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Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes

The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be consider...

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Autores principales: Wiegand, Sandra, Sobol, Morgan, Schnepp-Pesch, Luca Kristina, Yan, Geng, Iqbal, Sajid, Vollmers, John, Müller, Jochen A., Kaster, Anne-Kristin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10608941/
https://www.ncbi.nlm.nih.gov/pubmed/37894270
http://dx.doi.org/10.3390/microorganisms11102612
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author Wiegand, Sandra
Sobol, Morgan
Schnepp-Pesch, Luca Kristina
Yan, Geng
Iqbal, Sajid
Vollmers, John
Müller, Jochen A.
Kaster, Anne-Kristin
author_facet Wiegand, Sandra
Sobol, Morgan
Schnepp-Pesch, Luca Kristina
Yan, Geng
Iqbal, Sajid
Vollmers, John
Müller, Jochen A.
Kaster, Anne-Kristin
author_sort Wiegand, Sandra
collection PubMed
description The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.
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spelling pubmed-106089412023-10-28 Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes Wiegand, Sandra Sobol, Morgan Schnepp-Pesch, Luca Kristina Yan, Geng Iqbal, Sajid Vollmers, John Müller, Jochen A. Kaster, Anne-Kristin Microorganisms Article The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes. MDPI 2023-10-23 /pmc/articles/PMC10608941/ /pubmed/37894270 http://dx.doi.org/10.3390/microorganisms11102612 Text en © 2023 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
Wiegand, Sandra
Sobol, Morgan
Schnepp-Pesch, Luca Kristina
Yan, Geng
Iqbal, Sajid
Vollmers, John
Müller, Jochen A.
Kaster, Anne-Kristin
Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes
title Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes
title_full Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes
title_fullStr Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes
title_full_unstemmed Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes
title_short Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes
title_sort taxonomic re-classification and expansion of the phylum chloroflexota based on over 5000 genomes and metagenome-assembled genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10608941/
https://www.ncbi.nlm.nih.gov/pubmed/37894270
http://dx.doi.org/10.3390/microorganisms11102612
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