indicated in one subject co-colonization by different Akkermansia phylotypes. An additional 12 libraries also contained Akkermansia sequences, making a total of ∼16 Mbp of new Akkermansia pangenomic DNA. The relative abundance of Akkermansia DNA varied between <0.01% to nearly 4% of the assembled metagenomic reads. Finally, by testing a large collection of full length 16S sequences, we find at least eight different representative species in the genus Akkermansia.<h4>Conclusions/significance</h4>These large repositories allow us to further mine for genetic heterogeneity and species diversity in the genus Akkermansia, providing novel insight towards the functionality of this abundant inhabitant of the human intestinal tract.
format	article
author	Mark W J van Passel Ravi Kant Erwin G Zoetendal Caroline M Plugge Muriel Derrien Stephanie A Malfatti Patrick S G Chain Tanja Woyke Airi Palva Willem M de Vos Hauke Smidt
author_facet	Mark W J van Passel Ravi Kant Erwin G Zoetendal Caroline M Plugge Muriel Derrien Stephanie A Malfatti Patrick S G Chain Tanja Woyke Airi Palva Willem M de Vos Hauke Smidt
author_sort	Mark W J van Passel
title	The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
title_short	The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
title_full	The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
title_fullStr	The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
title_full_unstemmed	The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
title_sort	genome of akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/215154250c80462eb04e498316e186fa
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The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.

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