DOI: 10.5061/dryad.tmpg4f507
title: Data from: Polymicrobial Lysis-Hi-C experiments of three bacteria and plasmids derived from HiC-Pro

description: Microbes interact in biofilms and polymicrobial infections in a spatially
 structured manner, yet next-generation sequencing approaches generally
 fail to recover in situ spatial proximity between distinct genotypes in
 the interactome or eDNA matrix. This study explored a modified Hi-C
 approach involving an initial lysis phase prior to DNA cross-linking, to
 test whether adjacent cell chromatin can be cross-linked, anticipating
 that this could provide a new avenue for the study of spatial-mutational
 dynamics in structured microbial communities. An artificial polymicrobial
 mixture of Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia
 coli was lysed for 1 to 18 hours, then prepared for Hi-C. A murine biofilm
 infection model was treated with sonication, mechanical lysis, or chemical
 lysis before Hi-C. Bioinformatic analyses of resulting Hi-C interspecies
 chromatin links showed that while microbial species differed from one
 another, generally lysis significantly increased links between species and
 increased the distance of Hi-C links within species, while also increasing
 novel plasmid-chromosome links. The success of this modified lysis-Hi-C
 protocol in creating extracellular DNA links is a promising first step
 toward a new lysis-Hi-C-based method to recover genotypic microgeography
 in polymicrobial communities, with potential future applications in
 diseases with localized resistance, such as cystic fibrosis lung
 infections and chronic diabetic ulcers.
description: These data derive from a novel application of Hi-C which tests
 the effects of lysis prior to formaldehyde crosslinking to assess whether
 Hi-C links can form between species in either (1) mixed-species cell
 communities prepared, by culturing and partly drying cells of
 <em>Pseudomonas aeruginosa</em>, <em>Staphylococcus
 aureus</em>, and <em>E. coli</em> in a thin layer then
 treating with no lysis (controls) "CNL" or with either 1 hr
 "CSL" or 18 hr of lysis "CLL" with application of
 Igepal lysing buffer prior to formaldehyde crosslinking or (2) mouse wound
 biofilms prepared by inoculating dermal wound models with cultured
 microbes (<em>Pseudomonas aeruginosa</em> and
 <em>Staphylococcus aureus) </em>and collecting resulting
 biofilm+skin after 5 days, then treating with brief sonication (controls)
 "MS" or with mechanical lysis "MML" or mechanical
 lysis followed by 18 hr of lysis with Igepal lysing buffer "MLL"
 prior to formaldehyde crosslinking. After crosslinking, Hi-C libraries
 were prepared by standard protocols except with several modifications to
 precipitate and preserve eDNA. After Illumina sequencing of Hi-C
 libraries, data were analyzed following a modified bioinformatic pipeline
 using the HiC-Pro software. The output "raw" data deposited are
 the HiC-Pro Matrix (non-normalized) for links between self (same species)
 and non-self (other species) or plasmid. The corresponding code is
 attached.
description: HiC-Pro matrix link data filenames associated with this
 entry: CNL = cells no lysis CSL =
 cells short lysis CLL = cells long lysis
 MS = mouse sonication MML = mouse mechanical
 disruption MLL = mouse long lysis