ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data

Abstract

The introduction of high-throughput chromosome conformation capture (Hi-C) into metagenomics enables reconstructing high-quality metagenome-assembled genomes (MAGs) from microbial communities. Despite recent advances in recovering eukaryotic, bacterial, and archaeal genomes using Hi-C contact maps, few of Hi-C-based methods are designed to retrieve viral genomes. Here we introduce ViralCC, a publicly available tool to recover complete viral genomes and detect virus-host pairs using Hi-C data. Compared to other Hi-C-based methods, ViralCC leverages the virus-host proximity structure as a complementary information source for the Hi-C interactions. Using mock and real metagenomic Hi-C datasets from several different microbial ecosystems, including the human gut, cow fecal, and wastewater, we demonstrate that ViralCC outperforms existing Hi-C-based binning methods as well as state-of-the-art tools specifically dedicated to metagenomic viral binning. ViralCC can also reveal the taxonomic structure of viruses and virus-host pairs in microbial communities. When applied to a real wastewater metagenomic Hi-C dataset, ViralCC constructs a phage-host network, which is further validated using CRISPR spacer analyses. ViralCC is an open-source pipeline available at https://github.com/dyxstat/ViralCC.

Restructuring multi-phase interfaces from Cu-based metal–organic frameworks for selective electroreduction of CO2 to C2H4

“…The electron transfer between Ag and Cu may lead to the formation of Ag-Cu bonds, as well as the existence of an Ag-Cu interface. 42 Accordingly, the Cu K-edge analysis presented a slightly higher valence state of Cu than that of the Cu 2 O reference. Moreover, the k 2 -weighted Ag K-edge EXAFS showed that the bond length and coordination number of Ag in Ag/Cu/ Cu 2 O Ag 0.1 HKUST-1 were slightly reduced, suggesting the formation of a heterostructure rather than alloys.…”

“…An AgCu single-atom alloy blended with Ag nanoparticles showed a 94 ± 4% FE towards multicarbon products at a high current density of ∼720 mA cm −2 in a ow cell, but the FE of C 2 H 4 was below 40%. 42 In contrast, Ag/ Cu/Cu 2 O Ag 0.1 /HKUST-1 can achieve the superiority of C 2 H 4 FE (∼50%), current output (>180 mA cm −2 ), and stability (600 min) at the same time, underscoring its promise for practical use. When a membrane electrode assembly (MEA) reactor is rationally designed for such restructured catalysts, we believe greater advances in performance, in particular the greater current density and long-term stability, can be accomplished.…”

Single Amplified Genome Catalog Reveals the Dynamics of Mobilome and Resistome in the Human Microbiome

“…Single-cell genomics can address the limitations of conventional metagenomics, which struggles to detect ARGs within plasmids and phages. While some cutting-edge research aims to connect MAGs, MGEs, and ARGs using Hi-C metagenomics, the extensive sequence reads required often limit MGE and ARG detection [43][44][45][46][47] . Single-cell genomics, with its ability to overcome such challenges, offers a refined view of the complex dynamics among ARGs, MGEs, and their hosts.…”

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

“…In addition to bioinformatic approaches, proximity ligation information (e.g., Hi-C) can also be used to bin contigs (Burton et al 2014;Press et al 2017;DeMaere & Darling 2019). The ProxiMeta platform (Press et al 2017), MetaCC (Du & Sun 2023), and metaBAT-LR (Ho et al 2023) can perform binning using Hi-C data and a set of assembled contigs. Proximity ligation also allows mobile elements to be associated with their respective host genomes, offering a unique advantage.…”