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Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial ge...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10665431/ https://www.ncbi.nlm.nih.gov/pubmed/37993466 http://dx.doi.org/10.1038/s41467-023-43435-4 |
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author | Ramoneda, Josep Jensen, Thomas B. N. Price, Morgan N. Casamayor, Emilio O. Fierer, Noah |
author_facet | Ramoneda, Josep Jensen, Thomas B. N. Price, Morgan N. Casamayor, Emilio O. Fierer, Noah |
author_sort | Ramoneda, Josep |
collection | PubMed |
description | Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of ‘streamlined’ life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy. |
format | Online Article Text |
id | pubmed-10665431 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-106654312023-11-22 Taxonomic and environmental distribution of bacterial amino acid auxotrophies Ramoneda, Josep Jensen, Thomas B. N. Price, Morgan N. Casamayor, Emilio O. Fierer, Noah Nat Commun Article Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of ‘streamlined’ life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy. Nature Publishing Group UK 2023-11-22 /pmc/articles/PMC10665431/ /pubmed/37993466 http://dx.doi.org/10.1038/s41467-023-43435-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Ramoneda, Josep Jensen, Thomas B. N. Price, Morgan N. Casamayor, Emilio O. Fierer, Noah Taxonomic and environmental distribution of bacterial amino acid auxotrophies |
title | Taxonomic and environmental distribution of bacterial amino acid auxotrophies |
title_full | Taxonomic and environmental distribution of bacterial amino acid auxotrophies |
title_fullStr | Taxonomic and environmental distribution of bacterial amino acid auxotrophies |
title_full_unstemmed | Taxonomic and environmental distribution of bacterial amino acid auxotrophies |
title_short | Taxonomic and environmental distribution of bacterial amino acid auxotrophies |
title_sort | taxonomic and environmental distribution of bacterial amino acid auxotrophies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10665431/ https://www.ncbi.nlm.nih.gov/pubmed/37993466 http://dx.doi.org/10.1038/s41467-023-43435-4 |
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