Metagenomic microbial community profiling using unique clade-specific marker genes

Segata, Nicola, Waldron, Levi, Ballarini, Annalisa, Narasimhan, Vagheesh, Jousson, Olivier, Huttenhower, Curtis·2012·Nature Methods

DOI 10.1038/nmeth.2066

Cited by (1,002)

Items 701–800 of 1,002

Specific metagenomic asset drives the spontaneous fermentation of Italian sausages
Irene Franciosa, Ilario Ferrocino, Manuela Giordano, Jérôme Mounier, Kalliopi Rantsiou, Luca Cocolin · 2021 · Food Research International
Maternal regulation of biliary disease in neonates via gut microbial metabolites
Jai J. Jee, Li Yang, Pranavkumar Shivakumar, Pei-pei Xu, Reena Mourya, Unmesha Thanekar, Pu Yu, Yu Zhu, Yongkang Pan, Haibin Wang et al. · 2022 · Nature Communications
Impact of Exposure to Per- and Polyfluoroalkyl Substances on Fecal Microbiota Composition in Mother-Infant Dyads
Santosh Lamichhane, Taina Härkönen, Tommi Vatanen, Tuulia Hyötyläinen, Mikael Knip, Matej Orešič · 2022 · Environment International
Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants
Fuyong Li, Andre L. A. Neves, Bibaswan Ghoshal, Le Luo Guan · 2017 · Journal of Dairy Science
Using populations of human and microbial genomes for organism detection in metagenomes
Sasha K. Ames, Shea N. Gardner, Jose Manuel Martí, Tom Slezak, Maya B. Gokhale, Jonathan Allen · 2015 · Genome Research
New insight into the gut microbiome through metagenomics
Jens Nielsen, Boyang Ji · 2015 · Advances in Genomics and Genetics
Alterations of intestinal microbiota in liver cirrhosis with muscle wasting
Xiaojing Ren, Shasha Hao, Chuanli Yang, Lili Yuan, Xiaoshuang Zhou, Haoliang Zhao, Jia Yao · 2020 · Nutrition
Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet
Kelsey E. Witt, Karthik Yarlagadda, Julie M. Allen, Alyssa C. Bader, Mary L. Simon, Steven R. Kuehn, Kelly Scott Swanson, Tzu-Wen Cross, Kristin M. Hedman, Stanley H. Ambrose et al. · 2021 · Scientific Reports
Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models
Puzi Jiang, Sicheng Wu, Qibin Luo, Xing‐Ming Zhao, Wei-Hua Chen · 2021 · mSystems
Structure of the manure resistome and the associated mobilome for assessing the risk of antimicrobial resistance transmission to crops
Martyna Buta, Ewa Korzeniewska, Jakub Hubeny, Wiktor Zieliński, Damian Rolbiecki, Monika Harnisz, Łukasz Paukszto · 2021 · The Science of The Total Environment
Metagenomics analysis of probable transmission of determinants of antibiotic resistance from wastewater to the environment – A case study
Wiktor Zieliński, Jakub Hubeny, Martyna Buta, Damian Rolbiecki, Monika Harnisz, Łukasz Paukszto, Ewa Korzeniewska · 2022 · The Science of The Total Environment
A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response
Jordan C. Evans, Valentina Laclare McEneany, Michael J. Coyne, Elizabeth P. Caldwell, Madeline L. Sheahan, Salena S Von, Emily M. Coyne, Rodney K. Tweten, Laurie E. Comstock · 2022 · Nature Communications
Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects
Jonathan T. L. Kang, Jonathan J. Y. Teo, Denis Bertrand, Amanda Hui Qi Ng, Aarthi Ravikrishnan, Melvin Yong, Oon Tek Ng, Kalisvar Marimuthu, Swaine Lin Chen, Kern Rei Chng et al. · 2022 · Nature Microbiology
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
Heiner Klingenberg, Kathrin Petra Aßhauer, Thomas Lingner, Peter Meinicke · 2013 · Bioinformatics
taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
André Corvelo, Wayne E. Clarke, Nicolas Robine, Michael C. Zody · 2018 · Genome Research
Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand
Karlette A. Fernandes, Erica K. Gee, Chris W. Rogers, Sandra Kittelmann, Patrick J. Biggs, Emma N. Bermingham, Charlotte F. Bolwell, David G. Thomas · 2021 · Animals
Maternal high-fat diet-induced microbiota changes are associated with alterations in embryonic brain metabolites and adolescent behaviour
Anna Ratsika, Martín Gabriel Codagnone, Thomaz F. S. Bastiaanssen, Fabiana Andréa Hoffmann Sardá, Caoimhe M. K. Lynch, Ana Paula Ventura‐Silva, Cristina Rosell‐Cardona, Valentina Caputi, Catherine Stanton, Christine Fülling et al. · 2024 · Brain Behavior and Immunity
Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders
Nikolas Dovrolis, George C. Kolios, George M. Spyrou, Ioanna G Maroulakou · 2017 · Briefings in Bioinformatics
Health Outcomes, Pathogenesis and Epidemiology of Severe Acute Malnutrition (HOPE-SAM): rationale and methods of a longitudinal observational study
Mutsa Bwakura‐Dangarembizi, Beatrice Amadi, Claire D. Bourke, Ruairi C. Robertson, Benjamin Mwapenya, Kanta Chandwe, Chanda Kapoma, Kapula Chifunda, Florence D. Majo, Deophine Ngosa et al. · 2019 · BMJ Open
Metagenomic analysis of relationships between the denitrification process and carbon metabolism in a bioaugmented full-scale tannery wastewater treatment plant
S. Aalfin Emmanuel, Woo Jun Sul, Hoon Je Seong, Chaeyoung Rhee, Kalu I. Ekpheghere, In‐Soo Kim, Hong Gi Kim, Sung‐Cheol Koh · 2019 · World Journal of Microbiology and Biotechnology
Mercury contamination imposes structural shift on the microbial community of an agricultural soil
Lateef Babatunde Salam, Halima Shomope, Zainab Ummi, Fatima Bukar · 2019 · Bulletin of the National Research Centre/Bulletin of the National Research Center
Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment
Puzi Jiang, Senying Lai, Sicheng Wu, Xing‐Ming Zhao, Wei-Hua Chen · 2020 · BMC Genomics
White spot syndrome virus (WSSV) disturbs the intestinal microbiota of shrimp (Penaeus vannamei) reared in biofloc and clear seawater
Cecília de Souza Valente, Ana Rodiles, Maria Risoleta Freire Marques, Daniel Lee Merrifield · 2020 · Applied Microbiology and Biotechnology
Intermittent aeration of landfill simulation bioreactors: Effects on emissions and microbial community
Stefano Campanaro, Roberto Raga, Andrea Squartini · 2020 · Waste Management
Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease
Yangliu Xia, J. Wang, Xiaojie Fang, Tongyi Dou, Lijuan Han, Chao Yang · 2021 · Journal of Applied Microbiology
Mode of delivery modulates the intestinal microbiota and impacts the response to vaccination
Emma M. de Koff, Debbie van Baarle, Marlies A. van Houten, Marta Reyman, Guy A. M. Berbers, Femke van den Ham, Mei Ling J. N. Chu, Elisabeth A. M. Sanders, Debby Bogaert, Susana Fuentes · 2022 · Nature Communications
Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes
Aarthi Ravikrishnan, Indrik Wijaya, Eileen Png, Kern Rei Chng, Eliza Xin Pei Ho, Amanda Hui Qi Ng, Ahmad Nazri Mohamed Naim, Jean-Sébastien Gounot, Shou Ping Guan, Jasinda H. Lee et al. · 2024 · Nature Communications
LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes
Niels W. Hanson, Kishori M. Konwar, Steven Hallam · 2016 · Bioinformatics
Resolving Phylogenetic Relationships for Streptococcus mitis and Streptococcus oralis through Core- and Pan-Genome Analyses
Irina M. Velsko, Megan S Perez, Vincent P. Richards · 2019 · Genome Biology and Evolution
WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences
Ahmed A. Metwally, Yang David Dai, Patricia W. Finn, David L. Perkins · 2016 · PLoS ONE
High-resolution sweep metagenomics using fast probabilistic inference
Tommi Mäklin, Teemu Kallonen, Sophia David, Christine J. Boinett, Ben Pascoe, Guillaume Méric, David M. Aanensen, Edward J. Feil, Stephen G. Baker, Julian Parkhill et al. · 2021 · Wellcome Open Research
Toward a dynamical understanding of microbial communities
Paul B. Rainey, Steven D. Quistad · 2020 · Philosophical Transactions of the Royal Society B Biological Sciences
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju
Anna Tovo, Peter Menzel, Anders Krogh, Marco Cosentino Lagomarsino, Samir Simon Suweis · 2020 · Nucleic Acids Research
MetaBCC-LR: metagenomics binning by coverage and composition for long reads
Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin · 2020 · Bioinformatics
Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health
Himani Khurana, Durgesh Narain Singh, Anoop Singh, Yogendra Prakash Singh, Rup Lal, Ram Krishan Negi · 2020 · BMC Microbiology
Emerging carbapenem-resistant Klebsiella pneumoniae sequence type 16 causing multiple outbreaks in a tertiary hospital in southern Vietnam
To Nguyen Thi Nguyen, Phuong Luong Nha Nguyen, Ngan Thi Quynh Le, Lan Phu Huong Nguyen, Duong Bich Thuy, Nghia Ho Dang Trung, Quynh Pham Nhu Nguyen, Trung Duc Pham, Tuan-Anh Tran, Hao Chung The et al. · 2021 · Microbial Genomics
Mechanisms underlying interactions between two abundant oral commensal bacteria
Dasith Perera, Anthony R. McLean, Viviana Morillo-López, Kaileigh Cloutier-Leblanc, Eric Almeida, Kiana Cabana, Jessica L. Mark Welch, Matthew M. Ramsey · 2021 · The ISME Journal
Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies
Rebecca M. Lebeaux, Juliette C. Madan, Quang P. Nguyen, Modupe Oluseun Coker, Erika F. Dade, Yuka Moroishi, Thomas J. Palys, Benjamin D. Ross, Melinda M. Pettigrew, Hilary G. Morrison et al. · 2022 · Pediatric Research
Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation duringHelicobacter PyloriTreatment
Bumjo Oh, Ji Won Kim, Bong Soo Kim · 2016 · Helicobacter
Forensic analysis using microbial community between skin bacteria and fabrics
So-Yeon Lee, Seung‐Kyun Woo, So‐Min Lee, Yong‐Bin Eom · 2016 · Toxicology and Environmental Health Sciences
An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics
Jiaxian Shen, Alexander G. McFarland, Ryan A. Blaustein, Laura J. Rose, K Allison Perry-Dow, Anahid A. Moghadam, Mary K. Hayden, Vincent Bensan Young, Erica Marie Hartmann · 2022 · Microbiome
Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates
Bo Xu, Pengfei Song, Feng Jiang, Zhenyuan Cai, Haifeng Gu, Hongmei Gao, Bin Li, Chengbo Liang, Wen Qin, Jingjie Zhang et al. · 2024 · npj Biofilms and Microbiomes
Introducing an environmental assessment and intervention program in inner-city schools
Michelle Fox Huffaker, Wanda Phipatanakul · 2014 · Journal of Allergy and Clinical Immunology
Exploration and retrieval of whole-metagenome sequencing samples
Sohan Seth, Niko Välimäki, Samuel Kaski A, Antti Honkela · 2014 · Bioinformatics
Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications
Sofia Ahsanuddin, Ebrahim Afshinnekoo, Jorge A. Gandara, Mustafa Hakyemezoğlu, Daniela Bezdan, Samuel S. Minot, Nick Greenfield, Christopher E. Mason · 2017 · Journal of Biomolecular Techniques JBT
Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data
Zhigang Li, Katherine Lee, Margaret Rita Karagas, Juliette C. Madan, Anne Gatewood Hoen, A. James O’Malley, Hongzhe Li · 2018 · Statistics in Biosciences
Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics
Alexander Zaborin, Beatriz Peñalver Bernabé, Robert C. Keskey, Naseer Sangwan, Sanjiv K. Hyoju, Neil Gottel, Jack A. Gilbert, Olga Y. Zaborina, John C. Alverdy · 2020 · mSystems
TIPP2: metagenomic taxonomic profiling using phylogenetic markers
Nidhi Shah, Erin K. Molloy, Mihai Pop, Tandy J. Warnow · 2021 · Bioinformatics
High-resolution sweep metagenomics using fast probabilistic inference
Tommi Mäklin, Teemu Kallonen, Sophia David, Christine J. Boinett, Ben Pascoe, Guillaume Méric, David M. Aanensen, Edward J. Feil, Stephen G. Baker, Julian Parkhill et al. · 2020 · Wellcome Open Research
Strategies and tools in illumina and nanopore‐integrated metagenomic analysis of microbiome data
Yu Xia, Xiang Li, Ziqi Wu, Cailong Nie, Zhanwen Cheng, Yuhong Sun, Lei Liu, Tong Zhang · 2023 · iMeta
The Cystic Fibrosis Upper and Lower Airway Metagenome
Katarzyna Pienkowska, Marie‐Madlen Pust, Margaux Gessner, Svenja Gaedcke, Ajith Thavarasa, Ilona Rosenboom, Patricia Morán Losada, Rebecca Minso, Christin Arnold, Silke Hedtfeld et al. · 2023 · Microbiology Spectrum
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass
Joana Pereira‐Marques, Rui M. Ferreira, Céu Figueiredo · 2024 · Gut Microbes
Multimodal AI correlates of glucose spikes in people with normal glucose regulation, pre-diabetes and type 2 diabetes
Mattia Carletti, Jay A. Pandit, Matteo Gadaleta, Danielle C Chiang, Felipe Delgado, Katie Quartuccio, Brianna Fernandez, Juan A. Raygoza Garay, Ali Torkamani, Riccardo Miotto et al. · 2025 · Nature Medicine
Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi
Yan Zhang, Arthur Brady, Cheron E. Jones, Yang Song, Thomas C. Darton, Claire Jones, Christoph J. Blohmke, Andrew John Pollard, Laurence S. Magder, Alessio Fasano et al. · 2018 · mBio
Challenges of next-generation sequencing targeting anaerobes
Georg Conrads, Mohamed M. H. Abdelbary · 2019 · Anaerobe
Method development for cross-study microbiome data mining: Challenges and opportunities
Xiaoquan Su, Gongchao Jing, Yufeng Zhang, Shunyao Wu · 2020 · Computational and Structural Biotechnology Journal
A primer on metagenomics and next‐generation sequencing in fish gut microbiome research
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat · 2021 · Aquaculture Research
Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan
Amina Habib, Stéphane Lo, Khanh Villageois-Tran, Marie Petitjean, Shaheen Akhtar Malik, Laurence Armand-Lefèvre, Étienne Ruppé, Rabaab Zahra · 2022 · PLoS ONE
Alterations of Gut Microbiome, Metabolome, and Lipidome in Takayasu Arteritis
Luyun Fan, Junru Chen, Lili Pan, Xiaohong Xin, Bin Geng, Lirui Yang, Qian Wang, Wenjun Ma, Ying Lou, Jin‐Song Bian et al. · 2022 · Arthritis & Rheumatology
A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilising electronic probes
Andrés S. Espíndola, William L. Schneider, Peter R. Hoyt, Stephen M. Marek, Carla D. Garzón · 2015 · International Journal of Data Mining and Bioinformatics
Development of a synbiotic that protects against ovariectomy-induced trabecular bone loss
Lina Lawenius, Karin L. Gustafsson, Jianyao Wu, Karin H. Nilsson, Sofia Movérare‐Skrtic, Eric M. Schott, Maria Juliana Soto-Girón, Gerardo V. Toledo, Klara Sjögren, Claes Ohlsson · 2022 · American Journal of Physiology-Endocrinology and Metabolism
An In Silico Outlook for the Detection and Surveillance of Evolving and Persistent Plant Pathogens
Rahat Parveen, Noopur Khare, Sachidanand Singh, P. K. Johri · 2023 · Springer eBooks
Exploring the dynamic microbial tapestry of South Asian rivers: insights from the Ganges and Yamuna ecosystems
Sadashiv Chaturvedi, Biswameet Chakraborty, Min Liu, Amit Kumar, Bikram Pathak, Rupesh Kumar, Zhi‐Guo Yu · 2024 · Ecohydrology
Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Yan Wei Lim, Matthew R. Haynes, Mike Furlan, Charles E. Robertson, Jonathan Kirk Harris, Forest L. Rohwer · 2014 · Journal of Visualized Experiments
The Gastric Microbiome and Its Influence on Gastric Carcinogenesis
Chao Zhang, Sarah Ellen Powell, Doron Betel, Manish A. Shah · 2017 · Hematology/Oncology Clinics of North America
High-throughput DNA sequencing technologies for water and wastewater analysis
Alexander Wing Yip Chan, James Naphtali, Herb E Schellhorn · 2019 · Science Progress
HMPDACC: a Human Microbiome Project Multi-omic data resource
Heather Huot, Victor Felix, Jain Aluvathingal, Jonathan Crabtree, Olukemi O. Ifeonu, James Matsumura, Carrie L McCracken, Lance Nickel, Joshua Orvis, Mike Schor et al. · 2020 · Nucleic Acids Research
Bacterial composition and function during fermentation of Mongolia koumiss
Yue Wu, Yu Li, Qimu Gesudu, Juntao Zhang, Zhihong Sun, Halatu Haobisi, Bilege Menghe, Wenjun Liu · 2021 · Food Science & Nutrition
Highly Specialized Carbohydrate Metabolism Capability in Bifidobacterium Strains Associated with Intestinal Barrier Maturation in Early Preterm Infants
Bing Ma, Sripriya Sundararajan, Gita Nadimpalli, Michael France, Elias J. McComb, Lindsay Rutt, Jose M. Lemme‐Dumit, Elise Janofsky, Lisa S. Roskes, Pawel Gajer et al. · 2022 · mBio
Antibiotics in anaerobic digestion: Investigative studies on digester performance and microbial diversity
Jyoti Rani, Kailash Pati Pandey, Jeetesh Kushwaha, Madhumita Priyadarsini, Abhishek S. Dhoble · 2022 · Bioresource Technology
Pyrosequencing of rpoB uncovers a significant biogeographical pattern of rhizobial species in soybean rhizosphere
Xing Xing Zhang, Hui Juan Guo, Jian Jiao, Pan Zhang, Hui Yang Xiong, Wen Xin Chen, Chang Fu Tian · 2016 · Journal of Biogeography
Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes
Anukriti Sharma, Matthias Schmidt, Bärbel Kiesel, Nitish Kumar Mahato, Lauren E. Cralle, Yogendra Prakash Singh, Hans Hermann Richnow, Jack A. Gilbert, Wyatt Arnold, Rup Lal · 2018 · Frontiers in Microbiology
Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities
Gabriela Flores-Vargas, Darren R. Korber, Jordyn Bergsveinson · 2023 · Frontiers in Microbiology
Third-party fecal microbiota transplantation for high-risk treatment-naïve acute GVHD of the lower GI tract
Zachariah Michael DeFilipp, Ashish V. Damania, Haesook T. Kim, Chia‐Chi Chang, Areej R El-Jawahri, Steven L. McAfee, AJ S. Bottoms, Vesselina Toncheva, Melissa M. Smith, Maria Dolaher et al. · 2024 · Blood Advances
Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases
Ekaterina Avershina, A. Qureshi, Hanne Cecilie Winther-Larsen, Trine B. Rounge · 2025 · Microbiome
Biotic and abiotic factors shape the microbiota of wild‐caught populations of the arbovirus vector Culicoides imicola
Sandra Diaz Sanchez, Angélica Hernández-Jarguín, Alessandra Torina, Isabel G. Fernández de Mera, Agustín Estrada‐Peña, Margarita Villar, Francesco La Russa, Valeria Blanda, Joaquín Vicente, SANTO CARACAPPA et al. · 2018 · Insect Molecular Biology
Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacterium Proteus mirabilis strain SCDR1
Amr T. M. Saeb, Khalid A Al-Rubeaan, Mohamed Ibrahim Abouelhoda, Manojkumar Selvaraju, Hamsa T. Tayeb · 2017 · Antimicrobial Resistance and Infection Control
Oral microbiome diversity in chimpanzees from Gombe National Park
Andrew T. Ozga, Ian C. Gilby, Rebecca S. Nockerts, Michael Lawrence Wilson, Anne E. Pusey, Anne C. Stone · 2019 · Scientific Reports
Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades
Hyunmin Koo, Joseph A. Hakim, David K. Crossman, Elliot J. Lefkowitz, Casey D. Morrow · 2019 · PLoS ONE
A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota
Thomas H. A. Ederveen, Jos P.H. Smits, Karima Hajo, Saskia van Schalkwijk, Tessa A. Kouwenhoven, Sabina Lukovac, Michiel Wels, Ellen H. J. van den Bogaard, Joost Schalkwijk, Jos Boekhorst et al. · 2019 · Scientific Reports
An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community
Hyunmin Koo, Braden C. McFarland, Joseph A. Hakim, David K. Crossman, Michael R. Crowley, J. Martin Rodriguez, Etty N. Benveniste, Casey D. Morrow · 2020 · Royal Society Open Science
Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’
James Tan, Sida Wang, Gregory J. Dick, Vincent Bensan Young, David H. Sherman, Mark A. Burns, Xiaoxia Nina Lin · 2020 · Integrative Biology
An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent
April Murphy, Daniel Barich, M. Siobhan Fennessy, Joan L. Slonczewski · 2021 · Microbiology Spectrum
Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing
Daoming Wang, Tongda Zhang, Yueqi Lu, Changzheng Wang, Yumei Wu, Jiandong Li, Ye Tao, Le Deng, Xiaoyin Zhang, Jinmin Ma · 2022 · FEBS Open Bio
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils
Rachel Rui Xia Lim, Mi Ae Park, Long Hui Wong, Sumanto Haldar, Kevin Junliang Lim, Niranjan Nagarajan, Christiani Jeyakumar Henry, Yuan Rong Jiang, Oleg Vladimirovich Moskvin · 2022 · npj Biofilms and Microbiomes
VirusTaxo: Taxonomic classification of viruses from the genome sequence using k-mer enrichment
Rajan Saha Raju, Abdullah Al Nahid, Preonath Chondrow Dev, Rashedul Islam · 2022 · Genomics
Altered gut microbiome composition in nontreated plaque psoriasis patients
Chunmiao Wen, Yuanming Pan, Ming Jun Gao, Jianlei Wang, Kun Huang, Ping Tu · 2023 · Microbial Pathogenesis
Current Bioinformatics resources in combating infectious diseases
Amr T. M. Saeb · 2018 · Bioinformation
Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria
Rabindra K. Mandal, Anita Mandal, Joshua E. Denny, Ruth Namazi, Chandy C. John, Nathan W. Schmidt · 2023 · Nature Communications
Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS
Martin S. Lindner, Bernhard Y. Renard · 2015 · PLoS ONE
Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter
Marc Garcia‐Garcerà, Marie Touchon, Sylvain Brisse, Eduardo P. C. Rocha · 2017 · Environmental Microbiology
Considerations When Designing a Microbiome Study: Implications for Nursing Science
Katherine A. Maki, Ana Francisca Diallo, Mark B. Lockwood, Alexis T. Franks, Stefan J. Green, Paule V. Joseph · 2018 · Biological Research For Nursing
Dual RNA-seq in Streptococcus pneumoniae Infection Reveals Compartmentalized Neutrophil Responses in Lung and Pleural Space
Neil D Ritchie, Tom J. Evans · 2019 · mSystems
A Customizable Analysis Flow in Integrative Multi-Omics
Samuel M. Lancaster, Akshay Sanghi, Si Wu, Michael P. Snyder · 2020 · Biomolecules
A higher bacterial inward BCAA transport driven by Faecalibacterium prausnitzii is associated with lower serum levels of BCAA in early adolescents
Sofía Morán‐Ramos, Luis R. Macías Kauffer, Blanca Estela López-Contreras, Hugo Villamil‐Ramírez, Elvira Ocampo‐Medina, Paola León‐Mimila, Blanca Estela Del-Rio-Navarro, Omar Granados‐Portillo, Isabel Ibarra‐González, Marcela Beatriz Vela-Amieva et al. · 2021 · Molecular Medicine
The oral microbiome in relation to pancreatic cancer risk in African Americans
Jessica L. Petrick, Jeremy E. Wilkinson, Dominique S. Michaud, Qiuyin Cai, Hanna Gerlovin, Lisa B. Signorello, Brian Matthew Wolpin, Edward Ruiz-Narváez, Jirong Long, Yaohua Yang et al. · 2021 · British Journal of Cancer
Polyethylene Glycol Loxenatide Injection (GLP-1) Protects Vascular Endothelial Cell Function in Middle-Aged and Elderly Patients With Type 2 Diabetes by Regulating Gut Microbiota
Fengwu Chen, Lina He, Jilin Li, Shuhui Yang, Bangzhou Zhang, Dan Zhu, Zezhen Wu, Shuo Zhang, Ducheng Hou, Cong Ouyang et al. · 2022 · Frontiers in Molecular Biosciences
MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities
Billy Taj, Mobolaji Adeolu, Xuejian Xiong, Jordan Ang, Nirvana Nursimulu, John Parkinson · 2023 · Microbiome
Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations
Naseer Sangwan, Iratxe Zarraonaindia, Jarrad Hampton‐Marcell, Herbert Ssegane, Tifani W. Eshoo-Anton, Geeta Rijal, M. Cristina Negri, Jack A. Gilbert · 2016 · mSystems