Frontiers in Microbiology | Systems Microbiology

Review

Published on 19 Feb 2021

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

in Systems Microbiology

Laura Judith Marcos-Zambrano
Kanita Karaduzovic-Hadziabdic
Tatjana Loncar Turukalo
Piotr Przymus
Vladimir Trajkovik
Oliver Aasmets
Magali Berland
Aleksandra Gruca
Jasminka Hasic
Karel Hron

Frontiers in Microbiology

doi 10.3389/fmicb.2021.634511

93,326 views
340 citations

Original Research

Published on 18 Feb 2021

A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion

in Systems Microbiology

Deeya Saha
Sudip Kundu

Frontiers in Microbiology

doi 10.3389/fmicb.2021.613067

9,505 views
13 citations

Original Research

Published on 17 Feb 2021

Integrated Microbiome and Metabolome Analysis Reveals a Positive Change in the Intestinal Environment of Myostatin Edited Large White Pigs

in Systems Microbiology

Yangli Pei
Chujie Chen
Yulian Mu
Yalan Yang
Zheng Feng
Bugao Li
Hua Li
Kui Li

Frontiers in Microbiology

doi 10.3389/fmicb.2021.628685

6,988 views
23 citations

Original Research

Published on 17 Feb 2021

Enhanced Ohmyungsamycin A Production via Adenylation Domain Engineering and Optimization of Culture Conditions

in Systems Microbiology

Eunji Kim
Young Eun Du
Yeon Hee Ban
Yern-Hyerk Shin
Dong-Chan Oh
Yeo Joon Yoon

Frontiers in Microbiology

doi 10.3389/fmicb.2021.626881

3,568 views
14 citations

Original Research

Published on 10 Feb 2021

Impact of Temporal pH Fluctuations on the Coexistence of Nasal Bacteria in an in silico Community

in Systems Microbiology

Sandra Dedrick
M. Javad Akbari
Samantha K. Dyckman
Nannan Zhao
Yang-Yu Liu
Babak Momeni

Frontiers in Microbiology

doi 10.3389/fmicb.2021.613109

3,869 views
9 citations

Original Research

Published on 05 Feb 2021

Metagenomics Reveals That Intravenous Injection of Beta-Hydroxybutyric Acid (BHBA) Disturbs the Nasopharynx Microflora and Increases the Risk of Respiratory Diseases

in Systems Microbiology

Jiancheng Qi
Dongjie Cai
Yaocheng Cui
Tianyu Tan
Huawei Zou
Wei Guo
Yue Xie
Hongrui Guo
Shi-Yi Chen
Xiaoping Ma

Frontiers in Microbiology

doi 10.3389/fmicb.2020.630280

5,149 views
9 citations

Original Research

Published on 04 Feb 2021

Introduction of Colonic and Fecal Microbiota From an Adult Pig Differently Affects the Growth, Gut Health, Intestinal Microbiota and Blood Metabolome of Newborn Piglets

in Systems Microbiology

Renli Qi
Zhuo Zhang
Jing Wang
Xiaoyu Qiu
Qi Wang
Feiyun Yang
Jinxiu Huang
Zuohua Liu

Frontiers in Microbiology

doi 10.3389/fmicb.2021.623673

9,398 views
40 citations

Review

Published on 04 Feb 2021

Eradication of Helicobacter pylori and Gastric Cancer: A Controversial Relationship

in Systems Microbiology

Mariagrazia Piscione
Mariangela Mazzone
Maria Carmela Di Marcantonio
Raffaella Muraro
Gabriella Mincione

Frontiers in Microbiology

doi 10.3389/fmicb.2021.630852

35,742 views
106 citations

Original Research

Published on 29 Jan 2021

Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora

in Systems Microbiology

Zuo Wang
Yuannian Yu
Xinyao Li
Hongyan Xiao
Peihua Zhang
Weijun Shen
Fachun Wan
Jianhua He
Shaoxun Tang
Zhiliang Tan

Frontiers in Microbiology

doi 10.3389/fmicb.2021.625857

8,279 views
41 citations

Mini Review

Published on 28 Jan 2021

We Are One: Multispecies Metabolism of a Biofilm Consortium and Their Treatment Strategies

in Systems Microbiology

Ruchika Vinod Joshi
Cindy Gunawan
Riti Mann

Frontiers in Microbiology

doi 10.3389/fmicb.2021.635432

15,328 views
75 citations

Perspective

Published on 22 Jan 2021

Combating Antimicrobial Resistance Through Student-Driven Research and Environmental Surveillance

in Systems Microbiology

Erica R. Fuhrmeister
Jennifer R. Larson
Adam J. Kleinschmit
James E. Kirby
Amy J. Pickering
Carol A. Bascom-Slack

Frontiers in Microbiology

doi 10.3389/fmicb.2021.577821

9,072 views
15 citations

Original Research

Published on 21 Jan 2021

Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches

in Systems Microbiology

Sokratis Stergiadis
Irene Cabeza-Luna
Marina Mora-Ortiz
Robert D. Stewart
Richard J. Dewhurst
David J. Humphries
Mick Watson
Rainer Roehe
Marc D. Auffret

Frontiers in Microbiology

doi 10.3389/fmicb.2020.590441

10,177 views
24 citations

Original Research

Published on 21 Jan 2021

A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

in Systems Microbiology

Lydia Luise Bach
Asha Ram
Umer Z. Ijaz
Thomas J. Evans
Jan Lindström

Frontiers in Microbiology

doi 10.3389/fmicb.2020.573969

5,747 views
27 citations

Original Research

Published on 21 Jan 2021

DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors

in Systems Microbiology

Lezheng Yu
Fengjuan Liu
Yizhou Li
Jiesi Luo
Runyu Jing

Frontiers in Microbiology

doi 10.3389/fmicb.2021.605782

5,104 views
15 citations

Technology and Code

Published on 21 Jan 2021

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts

in Systems Microbiology

Beibei Wang
Huayi Yang
Jianan Sun
Chuhao Dou
Jian Huang
Feng-Biao Guo

Frontiers in Microbiology

doi 10.3389/fmicb.2021.593979

6,069 views
7 citations

Review

Published on 20 Jan 2021

The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions

in Systems Microbiology

Enrica Pessione

Frontiers in Microbiology

doi 10.3389/fmicb.2020.571417

5,553 views
15 citations

Original Research

Published on 20 Jan 2021

Students’ Experiences of Working With a Socio-Scientific Issues-Based Curriculum Unit Using Role-Playing to Negotiate Antibiotic Resistance

in Systems Microbiology

Konstantin J. Sagmeister
Christoph W. Schinagl
Suzanne Kapelari
Pamela Vrabl

Frontiers in Microbiology

doi 10.3389/fmicb.2020.577501

9,288 views
26 citations

Original Research

Published on 14 Jan 2021

Organic Acids as Alternatives for Antibiotic Growth Promoters Alter the Intestinal Structure and Microbiota and Improve the Growth Performance in Broilers

in Systems Microbiology

Dong Dai
Kai Qiu
Hai-jun Zhang
Shu-geng Wu
Yan-ming Han
Yuan-yuan Wu
Guang-hai Qi
Jing Wang

Frontiers in Microbiology

doi 10.3389/fmicb.2020.618144

12,600 views
82 citations

Original Research

Published on 14 Jan 2021

Integrative Analysis of Whole Genome Sequencing and Phenotypic Resistance Toward Prediction of Trimethoprim-Sulfamethoxazole Resistance in Staphylococcus aureus

in Systems Microbiology

Dennis Nurjadi
Elfi Zizmann
Quan Chanthalangsy
Klaus Heeg
Sébastien Boutin

Frontiers in Microbiology

doi 10.3389/fmicb.2020.607842

5,596 views
25 citations

Original Research

Published on 14 Jan 2021

The Therapeutic Efficacy of Curcumin vs. Metformin in Modulating the Gut Microbiota in NAFLD Rats: A Comparative Study

in Systems Microbiology

Ruifang Li
Yurong Yao
Pengfei Gao
Shurui Bu

Frontiers in Microbiology

doi 10.3389/fmicb.2020.555293

12,278 views
59 citations

Review

Published on 14 Jan 2021

Probiotics and MicroRNA: Their Roles in the Host–Microbe Interactions

in Systems Microbiology

Ying Zhao
Yan Zeng
Dong Zeng
Hesong Wang
Mengjia Zhou
Ning Sun
Jinge Xin
Abdul Khalique
Danish Sharafat Rajput
Kangcheng Pan

Frontiers in Microbiology

doi 10.3389/fmicb.2020.604462

13,246 views
54 citations

Original Research

Published on 13 Jan 2021

A Culturally Responsive Curricular Revision to Improve Engagement and Learning in an Undergraduate Microbiology Lab Course

in Systems Microbiology

Karla S. Fuller
Camila Torres Rivera

Frontiers in Microbiology

doi 10.3389/fmicb.2020.577852

5,986 views
11 citations

Original Research

Published on 13 Jan 2021

Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles

in Systems Microbiology

Jennifer M. DeBruyn
Katharina M. Hoeland
Lois S. Taylor
Jessica D. Stevens
Michelle A. Moats
Sreejata Bandopadhyay
Stephen P. Dearth
Hector F. Castro
Kaitlin K. Hewitt
Shawn R. Campagna

Frontiers in Microbiology

doi 10.3389/fmicb.2020.608856

18,039 views
42 citations

Original Research

Published on 12 Jan 2021

Effects of Rare Microbiome Taxa Filtering on Statistical Analysis

in Systems Microbiology

Quy Cao
Xinxin Sun
Karun Rajesh
Naga Chalasani
Kayla Gelow
Barry Katz
Vijay H. Shah
Arun J. Sanyal
Ekaterina Smirnova

Frontiers in Microbiology

doi 10.3389/fmicb.2020.607325

28,266 views
158 citations

1,790 articles

articles

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion

Integrated Microbiome and Metabolome Analysis Reveals a Positive Change in the Intestinal Environment of Myostatin Edited Large White Pigs

Enhanced Ohmyungsamycin A Production via Adenylation Domain Engineering and Optimization of Culture Conditions

Impact of Temporal pH Fluctuations on the Coexistence of Nasal Bacteria in an in silico Community

Metagenomics Reveals That Intravenous Injection of Beta-Hydroxybutyric Acid (BHBA) Disturbs the Nasopharynx Microflora and Increases the Risk of Respiratory Diseases

Introduction of Colonic and Fecal Microbiota From an Adult Pig Differently Affects the Growth, Gut Health, Intestinal Microbiota and Blood Metabolome of Newborn Piglets

Eradication of Helicobacter pylori and Gastric Cancer: A Controversial Relationship

Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora

We Are One: Multispecies Metabolism of a Biofilm Consortium and Their Treatment Strategies

Combating Antimicrobial Resistance Through Student-Driven Research and Environmental Surveillance

Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches

A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts

The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions

Students’ Experiences of Working With a Socio-Scientific Issues-Based Curriculum Unit Using Role-Playing to Negotiate Antibiotic Resistance

Organic Acids as Alternatives for Antibiotic Growth Promoters Alter the Intestinal Structure and Microbiota and Improve the Growth Performance in Broilers

Integrative Analysis of Whole Genome Sequencing and Phenotypic Resistance Toward Prediction of Trimethoprim-Sulfamethoxazole Resistance in Staphylococcus aureus

The Therapeutic Efficacy of Curcumin vs. Metformin in Modulating the Gut Microbiota in NAFLD Rats: A Comparative Study

Probiotics and MicroRNA: Their Roles in the Host–Microbe Interactions

A Culturally Responsive Curricular Revision to Improve Engagement and Learning in an Undergraduate Microbiology Lab Course

Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles

Effects of Rare Microbiome Taxa Filtering on Statistical Analysis