Frontiers in Microbiology | Systems Microbiology

Original Research

Published on 19 Jul 2024

Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs

in Systems Microbiology

Bojana Banović Đeri
Sofija Nešić
Ivan Vićić
Jelena Samardžić
Dragana Nikolić

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1401985

5,732 views
2 citations

Original Research

Published on 18 Jul 2024

Gut microbiota causally affects drug-induced liver injury via plasma metabolites: a Mendelian randomization study

in Systems Microbiology

Haoshuang Fu
Shuang Zhao
Shuying Song
Qing Xie

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1432049

4,803 views
8 citations

Original Research

Published on 17 Jul 2024

The effect of gut microbiome and plasma metabolome on systemic sclerosis: a bidirectional two-sample Mendelian randomization study

in Systems Microbiology

Shasha Xie
Qiming Meng
Lin Wang

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1427195

2,910 views
3 citations

Editorial

Published on 17 Jul 2024

Editorial: Combining machine learning, computational modeling, and high throughput experimentation to accelerate discovery in systems microbiology

in Systems Microbiology

Miguel Fuentes-Cabrera
Paolo Zuliani
Bowen Li
Jared L. Wilmoth
Aivett Bilbao
Alice C. Dohnalkova

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1451243

1,793 views

Original Research

Published on 16 Jul 2024

Age-correlated changes in the canine oral microbiome

in Systems Microbiology

Gregory Kislik
Lin Zhou
Liudmilla Rubbi
Matteo Pellegrini

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1426691

4,149 views
6 citations

Original Research

Published on 15 Jul 2024

Gut microbiota, plasma metabolites, and osteoporosis: unraveling links via Mendelian randomization

in Systems Microbiology

Yi Lu
Xiaobing Cai
Baohua Shi
Haitao Gong

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1433892

6,854 views
8 citations

Original Research

Published on 12 Jul 2024

Causal effects of gut microbiota on risk of interstitial cystitis: a two-sample Mendelian randomization study

in Systems Microbiology

Jianguo Gao
Sihai Shao
Yuefan Shen

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1434117

3,412 views
1 citation

Original Research

Published on 12 Jul 2024

The causal relationship between gut microbiota and alopecia areata: a Mendelian randomization analysis

in Systems Microbiology

Dezhao Bi
Jin Tong Tey
Dan Yao
Yutian Cao
Minyu Qian
Jianxin Shi
Shun Guo

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1431646

5,519 views
4 citations

Editorial

Published on 10 Jul 2024

Editorial: Untangle the broad connections and tight interactions between human microbiota and complex diseases through data-driven approaches, volume II

in Systems Microbiology

Qi Zhao
Zuo-Bin Zhu
Jian Li
Li Zhang
Liang Wang

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1449474

1,549 views

Original Research

Published on 03 Jul 2024

Viability-PCR for the selective detection of Lactobacillus acidophilus and Bifidobacterium bifidum in live bacteria-containing products

in Systems Microbiology

Stefania Catone
Serena Iannantuono
Domenico Genovese
Christina Von Hunolstein
Giovanna Franciosa

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1400529

4,316 views
5 citations

Review

Published on 19 Jun 2024

Microbiome modeling: a beginner's guide

in Systems Microbiology

Emanuel Lange
Lena Kranert
Jacob Krüger
Dirk Benndorf
Robert Heyer

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1368377

12,295 views
13 citations

Original Research

Published on 19 Jun 2024

Proof of concept: real-time viability and metabolic profiling of probiotics with isothermal microcalorimetry

in Systems Microbiology

Carlotta Morazzoni
Madle Sirel
Serena Allesina
Marta Veses Garcia
Kasper Kragh
Marco Pane
Katrin Beilharz

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1391688

3,920 views
9 citations

Original Research

Published on 12 Jun 2024

Specific cultivation-independent enumeration of viable cells in probiotic products using a combination of fluorescence in situ hybridization and flow cytometry

in Systems Microbiology

Laura Snaidr
Peter Mühlhahn
Claudia Beimfohr
Christian Kreuzer
Carolin Richly
Jiri Snaidr

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1410709

6,126 views
7 citations

Original Research

Published on 04 Jun 2024

Genetically supported causality between gut microbiota, immune cells, and ischemic stroke: a two-sample Mendelian randomization study

in Systems Microbiology

Han Shuai
Zi Wang
Yinggang Xiao
Yali Ge
Hua Mao
Ju Gao

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1402718

3,493 views
4 citations

Original Research

Published on 03 Jun 2024

Explainable artificial intelligence and microbiome data for food geographical origin: the Mozzarella di Bufala Campana PDO Case of Study

in Systems Microbiology

Michele Magarelli
Pierfrancesco Novielli
Francesca De Filippis
Raffaele Magliulo
Pierpaolo Di Bitonto
Domenico Diacono
Roberto Bellotti
Sabina Tangaro

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1393243

2,822 views
9 citations

Original Research

Published on 30 May 2024

Genomic and functional diversity of the human-derived isolates of Faecalibacterium

in Systems Microbiology

Wenxi Li
Xiaoqian Lin
Hewei Liang
Zhinan Wu
Mengmeng Wang
Jingxi Sun
Xiaofang Li
Wenxin He
Xiaowei Gao
Tongyuan Hu

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1379500

6,749 views
14 citations

Methods

Published on 30 May 2024

A GLM-based zero-inflated generalized Poisson factor model for analyzing microbiome data

in Systems Microbiology

Jinling Chi
Jimin Ye
Ying Zhou

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1394204

3,976 views
1 citation

Original Research

Published on 30 May 2024

Identification of microbial diversity in buried ivory soil at the Sanxingdui site in Guanghan City, China, using high-throughput sequencing

in Systems Microbiology

Siyu Sun
Zhe Xu
Mengjia Ren
Sifan Li
Zhenbin Xie
Yanbing Luo
Yongqiang Tian

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1384650

3,066 views
5 citations

Systematic Review

Published on 29 May 2024

Oropharyngeal cancer and human papillomavirus: a visualization based on bibliometric analysis and topic modeling

in Systems Microbiology

Zhu Liu
Haixu Wang
Yang Xu
Hongming Wei
Yuchong Zhang
Huilei Dong

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1387679

3,272 views
2 citations

Original Research

Published on 23 May 2024

Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics

in Systems Microbiology

Meina Yang
Hongxia Deng
Siyu Zhou
Danhua Lu
Xiaoyang Shen
Lu Huang
Yan Chen
Liangzhi Xu

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1373077

6,071 views
11 citations

Original Research

Published on 23 May 2024

LCASPMDA: a computational model for predicting potential microbe-drug associations based on learnable graph convolutional attention networks and self-paced iterative sampling ensemble

in Systems Microbiology

Zinuo Yang
Lei Wang
Xiangrui Zhang
Bin Zeng
Zhen Zhang
Xin Liu

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1366272

2,153 views
6 citations

Opinion

Published on 20 May 2024

The invisible life

in Systems Microbiology

Francesca Guerrieri
Cédric Libert

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1401487

3,057 views

Original Research

Published on 15 May 2024

Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis

in Systems Microbiology

Priyansha Raj Sinha
Rami Balasubramanian
Shubhada R. Hegde

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1335310

4,881 views
1 citation

Original Research

Published on 10 May 2024

Bacterial–fungal interactions and response to heavy metal contamination of soil in agricultural areas

in Systems Microbiology

Jia Li
Qiwen Zheng
Jiangyun Liu
Shuwei Pei
Zhen Yang
Rentong Chen
Li Ma
Jingping Niu
Tian Tian

Frontiers in Microbiology

doi 10.3389/fmicb.2024.1395154

4,842 views
21 citations

1,792 articles

articles

Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs

Gut microbiota causally affects drug-induced liver injury via plasma metabolites: a Mendelian randomization study

The effect of gut microbiome and plasma metabolome on systemic sclerosis: a bidirectional two-sample Mendelian randomization study

Editorial: Combining machine learning, computational modeling, and high throughput experimentation to accelerate discovery in systems microbiology

Age-correlated changes in the canine oral microbiome

Gut microbiota, plasma metabolites, and osteoporosis: unraveling links via Mendelian randomization

Causal effects of gut microbiota on risk of interstitial cystitis: a two-sample Mendelian randomization study

The causal relationship between gut microbiota and alopecia areata: a Mendelian randomization analysis

Editorial: Untangle the broad connections and tight interactions between human microbiota and complex diseases through data-driven approaches, volume II

Viability-PCR for the selective detection of Lactobacillus acidophilus and Bifidobacterium bifidum in live bacteria-containing products

Microbiome modeling: a beginner's guide

Proof of concept: real-time viability and metabolic profiling of probiotics with isothermal microcalorimetry

Specific cultivation-independent enumeration of viable cells in probiotic products using a combination of fluorescence in situ hybridization and flow cytometry

Genetically supported causality between gut microbiota, immune cells, and ischemic stroke: a two-sample Mendelian randomization study

Explainable artificial intelligence and microbiome data for food geographical origin: the Mozzarella di Bufala Campana PDO Case of Study

Genomic and functional diversity of the human-derived isolates of Faecalibacterium

A GLM-based zero-inflated generalized Poisson factor model for analyzing microbiome data

Identification of microbial diversity in buried ivory soil at the Sanxingdui site in Guanghan City, China, using high-throughput sequencing

Oropharyngeal cancer and human papillomavirus: a visualization based on bibliometric analysis and topic modeling

Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics

LCASPMDA: a computational model for predicting potential microbe-drug associations based on learnable graph convolutional attention networks and self-paced iterative sampling ensemble

The invisible life

Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis

Bacterial–fungal interactions and response to heavy metal contamination of soil in agricultural areas