MetaMetaDB: a database and analytic system for investigating microbial habitability.

MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryot...

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Autores principales:	Ching-chia Yang, Wataru Iwasaki
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1f36080c65ff46b8b4a824c193ed591f
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spelling	oai:doaj.org-article:1f36080c65ff46b8b4a824c193ed591f2021-11-18T08:35:35ZMetaMetaDB: a database and analytic system for investigating microbial habitability.1932-620310.1371/journal.pone.0087126https://doaj.org/article/1f36080c65ff46b8b4a824c193ed591f2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24475242/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA) sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase), which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.Ching-chia YangWataru IwasakiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e87126 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ching-chia Yang Wataru Iwasaki MetaMetaDB: a database and analytic system for investigating microbial habitability.
description	MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA) sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase), which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.
format	article
author	Ching-chia Yang Wataru Iwasaki
author_facet	Ching-chia Yang Wataru Iwasaki
author_sort	Ching-chia Yang
title	MetaMetaDB: a database and analytic system for investigating microbial habitability.
title_short	MetaMetaDB: a database and analytic system for investigating microbial habitability.
title_full	MetaMetaDB: a database and analytic system for investigating microbial habitability.
title_fullStr	MetaMetaDB: a database and analytic system for investigating microbial habitability.
title_full_unstemmed	MetaMetaDB: a database and analytic system for investigating microbial habitability.
title_sort	metametadb: a database and analytic system for investigating microbial habitability.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/1f36080c65ff46b8b4a824c193ed591f
work_keys_str_mv	AT chingchiayang metametadbadatabaseandanalyticsystemforinvestigatingmicrobialhabitability AT wataruiwasaki metametadbadatabaseandanalyticsystemforinvestigatingmicrobialhabitability
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MetaMetaDB: a database and analytic system for investigating microbial habitability.

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