Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.

As obesity and Western diet consumption are key factors contributing to gut dysbiosis, we investigated the relationship between intestinal microbiota, obesity, and psoriasis in an imiquimod-based model. C57BL/6 mice were used as follows: psoriasis-induced groups fed continuously with a standard or Western diet, psoriasis-induced group fed with a Western diet and then returned to a standard diet, and controls. For each group, clinicopathological, immune, and metabolic parameters were integrated with microbiome data. The imiquimod-based models displayed human psoriasis features and significant changes in immune parameters. Hence, psoriatic mice on prolonged high-fat intake presented decreased microbial richness and evenness and a gut microbiome composition resembling that of obese mice. Ruminococcus, Clostridium, Desulfovibrio, and Enterorhabdus were the most abundant genera in the obesity-enhanced psoriasis group. Raoultella abundance was linked with psoriasis. Yet, the same pathobionts over-represented in the obese psoriatic mice displayed positive correlations with metabolic stress indicators and proinflammatory factors, indicating potential biomarkers of disease severity. Conversely, Lactobacillus taiwanensis, Alistipes putredinis, and Eubacterium hadrum might be potential taxa for attenuating the metabolic burden in obesity-enhanced psoriasis. Here, we depict the microbial signatures associated with inflammation and metabolic stress in an obesity-aggravated psoriasis mouse model.

Background Bacteriophages (phages) are recognized as key regulators of microbial communities, and it is pivotal to understand viral ecology, diversity, and evolution. However, identification and characterization of phages from shotgun metagenome sequencing pose unique bioinformatic challenges owing to the inherent complexity and scale of the data. Results Here, we introduce VirMake, a comprehensive, flexible, and scalable pipeline developed for viral taxonomic and functional analysis of shotgun metagenome data. It enables high-throughput end-to-end processing, assembly, and annotation of metagenomic data, including viral sequence identification, taxonomic and functional annotation, and using a modular framework, allows users to integrate viral analysis at different stages of metagenome data analysis. VirMake can be installed on Linux operating systems that support Conda and is freely available at https://github.com/Rounge-lab/VirMake. Here, we showcase VirMake capabilities using three metagenome datasets of varying sizes (up to 2.9 Tbp), generated from various environments (human gut and water) and using different sample preparation protocols (VLP enrichment and bulk DNA extraction). Conclusions VirMake enabled robust processing of all datasets, showing viral genome richness, taxonomy and integration status to vary according to sampling environments and laboratory protocols.

Este estudo descreve a prospecção biotecnológica de enzimas hidrolíticas e genes envolvidos na biossíntese de biopolímeros a partir de uma biblioteca metagenômica construída com DNA ambiental (eDNA) extraído de terra preta de índio (TPI), um solo antropogênico da Amazônia reconhecido por sua elevada diversidade microbiana. A biblioteca foi construída utilizando como vetor o fosmídeo pCC1Fos e compreendeu aproximadamente 10.000 clones recombinantes independentes, totalizando cerca de 400 Mb de informação genética. A triagem funcional revelou 226 clones com atividades enzimáticas distintas, com predominância de atividades amilolíticas e de clones produtores de polihidroxialcanoatos (PHA), além de atividades lipolíticas, celulolíticas e xilanolíticas. A análise por bioinformática das sequências de DNA dos fosmídeos recombinantes de clones selecionados permitiu a identificação de genes com potencial aplicação industrial, incluindo lipases, esterases e amilases, apresentando diferentes níveis de similaridade com enzimas previamente descritas. Em conjunto, os resultados demonstram que a integração entre triagem funcional e sequenciamento de grandes fragmentos de DNA metagenômico constitui uma estratégia eficaz para a descoberta de genes de biocatalisadores com potencial biotecnológico, refletindo a vasta diversidade inerente aos solos de terra preta de índio.