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Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics

Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consis...

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Detalles Bibliográficos
Autores principales: Engel, Philipp, Stepanauskas, Ramunas, Moran, Nancy A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161309/
https://www.ncbi.nlm.nih.gov/pubmed/25210772
http://dx.doi.org/10.1371/journal.pgen.1004596
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author Engel, Philipp
Stepanauskas, Ramunas
Moran, Nancy A.
author_facet Engel, Philipp
Stepanauskas, Ramunas
Moran, Nancy A.
author_sort Engel, Philipp
collection PubMed
description Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification.
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spelling pubmed-41613092014-09-17 Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics Engel, Philipp Stepanauskas, Ramunas Moran, Nancy A. PLoS Genet Research Article Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification. Public Library of Science 2014-09-11 /pmc/articles/PMC4161309/ /pubmed/25210772 http://dx.doi.org/10.1371/journal.pgen.1004596 Text en © 2014 Engel et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Engel, Philipp
Stepanauskas, Ramunas
Moran, Nancy A.
Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
title Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
title_full Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
title_fullStr Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
title_full_unstemmed Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
title_short Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
title_sort hidden diversity in honey bee gut symbionts detected by single-cell genomics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161309/
https://www.ncbi.nlm.nih.gov/pubmed/25210772
http://dx.doi.org/10.1371/journal.pgen.1004596
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