Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Abstract 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 bac...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-43435-4 |
| _version_ | 1797452099968040960 |
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| author | Josep Ramoneda Thomas B. N. Jensen Morgan N. Price Emilio O. Casamayor Noah Fierer |
| author_facet | Josep Ramoneda Thomas B. N. Jensen Morgan N. Price Emilio O. Casamayor Noah Fierer |
| author_sort | Josep Ramoneda |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-09T15:03:53Z |
| format | Article |
| id | doaj.art-59b6278643534db3957a3fdd4e82398f |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-09T15:03:53Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-59b6278643534db3957a3fdd4e82398f2023-11-26T13:46:15ZengNature PortfolioNature Communications2041-17232023-11-0114111110.1038/s41467-023-43435-4Taxonomic and environmental distribution of bacterial amino acid auxotrophiesJosep Ramoneda0Thomas B. N. Jensen1Morgan N. Price2Emilio O. Casamayor3Noah Fierer4Cooperative Institute for Research in Environmental Sciences (CIRES), University of ColoradoCooperative Institute for Research in Environmental Sciences (CIRES), University of ColoradoEnvironmental Genomics and Systems Biology, Lawrence Berkeley National LaboratorySpanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB)Cooperative Institute for Research in Environmental Sciences (CIRES), University of ColoradoAbstract 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.https://doi.org/10.1038/s41467-023-43435-4 |
| spellingShingle | Josep Ramoneda Thomas B. N. Jensen Morgan N. Price Emilio O. Casamayor Noah Fierer Taxonomic and environmental distribution of bacterial amino acid auxotrophies Nature Communications |
| 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 |
| url | https://doi.org/10.1038/s41467-023-43435-4 |
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