iMeta | Efficient and easy-to-use capturing 3D metagenome interactions with GutHi-C

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Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C
Yu-Xi Lu, Jin-Bao Yang, Chen-Ying Li, Yun-Han Tian, Rong-Rong Chang, Da-Shuai Kong, Shu-Lin Yang, Yan-Fang Wang, Yu-Bo Zhang, Xiu-Sheng Zhu, Wei-Hua Pan, Si-Yuan Kong
First published: 22 July 2024 doi.org/10.100...
Graphical Abstract
Hi-C can obtain three-dimensional chromatin structure information and is widely used for genome assembly. We constructed the GutHi-C technology. As shown in the graphical abstract, it is a highly efficient and quick-to-operate method and can be widely used for human, livestock, and poultry gut microorganisms. It provides a reference for the Hi-C methodology of the microbial metagenome. DPBS, Dulbecco's phosphate-buffered saline; Hi-C, high-through chromatin conformation capture; LB, Luria-Bertani; NGS, next-generation sequencing; PCR, polymerase chain reaction; QC, quality control.
Abstract
Microorganisms play a key role in ecosystems, and understanding their metagenomic organization is important for understanding the function and interrelationships of microbial populations1-3. Shotgun technology, which is widely used in microbial metagenome research, produces a large number of redundant sequences that can not be classified at the species and strain level4,5. Hi-C has some obvious advantages in three-dimensional (3D) organization analysis and genome-assisted assembly, but it is rarely used in microbes6-8. Therefore, there is an important need for a more efficient and easy-to-use Hi-C technology that can be widely used in human, livestock, or poultry gut microbes. This study introduces a metagenome GutHi-C technology suitable for microbial populations(Figure 1A). Our method further optimized the experimental conditions, significantly reducing library waste and losses, and conserving experimental reagents. We also created an technical operations video to facilitate academic exchange of the technology. Results show that the quality control parameters of GutHi-C (such as unique alignment rate, valid data output rate and ,valid interaction pair proportion and cis-interaction ratios) are superior to the data generated by previous methods. GutHi-C also has a good repeatability. With big data, it exhibited pronounced Hi-C signal intensity and presented strong chromatin interaction domains, such as CIDs and loop domains. For applications in assembly, GutHi-C help HiFi presents a 38.6% increase of high-quality metagenomes. Consequently, based on the assessment analysis of GutHi-C, it would have broad applications in gut microbes of animals, humans, and wide microbial communities, including soil or environmental microorganisms.