Abstract: Many microorganisms are auxotrophic – unable to synthesize the compounds they require for growth. Auxotrophies are important drivers of the interactions that structure microbial communities. However, we still lack empirical information about the metabolic capabilities of most bacterial taxa, and the metabolic models often used to predict the metabolic capabilities of bacteria based on genomic information frequently underestimate these capabilities. The goal of this study was to provide a comprehensive perspective on the prevalence of amino acid auxotrophies across a broad diversity of bacteria and across habitats. We predicted the amino acid biosynthesis capabilities of 31,661 unique bacterial genomes from 13 different phyla using a metabolic model that we validated with empirical data. While most bacterial phyla contain auxotrophic taxa, we found that the majority (72%) are able to synthesize all amino acids. Amino acid auxotrophy was predominant only in bacterial families of intracellular parasites (Mycoplasmataceae, 100% auxotrophs) and host-associated taxa (e.g. Enterobacteriaceae, 81.5% auxotrophs). We then predicted the amino acid biosynthesis capabilities of 13,539 representative genomes from taxa found across 12 unique habitats (3,813 samples across soil, aquatic, plant and human-associated environments, engineered environments, and food products) to investigate environmental associations with auxotrophy. To this end, we used the 16S rDNA sequence information from the taxa found across these habitats and matched these sequences to reference genomes in the Genome Taxonomy Database (GTDB). We found that the proportion of auxotrophic taxa was highest in host-associated environments dominated by Firmicutes such as the human oral cavity (76.6%), and lowest in environments dominated by Proteobacteria such as soils (3%). Overall, free-living lifestyles were associated to the ability to synthesize all amino acids, and only parasitic and host-associated lifestyles had significant proportions of auxotrophs. This work provides a comprehensive view on amino acid auxotrophy across the bacterial tree of life, showing that bacterial amino acid auxotrophies are less common than expected from previous work. Our findings can point at potential biotic interactions, provide novel trait information on thousands of uncultured taxa, and help understand how microorganisms adapt to their respective environments.
