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Related Experiment Video

Updated: Sep 10, 2025

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Unexplored diversity and potential functions of extra-chromosomal elements.

Haoyu Liu1, Jia Sun1, JuanJuan Si1

  • 1College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.

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|August 19, 2025
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Summary

This study identifies and characterizes bacterial chromids, large secondary replicons carrying essential genes. A new tool, Chromid-Finder, aids in their discovery within metagenomic data, revealing their diverse distribution and functional roles in bacteria.

Keywords:
antiviral systemsbacterial respiratory chainchromidchromid-finder tool

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Area of Science:

  • Genomics and Microbiology
  • Bacterial Genetics
  • Bioinformatics

Background:

  • Bacterial genomes often contain large secondary replicons beyond the main chromosome.
  • Chromids, a unique type of secondary replicon, possess plasmid-like replication but carry core genes.
  • The distribution, characteristics, and functions of chromids are not well understood.

Purpose of the Study:

  • To establish a workflow for identifying chromids in bacterial genomes.
  • To analyze the distribution, characteristics, and functions of chromids.
  • To develop an automated tool for chromid identification in metagenomic data.

Main Methods:

  • Developed and applied a workflow to screen 36,322 complete bacterial genomes for chromids.
  • Analyzed chromid size, gene content (respiratory enzymes, antiviral systems), and co-occurrence with main chromosomes.
  • Created and validated the Chromid-Finder program for automated identification in metagenomic datasets, including 92,143 human gut MAGs.

Main Results:

  • Identified 1,104 bacterial genomes containing chromids across eight phyla and 73 genera, indicating wide distribution.
  • Chromids are larger than megaplasmids and can exist in multi-chromid bacteria.
  • Chromids encode genes enhancing metabolic capabilities and antiviral defense; their presence in the human gut correlates with host factors.

Conclusions:

  • Bacterial chromids are widespread and functionally significant, contributing to bacterial adaptation and defense.
  • The Chromid-Finder tool enables efficient identification of chromids in large-scale metagenomic data.
  • Chromid-carrying bacteria in the human gut show distinct distributions linked to host characteristics, suggesting ecological importance.