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
COMMENTARY
Open access

The Microbiome Protocols eBook initiative: Building a bridge to microbiome research

Yunyun Gao, Kai Peng, Defeng Bai, Xiao-Ye Bai, Yujing Bi, Anqi Chen, Baodong Chen, Feng Chen, Juan Chen, Lei Chen, Tong Chen, Wei Chen, Xu Cheng, Yanfen Cheng, Jie Cui, Jingjing Dai, Junbiao Dai, Zhaolai Dai, Ye Deng, Yi-Zhen Deng, Wei Ding, Zhencheng Fang, Wei Fu, Hanbing Gao, Shaohua Gu, Xue Guo, Xuguang Guo, Dongfei Han, Lele He, Yatao He, Hui-Yu Hou, Baolei Jia, Gengjie Jia, Shuo Jiao, Wei Jin, Feng Ju, Zhicheng Ju, Siyuan Kong, Canhui Lan, Bing Li, Da Li, Diyan Li, Jingdi Li, Meng Li, Qi Li, Qiang Li, Wen-Jun Li, Xiaofang Li, Xuemeng Li, Yahui Li, You-Gui Li, Zhibin Liang, Ning Ling, Fufeng Liu, Qing Liu, Shuang-Jiang Liu, Hongye Lu, Qi Lu, Guangwen Luo, Hao Luo, Yuheng Luo, Hujie Lyu, Chuang Ma, Liyuan Ma, Tengfei Ma, Jinfeng Ni, Ziqin Pang, Xiaojing Qiang, Yuan Qin, Qingyue Qu, Chao Ran, Shuqiang Ren, Haitao Shang, Luyang Song, Linyang Sun, Weimin Sun, Liping Tang, Jian Tian, Kai Wang, Mengzhi Wang, Ming-Ke Wang, Tao Wang, Xiao-Yan Wang, Yao Wang, Yiwen Wang, Youshan Wang, Hailei Wei, Hong Wei, Zhong Wei, Tao Wen, Jiqiu Wu, Linhuan Wu, Linkun Wu, Jiao Xi, Bo Xie, Guofang Xu, Jun Xu, Shanshan Xu, Qing Xue, Liping Yan, Haifei Yang, Jun Yang, Junbo Yang, Ruifu Yang, Yalin Yang, Ying-Jie Yang, Xiaofang Yao, Yanpo Yao, Salsabeel Yousuf, Ke Yu, Zhengrong Yuan, Zhilin Yuan, Dong Zhang, Tianyuan Zhang, Weipeng Zhang, Yunzeng Zhang, Zhaonan Zhang, Zhen Zhang, Zhi-Feng Zhang, Shengguo Zhao, Wei Zhao, Maosheng Zheng, Ziqiang Zheng, Xin Zhou, Yuanping Zhou, Zhigang Zhou, Mo Zhu, Yong-Guan Zhu, Haiyan Chu, Yang Bai, Yong-Xin Liu
  •  11 March 2024
Description unavailable

The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. The first edition, launched in 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend a sincere invitation to researchers to participate in the upcoming 2nd version of MPB, contributing their valuable protocols to advance microbiome research.

RESEARCH ARTICLE
Open access

The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus

  •  11 March 2024
Description unavailable

Sanghuangporus is a medical mushroom with potent anticolitic effects. It modulates the gut microbiota and specifically enriches Alistipes onderdonkii, which can produce 5-hydroxyindole-3-acetic acid, thus activating the aryl hydrocarbon receptor pathway and ameliorating colitis.

COMMENTARY
Open access

Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs

  •  13 March 2024
Description unavailable

The administration of oral antidiabetic drugs (OADs) to patients with type 2 diabetes elicits distinct and shared changes in the gut microbiota, with acarbose and berberine exhibiting greater impacts on the gut microbiota than metformin, vildagliptin, and glipizide. The baseline gut microbiota strongly associates with treatment responses of OADs.

RESEARCH ARTICLE
Open access

Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life

  •  31 January 2024
Description unavailable

We infer that the maturation of infant resistome is not a random change but a programmed modification in the gut microbiome, which is due to resistance genes being disproportionally distributed across taxa. The decline of overall resistance is possibly due to the diminishment of Pseudomonadota, which is often equipped with antimicrobial resistance genes (ARGs), whereas the transition into table food creates a nutritional niche for Bacteriodota in the infant gut, which is a relatively small reservoir of resistance genes. The maturation of gut resistome is driven by infants’ changing carbohydrate metabolism, which demonstrated an increasing need for carbohydrate-active enzymes from Bacteroidota and decreasing involvements from Pseudomonadota during infancy. AA, auxiliary activities; CAZy, carbohydrate-active enzymes; GH, glycoside hydrolases; GT, glycosyltransferases; PL, polysaccharide lyases.

REVIEW ARTICLE
Open access

“Nutrient–fungi–host” tripartite interaction in cancer progression

  •  26 January 2024
Description unavailable

Interactions between nutrient and fungi in cancer development and treatment remain under investigation. In this article, we aim to provide insights into the relationships between fungi and various categories of cancer, mediated by diverse nutrient sensing pathways of fungi in response to external environment. Moreover, we highlight the potential application of fungi-targeted strategies in precision nutrition for both cancer prevention and treatment.

RESEARCH ARTICLE
Open access

Photoaffinity probe-based antimalarial target identification of artemisinin in the intraerythrocytic developmental cycle of Plasmodium falciparum

  •  19 February 2024
Description unavailable

Here, both the covalent and noncovalent binding targets of artemisinin at different stages of the intraerythrocytic developmental cycle of Plasmodium falciparum were identified using a photoaffinity probe. The results suggest that interfering with the protein synthesis, glycolysis, and oxidative homeostasis pathways of parasites underlies the antimalarial effects of artemisinin. ABPP, activity-based protein profiling; APP, artemisinin photoaffinity probe; ART, artemisinin; RBC, red blood cell; UV, ultraviolet.

RESEARCH ARTICLE
Open access

Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae

  •  13 February 2024
Description unavailable

We present a comprehensive exploration of Lachnospiraceae, leveraging an extensive cultured-based genome collection. Phylogenetic analysis reveals previously underestimated taxonomic diversity. A thorough gene set analysis, comprising a 1.5 M gene catalog, sheds light on the functional richness of Lachnospiraceae. Notably, exploration of short-chain fatty acid synthesis pathways highlights their synthetic potential, with strains displaying distinct capacities for butyrate and propionate production. Disease association analysis establishes correlations between Lachnospiraceae strains and atherosclerotic cardiovascular disease and inflammatory bowel disease, offering valuable insights into their potential roles in human health and disease.

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

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.

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.