Efficient and easy‐to‐use capturing three‐dimensional metagenome interactions with GutHi‐C

Abstract

Microorganisms play a key role in ecosystems, and understanding their metagenomic organization is important for understanding the function and interrelationships of microbial populations [1,2]. 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 level [3,4]. High-through chromatin conformation capture (Hi-C) has some obvious advantages in three-dimensional (3D) organization analysis and genome-assisted assembly, but it is rarely used in microbes [5][6][7]. 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 reduced library waste and losses, and conserved experimental reagents (Figure S1). We also created a technical operations video to facilitate the academic exchange of the technology (https://youtu.be/aYEhhRO3eBk). The results show that the quality control parameters of GutHi-C (such as unique alignment rates, valid data output rates, 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 (Figure S2). With big data, it exhibited pronounced Hi-C signal intensity and presented strong chromatin interaction domains, such as chromosomal interaction domains (CIDs) and loop domains. For applications in assembly, assisted by the GutHi-C, high fidelity (HiFi) platform presents a 38.6% increase in 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.