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
EDITORIAL
Open access

ChatGPT and generative AI are revolutionizing the scientific community: A Janus-faced conundrum

  •  27 February 2024
Description unavailable

The advent of generative artificial intelligence (AI) technologies marks a transformative moment for the scientific sphere, unlocking novel avenues to elevate scientific writing's efficiency and quality, expedite insight discovery, and enhance code development processes. Essential to leveraging these advancements is prompt engineering, a method that enhances AI interaction efficiency and quality. Despite its benefits, effective application requires blending researchers' expertise with AI, avoiding overreliance. A balanced strategy of integrating AI with independent critical thinking ensures the advancement and quality of scientific research, leveraging innovation while maintaining research integrity.

RESEARCH ARTICLE
Open access

From mechanism to application: Decrypting light-regulated denitrifying microbiome through geometric deep learning

  •  06 January 2024
Description unavailable

This study proposed and showcased the discover–model–learn–advance (DMLA) cycle for unlocking nature as codebases to empower biological mechanisms decryption and biotechnology development. At the discovering stage, we found the bidirectionally light-regulated denitrification. Then, metatranscriptomic was utilized for geometric deep learning to obtain coexpressed gene panels. On the basis of that, we developed toolkits to learn underlying mechanisms and advance biotechnology, which were validated in the wet lab. Deepening recognition can further drive continuous DMLA cycles to accelerate scientific and biotechnology development.

RESEARCH ARTICLE
Open access

Changes in seminal plasma microecological dynamics and the mechanistic impact of core metabolite hexadecanamide in asthenozoospermia patients

  •  25 January 2024
Description unavailable

In the onset of asthenozoospermia (AZS), the presence of six genera of bacteria (Pseudomonas, Serratia, Methylobacterium-Methylorubrum, Uruburuella, Vibrio, and Pseudoalteromonas) in the seminal plasma potentially induces dynamic changes that ultimately diminish the synthesis of hexadecanamide. This reduction in hexadecanamide content in seminal plasma contributes to a subsequent decline in sperm motility. This reduced motility can be attributed to the downregulation of the levels of two key proteins, PAOX and CA2, within sperm cells.

REVIEW ARTICLE
Open access

Promising dawn in the management of pulmonary hypertension: The mystery veil of gut microbiota

  •  01 January 2024
Description unavailable

With the rapid development of technologies, including metagenomic and nontargeted or targeted metabolomics, the knowledge of gut microbiota and their related metabolites is constantly growing. Dysfunctions of microorganisms are associated with cardiovascular diseases, and gut microbiota and its associated metabolites are also involved in the pathogenesis of pulmonary hypertension. In addition, pulmonary hypertension might result in the alteration of bacterial flora. Here, we provide a comprehensive landscape of gut microbiota and metabolites in pulmonary hypertension, emphasizing the interplay between microorganisms and hosts in modulating pulmonary hypertension.

RESEARCH ARTICLE
Open access

Storage-D: A user-friendly platform that enables practical and personalized DNA data storage

  •  21 January 2024
Description unavailable

Deoxyribonucleic acid (DNA) has been suggested as a very promising medium for data storage in recent years. Although numerous studies have advocated for DNA data storage, its practical application remains obscure and there is a lack of a user-oriented platform. Here, we developed a DNA data storage platform, named Storage-D, which modularized essential functions for DNA data storage and provided personalized codec choices for users. A new codec algorithm called “Wukong” was specially designed and integrated into the tool, which outperforms previous algorithms in key practical application considerations. By connecting to commercial DNA synthesis and sequencing platform with “Storage-D,” “Diagnosis and treatment protocol for COVID-19 patients” was successfully stored in DNA both in vitro and in vivo. This platform allows for practical and personalized DNA data storage, potentially with a wide range of applications. The web server and codes of the platform are available at http://storage.dailab.xyz:16666/ and https://github.com/DNAstorage-iSynBio/Storage-D/, respectively.

REVIEW ARTICLE
Open access

Intestinal flora and pregnancy complications: Current insights and future prospects

  •  22 January 2024
Description unavailable

Gut microbiota is crucial for a healthy pregnancy, being affected by factors such as hormones, diet, obesity, nicotine, antibiotics, and microplastics. This article emphasizes the impact of gut microbiome changes on pregnancy complications and outcomes, delving into the underlying mechanisms and potential gut microbe-based therapies. Additionally, it explores the contentious issue of bacterial presence in the uterine environment. FGR, fetal growth restriction; HT, hypothyroidism in pregnancy; ICP, intrahepatic cholestasis of pregnancy; PE, pre-eclampsia; GDM, gestational diabetes mellitus; PROM, premature rupture of membranes; PTB, preterm birth.

COMMENTARY
Open access

PHGD: An integrative and user-friendly database for plant hormone-related genes

  •  08 January 2024
Description unavailable

Plant Hormone Gene Database (PHGD) database platform construction pipeline. First, we collected all reported hormone-related genes in the model plant Arabidopsis thaliana, and combined with the existing experimental background, mapped the hormone–gene interaction network to provide a blueprint. Next, we collected 469 high-quality plant genomes. Then, bioinformatics was used to identify hormone-related genes in these plants. Finally, these genetic data were programmed to be stored in a database and a platform website PHGD was built. PHGD was divided into eight modules, namely Home, Browse, Search, Resources, Download, Tools, Help, and Contact. We provided data resources and platform services to facilitate the study of plant hormones.

REVIEW ARTICLE
Open access

Recent advances in the characterization of essential genes and development of a database of essential genes

  •  02 January 2024
Description unavailable

Essential genes are indispensable for the survival and development of organisms, and have been successfully identified using various experimental methods across diverse organisms. DEG, a database of essential genes is dedicated to collecting experimental results on essential genes and has become one of the most commonly used tools for studying essential genes, where the information on essential genes for a specific species can be quickly accessed, with a broad range of applications, such as essential gene feature analysis and prediction, drug and vaccine design, as well as artificial genome design and construction. The definition of essential genes is environment-specific rather than simple binary, which should not be overlooked in the study of essential genes.

REVIEW ARTICLE
Open access

Gut microbiota reshapes cancer immunotherapy efficacy: Mechanisms and therapeutic strategies

  •  01 January 2024
Description unavailable

The role of gut microbiota in cancer immunotherapy. Through manipulation of commensals in cancer patients by diet interventions, fecal microbial transplant, prebiotics, probiotics and bacteria consortia, host antitumor immunity can be enhanced by dominance of “beneficial” bacteria in gut lumen and their metabolites. Increased effector T cells and induction of regulatory T cells (Tregs) can be seen in gut-associated lymphoid tissue, which leads to improved clinical outcomes of cancer immunotherapy with lower incidence of immune-related adverse events (fecal microbiota transplant; perforin; granzyme B; Treg).

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.