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
Short Communication
Open access

Establishing a novel inflammatory bowel disease prediction model based on gene markers identified from single nucleotide variants of the intestinal microbiota

  •  24 July 2022
Description unavailable

Specific gene characteristics based on SNVs were identified in intestinal microbiota genes of IBD patients. A novel diagnostic method for predicting IBD was established. F. prausnitzii showed decreased abundance in different diseases and different mutation sites within genes.

Research Article
Open access

TCM2COVID: A resource of anti-COVID-19 traditional Chinese medicine with effects and mechanisms

  •  05 August 2022
Description unavailable

TCM2COVID documents over 280 traditional Chinese medicine formulas (including over 300 herbs) with detailed clinical evidence and therapeutic mechanism information; TCM2COVID records over 80 natural products with detailed potential therapeutic mechanisms; TCM2COVID launches a useful web server for querying, analyzing, and visualizing documented formulas similar to those supplied by the user (formula similarity analysis).

Research Article
Open access

StrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

  •  01 August 2022
Description unavailable

Strain-level Pangenome Decomposition Analysis (StrainPanDA) uses the pangenome coverage profile of multiple metagenomic samples to simultaneously reconstruct the composition and gene content variation of coexisting strains in microbial communities. StrainPanDA allows accurate and robust inference of strain composition and gene content profiles on synthetic data sets. Linked reconstruction of strain composition and gene content profiles provided by StrainPanDA furthers our understanding of the relationship between microbial adaptation and strain-specific functions (e.g., nutrient utilization and pathogenicity).

Commentary
Open access

Impact of tobacco smoking on oral cancer genetics—A next-generation sequencing perspective

  •  04 August 2022
Description unavailable

This study identified a total of 28 genetic loci (comprising 31 genes), which were found to be altered in oral cancer patients having a habit of tobacco smoking. Three loci, that is, 17p13.1 (TP53), 9p21.3 (CDKN2A), and 9q34.3 (NOTCH1) were found to be modified and common in three records whereas one locus, that is, 3q26.32 (PIK3CA) was found to be modified and common in two records. This study suggests that oral cancer patients should be categorized into different subgroups based on (i) genetic signatures, and (ii) smoking status, then the treatment strategies for each group should be precisely defined.

Protocol
Open access

Complex heatmap visualization

  •  01 August 2022
Description unavailable

Complex heatmap is a powerful visualization method for revealing associations between multiple sources of information. We have developed an R package named ComplexHeatmap that provides comprehensive functionalities for heatmap visualization. It has been widely used in the bioinformatics community. We give a comprehensive introduction to the current state of ComplexHeatmap in this article.

Commentary
Open access

Sangerbox: A comprehensive, interaction-friendly clinical bioinformatics analysis platform

  •  08 July 2022
Description unavailable

Sangerbox with a user-friendly interface supports differential analysis, correlation analyses, pathway enrichment analysis, weighted correlation network analysis, and so on. A new interactive plotting system that allows users to adjust the parameters in the image. It has organized GEO, TCGA, ICGC, and other databases; a rapid batch processing reduces the difficulty in data acquirement, greatly improving the efficiency.

Perspective
Open access

Are short-read amplicons suitable for the prediction of microbiome functional potential? A critical perspective

  •  04 July 2022
Description unavailable

We raise concerns regarding the biological validity of predicting functional potential from microbiome taxonomic profiles generated by short-read amplicon sequencing. We reason that predicted functional potential profiles can be improved by employing long-read sequencing technologies, which in combination with independent measurements of actual functions can constitute a powerful approach to understanding microbiome functioning.

Research Article
Open access

Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana

  •  13 June 2022
Description unavailable

Parasitic weed growth is influenced by microbes in the sunflower rhizosphere. The germination of Orobanche cumana seeds can be facilitated by Lysobacter antibioticus HX79 metabolites. The molecular docking strategy can be used for screening active chemicals.

Research Article
Open access

Biochar stimulates tomato roots to recruit a bacterial assemblage contributing to disease resistance against Fusarium wilt

  •  23 June 2022
Description unavailable

Biochar enhances the disease suppressiveness of tomato rhizosphere microbiome. Biochar stimulates tomato to actively recruit plant-beneficial bacterial taxa. The ability of tomato root exudates to recruit beneficial bacteria is enhanced by biochar.

Protocol
Open access

A painless way to customize Circos plot: From data preparation to visualization using TBtools

  •  04 July 2022
Description unavailable

An out-of-the-box solution for genome-scale data visualization. A step-by-step protocol for Circos plot configuration. Reproducible and resumable project management

Review Article
Open access

Dynamics, gene transfer, and ecological function of intracellular and extracellular DNA in environmental microbiome

  •  20 June 2022
Description unavailable

Extracellular or intracellular DNA (e/iDNA) extensively exists in soil environment. e/iDNA indicates the functional gene variety and microbial activity. e/iDNA can transform into each other biologically. e/iDNA is essential for nutrient transformation and gene communication.

Research Article
Open access

ggClusterNet: An R package for microbiome network analysis and modularity-based multiple network layouts

  •  13 June 2022
Description unavailable

ggClusterNet is an R package for microbial networks analysis and interpretation. Ten network layout algorithms allow users more alternatives to plot the network and generate published-ready figures. It is free to access on GitHub and Gitee.

Review Article
Open access

The human lung microbiome—A hidden link between microbes and human health and diseases

  •  16 June 2022
Description unavailable

Sputum, bronchoalveolar lavage, bronchial brushing, and lung tissue are the routine sample types for the lung microbiome. Multiomics have been increasingly applied for characterizing the lung microbiome. Lung microbiome is broadly implicated in chronic and acute lung diseases, lung cancer, and other lung diseases, with potential mechanistic implications. Current challenges of the lung microbiome studies include low microbial-to-host ratio, high disease heterogeneity, and the difficulty in precisely manipulating and culturing the lung microbiome. Future potential topics for lung microbiome studies include understanding the diagnostic potential of the lung microbiome, its spatial dynamics, its mechanistic interaction with the host, and the crosstalk between the lung and distal organs.