Original Research

Published on 16 Oct 2023

Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics

in Systems Microbiology

David Gómez-Varela
Feng Xian
Sabrina Grundtner
Julia Regina Sondermann
Giacomo Carta
Manuela Schmidt

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1258703

4,778 views
22 citations

Original Research

Published on 12 Oct 2023

Transcriptomic and metabolomic analyses to study the key role by which Ralstonia insidiosa induces Listeria monocytogenes to form suspended aggregates

in Systems Microbiology

Xifeng Zuo
Meilin Chen
Xinshuai Zhang
Ailing Guo
Si Cheng
Rong Zhang

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1260909

2,098 views

Original Research

Published on 10 Oct 2023

Casual effects of gut microbiota on risk of infections: a two-sample Mendelian randomization study

in Systems Microbiology

Beibei Lyu
Jinghang Ma
Yongyu Bai
Zhen Feng

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1284723

3,246 views
4 citations

Original Research

Published on 09 Oct 2023

Returning ryegrass to continuous cropping soil improves soil nutrients and soil microbiome, producing good-quality flue-cured tobacco

in Systems Microbiology

Hanjun Zhou
Mingjie Zhang
Jiahao Yang
Jing Wang
Yulu Chen
Xiefeng Ye

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1257924

2,185 views
5 citations

Technology and Code

Published on 06 Oct 2023

plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph

in Systems Microbiology

Janik Sielemann
Katharina Sielemann
Broňa Brejová
Tomáš Vinař
Cedric Chauve

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1267695

3,087 views
2 citations

Original Research

Published on 06 Oct 2023

Causal relationship between Butyricimonas and allergic asthma: a two-sample Mendelian randomization study

in Systems Microbiology

Wei Wan
Yi Qiu
Xinyi Huang
Yingxiang Ren
Andi Peng
Chunping Yang

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1190765

3,383 views
1 citation

Original Research

Published on 05 Oct 2023

Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment

in Systems Microbiology

Sebastian L. Singleton
Edward W. Davis
Holly K. Arnold
An Mei Y. Daniels
Susanne M. Brander
Rachel J. Parsons
Thomas J. Sharpton
Stephen J. Giovannoni

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1259014

3,527 views
5 citations

Mini Review

Published on 05 Oct 2023

Overview of data preprocessing for machine learning applications in human microbiome research

in Systems Microbiology

Eliana Ibrahimi
Marta B. Lopes
Xhilda Dhamo
Andrea Simeon
Rajesh Shigdel
Karel Hron
Blaž Stres
Domenica D’Elia
Magali Berland
Laura Judith Marcos-Zambrano

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1250909

5,301 views
9 citations

Methods

Published on 03 Oct 2023

Culturing the Plastisphere: comparing methods to isolate culturable bacteria colonising microplastics

in Systems Microbiology

Emily M. Stevenson
Angus Buckling
Matthew Cole
Penelope K. Lindeque
Aimee K. Murray

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1259287

5,878 views
7 citations

Original Research

Published on 29 Sep 2023

Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

in Systems Microbiology

Mitiku Mihiret Seyoum
Amanda J. Ashworth
Kristina M. Feye
Steven C. Ricke
Phillip R. Owens
Philip A. Moore
Mary Savin

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1227006

3,579 views

Original Research

Published on 28 Sep 2023

Application of multi-omic features clustering and pathway enrichment to clarify the impact of vitamin B2 supplementation on broiler caeca microbiome

in Systems Microbiology

Carlo Mengucci
Simone Rampelli
Gianfranco Picone
Alex Lucchi
Gilberto Litta
Elena Biagi
Marco Candela
Gerardo Manfreda
Patrizia Brigidi
Francesco Capozzi

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1264361

1,465 views
1 citation

Correction

Published on 27 Sep 2023

Corrigendum: Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov., two IAA-producing novel rare bacterial species inhabiting desert biological soil crusts

in Systems Microbiology

Zhu-Ming Jiang
Yang Deng
Xue-Fei Han
Jing Su
Hao Wang
Li-Yan Yu
Yu-Qin Zhang

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1285950

882 views

Original Research

Published on 27 Sep 2023

Machine learning strategy for identifying altered gut microbiomes for diagnostic screening in myasthenia gravis

in Systems Microbiology

Che-Cheng Chang
Tzu-Chi Liu
Chi-Jie Lu
Hou-Chang Chiu
Wei-Ning Lin

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1227300

2,587 views
4 citations

Review

Published on 26 Sep 2023

Gut macrobiotic and its metabolic pathways modulate cardiovascular disease

in Systems Microbiology

Junwen Zhu
Jin Lyu
Ruochi Zhao
Gang Liu
Shuangshuang Wang

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1272479

4,044 views
2 citations

Review

Published on 22 Sep 2023

Machine learning approaches in microbiome research: challenges and best practices

in Systems Microbiology

Georgios Papoutsoglou
Sonia Tarazona
Marta B. Lopes
Thomas Klammsteiner
Eliana Ibrahimi
Julia Eckenberger
Pierfrancesco Novielli
Alberto Tonda
Andrea Simeon
Rajesh Shigdel

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1261889

11,288 views
24 citations

Editorial

Published on 19 Sep 2023

Editorial: Soil microbe-arthropod interactions under global change

in Systems Microbiology

Rentao Liu
Bing Yang

Frontiers in Microbiology

doi 10.3389/fmicb.2023.1280103

1,098 views

Navigation group

Articles

Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics

Transcriptomic and metabolomic analyses to study the key role by which Ralstonia insidiosa induces Listeria monocytogenes to form suspended aggregates

Casual effects of gut microbiota on risk of infections: a two-sample Mendelian randomization study

Returning ryegrass to continuous cropping soil improves soil nutrients and soil microbiome, producing good-quality flue-cured tobacco

plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph

Causal relationship between Butyricimonas and allergic asthma: a two-sample Mendelian randomization study

Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment

Overview of data preprocessing for machine learning applications in human microbiome research

Culturing the Plastisphere: comparing methods to isolate culturable bacteria colonising microplastics

Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

Application of multi-omic features clustering and pathway enrichment to clarify the impact of vitamin B2 supplementation on broiler caeca microbiome

Corrigendum: Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov., two IAA-producing novel rare bacterial species inhabiting desert biological soil crusts

Machine learning strategy for identifying altered gut microbiomes for diagnostic screening in myasthenia gravis

Gut macrobiotic and its metabolic pathways modulate cardiovascular disease

Machine learning approaches in microbiome research: challenges and best practices

Editorial: Soil microbe-arthropod interactions under global change