Archivo de la etiqueta: Microbiota

The Potential of Hi-c Sequencing for Unlocking Plasmid-Bacteria Host Interactions in Animal Health Research

The Game-Changing Potential of Hi-c Sequencing for Unlocking Plasmid-Bacteria Host Interactions in Animal Health Research

 

At DataOmics, we are always eager to learn about new technologies and techniques in bioinformatics with application to animal science. That’s why we are thrilled to explore the potential of Hi-c sequencing applications in microbiome and animal health research.

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 Hi-C sequencing and its benefits.

Hi-C sequencing 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.

One of the most promising applications of Hi-C sequencing is elucidating plasmid-bacteria host interactions. This method explores the cross-links between plasmid genes (and other elements)  and their host bacteria and how these interactions affect genetic processes such as gene regulation and expression.

Plasmids are mobile genetic elements that can carry not only genes related to beneficial traits but also antibiotic resistance genes among others, which are particularly relevant to animal health.  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 track how these genes spread among bacterial populations.

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 species-level deconvolution of microbiota that inhabits an animal gut.

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.

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.

But not only that; Hi-C sequencing combined with long-read sequencing holds the potential to improve De novo genome assembly for species without a high-quality reference genome. For instance, it can be particularly useful in aquaculture R&D, as demonstrated by recent studies. The potential of incorporating Hi-c data to perform De novo assemblies was successfully exemplified by the high-quality genome assemblies of Trachidermus fasciatue and Pelteobagrus vachelli genomes.

 

Additionally, ultra-long-range Hi-c chromatin interaction data used by a phasing tool enables the generation of haplotype-resolved genome assemblies. 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.

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 genomic research of non-model species and exploring the effect of feeds and additives on animal gut microbiota and health.

Although Hi-c data can be highly complex and require careful experimental design, appropriate data processing, and bioinformatic analysis, DataOmics team has experience working with Hi-c sequencing data and can provide the necessary computational resources and bioinformatics services to handle the demanding nature of this technology.

 

If you’re interested in Hi-C technology, DataOmics experts can help your team overcome these challenges and make the most of this groundbreaking technology for your research.

 

Contact us!