ArticlemSystems2025
Unexplored diversity and potential functions of extra-chromosomal elements.
Article in mSystems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
5 citing papers in PubMed.
- Complete genome sequencing and assembly of twoMicrobiology resource announcements · 2026Article
- Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters inmSystems · 2026Article
- Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome.Nature communications · 2026Article
- Establishment of the chromid database and analysis of evolutionary research.Molecular genetics and genomics : MGG · 2026Article
- Megaplasmids associate withbioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.