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Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Author

Listed:
  • Josep Ramoneda

    (University of Colorado)

  • Thomas B. N. Jensen

    (University of Colorado
    Aalborg University)

  • Morgan N. Price

    (Lawrence Berkeley National Laboratory)

  • Emilio O. Casamayor

    (Center for Advanced Studies of Blanes (CEAB))

  • Noah Fierer

    (University of Colorado
    University of Colorado)

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.

Suggested Citation

  • Josep Ramoneda & Thomas B. N. Jensen & Morgan N. Price & Emilio O. Casamayor & Noah Fierer, 2023. "Taxonomic and environmental distribution of bacterial amino acid auxotrophies," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43435-4
    DOI: 10.1038/s41467-023-43435-4
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    References listed on IDEAS

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    1. Christopher E. Lawson & Sha Wu & Ananda S. Bhattacharjee & Joshua J. Hamilton & Katherine D. McMahon & Ramesh Goel & Daniel R. Noguera, 2017. "Metabolic network analysis reveals microbial community interactions in anammox granules," Nature Communications, Nature, vol. 8(1), pages 1-12, August.
    2. H. James Tripp & Joshua B. Kitner & Michael S. Schwalbach & John W. H. Dacey & Larry J. Wilhelm & Stephen J. Giovannoni, 2008. "SAR11 marine bacteria require exogenous reduced sulphur for growth," Nature, Nature, vol. 452(7188), pages 741-744, April.
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    Cited by:

    1. György Abrusán & Aleksej Zelezniak, 2024. "Cellular location shapes quaternary structure of enzymes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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