•Exploration of microbiome-related metabolites (trimethylamine N-oxide [TMAO], choline, betaine, L-carnitine, and deoxycarnitine) in 7834 participants from five population cohorts. •Cardiovascular risk was associated with elevated choline concentrations, but not with TMAO concentrations. •Characterization of the genetic architecture behind metabolite concentration variability. •Identification of gut microbial taxonomic abundance associated with metabolite’s plasma concentration levels. •Fish intake is the major dietary driver of TMAO concentrations, and betaine is related to grains and vegetable intake.
•Comprehensive Venn functionality: EVenn introduces a unified platform with diverse Venn diagram tools, from interactive diagrams to network representations, catering to the intricate needs of multiomics data analysis across metabolomics, genomics, transcriptomics, and proteomics. •Efficient data exploration: EVenn’s data center streamlines exploration by supporting a standardized data format, allowing researchers to effortlessly upload and analyze data. The manuscript demonstrates its practical utility through representative results and detailed case demonstrations. •User-friendly interface: With a user-friendly interface, EVenn simplifies the generation of various Venn diagrams, Euler diagrams, UpSet plots, and more. This protocol establishes EVenn as a valuable resource for researchers seeking a cohesive and accessible tool for multiomics data interpretation.
•Pregnancy rates vary among women with different vaginal microbiome communities. •Too high abundances of both Lactobacillus crispatus and Lactobacillus iners have negative effects on in vitro fertilization (IVF) outcomes. •A moderate abundance (around 80%) of Lactobacillus is more beneficial for pregnancy.
•Bacmethy tool provides a one-stop analysis and visualization pipeline for effectively characterizing bacterial DNA methylation modification features and predicting the regulation patterns. •Bacmethy offers both a local run function and an online interface analysis service, providing significant convenience for researchers without coding abilities. •Bacmethy provides useful information for decoding the underlying molecular mechanisms of how DNA methylation regulates bacterial cellular and physiological functions.
•Robinia pseudoacacia strategically recruited AM fungi to cope with phosphorus limitation. •AMfungi interacted with the assembly and composition of bacteria and rhizobia. •AM fungal-centered underground network supported slope multifunctionality. •The R. pseudoacacia–AM fungi–rhizobia association restores eroded ecosystems.
•This study comprehensively compared viral-like particle-concentrated (VPC) and non-concentrated (NC) metagenomic approaches in virome investigation, highlighting their respective efficacies in detecting different viral communities and functional elements in wastewater treatment plants (WWTPs). •Eukaryotic viruses belonging to Cressdnaviricota were the most prevalent in VPC metagenomes, while bacterial viruses belonging to Uroviricota were the most abundant in NC metagenomes. •Diverse phage-born auxiliary metabolic genes (AMGs) were discovered in the virome of WWTPs, and a large array of AMGs involved in biogeochemical cycles like carbon, sulfur, and phosphorus cycling showed transcriptional activation in wastewater treatment systems. •A tiny proportion (less than 0.08% of viral operational taxonomic units) of viruses was discovered to harbor antibiotic resistance genes (ARGs) (29 phage-born ARGs) only in the cellular fraction, and phage-born ARG types primarily included macrolide–lincosamide–streptogramin, tetracycline, and aminoglycoside resistance.
•Four distinct cuproptosis signature-based clusters are associated with different clinical outcomes and biological pathways and are highly consistent with distinct tumor immune contextures, respectively. •Based on the cuproptosis signature risk score, GC patients with a higher CSRS score were characterized by decreased survival time and correlated with tumor adhesion state and lower tumor mutation loads. •DBT, MTF1, or ATP7A were significantly elevated in the CSRS-High subtype, while ATP7B, SLC31A1, GCSH, LIAS, DLAT, FDX1, DLD, and PDHA1 were increased in the CSRS-Low subtype. •Drug sensitivity analyses revealed potential therapeutic compounds for GC with high CSRS scores.
•SeqKit2 expands its capabilities, doubling the number of subcommands from 19 to 38, and adding support for three more compression file formats. •SeqKit2 outperforms its predecessor and maintains competitive with other tools. •SeqKit2 improves user-friendliness with new features, like, autocompletion, progress bars, and enhanced error handling.
•Shaped by both genetic and environmental factors, gut microbiota significantly influences the host’s drug absorption, distribution, metabolism, and excretion (ADME) microenvironment, highlighting the need for a new evaluation system for drug-microbiome interactions. •To investigate the intricate nature of interactions between gut microbiota and drugs in vivo, a novel top-down research approach utilizing germ-free animal models is proposed.
•The progression of Clostridioides difficile infection (CDI) is influenced by various factors, including the use of antibiotics, age, comorbidities, immune gene polymorphisms, and antibody levels. •Immune response plays a critical role in controlling both the course and severity of CDI. •Immunotherapy holds significant promise for advancing both treatment and prevention strategies for CDI. This encompasses the application of monoclonal antibodies, vaccines, and fecal microbiota transplantation (FMT).