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Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches

Rothia species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity, including the palatine tonsils, is colonized by a complex microbial community, which compete for resources, actively suppres...

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Detalles Bibliográficos
Autores principales: de Oliveira, Isabela M. Fernandes, Ng, Duncan Y. K., van Baarlen, Peter, Stegger, Marc, Andersen, Paal Skytt, Wells, Jerry M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9676035/
https://www.ncbi.nlm.nih.gov/pubmed/36165601
http://dx.doi.org/10.1099/mgen.0.000854
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author de Oliveira, Isabela M. Fernandes
Ng, Duncan Y. K.
van Baarlen, Peter
Stegger, Marc
Andersen, Paal Skytt
Wells, Jerry M.
author_facet de Oliveira, Isabela M. Fernandes
Ng, Duncan Y. K.
van Baarlen, Peter
Stegger, Marc
Andersen, Paal Skytt
Wells, Jerry M.
author_sort de Oliveira, Isabela M. Fernandes
collection PubMed
description Rothia species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity, including the palatine tonsils, is colonized by a complex microbial community, which compete for resources, actively suppress competitors and influence host physiology. We analysed genomic data from 43 new porcine Rothia isolates, together with 112 publicly available draft genome sequences of Rothia isolates from humans, animals and the environment. In all Rothia genomes, we identified biosynthetic gene clusters predicted to produce antibiotic non-ribosomal peptides, iron scavenging siderophores and other secondary metabolites that modulate microbe–microbe and potentially microbe–host interactions. In vitro overlay inhibition assays corroborated the hypothesis that specific strains produce natural antibiotics. Rothia genomes encode a large number of carbohydrate-active enzymes (CAZy), with varying CAZy activities among the species found in different hosts, host niches and environments. These findings reveal competition mechanisms and metabolic specializations linked to ecological adaptation of Rothia species in different hosts.
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spelling pubmed-96760352022-11-21 Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches de Oliveira, Isabela M. Fernandes Ng, Duncan Y. K. van Baarlen, Peter Stegger, Marc Andersen, Paal Skytt Wells, Jerry M. Microb Genom Research Articles Rothia species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity, including the palatine tonsils, is colonized by a complex microbial community, which compete for resources, actively suppress competitors and influence host physiology. We analysed genomic data from 43 new porcine Rothia isolates, together with 112 publicly available draft genome sequences of Rothia isolates from humans, animals and the environment. In all Rothia genomes, we identified biosynthetic gene clusters predicted to produce antibiotic non-ribosomal peptides, iron scavenging siderophores and other secondary metabolites that modulate microbe–microbe and potentially microbe–host interactions. In vitro overlay inhibition assays corroborated the hypothesis that specific strains produce natural antibiotics. Rothia genomes encode a large number of carbohydrate-active enzymes (CAZy), with varying CAZy activities among the species found in different hosts, host niches and environments. These findings reveal competition mechanisms and metabolic specializations linked to ecological adaptation of Rothia species in different hosts. Microbiology Society 2022-09-27 /pmc/articles/PMC9676035/ /pubmed/36165601 http://dx.doi.org/10.1099/mgen.0.000854 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
spellingShingle Research Articles
de Oliveira, Isabela M. Fernandes
Ng, Duncan Y. K.
van Baarlen, Peter
Stegger, Marc
Andersen, Paal Skytt
Wells, Jerry M.
Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches
title Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches
title_full Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches
title_fullStr Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches
title_full_unstemmed Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches
title_short Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches
title_sort comparative genomics of rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9676035/
https://www.ncbi.nlm.nih.gov/pubmed/36165601
http://dx.doi.org/10.1099/mgen.0.000854
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