Lysis-Hi-C as a method to study polymicrobial communities and eDNA.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Microbes form structured communities in biofilms and infections.
• Next-generation sequencing struggles to map in situ spatial proximity of microbial genotypes.
• Hi-C sequencing aids microbiome analysis by linking adjacent DNA for improved assembly.

Purpose of the Study:

• To explore a modified Hi-C approach with an initial lysis phase.
• To test if adjacent cell chromatin can be cross-linked after lysis.
• To study spatial-mutational dynamics in structured microbial communities.

Main Methods:

• An artificial polymicrobial mixture (Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli) was lysed (1-18h) then prepared for Hi-C.
• A murine biofilm infection model underwent sonication, mechanical lysis, or chemical lysis before Hi-C.
• Bioinformatic analysis of Hi-C interspecies chromatin links.

Main Results:

• Lysis significantly increased interspecies DNA links.
• Lysis increased the distance of intraspecies Hi-C links.
• Novel plasmid-chromosome links were increased by lysis.

Conclusions:

• The modified lysis-Hi-C protocol successfully created extracellular DNA links.
• This method is a promising step toward mapping genotypic microgeography in polymicrobial communities.
• Potential applications exist for diseases with localized resistance, like cystic fibrosis and diabetic ulcers.