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Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella

Gilliamella and Snodgrassella, members of core gut microbiota in corbiculate bees, have high species diversity and adaptability to a wide range of hosts. In this study, we performed species taxonomy and phylogenetic analysis for Gilliamella and Snodgrassella strains that we isolated in our laborator...

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Autores principales: Zhang, Zhengyi, Guo, Yulong, Yang, Fan, Li, Jilian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9598484/
https://www.ncbi.nlm.nih.gov/pubmed/36290512
http://dx.doi.org/10.3390/bioengineering9100544
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author Zhang, Zhengyi
Guo, Yulong
Yang, Fan
Li, Jilian
author_facet Zhang, Zhengyi
Guo, Yulong
Yang, Fan
Li, Jilian
author_sort Zhang, Zhengyi
collection PubMed
description Gilliamella and Snodgrassella, members of core gut microbiota in corbiculate bees, have high species diversity and adaptability to a wide range of hosts. In this study, we performed species taxonomy and phylogenetic analysis for Gilliamella and Snodgrassella strains that we isolated in our laboratory, in combination with published whole-genome. Functional effects of accessory and unique genes were investigated by KEGG category and pathway annotation in pan-genome analysis. Consequently, in Gilliamella, we inferred the importance of carbohydrate metabolism, amino acid metabolism, membrane transport, energy metabolism, and metabolism of cofactors and vitamins in accessory or unique genes. The pathway mentioned above, plus infectious disease, lipid metabolism, nucleotide metabolism as well as replication and repair exert a pivotal role in accessory or unique genes of Snodgrassella. Further analysis revealed the existence of functional differentiation of accessory and unique genes among Apis-derived genomes and Bombus-derived genomes. We also identified eight and four biosynthetic gene clusters in all Gilliamella and Snodgrassella genomes, respectively. Our study provides a good insight to better understand how host heterogeneity influences the bacterial speciation and affects the versatility of the genome of the gut bacteria.
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spelling pubmed-95984842022-10-27 Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella Zhang, Zhengyi Guo, Yulong Yang, Fan Li, Jilian Bioengineering (Basel) Article Gilliamella and Snodgrassella, members of core gut microbiota in corbiculate bees, have high species diversity and adaptability to a wide range of hosts. In this study, we performed species taxonomy and phylogenetic analysis for Gilliamella and Snodgrassella strains that we isolated in our laboratory, in combination with published whole-genome. Functional effects of accessory and unique genes were investigated by KEGG category and pathway annotation in pan-genome analysis. Consequently, in Gilliamella, we inferred the importance of carbohydrate metabolism, amino acid metabolism, membrane transport, energy metabolism, and metabolism of cofactors and vitamins in accessory or unique genes. The pathway mentioned above, plus infectious disease, lipid metabolism, nucleotide metabolism as well as replication and repair exert a pivotal role in accessory or unique genes of Snodgrassella. Further analysis revealed the existence of functional differentiation of accessory and unique genes among Apis-derived genomes and Bombus-derived genomes. We also identified eight and four biosynthetic gene clusters in all Gilliamella and Snodgrassella genomes, respectively. Our study provides a good insight to better understand how host heterogeneity influences the bacterial speciation and affects the versatility of the genome of the gut bacteria. MDPI 2022-10-12 /pmc/articles/PMC9598484/ /pubmed/36290512 http://dx.doi.org/10.3390/bioengineering9100544 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhang, Zhengyi
Guo, Yulong
Yang, Fan
Li, Jilian
Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella
title Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella
title_full Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella
title_fullStr Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella
title_full_unstemmed Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella
title_short Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella
title_sort pan-genome analysis reveals functional divergences in gut-restricted gilliamella and snodgrassella
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9598484/
https://www.ncbi.nlm.nih.gov/pubmed/36290512
http://dx.doi.org/10.3390/bioengineering9100544
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