{"id":934,"date":"2023-03-24T14:18:41","date_gmt":"2023-03-24T14:18:41","guid":{"rendered":"https:\/\/dataomics.tech\/?p=934"},"modified":"2025-10-29T12:24:11","modified_gmt":"2025-10-29T12:24:11","slug":"hi-c-sequencing-plasmid-bacteria-host-interactions-animal-health","status":"publish","type":"post","link":"https:\/\/dataomics.tech\/en\/hi-c-sequencing-plasmid-bacteria-host-interactions-animal-health\/","title":{"rendered":"The Potential of Hi-c Sequencing for Unlocking Plasmid-Bacteria Host Interactions in Animal Health Research"},"content":{"rendered":"<p><span style=\"font-family: georgia, palatino, serif; font-size: 24pt; color: #0000ff;\"><strong>The Game-Changing Potential of Hi-c Sequencing for Unlocking Plasmid-Bacteria Host Interactions in Animal Health Research<\/strong><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: 14pt;\">At <strong>DataOmics<\/strong>, we are always eager to learn about new technologies and techniques in bioinformatics with application to animal science. That&#8217;s why we are thrilled to explore the potential of <strong>Hi-c sequencing applications <\/strong>in <strong>microbiome and animal health <\/strong>research.<\/span><\/p>\n<p><span style=\"font-size: 14pt;\">So, if you are interested in applying the latest and most creative solutions to develop more effective strategies for promoting animal health, we invite you to join us and learn more about <strong>Hi-C sequencing and its benefits<\/strong>.<\/span><\/p>\n<p><span style=\"font-size: 14pt;\"><strong>Hi-C sequencing<\/strong> combines Chromosome Conformation Capture (3C) technology with next-generation sequencing (NGS) to study the three-dimensional structure of chromosomes. This method gives a detailed and extensive view at how genes interact throughout the whole genome, allowing researchers to understand the importance of genome organization on various levels for different organisms and cell types.<\/span><\/p>\n<p><span style=\"font-size: 14pt;\">One of the most promising applications of <strong>Hi-C sequencing<\/strong> is elucidating <strong>plasmid-bacteria host interactions<\/strong>. This method explores the cross-links between <strong>plasmid genes (and other elements)<\/strong> \u00a0<strong>and their host bacteria<\/strong> and how these interactions affect genetic processes such as gene regulation and expression.<\/span><\/p>\n<p><span style=\"font-size: 14pt;\"><strong>Plasmids<\/strong> are mobile genetic elements that can carry not only <span style=\"color: #0000ff;\"><a style=\"color: #0000ff;\" href=\"https:\/\/doi.org\/10.1101\/2022.09.16.508255\"><strong>genes related to beneficial traits<\/strong><\/a><\/span> but also <span style=\"color: #0000ff;\"><a style=\"color: #0000ff;\" href=\"https:\/\/www.nature.com\/articles\/s41467-020-18164-7\"><strong>antibiotic resistance genes<\/strong><\/a> <\/span>among others, which are particularly relevant to animal health.\u00a0 Therefore, as a practical example, the Hi-c proximity-ligation method can helps us recognize the bacterial hosts more likely to carry antibiotic resistance genes and <strong>track how these genes spread among bacterial populations<\/strong>.<\/span><\/p>\n<p><span style=\"font-size: 14pt;\">Moreover, the Hi-c chromatin-level contact probability maps can also be used to reconstruct the individual genomes of microbial species obtained from metagenomic shotgun sequencing. Hi-C data provides intracellular contiguity information and contains both intrachromosomal and interchromosomal data, making it a powerful tool for <span style=\"color: #0000ff;\"><strong><a style=\"color: #0000ff;\" href=\"https:\/\/doi.org\/10.1534\/g3.114.011825\">species-level deconvolution of microbiota<\/a><\/strong><\/span> that inhabits an animal gut.<\/span><\/p>\n<figure id=\"attachment_969\" aria-describedby=\"caption-attachment-969\" style=\"width: 681px\" class=\"wp-caption alignright\"><img fetchpriority=\"high\" decoding=\"async\" class=\"wp-image-969\" src=\"https:\/\/dataomics.tech\/wp-content\/uploads\/2023\/03\/Hi-c-proximity-map-plasmid-host-adapted-1-e1679912398628.jpg\" alt=\"Featured figure adapted from Maximiliam et al. 2017: copyright available under a CC-BY-NC-ND 4.0 International license. Closer look at the chromatin-level DNA cross-links, e.g. plasmid genes and bacteria chromosome (red highlighted), in a microbiota metagenome and sequencing linkages between DNA contigs or scaffolds are used to deconvolute DNAs derived from the same organisms.\" width=\"681\" height=\"243\" srcset=\"https:\/\/dataomics.tech\/wp-content\/uploads\/2023\/03\/Hi-c-proximity-map-plasmid-host-adapted-1-e1679912398628.jpg 684w, https:\/\/dataomics.tech\/wp-content\/uploads\/2023\/03\/Hi-c-proximity-map-plasmid-host-adapted-1-e1679912398628-300x107.jpg 300w\" sizes=\"(max-width: 681px) 100vw, 681px\" \/><figcaption id=\"caption-attachment-969\" class=\"wp-caption-text\">Featured figure adapted from Maximiliam et al. 2017: copyright available under a CC-BY-NC-ND 4.0 International license. Closer look at the chromatin-level DNA cross-links, e.g. plasmid genes and bacteria chromosome (red highlighted), in a microbiota metagenome and sequencing linkages between DNA contigs or scaffolds are used to deconvolute DNAs derived from the same organisms.<\/figcaption><\/figure>\n<p style=\"text-align: justify;\"><span style=\"font-size: 14pt;\">But not only that; <strong>Hi-C sequencing<\/strong> combined with long-read sequencing holds the potential <strong>to<\/strong> <strong>improve<\/strong> <strong><em>De novo <\/em>genome assembly<\/strong> for species without a high-quality reference genome. For instance, it can be particularly useful in <strong>aquaculture R&amp;D,<\/strong> as demonstrated by r<\/span><span style=\"font-size: 14pt;\">ecent studies. The potential of <strong>incorporating Hi-c data to perform<\/strong> <strong><em>De novo<\/em> assemblies <\/strong>was successfully exemplified by the high-quality genome assemblies of <a href=\"ttps:\/\/doi.org\/10.3390\/ijms24032904\"><span style=\"color: #0000ff;\"><em><span style=\"text-decoration: underline; color: #0000ff;\">Trachidermus<\/span><\/em><span style=\"text-decoration: underline;\"> <em>fasciatu<\/em>e<\/span><\/span><\/a><span style=\"color: #0000ff;\"> and <em><a style=\"color: #0000ff;\" href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2022.1050192\/full\">Pelteobagrus vachelli<\/a> <\/em><span style=\"color: #000000;\">genomes.<\/span><\/span><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: 14pt;\">Additionally, ultra-long-range Hi-c chromatin interaction data used by a phasing tool enables the generation of <strong><span style=\"color: #0000ff;\"><a style=\"color: #0000ff;\" href=\"https:\/\/www.nature.com\/articles\/s41467-020-20536-y\">haplotype-resolved genome assemblies<\/a><\/span><\/strong>. It works as an alternative to other complex and unfeasible protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approaches.<\/span><\/p>\n<p><span style=\"font-size: 14pt;\">There is no doubt that Hi-c sequencing is a game-changing technology with a broad range of applications. It is specially true in the <strong>genomic research of non-model species<\/strong> and exploring the effect of <strong>feeds and additives on animal gut microbiota and health.<\/strong><\/span><\/p>\n<p><span style=\"font-size: 14pt;\">Although Hi-c data can be highly complex and require careful experimental design, appropriate data processing, and bioinformatic analysis, <strong>DataOmics<\/strong> team has experience working with Hi-c sequencing data and can provide the necessary computational resources and <strong><span style=\"color: #0000ff;\"><a style=\"color: #0000ff;\" href=\"https:\/\/dataomics.tech\/en\/bioinformatic-services\/metagenomics\/\">bioinformatics services<\/a><\/span><\/strong> to handle the demanding nature of this technology.<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: 14pt; color: #333399;\">If you&#8217;re interested in <strong>Hi-C technology<\/strong>, <strong>DataOmics<\/strong> experts can help your team overcome these challenges and make the most of this groundbreaking technology for your research.<br \/>\n<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"font-size: 14pt;\"><a href=\"https:\/\/dataomics.tech\/en\/contact-us\/\"><span style=\"font-size: 14pt;\"><strong><span style=\"font-size: 18pt;\"><span style=\"color: #333399;\">Contact us!<\/span><\/span><\/strong><\/span><\/a><\/span><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>","protected":false},"excerpt":{"rendered":"<p>The Game-Changing Potential of Hi-c Sequencing for Unlocking Plasmid-Bacteria Host Interactions in Animal Health Research &nbsp; At DataOmics, we are always eager to learn about new technologies and techniques in bioinformatics with application to animal science. That&#8217;s why we are thrilled to explore the potential of Hi-c sequencing applications in microbiome and animal health research. [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":1245,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[45,46],"tags":[50,54,52,49,48],"class_list":["post-934","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-bioinformatics","category-genome-assembly","tag-animal-health","tag-genome-assembly","tag-hi-c","tag-metagenome","tag-microbiota"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>The Game-Changing Potential of Hi-c Sequencing for Unlocking Plasmid-Bacteria Host Interactions in Animal Health Research<\/title>\n<meta name=\"description\" content=\"One of the most promising applications of Hi-C sequencing is elucidating plasmid-bacteria host interactions.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, 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