Shuang-Jiang Liu
Principal Investigator, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
Dr. Liu’s research interest covers environmental microbiology, microbial cultivation and gut microbiomes.
Jingyuan Fu
Professor, University of Groningen, The Netherlands
Dr. Fu’s research is focused on integrative genomics and host-microbe interactions in complex diseases.
James M. Tiedje
Michigan State University, USA
Yong-Guan Zhu
Institute of Urban Environment Chinese Academy of Sciences
Jun Yu
Chinese University of Hong Kong
Ji-Zheng He
The University of Melbourne, Australia
Hans-Peter Grossart
Leibniz Institute for Freshwater Ecology and Inland Fisheries, Germany
Shuang-Jiang Liu
Principal Investigator, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
Dr. Liu’s research interest covers environmental microbiology, microbial cultivation and gut microbiomes.
Jingyuan Fu
Professor, University of Groningen, The Netherlands
Dr. Fu’s research is focused on integrative genomics and host-microbe interactions in complex diseases.
James M. Tiedje
Michigan State University, USA
Yong-Guan Zhu
Institute of Urban Environment Chinese Academy of Sciences
Jun Yu
Chinese University of Hong Kong
Ji-Zheng He
The University of Melbourne, Australia
Hans-Peter Grossart
Leibniz Institute for Freshwater Ecology and Inland Fisheries, Germany
Most recent articles
RESEARCH ARTICLE
Open access

Comammox Nitrospira act as key bacteria in weakly acidic soil via potential cobalamin sharing

  •  04 February 2025
Description unavailable

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.

CORRESPONDENCE
Open access

The HTIRDB: A resource containing a transcriptional atlas for 105 different tissues from each of seven species of domestic herbivore

  •  28 January 2024
Description unavailable

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.

METHOD
Open access

Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree

  •  12 January 2024
Description unavailable

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.

RESEARCH ARTICLE
Open access

The prognostic and therapeutic significance of polyunsaturated fatty acid-derived oxylipins in ST-segment elevation myocardial infarction

  •  09 January 2024
Description unavailable

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.

CORRESPONDENCE
Open access

Gut microbiota in treating inflammatory digestive diseases: Current challenges and therapeutic opportunities

  •  31 December 2024
Description unavailable

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.

COMMENTARY
Open access

Integrating gut and IgA-coated microbiota to identify Blautia as a probiotic for enhancing feed efficiency in chickens

  •  23 December 2024
Description unavailable

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.

CORRESPONDENCE
Open access

EGDB: A comprehensive multi-omics database for energy grasses and the epigenomic atlas of pearl millet

  •  28 December 2024
Description unavailable

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.

SHORT COMMUNICATION
Open access

Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp

  •  08 May 2023
Description unavailable

Fastp is a widely adopted tool for FASTQ data preprocessing and quality control. It is ultrafast and versatile and can perform adapter removal, global or quality trimming, read filtering, unique molecular identifier processing, base correction, and many other actions within a single pass of data scanning. Fastp has been reconstructed and upgraded with some new features. Compared to fastp 0.20.0, the new fastp 0.23.2 is even 80% faster.

SHORT COMMUNICATION
Open access

ImageGP: An easy‐to‐use data visualization web server for scientific researchers

  •  21 February 2022
Description unavailable

Representative visualization results of ImageGP. ImageGP supports 16 types of images and four types of online analysis with up to 26 parameters for customization. ImageGP also contains specialized plots like volcano plot, functional enrichment plot for most omics-data analysis, and other 4 specialized functions for microbiome analysis. Since 2017, ImageGP has been running for nearly 5 years and serving 336,951 visits from all over the world. Together, ImageGP (http://www.ehbio.com/ImageGP/) is an effective and efficient tool for experimental researchers to comprehensively visualize and interpret data generated from wet-lab and dry-lab.

SHORT COMMUNICATION
Open access

Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data

  •  28 September 2022
Description unavailable

The ggtree object is designed to store phylogenetic tree and associated data, and the object itself is a graphic object that can be rendered as an image file. This work will increase the reproducibility and reusability of phylogenetic data, as well as facilitate integrative and comparative studies.

PROTOCOL
Open access

Using PhyloSuite for molecular phylogeny and tree-based analyses

  •  16 February 2023
Description unavailable

A new release of PhyloSuite, capable of conducting tree-based analyses. Detailed guidelines for each step of phylogenetic and tree-based analyses, following the “What? Why? and How?” structure. This protocol will help beginners learn how to conduct multilocus phylogenetic analyses and help experienced scientists improve their efficiency.