In this study, we comprehensively profiled plasma oxylipin alterations in patients with ST-segment elevation myocardial infarction (STEMI) with and without recurrent major adverse cardiovascular events (MACE) in a prospective cohort (n = 645) with 2 years of follow-up. Using a multivariate random forest algorithm, we identified a panel of 14 oxylipin markers that showed powerful performance in predicting recurrent MACE. The predictive performance of the oxylipin marker panel was confirmed in an independent external validation cohort (n = 401). Using functional metabolomics strategies, we found that six anti-inflammatory/pro-resolving oxylipin combinations had synergistic and cardioprotective effects on a murine model of myocardial ischemia‒reperfusion injury. Mechanistically, we demonstrated that inflammatory/pro-resolving oxylipins could reinstate the synthesis of ceramides and lysophosphatidylcholines and ameliorate inflammatory responses. Collectively, our studies highlight the great potential of bioactive oxylipins in prognostic prediction and therapeutics after STEMI.

In this study, we examine the disruption of microbial ecological interactions, as reflected by co-abundances, in relation to hypertension and its severity in a large-scale, population-based cohort from the Guangdong Gut Microbiome Project (GGMP, n = 6999). We characterized 581 hypertension-related co-abundances that are robust against comorbidities and exhibit a 68.7% replication rate in two independent cohorts. Notably, 40.3% of genera without significant differential abundance, yet they contribute to majority (68.2%) of the hypertension-related co-abundances. Additionally, 14.1% of these co-abundances varied across different hypertension grades, with the strength of 21 differential co-abundances significantly associated with hypertension severity, including key ecology niches dominated by Comamonas and Ruminococcaceae. Importantly, the interactions between microbes in these co-abundances contribute extra variance to hypertension-related pathways, such as tryptophan degradation, methionine, and O-antigen biosynthesis.

EasyMetagenome is a user-friendly shotgun metagenomics pipeline designed for comprehensive microbiome analysis, supporting quality control, host removal, read-based, assembly-based, binning, genome and pan-genome analysis. It offers customizable settings, data visualizations, and parameter explanations. The pipeline is freely available at https://github.com/YongxinLiu/EasyMetagenome.

Comammox Nitrospira are the dominant ammonia oxidizers in weakly acidic soil. They are the K-strategy species in weakly acidic soil and may promote bacterial cooperation under low pH conditions via cobalamin sharing.

We present a multi-organ single-cell, spatial transcriptomics, and BA omics atlas of specific pathogen-free (SPF) and germ-free (GF) mice. We found plasma cell aggregation displays significant tissue heterogeneity depending on the gut microbiota. GF mice exhibit impaired follicular and marginal zone B cell maturation, linked to microbiota-mediated modulation of Cr2 gene expression. The microbiota regulates the development and survival of neutrophils in the bone marrow, influences the development and differentiation of T cells in the thymus, and modulates intraepithelial γδ T cell composition and lipid absorption in the small intestine. The absence of microbiota in GF mice alters the intestinal mucosa zonation and triggers coordinated dynamics in intestinal lipid absorption, transport, chylomicron synthesis, lipid droplet formation, lipolysis, and fatty acid oxidation in the small intestine enterocytes. The liver microbiota-dependent zinc finger and BTB domain-containing protein (ZBTB20)-Lipoprotein lipase (LPL) axis plays a role in plasma lipid homeostasis.

Alterations in gut microbial composition and fecal metabolome have been reported in patients with gallstones. The gut microbiota plays a crucial role in shaping the host's fecal metabolic profile. Specifically, metabolites of amino acids, fatty acids, and nicotinic acid may affect the synthesis, transport, or metabolism of cholesterol, thereby impacting gallstone formation. Oral administration of C. glycyrrhizinilyticum can promote histological liver damage and affect liver lipid metabolism, contributing to cholesterol gallstone formation. Fructooligosaccharides can be a new, cost-effective, and relatively simple microbiota-targeted therapeutic approach for cholesterol gallstones. Microbiome-targeted therapies, involving the modulation of gut microbiota, should be explored as potential treatments for gallstones.

We have intensively searched existing literature repositories and databases. Using microbial disturbance as a robust index, we systematically revealed the complex relationships among dietary fiber, microbiota, and diseases. Key challenges include quantifying the multi-taxonomic microbiota disturbances induced by dietary fibers or disease onset, as well as determining the associations between dietary fibers and diseases. We developed the Bio-taxonomic Hierarchy Weighted Aggregation algorithm and generated a candidate list of dietary fibers with therapeutic potential. Notably, several of these fibers have been validated by previous studies, clinical trials, or our murine models, which underscores their relevance in potential therapeutic applications.

MicrobiomeStatPlots is a comprehensive platform for microbiome data analysis and visualization, offering bioinformatics tips, integrating multi-omics pipelines, and featuring 82 visualization and interpretation cases. The platform allows users to customize the code and encourages contributions to expand its content, with plans for future updates. This platform is available at https://github.com/YongxinLiu/MicrobiomeStatPlot.

The treeio and ggtree packages provide robust tools for the comprehensive parsing and visualization of phylogenetic placement data. These tools enable detailed analyses, including placement filtration and uncertainty assessment, thereby facilitating deeper insights into evolutionary relationships within metagenomic datasets.

The concept of “gut–X axis”: the intestine and intestinal microbiota are proven to be able to modulate the pathophysiologic progressions of the extraintestinal organs' diseases. The bioactive chemicals and/or intestinal immune cells can translocate into the circulatory system and other organs and influence the immune reactions, metabolic status, cells physiology, and so forth of extraintestinal organs, finally regulating these organs' homeostasis. Meanwhile, other organs may reversely impact the intestine, namely such regulatory axis is bidirectional.

This study explores the role of IgA-coated bacteria in improving feed efficiency in chickens, offering a novel perspective for probiotic screening. Chickens with high feed efficiency were found to have a greater abundance of Gram-positive bacteria, while low feed efficiency chickens exhibited higher levels of Gram-negative bacteria and potential pathogens. Through fecal microbiota transplantation (FMT) and integrating analysis of cecal and IgA-coated microbiota, we precisely identified Blautia as a key genus linked to improved feed efficiency. Further validation demonstrated that Blautia coccoides, a representative species of this genus, enhances feed efficiency and activates B cells to produce Immunoglobulin A (IgA), both in vivo and in vitro. Our findings provide new insights into the potential of IgA-coated bacteria as functional probiotics, offering a promising strategy for enhancing feed efficiency in animal production.

Given the key role of energy grasses in biomass energy, electricity, biofuels, and carbon sequestration, the Energy Grass Omics Database (EGDB) integrates germplasm data with genomics, transcriptomics, epigenomics, and phenomics data to support functional genomic research on diverse energy grass species. EGDB also currently supplies the largest epigenetic data set of energy grasses: a high-resolution chromatin modification, chromatin accessibility, and gene expression landscape of pearl millet to provide insights into regulatory traits essential for sustainable energy production.

Accumulating evidence indicates that the gut microbiota is intricately involved in the initiation and progression of human diseases, forming a multidirectional regulatory axis centered on intestinal microbiota. This article illustrates the challenges in exploring the role of the gut microbiota in inflammatory digestive diseases, such as metabolic dysfunction-associated steatotic liver disease (MASLD) and inflammatory bowel disease (IBD), and summarizes the existing microbiome-focused treatment strategies (probiotics, prebiotics, symbiotics, fecal microbiota transplantation, and bacteriophages therapy), emerging technologies (gut microbiome-on-a-chip and artificial intelligence), as well as possible future research directions. Taken together, these therapeutic strategies and technologies present both opportunities and challenges, which require researchers and clinicians to test the rationality and feasibility of various therapeutic modalities in continuous practice.

Here, we describe the Herbivore Transcriptome Integrated Resource Database (HTIRDB, https://yanglab.hzau.edu.cn/HTIRDB#/). The HTIRDB comprises the self-generated transcriptomic data from 100 to 105 tissues from two female domestic herbivores from six species (cattle, donkey, goat, horse, rabbit, and sika deer) and two breeds of sheep, and an extra 28,710 related published datasets. The HTIRDB user-friendly interface provides tools and functionalities that facilitate the exploration of gene expression between tissues and species. The tools for comparative transcriptomics can be used to identify housekeeping genes, tissue-specific genes, species-specific genes, and species-conserved genes. To date, the HTIRDB is the most extensive transcriptome data resource for domestic herbivores that is freely available.

Hypertriglyceridemia (HTG) can lead to the disorder of gut microbiota in mice, resulting in the increase of endotoxin content. HTG can also aggravate the damage of intestinal barrier function and intestinal bacterial translocation in acute pancreatitis (AP) mice. Toll-like receptor 4 gene (Tlr4) knockout can significantly reduce gut permeability and endotoxin invasion in AP mice. In addition, HTG-modulated gut microbiota could up-regulate glycerophospholipid metabolism and increase lysophosphatidylcholine (LysoPC) content in a TLR4-dependent manner, thereby aggravating pancreatic injury in AP.