nature.com
A genomic catalog of Earth's bacterial and archaeal symbionts
Symbiont genome dataset and feature extraction We constructed a comprehensive symbiont proteome database and extracted genomic features to enable lifestyle classification (Fig. 1). The first part included a reference set of 792 symbiont proteomes from across major clades (Fig. 1a) that was used to capture functional signals of symbiosis. The manually curated origin of the 792 symbiont proteomes and the expert-guided labeling criteria for the 6,751 genomes are described in the Methods. We performed orthogroup inference on these symbiont proteomes, from which we built 20,063 high-confidence profile hidden Markov models (HMMs) for orthogroups that contained ≥5 member proteins. The HMMs serve as potential markers of symbiotic gene content (Fig. 1a). Next, we built a dataset comprising 6,751 labeled microbial genomes (Fig. 1b and Supplementary Table 1) available in the Integrated Microbial Genomes and Metagenomes (IMG/M) database29, spanning three lifestyle classes: free-living (n = 5,959), host-associated (n = 409) and obligately intracellular (n = 383). Detailed definitions of these lifestyle labels are provided in the Methods. With the aim of accounting for the effect of genome incompleteness in the downstream training of our models, all the genomes were artificially reduced to different levels of genome completeness and fragmentation lengths (Fig. 1b)...
