•We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98Mb new sequences absent from the reference genome. •We find a significant portion of the detected structural variants were derived from transposable element (TE) activity. Many of these are located within gene bodies or regulatory regions, potentially linked to duck domestication and enhancement. •We used two representative examples to show how TE insertions can lead phenotypic diversity, highlighting IGF2BP1’s role in bodyweight and MITF’s influence on white plumage in ducks. •Notably, the Gypsy insertion in the IGF2BP1 promoter, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation).
•CBD2 integrates biomarkers derived from diverse biological sources and clinical applications, employing a standardized approach for annotation and classification. •CBD2 facilitates precision medicine in colorectal cancer by providing abundant data, including drug–target information and visualized network analysis functions. •With its user-friendly interface, CBD2 aids in the identification and development of biomarkers for colorectal cancer.
•Gut microbiota has been acknowledged as key regulators in host-mediated anticancer immune response especially during immunotherapy, and antibiotics-induced dysbiosis often leads to resistance to immunotherapy and poor clinical outcomes. •Although the mechanisms underlying gut microbiota-mediated potentiating efficacy while ameliorating side effects of immunotherapy differs across bacteria genus and immunotherapy types, it’s generally via enhancing anticancer immunity and remodulating the tumor microenvironment. •We reviewed the commensal bacteria profiles associated with responders to immunotherapy in various cancer types, characterized by a high diversity with abundance of specific species, which may help predict patients; sensitivity to immunotherapy before treatment. •Since the causal relationship between individual gut microbiota and response to immunotherapy, we propose gut microbiota act as the future therapeutic target and adjuvant in personalized anticancer regimen, and reviewed the current dilemma and potential strategies to manipulate gut microbiota towards “beneficial bacteria.”
•Essential genes are crucial for organism survival and development, which have been identified using various experimental methods across different organisms, providing valuable resources for studying their characteristics and developing predictive algorithms. •The database of essential genes (DEG) collects experimental results on essential genes and serves as a widely used resource for studying them. It enables quick access to essential gene information for specific species and has applications in essential gene analysis, prediction, drug and vaccine design, and artificial genome construction. •The definition of essential genes is context-dependent, not a simple binary classification. Integrating different experimental results of essential genes is challenging but offers opportunities to explore gene interaction mechanisms.
•Exposure to livestock-associated environment, more microbially enriched than school environment, can remodel the human skin microbiome and antibiotic resistome. •The 5 h of exposure is sufficient to alter the microbiota and antibiotic resistance genes (ARGs) structure of skin and these changes were retained once formed. •ARGs carried by host microbes were transferred between the environment and workers’ skin.
•Significant differences in microbial composition and potential functional capacity among different gut locations were found in Jinhua pigs with distinct fatness phenotypes. •Jinhua pigs with lower fatness exhibited higher levels of short-chain fatty acids in the colon, highlighting their enhanced carbohydrate fermentation capacity. •Clostridium butyricum might be a representative bacterial species from Jinhua pigs with lower fatness, and a significantly higher percentage of its genome was dedicated to CAZyme glycoside hydrolase family 13 (GH13). •Isolated C. butyricum alleviated fat accumulation and increased the enrichment of GH13 in obese mice.
•Soil enzyme profile analysis for indicating decomposer micro-food web features was first proposed. •Diversity indication utilities for contrasting enzyme profiles were different. •Protozoa channel index and enzymatic channel index were proposed.
•Graph neural networks (GNNs)-based biology-contextualized computational framework exhibited superior performance in identifying coexpressed gene panels and decrypting wavelength-dependent denitrification. •Wet-lab demonstrations validated the wavelength-divergent secretion system and nitrate-superoxide co-regulation as unveiled by GNNs, which could be utilized for nitrate removal and resource recovery. •The coexpressed gene panels and topological network toolkits were developed to guide scientific discovery and versatile biotechnology development.
•Supplementation with glucomannan alleviates insulin resistance. •Glucomannan promotes the growth of Bacteroides ovatus, accompanied by improved intestinal barrier integrity and reduced systemic inflammation. •B. ovatus-derived indoleacetic acid is a key bioactive metabolite that fortifies intestinal barrier function via the activation of intestinal aryl hydrocarbon receptor.
•The black rice diet (BRD) can slow down the development of colorectal tumors in ApcMin/+ and azoxymethane/dextran sulfate sodium (AOM/DSS) colorectal cancer (CRC) model mice. •The BRD increases the abundance of intestinal probiotics, such as Bacteroides uniformis and Lactobacillus, while reducing potential intestinal pathogens. •The upregulated metabolites indole and indole-3-lactic acid in BRD are ligands of the aryl hydrocarbon receptor (AHR) pathway, which slow down the development of CRC by activating intestinal AHR receptor gene expression. •A moderate consumption of BRD is expected to become a potential strategy for the prevention and treatment of CRC by improving gut microbiota and metabolites.
•Wekemo Bioincloud offers not just workflows for diverse meta-omics data analysis but also a rich array of tools for effective data visualization. •Enables modifying vector outputs online, achieving publication-ready figures. •Displays tools’ popularity/usage trends, enhancing the platform’s flexibility and user-friendly experience.