Unexplored diversity and potential functions of extra-chromosomal elements

In addition to the main chromosome, approximately 10% bacterial genomes have one or more large secondary replicons, including a unique type of replicon known as "chromid," which has plasmid-type replication and partition systems but carries core genes. Their nucleotide composition of chromids is very similar to that of their related chromosomes. However, the distribution, characteristics, functions, and origins of these chromids remain unclear. In this study, we established a workflow to identify chromids from complete bacterial genomes and screened 36,322 complete bacterial genomes, resulting in the identification of 1,104 bacterial genomes with chromids as secondary replicons. These chromid-carrying bacteria belong to eight phyla and 73 genera, exhibiting diversity and a wide global distribution. We analyzed the characteristics of chromids and found that their average size is larger than that of "megaplasmids" and that multi-chromid bacteria exist. Furthermore, chromids encode genes related to bacterial respiratory chain enzyme complexes and antiviral systems, expanding bacterial metabolic capabilities and enhancing their antiviral defenses. In addition, we developed an automated identification program, Chromid-Finder, for identifying chromid sequences in metagenomic data, which has demonstrated outstanding performance. To demonstrate its application, we analyzed 92,143 metagenome-assembled genomes (MAGs) from the human gut microbiome. We found that the distribution of chromid-carrying bacteria in the human gut is closely associated with host age, health status, and geographic location. Species with chromids exhibit unique functional capabilities, showing good separation at the phylum level.IMPORTANCEIn this study, we have developed a workflow to identify chromids from complete bacterial genomes. We utilized this workflow to search for chromids in the latest NCBI RefSeq databases, to map the distribution of bacteria carrying chromids, to identify the characteristics of bacterial chromids, to discuss their origins, and to investigate their roles in bacterial life. To address the growing volume of metagenomic data, we developed a high-performance automated identification program, Chromid-Finder, designed to identify chromids and their corresponding bacterial main chromosomes within extensive metagenomic data sets. Using this tool, we analyzed 92,143 metagenome-assembled genomes (MAGs) from the human gut microbiome.