Frontiers in Microbiology | Systems Microbiology

Review

Published on 18 Dec 2025

Mechanisms of gut microbiota in host fat deposition: metabolites, signaling pathways, and translational applications

in Systems Microbiology

Sha Liu

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1675155

294 views

Original Research

Accepted on 16 Dec 2025

Feeding Patterns Reprogram a Gut Microbial Virulence–Iron–Quorum Sensing Functional Axis Linked to Atherosclerotic Risk

in Systems Microbiology

He Zhang
Keyu Chen
Renjin Chen
Erteng Jia

Frontiers in Microbiology

182 views

Mini Review

Accepted on 15 Dec 2025

Pharmacomicrobiomics in Inflammatory Skin Disease: Past, Present, and the Future

in Systems Microbiology

Juna Khang
Rebeca Martinez
Katherine Brag
Jean McGee

Frontiers in Microbiology

103 views

Original Research

Published on 15 Dec 2025

Third-generation sequencing reveals the spatial variation of microbial composition of airborne bacteria in an intensive dairy farm

in Systems Microbiology

Qianqian Zhang
Luyu Ding
Xueying Xie
Lin Ru
Qifeng Li
Chunxia Yao
Johann Solkner
Ruixiang Jiang

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1688472

359 views

Original Research

Published on 15 Dec 2025

Gut microbiota dysbiosis impairs TGF-β/Smad4 signaling to drive postoperative metastasis in colorectal cancer

in Systems Microbiology

Tongtong Lan
Qilong Hou
Huichao Zhao
Yiman Luan
Yuying Shi
Shengrui Hu
Ningrui Wang
Shiyu Yan
Xinyi Gong
Yang Song

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1654227

431 views

Original Research

Published on 15 Dec 2025

Gut microbiome associated with melanin deposition by supporting energy metabolism in Sichuan mountainous black-bone chickens

in Systems Microbiology

Juan Liao
Ling Duan
Gang Wang
Shigang Yu
Xuemei Shen
Min Jiang
Ke Shen
Rajeev K. Singla
Bairong Shen
Yi Zhou

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1682376

798 views

Review

Accepted on 11 Dec 2025

A comprehensive comparison of web-based tools for amplicon-metagenomic analysis

in Systems Microbiology

Yuhe Kan
Xiao-Yu Ma
Yi-Lu Wang
Baiye Sun
Shoule Wang

Frontiers in Microbiology

147 views

Original Research

Published on 11 Dec 2025

Effect of IFN-τ on intestinal flora and metabolomics of Escherichia coli-mediated endometritis in mice

in Systems Microbiology

Pan Liu
Yaofeng Zhang
Xu Chen
Lijun Tang
Wenxiu Xu
Guigui Wang
Duoqi Zhang
Junfeng Liu

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1687781

717 views

Original Research

Published on 11 Dec 2025

Integrated transcriptomic and metabolomic analyses reveal the antibacterial mechanism of isocorydine against Mycobacterium bovis

in Systems Microbiology

Xia Wang
Weichao Ma
Yijun Yuan
Xiang Gao
Tianyu Zhao
Peng Wang
Yanmei Liu
Tingpu Wang

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1717499

473 views

Systematic Review

Published on 10 Dec 2025

Efficacy and safety of probiotics as a complementary treatment for urticaria: a systematic review and meta-analysis

in Systems Microbiology

Danni Tan
Ke Liao
Yunfeng Yu
Yuman Yin
Lina Qin
Qin Xiang
Rong Yu

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1634990

691 views

Review

Published on 10 Dec 2025

Understanding gut microbial diversity using systems based on the Constrained-Disorder Principle provides a novel approach to targeting gut microbiome therapies

in Systems Microbiology

Ofer Perzon
Yaron Ilan

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1713775

414 views

Original Research

Accepted on 09 Dec 2025

The application value and limitations of metagenomic detection technology based on cerebrospinal fluid samples in suspected central nervous system infection: a retrospective study

in Systems Microbiology

Qiujuan Feng
Baoyi Liu
Huazhao Liu
Yaqin Fan
Shanshan Gao
Jia Zhang
Yingjie Kuang
Wenshan Wang
Huiqiang Liang
Yulan Qiu

Frontiers in Microbiology

Original Research

Published on 08 Dec 2025

Spatial microbiome-metabolic crosstalk drives CD8+ T-cell exhaustion through the butyrate-HDAC axis in colorectal cancer

in Systems Microbiology

Xiaoyang Chen
Yinxu Zhang
Guangyu Zhang
Dai Wang
Linhua Dou
Yuxi Wang
Zining Huang
Xiaomei Liu

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1704491

718 views

Perspective

Published on 05 Dec 2025

Generative AI in microbial evolution and resistance: toward robust, explainable, and equitable predictions

in Systems Microbiology

Fahim Sufi

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1705320

1,026 views

Original Research

Accepted on 03 Dec 2025

Comparison between metatranscriptomics and viral metagenomics, 16S and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response

in Systems Microbiology

Grégory Destras
M Sabatier
Antonin BAL
B Simon
Q Semanas
H Regue
T Boyer
D Ploin
Yves Gillet
B Lina

Frontiers in Microbiology

223 views

Original Research

Published on 03 Dec 2025

Multi-omics reveals novel forage advantages of Potentilla anserina Linnaeus in high-salt habitats

in Systems Microbiology

Zhijia Cui
Xiaoling Zhang
Ziyang Lv
Shangkun Yang
Miaomiao Zhang
Hanghang Hou
Jing Li
Yuhao Yuan
Junqiao Li
Baili Feng

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1659904

904 views

Review

Published on 27 Nov 2025

Bacterial colonization of bone substitute materials used in oral surgery: mechanisms, clinical implications, and preventive strategies—A narrative review

in Systems Microbiology

Wojciech Popowski
Damian Koseski
Dominika Domanowska
Magdalena Zalewska
Magdalena Popowska

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1715632

822 views

Perspective

Accepted on 26 Nov 2025

Without Safeguard, AI-Bio Integration Risks Accelerating Future Pandemics

in Systems Microbiology

Dianzhuo Wang
Marian Huot
Zechen Zhang
Kaiyi Jiang
Eugene I. Shakhnovich
Kevin M. Esvelt

Frontiers in Microbiology

236 views

Original Research

Published on 26 Nov 2025

Comparative metagenomic analysis on COPD and health control samples reveals taxonomic and functional motifs

in Systems Microbiology

Guangyi Chen
Chantal Wiegand
Andreas Willett
Christian Herr
Rolf Müller
Robert Bals
Olga V. Kalinina

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1636322

823 views

Original Research

Accepted on 24 Nov 2025

Gene and Function Diversity-Area Relationships (DAR) in the Inflammatory Bowel Disease (IBD) Fecal and Mucosal Microbiome

in Systems Microbiology

Fubing Yu
Song Jiyang
Linyi Qi
Jinghua Liu
Yintiantian Yang
Wendy Li
Lianwei Li
Zhanshan Ma

Frontiers in Microbiology

130 views

Original Research

Published on 24 Nov 2025

Tripartite exacerbation stratification in AECOPD suggests a gradient of lower airway dysbiosis: a metagenomic transition from commensal taxa to pseudomonadota dominance

in Systems Microbiology

Yunxia An
Min Xu
Yi Kang
Jinzhou Fang
Xiaoju Zhang

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1588029

795 views

Original Research

Published on 20 Nov 2025

Genetically engineered Pseudomonas aeruginosa with lipase regulation for production of rhamnolipids from waste frying oil

in Systems Microbiology

Runyu Yang
Yitong Shi
Jinyu Bian
Mengxiao Sun
Junchi Ma
Cailing Ren
Xueyan Feng
Yun Wang
Yuanhui Yang
Jianqiang Zhou

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1691217

1,247 views

Review

Published on 12 Nov 2025

The “gut microbiota-ferroptosis axis”: a hypothesis for osteoarthritis pathogenesis and therapeutic implications

in Systems Microbiology

Tao Wang
Yuanze Xu
Haorui Zha
Lianguo Wu

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1685962

1,673 views

Original Research

Published on 12 Nov 2025

Microbiome-metabolome dysbiosis of bronchoalveolar lavage fluid of lung cancer patients

in Systems Microbiology

Jing Wang
Wei Su
Qin Chen
Jiemin Zhou
Xinyue Wang
Richeng Jiang
Junling Li
Puyuan Xing

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1669172

1,178 views

1,780 articles

articles

Mechanisms of gut microbiota in host fat deposition: metabolites, signaling pathways, and translational applications

Feeding Patterns Reprogram a Gut Microbial Virulence–Iron–Quorum Sensing Functional Axis Linked to Atherosclerotic Risk

Pharmacomicrobiomics in Inflammatory Skin Disease: Past, Present, and the Future

Third-generation sequencing reveals the spatial variation of microbial composition of airborne bacteria in an intensive dairy farm

Gut microbiota dysbiosis impairs TGF-β/Smad4 signaling to drive postoperative metastasis in colorectal cancer

Gut microbiome associated with melanin deposition by supporting energy metabolism in Sichuan mountainous black-bone chickens

A comprehensive comparison of web-based tools for amplicon-metagenomic analysis

Effect of IFN-τ on intestinal flora and metabolomics of Escherichia coli-mediated endometritis in mice

Integrated transcriptomic and metabolomic analyses reveal the antibacterial mechanism of isocorydine against Mycobacterium bovis

Efficacy and safety of probiotics as a complementary treatment for urticaria: a systematic review and meta-analysis

Understanding gut microbial diversity using systems based on the Constrained-Disorder Principle provides a novel approach to targeting gut microbiome therapies

The application value and limitations of metagenomic detection technology based on cerebrospinal fluid samples in suspected central nervous system infection: a retrospective study

Spatial microbiome-metabolic crosstalk drives CD8+ T-cell exhaustion through the butyrate-HDAC axis in colorectal cancer

Generative AI in microbial evolution and resistance: toward robust, explainable, and equitable predictions

Comparison between metatranscriptomics and viral metagenomics, 16S and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response

Multi-omics reveals novel forage advantages of Potentilla anserina Linnaeus in high-salt habitats

Bacterial colonization of bone substitute materials used in oral surgery: mechanisms, clinical implications, and preventive strategies—A narrative review

Without Safeguard, AI-Bio Integration Risks Accelerating Future Pandemics

Comparative metagenomic analysis on COPD and health control samples reveals taxonomic and functional motifs

Gene and Function Diversity-Area Relationships (DAR) in the Inflammatory Bowel Disease (IBD) Fecal and Mucosal Microbiome

Tripartite exacerbation stratification in AECOPD suggests a gradient of lower airway dysbiosis: a metagenomic transition from commensal taxa to pseudomonadota dominance

Genetically engineered Pseudomonas aeruginosa with lipase regulation for production of rhamnolipids from waste frying oil

The “gut microbiota-ferroptosis axis”: a hypothesis for osteoarthritis pathogenesis and therapeutic implications

Microbiome-metabolome dysbiosis of bronchoalveolar lavage fluid of lung cancer patients