Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Abstract
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 canmore »
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 2217635
- Resource Type:
- Published Article
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Name: Nature Communications Journal Volume: 14 Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Ramoneda, Josep, Jensen, Thomas B. N., Price, Morgan N., Casamayor, Emilio O., and Fierer, Noah. Taxonomic and environmental distribution of bacterial amino acid auxotrophies. United Kingdom: N. p., 2023.
Web. doi:10.1038/s41467-023-43435-4.
Ramoneda, Josep, Jensen, Thomas B. N., Price, Morgan N., Casamayor, Emilio O., & Fierer, Noah. Taxonomic and environmental distribution of bacterial amino acid auxotrophies. United Kingdom. https://doi.org/10.1038/s41467-023-43435-4
Ramoneda, Josep, Jensen, Thomas B. N., Price, Morgan N., Casamayor, Emilio O., and Fierer, Noah. Wed .
"Taxonomic and environmental distribution of bacterial amino acid auxotrophies". United Kingdom. https://doi.org/10.1038/s41467-023-43435-4.
@article{osti_2217635,
title = {Taxonomic and environmental distribution of bacterial amino acid auxotrophies},
author = {Ramoneda, Josep and Jensen, Thomas B. N. and Price, Morgan N. and Casamayor, Emilio O. and Fierer, Noah},
abstractNote = {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.},
doi = {10.1038/s41467-023-43435-4},
journal = {Nature Communications},
number = 1,
volume = 14,
place = {United Kingdom},
year = {Wed Nov 22 00:00:00 EST 2023},
month = {Wed Nov 22 00:00:00 EST 2023}
}
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