Frontiers in Microbiology | Systems Microbiology

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

1,296 views

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

1,884 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

1,936 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

1,528 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

1,467 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

1,521 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

1,338 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

1,919 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

2,790 views
1 citation

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

2,068 views

Editorial

Published on 11 Nov 2025

Editorial: Resources for developing plasmid databases

in Systems Microbiology

Haruo Suzuki
Masato Suzuki
Masaki Shintani

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1719919

865 views

Original Research

Published on 11 Nov 2025

1DCNN-BiLSTM-transformer hypertension risk prediction model based on APW

in Systems Microbiology

Yan Peng
Lu Ma
Huiyu Zhou
Jiao Li
Jie Wang

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1714654

1,455 views

Correction

Published on 06 Nov 2025

Correction: Microbiome and metabolome integrated analysis: exploring potential diagnostic approaches for Parkinson's disease using tongue coating samples

in Systems Microbiology

Runjuan Yang
Mengqi Jia
Ying Xu
Zhenghua Wu
Dongying Wu
Yaxing Gui

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1721341

1,131 views

Editorial

Published on 03 Nov 2025

Editorial: Investigating the role of microorganisms in ecosystems and their interactions with the humans, animals, plants, and environment interface

in Systems Microbiology

Wen-Jun Li
Juan M. Gonzalez
Bhagwan Narayan Rekadwad

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1710906

1,557 views

Original Research

Published on 30 Oct 2025

Rapid and accurate recognition of erythrocytic stage parasites of Plasmodium falciparum via a deep learning-based YOLOv3 platform

in Systems Microbiology

Wei He
Huiyin Zhu
Junjie Geng
Daiqian Zhu
Kai Wu
Li Xie
Jian Li
Hailin Yang

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1471436

1,927 views

Original Research

Published on 27 Oct 2025

Dynamic multi-omics mechanisms underpinning retinol tolerance: stage-specific reconstruction of skin barrier function and host–microbiome metabolic interactions

in Systems Microbiology

Yixuan Huang
Qi Zhou
Minyan Gui
Danni Guo
Jingmin Cheng
Wentao Ma
Peng Shu
Xiao Liu

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1668712

2,342 views

Original Research

Published on 17 Oct 2025

Microbial cross contamination in household laundering and microbial ecology of household washing machines

in Systems Microbiology

Kelly Whitehead
Jake Eppinger
Vanita Srinivasan
Juan A. Ugalde

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1667606

4,251 views

Original Research

Published on 14 Oct 2025

Spatiotemporal dynamics of Bacillus anthracis under climate change: a machine learning approach

in Systems Microbiology

Sameh M. H. Khalaf
Monerah S. M. Alqahtani
Yousef A. Selim
Kenoz O. Elsayed
Hager A. Bendary

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1659876

2,644 views

Original Research

Published on 10 Oct 2025

Exploring the fungal community structure and assembly in different tissues of Gymnadenia conopsea

in Systems Microbiology

Xiu Yin
Yazhou Lu
Hong Quan
Erhao Zhang
Zhongbin Wang

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1640133

1,589 views

Original Research

Published on 06 Oct 2025

Microbial-driven valorization of tannery sludge for fatty acids production: unraveling microbiome activity and functional redundancy

in Systems Microbiology

Barbara Tonanzi
Alessio Massimi
Francesco Valentino
Giulia Adele Tuci
Marco Gottardo
Simona Rossetti
Simona Crognale

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1675618

2,908 views

Original Research

Published on 03 Oct 2025

Stage-specific fecal and salivary microbiota signatures for noninvasive detection of colorectal cancer

in Systems Microbiology

Zhenzhen Wu
Zhenzheng Zhu
Chenxi Zhou
Zhenyi Lin
Hujia Yang
Guanjun Jiang
Shuning Ding
Jieru Yu
Leitao Sun

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1658693

2,261 views

Systematic Review

Published on 01 Oct 2025

Beyond just correlation: causal machine learning for the microbiome, from prediction to health policy with econometric tools

in Systems Microbiology

Issam Khelfaoui
Wenxin Wang
Hicham Meskher
Akram Ismael Shehata
Mohammed F. El Basuini
Mohamed F. Abouelenein
Houssem Eddine Degha
Mayada Alhoshy
Islam I. Teiba
Seedahmed S. Mahmoud

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1691503

3,100 views
1 citation

Review

Published on 30 Sep 2025

Potential and application of Fusobacterium nucleatum in the diagnosis and treatment of colorectal cancer

in Systems Microbiology

Xin He
Qing Zhao
Jianhong Zhang
Jing Shi
Ningyi Wan
Bin Tang
Bo Tian
Pu Li

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1652702

4,346 views
1 citation

Original Research

Published on 30 Sep 2025

Parkin overexpression modulates gut-microbiota composition during aging in Drosophila melanogaster

in Systems Microbiology

Larisa Sarghie
Paula Istvan
Ricardo Aparicio
David W. Walker
Robi Tacutu
Marius Surleac

Frontiers in Microbiology

doi 10.3389/fmicb.2025.1672083

2,891 views

1,789 articles

articles

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

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

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

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

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

Editorial: Resources for developing plasmid databases

1DCNN-BiLSTM-transformer hypertension risk prediction model based on APW

Correction: Microbiome and metabolome integrated analysis: exploring potential diagnostic approaches for Parkinson's disease using tongue coating samples

Editorial: Investigating the role of microorganisms in ecosystems and their interactions with the humans, animals, plants, and environment interface

Rapid and accurate recognition of erythrocytic stage parasites of Plasmodium falciparum via a deep learning-based YOLOv3 platform

Dynamic multi-omics mechanisms underpinning retinol tolerance: stage-specific reconstruction of skin barrier function and host–microbiome metabolic interactions

Microbial cross contamination in household laundering and microbial ecology of household washing machines

Spatiotemporal dynamics of Bacillus anthracis under climate change: a machine learning approach

Exploring the fungal community structure and assembly in different tissues of Gymnadenia conopsea

Microbial-driven valorization of tannery sludge for fatty acids production: unraveling microbiome activity and functional redundancy

Stage-specific fecal and salivary microbiota signatures for noninvasive detection of colorectal cancer

Beyond just correlation: causal machine learning for the microbiome, from prediction to health policy with econometric tools

Potential and application of Fusobacterium nucleatum in the diagnosis and treatment of colorectal cancer

Parkin overexpression modulates gut-microbiota composition during aging in Drosophila melanogaster