cran: uclust | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.550420

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Cited by: 91
Author(s): Daniel Straub, Nia Blackwell, Adrian Langarica‐Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
Software Mentions: 22
Published: about 4 years ago

10.1371/journal.pone.0243241

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
Cited by: 15
Author(s): Sebastian Hupfauf, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandòn, Heribert Insam, Sabine Marie Podmirseg
Software Mentions: 13
Published: almost 4 years ago

10.7717/peerj.4395

COREMIC: a web-tool to search for a niche associated CORE MICrobiome
Cited by: 17
Author(s): Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams
Software Mentions: 11
Published: over 6 years ago

10.7717/peerj.8027

Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps
Cited by: 0
Author(s): Cédric Boué, Tonia DeBellis, Lisa Venier, Timothy T. Work, Steven W. Kembel
Software Mentions: 10
Published: almost 5 years ago

10.3389/fmicb.2018.01323

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish
Cited by: 37
Author(s): Dylan Dahan, Brooke A. Jude, Regina Lamendella, Felicia Keesing, Gabriel G. Perron
Software Mentions: 9
Published: over 6 years ago

10.1186/s12866-020-1704-3

The canine oral microbiome: variation in bacterial populations across different niches
Cited by: 36
Author(s): Avika Ruparell, Taichi Inui, Ruth Staunton, Corrin Wallis, Oliver Deusch, Lucy J. Holcombe
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-020-62186-6

Site-specific molecular analysis of the bacteriota on worn spectacles
Cited by: 4
Author(s): Birgit Fritz, Melanie März, Severin Weis, Siegfried Wahl, Focke Ziemssen, Markus Egert
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2019.01805

Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing
Cited by: 44
Author(s): Josephine Grützke, Burkhard Malorny, Jens A. Hammerl, Anne Busch, Simon H. Tausch, Herbert Tomaso, Carlus Deneke
Software Mentions: 8
Published: over 5 years ago

10.1128/mBio.02293-19

Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria
Cited by: 43
Author(s): Grace Pold, Luiz A. Domeignoz‐Horta, Eric W. Morrison, Serita D. Frey, Seeta A. Sistla, Kristen M. DeAngelis
Software Mentions: 8
Published: over 4 years ago

10.3389/fmicb.2021.654108

Gut Microbiota of Drosophila subobscura Contributes to Its Heat Tolerance and Is Sensitive to Transient Thermal Stress
Cited by: 22
Author(s): Angélica Jaramillo, Luis E. Castañeda
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2017.02414

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field
Cited by: 48
Author(s): Bryan D. Emmett, Nicholas D. Youngblut, Daniel H. Buckley, Laurie E. Drinkwater
Software Mentions: 8
Published: almost 7 years ago

10.7717/peerj.3944

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
Cited by: 24
Author(s): Ara S. Winter, Jennifer J.M. Hathaway, Jason C. Kimble, Debbie C. Buecher, Ernest W. Valdez, Andrea Porras-Alfaro, Jesse M. Young, Kaitlyn J. H. Read, Diana E. Northup
Software Mentions: 7
Published: about 7 years ago

10.1038/s41598-019-54039-8

High-starch diets alter equine faecal microbiota and increase behavioural reactivity
Cited by: 27
Author(s): L. Bulmer, Jo Anne Murray, Neil M. Burns, A. Garber, Françoise Wemelsfelder, Neil McEwan, P.M. Hastie
Software Mentions: 7
Published: almost 5 years ago

10.3389/fmicb.2017.02624

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica
Cited by: 15
Author(s): Juan G. Abarca, Ibrahim Zuñiga, Gilmary Ortiz-Morales, Armando Lugo, Mariel Viquez-Cervilla, Natalia Rodríguez-Hernández, Frances Vázquez-Sánchez, Catalina Murillo‐Cruz, Ernesto A. Torres-Rivera, Adrián A. Pinto‐Tomás, Filipa Godoy-Vitorino
Software Mentions: 7
Published: almost 7 years ago

10.1111/mec.13891

Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African <scp>HIV</scp>/<scp>AIDS</scp> cohort
Cited by: 51
Author(s): Mathieu Vanhove, Mathew A. Beale, Johanna Rhodes, Duncan Chanda, Shabir Lakhi, Geoffrey Kwenda, Síle F. Molloy, Natasha Karunaharan, Neil Stone, Thomas S. Harrison, Tihana Bicanic, Matthew C. Fisher
Software Mentions: 7
Published: almost 8 years ago

10.3390/ani10020242

Applicability of an Unmedicated Feeding Program Aimed to Reduce the Use of Antimicrobials in Nursery Piglets: Impact on Performance and Fecal Microbiota
Cited by: 2
Author(s): Paola López-Colom, Jordi Estellé, Jordi Bonet, Julià Coma, S. M. Martín‐Orúe
Software Mentions: 7
Published: almost 5 years ago

10.1002/1873-3468.13278

The gut microbiome participates in transgenerational inheritance of low‐temperature responses in Drosophila melanogaster
Cited by: 23
Author(s): Aman Zare, Anna-Mia Johansson, Edvin Karlsson, Nicolas Delhomme, Per Stenberg
Software Mentions: 7
Published: almost 6 years ago

10.1186/s40104-019-0393-y

Efficacy of medium-chain fatty acid salts distilled from coconut oil against two enteric pathogen challenges in weanling piglets
Cited by: 23
Author(s): Paola López-Colom, Lorena Castillejos, Agustina Rodríguez-Sorrento, Mónica Puyalto, J. J. Mallo, S. M. Martín‐Orúe
Software Mentions: 7
Published: almost 5 years ago

10.1128/mBio.01432-18

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes
Cited by: 31
Author(s): David Wood, Nancy Lachner, Jean-Marie Tan, Stephanie Tang, Nicola Angel, Antonia Laino, Richard Linedale, Kim‐Anh Lê Cao, Mark Morrison, Ian H. Frazer, H. Peter Soyer, Philip Hugenholtz
Software Mentions: 7
Published: almost 6 years ago

10.1111/mec.14860

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
Cited by: 43
Author(s): Robert Hooper, Jaelle C. Brealey, Tom van der Valk, Antton Alberdi, John W. Durban, Holly Fearnbach, Kelly M. Robertson, Robin W. Baird, M. Bradley Hanson, Paul R. Wade, M. Thomas P. Gilbert, Phillip A. Morin, Jochen B. W. Wolf, Andrew D. Foote, Katerina Guschanski
Software Mentions: 7
Published: about 6 years ago

10.1186/s40104-021-00601-2

Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets
Cited by: 13
Author(s): Yan Hui, Paulina Tamez-Hidalgo, Tomasz Cieplak, Gizaw Dabessa Satessa, Witold Kot, Søren Kjærulff, Mette Olaf Nielsen, Dennis Sandris Nielsen, Łukasz Krych
Software Mentions: 7
Published: over 3 years ago

10.4056/sigs.3377516

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.
Cited by: 8
Author(s): Kristen M. DeAngelis, Patrik D’haeseleer, Dylan Chivian, Blake A. Simmons, Adam P. Arkin, Konstantinos Mavromatis, Stephanie Malfatti, Susannah G. Tringe, Terry C. Hazen
Software Mentions: 7
Published: almost 12 years ago

10.3389/fmicb.2014.00541

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland
Cited by: 71
Author(s): Antje Gittel, Jiří Bárta, Iva Kohoutová, Jörg Schnecker, Birgit Wild, Petr Čapek, Christina Kaiser, Vigdis Torsvik, Andreas Richter, Christa Schleper, Tim Urich
Software Mentions: 6
Published: about 10 years ago

10.3389/fmicb.2018.02533

Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population
Cited by: 57
Author(s): Filipa Godoy-Vitorino, Josefina Romaguera, Chunyu Zhao, Daniela Vargas-Robles, Gilmary Ortiz-Morales, Frances Vázquez-Sánchez, María M. Sánchez-Vázquez, Manuel de la Garza-Casillas, Magaly Martínez‐Ferrer, James R. White, Kyle Bittinger, Maria Gloria Domínguez-Bello, Martin J. Blaser
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.21887

A phylogenetic transform enhances analysis of compositional microbiota data
Cited by: 239
Author(s): Justin D. Silverman, Alex D. Washburne, Sayan Mukherjee, Lawrence A. David
Software Mentions: 6
Published: over 7 years ago

10.7717/peerj.5715

Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests
Cited by: 24
Author(s): Luis E. Castañeda, Tohru Miura, Roland Sánchez, Olga Barbosa
Software Mentions: 6
Published: about 6 years ago

10.7717/peerj.5960

Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia
Cited by: 11
Author(s): Chava L. Weitzman, Karen S. Gibb, Keith A. Christian
Software Mentions: 6
Published: almost 6 years ago

10.3389/fmicb.2018.01892

Identification of Halophilic Microbes in Lung Fibrotic Tissue by Oligotyping
Cited by: 11
Author(s): Corina N. D’Alessandro-Gabazza, Celia Méndez–García, Osamu Hataji, Sara Westergaard, Fumiaki Watanabe, Taro Yasuma, Masaaki Toda, Hajime Fujimoto, Kota Nishihama, Kentaro Fujiwara, Osamu Taguchi, Tetsu Kobayashi, Roderick I. Mackie, Isaac Cann, Esteban C. Gabazza
Software Mentions: 6
Published: about 6 years ago

10.1186/s40168-015-0107-4

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa
Cited by: 109
Author(s): Pål Trosvik, Eric J. de Muinck
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0184890

Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology
Cited by: 92
Author(s): Sarah E. Macdonald, Matthew J. Nolan, Kimberley Harman, Kay Boulton, David Hume, Fiona M. Tomley, Richard A. Stabler, Damer P. Blake
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0169339

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA
Cited by: 51
Author(s): Kathleen H. Lavoie, Ara S. Winter, Kaitlyn J. H. Read, Evan M. Hughes, M. Spilde, Diana E. Northup
Software Mentions: 6
Published: over 7 years ago

10.1186/s12917-014-0282-8

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives
Cited by: 115
Author(s): Brian B. Oakley, R. J. Buhr, Casey W. Ritz, Brian H. Kiepper, M. E. Berrang, Bruce S. Seal, N. A. Cox
Software Mentions: 6
Published: almost 10 years ago

10.3389/fmicb.2017.01011

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir
Cited by: 45
Author(s): Xiaoxiao Li, Jinfeng Liu, Lei Zhou, Serge Maurice Mbadinga, Shi‐Zhong Yang, Ji‐Dong Gu, Bo‐Zhong Mu
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0221408

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea
Cited by: 16
Author(s): Jong-Geol Kim, Joo-Han Gwak, Man‐Young Jung, Sung‐Uk An, Jung‐Ho Hyun, Sanghoon Kang, Sung‐Keun Rhee
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-018-25450-4

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare
Cited by: 34
Author(s): Jessica Dittmer, Didier Bouchon
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-021-01108-8

Human gut-derived B. longum subsp. longum strains protect against aging in a d-galactose-induced aging mouse model
Cited by: 13
Author(s): Yue Xiao, Chao Yang, Leilei Yu, Fengwei Tian, Yarong Wu, Hao Zhang, Ruifu Yang, Colin Hill, Yu‐Jun Cui, Qixiao Zhai
Software Mentions: 6
Published: about 3 years ago

10.3389/fmicb.2016.00399

Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities
Cited by: 21
Author(s): Megan A. Rúa, Emily Wilson, S. D. Steele, Arielle R. Munters, Jason D. Hoeksema, A. Carolin Frank
Software Mentions: 6
Published: over 8 years ago

10.3389/fmicb.2016.00563

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
Cited by: 21
Author(s): Jeffrey J. Marlow, Connor T. Skennerton, Li Zhou, Karuna Chourey, Robert L. Hettich, Chongle Pan, Victoria J. Orphan
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pntd.0003240

Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments
Cited by: 13
Author(s): Katrine Whiteson, Vladimir Lazarević, Manuela Tangomo-Bento, Myriam Girard, Heather Maughan, Didier Pittet, Patrice François, Jacques Schrenzel
Software Mentions: 6
Published: almost 10 years ago

10.1038/s41598-018-25927-2

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses
Cited by: 24
Author(s): Zhongming Ge, Alexander Sheh, Yan Feng, Sureshkumar Muthupalani, Lili Ge, Chuanwu Wang, Susanna Kurnick, Anthony Mannion, Mark T. Whary, James G. Fox
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2019.03153

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing
Cited by: 33
Author(s): Genevieve L. Fernandes, Belle Damodara Shenoy, Samir Damare
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2019.01204

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria
Cited by: 22
Author(s): Laura Gómez‐Consarnau, David M. Needham, Peter K. Weber, Jed A. Fuhrman, Xavier Mayali
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2017.00655

Lactobacillus johnsonii N6.2 Modulates the Host Immune Responses: A Double-Blind, Randomized Trial in Healthy Adults
Cited by: 66
Author(s): Guillermo Marcial, Amanda Ford, Michael J. Haller, Salvador A. Gezan, Natalie A. Harrison, David Cai, Julie Meyer, Daniel J. Perry, Mark A. Atkinson, Clive Wasserfall, Timothy J. Garrett, Claudio F. González, Todd M. Brusko, Wendy J. Dahl, Graciela L. Lorca
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2019.02999

Opioids Impair Intestinal Epithelial Repair in HIV-Infected Humanized Mice
Cited by: 37
Author(s): Jingjing Meng, Santanu Banerjee, Li Zhang, Gregory M. Sindberg, Shamsudheen Moidunny, Bin Li, David J. Robbins, Mohit Girotra, Bradley J. Segura, Sundaram Ramakrishnan, Sabita Roy
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2021.617280

Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments
Cited by: 9
Author(s): Annika Schnakenberg, David A. Aromokeye, Ajinkya Kulkarni, Lisa Maier, Lea C Wunder, Tim Richter-Heitmann, Thomas Pape, Petra Pop Ristova, Solveig I Bühring, Ingrid Dohrmann, Gerhard Bohrmann, Sabine Kasten, Michael W. Friedrich
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-46923-0

The Predominant Oral Microbiota Is Acquired Early in an Organized Pattern
Cited by: 63
Author(s): Rosalyn Sulyanto, Zachary A. Thompson, Clifford J. Beall, Eugene J. Leys, Ann L. Griffen
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0125393

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation
Cited by: 45
Author(s): Samuel Gregory, Christopher Anderson, Marta Camps Arbestain, Patrick J. Biggs, Austen R. D. Ganley, Justin M. O’Sullivan, Michael T. McManus
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0226616

Insights into fungal diversity of a shallow-water hydrothermal vent field at Kueishan Island, Taiwan by culture-based and metabarcoding analyses
Cited by: 25
Author(s): Ka−Lai Pang, Sheng−Yu Guo, I-An Chen, Gaëtan Burgaud, Zengwei Luo, Hans-Uwe Dahms, Jiang‐Shiou Hwang, Yi-Li Lin, Jian-Shun Huang, Tsz-Wai Ho, Ling Ming Tsang, Michael Chiang, Hyojung Cha
Software Mentions: 5
Published: almost 5 years ago

10.1002/ece3.5711

Site‐specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales
Cited by: 15
Author(s): Candice Y. Lumibao, Elizabeth T. Borer, Bradford Condon, Linda L. Kinkel, Georgiana May, Eric W. Seabloom
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2016.00565

Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology
Cited by: 59
Author(s): Jane Debode, Caroline De Tender, Saman Soltaninejad, Cinzia Van Malderghem, Annelies Haegeman, Inge Van der Linden, Bart Cottyn, Marc Heyndrickx, Martine Maes
Software Mentions: 5
Published: over 8 years ago

10.1002/ece3.5538

Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes
Cited by: 2
Author(s): Luis Alza, Philip Lavretsky, Jeffrey L. Peters, Gerardo Cerón, Matthew J. Smith, Cecilia Kopuchian, Andrea A. Astié, Kevin G. McCracken
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2015.00031

Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils
Cited by: 22
Author(s): Jing Li, Yibing Ma, Hang‐Wei Hu, Juntao Wang, Yurong Liu, Ji‐Zheng He
Software Mentions: 5
Published: almost 10 years ago

10.1038/s41598-017-03489-z

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli
Cited by: 38
Author(s): Tracy H. Hazen, Jane Michalski, Qingwei Luo, Amol C. Shetty, Sean C. Daugherty, James M. Fleckenstein, David A. Rasko
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0057190

The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations
Cited by: 103
Author(s): Brian B. Oakley, Cesar A. Morales, J. Eric Line, M. E. Berrang, Richard J. Meinersmann, Glenn E. Tillman, Mark G. Wise, Gregory R. Siragusa, Kelli L. Hiett, Bruce S. Seal
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0217001

Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile
Cited by: 26
Author(s): Vincenzo Motta, Diana Luise, Paolo Bosi, Paolo Trevisi
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-021-01037-6

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis
Cited by: 15
Author(s): Jessica Dittmer, Robert M. Brucker
Software Mentions: 5
Published: over 3 years ago

10.3390/pathogens3020356

Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis
Cited by: 22
Author(s): Akifumi Yamashita, Tsuyoshi Sekizuka, Makoto Kuroda
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0047879

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities
Cited by: 281
Author(s): Sandra Kittelmann, Henning Seedorf, William A. Walters, José C. Clemente, Rob Knight, Jeffrey I. Gordon, Peter H. Janssen
Software Mentions: 4
Published: over 11 years ago

10.3389/fmicb.2012.00293

Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat
Cited by: 30
Author(s): David Armitage, Kimberley L. Gallagher, Nicholas D. Youngblut, Daniel H. Buckley, Stephen H. Zinder
Software Mentions: 4
Published: almost 13 years ago

10.1186/2042-5783-2-3

Metagenomics - a guide from sampling to data analysis
Cited by: 673
Author(s): Torsten Thomas, Jack Gilbert, Patrick Meyer
Software Mentions: 4
Published: over 12 years ago

10.3390/nu11061390

Influence of Socio-Economic and Psychosocial Profiles on the Human Breast Milk Bacteriome of South African Women
Cited by: 14
Author(s): Anna Ojo-Okunola, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Sugnet Gardner-Lubbe, Dan J. Stein, Heather J. Zar, Mark P. Nicol, Elloise du Toit
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.604964

Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding
Cited by: 24
Author(s): Pasquale Alibrandi, Sylvia Schnell, Silvia Perotto, Massimiliano Cardinale
Software Mentions: 4
Published: almost 4 years ago

10.1128/mSphere.00558-19

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia
Cited by: 41
Author(s): Lu Wu, Tiansheng Zeng, Massimo Deligios, Luciano Milanesi, Morgan G. I. Langille, Angelo Zinellu, Salvatore Rubino, Ciriaco Carru, David J. Kelvin
Software Mentions: 4
Published: over 4 years ago

10.1128/mSystems.00024-17

Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions
Cited by: 11
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2020.00867

Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility
Cited by: 10
Author(s): Benjamin Schwan, Christian Abendroth, Adriel Latorre‐Pérez, Manuel Porcar, Cristina Vilanova, Christina Dornack
Software Mentions: 4
Published: over 4 years ago

10.1128/mSphere.00226-16

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City
Cited by: 22
Author(s): Holly M. Bik, Julia M. Maritz, Albert Luong, Hakdong Shin, Maria Gloria Domínguez-Bello, Jane M. Carlton
Software Mentions: 4
Published: almost 8 years ago

10.1093/femsec/fiy194

Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny
Cited by: 24
Author(s): Thomas Swierts, Daniel F. R. Cleary, Nicole J. de Voogd
Software Mentions: 4
Published: about 6 years ago

10.1111/1574-6941.12362

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska
Cited by: 100
Author(s): Hye Min Kim, Jae Chang Jung, Étienne Yergeau, Chung Yeon Hwang, L. D. Hinzman, Sang Heon Nam, Soon Gyu Hong, Ok-Sun Kim, Jongsik Chun, Yoo Kyung Lee
Software Mentions: 4
Published: over 10 years ago

10.1128/mBio.02262-18

Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role
Cited by: 13
Author(s): Jolene R. Bowers, Michael Valentine, Veronica Harrison, Viacheslav Y. Fofanov, John D. Gillece, Josie Delisle, Bethany K. Patton, James M. Schupp, Krystal Sheridan, Darrin Lemmer, Scott Ostdiek, Harlori K. Bains, Jennifer Heim, Tammy Sylvester, Siru Prasai, Melissa Kretschmer, Nicole Fowle, Kenneth Komatsu, Shane Brady, Susan Robinson, Kathryn Fitzpatrick, Gholamabbas Amin Ostovar, Eric Alsop, Elizabeth Hutchins, Kendall Jensen, Paul Keim, David M. Engelthaler
Software Mentions: 4
Published: over 5 years ago

10.1111/1751-7915.12751

The dynamics of the bacterial communities developed in maize silage
Cited by: 66
Author(s): Javad Gharechahi, Zohreh Akhavan Kharazian, Sajjad Sarikhan, Gholamreza Salehi Jouzani, Mahnaz Aghdasi, Ghasem Hosseini Salekdeh
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.05224

Social networks predict gut microbiome composition in wild baboons
Cited by: 384
Author(s): Jenny Tung, Luis B. Barreiro, Michael B. Burns, Jean Grenier, Joshua Lynch, Laura Grieneisen, Jeanne Altmann, Susan C. Alberts, Ran Blekhman, Elizabeth A. Archie
Software Mentions: 4
Published: over 9 years ago

10.14814/phy2.14012

Fecal transplant modifies urine chemistry risk factors for urinary stone disease
Cited by: 18
Author(s): Joshua M. Stern, Marcia Urban‐Maldonado, Mykhaylo Usyk, Ignacio Granja, Daniel Schoenfeld, Kelvin P. Davies, Ilir Agalliu, John R. Asplin, Robert D. Burk, Sylvia O. Suadicani
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-018-24040-8

Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China
Cited by: 80
Author(s): Baihui Ren, Yuanman Hu, Baodong Chen, Ying Zhang, Jan Thiele, Ronghua Shi, Miao Liu, Rencang Bu
Software Mentions: 4
Published: over 6 years ago

10.1038/srep16807

Application of density gradient for the isolation of the fecal microbial stool component and the potential use thereof
Cited by: 40
Author(s): Arancha Hevia, Susana Delgado, Abelardo Margollés, Borja Sánchez
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pbio.3000106

A census-based estimate of Earth's bacterial and archaeal diversity
Cited by: 124
Author(s): Stilianos Louca, Florent Mazel, Michael Doebeli, Laura Wegener Parfrey
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12940-018-0394-x

The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome
Cited by: 78
Author(s): Qixing Mao, Fabiana Manservisi, Simona Panzacchi, Daniele Mandrioli, I Menghetti, Andrea Vornoli, Luciano Bua, Laura Falcioni, Corina Lesseur, Jia Chen, Fiorella Belpoggi, Jianzhong Hu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-00650-6

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration
Cited by: 34
Author(s): Deepak Kumaresan, Adam T. Cross, Benjamin Moreira‐Grez, Khalil Kariman, Paul Nevill, Jason C. Stevens, Richard J. N. Allcock, Anthony G. O'Donnell, Kingsley W. Dixon, Andrew S. Whiteley
Software Mentions: 4
Published: over 7 years ago

10.1186/s13099-014-0039-8

Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs
Cited by: 44
Author(s): Husen Zhang, Haifeng Wang, Megan Shepherd, Ke Wen, Guohua Li, Xing-Dong Yang, Jacob Kocher, Ernawati Arifin Giri-Rachman, Allan W. Dickerman, Robert E. Settlage, Lijuan Yuan
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-015-2194-9

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
Cited by: 311
Author(s): R. D'Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John Kenny, Richard I. Gregory, Alistair C. Darby, Migun Shakya, Mircea Podar, Christopher Quince, Neil Hall
Software Mentions: 4
Published: almost 9 years ago

10.1038/hdy.2016.103

Detection of genetic incompatibilities in non-model systems using simple genetic markers: hybrid breakdown in the haplodiploid spider mite Tetranychus evansi
Cited by: 21
Author(s): Bram Knegt, Tomos Potter, Nicole A Pearson, Yuuji Sato, Heike Staudacher, Bernardus C. J. Schimmel, E. Toby Kiers, Martijn Egas
Software Mentions: 4
Published: about 8 years ago

10.1186/s13068-018-1193-x

Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production
Cited by: 91
Author(s): Matthew Scarborough, Griffin Lynch, Mitch Dickson, Mick McGee, Timothy J. Donohue, Daniel R. Noguera
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.02499

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium
Cited by: 36
Author(s): Elham Karimi, Maria João Ramos, Jorge M. S. Gonçalves, Joana R. Xavier, Margarida Reis, Rodrigo Costa
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2016.02125

Characterization of Gut Microbiome Dynamics in Developing Pekin Ducks and Impact of Management System
Cited by: 36
Author(s): Aaron A. Best, Amanda Porter, Susan M. Fraley, Gregory S. Fraley
Software Mentions: 4
Published: almost 8 years ago

10.1186/s40168-019-0715-5

Active eukaryotes in drinking water distribution systems of ground and surface waterworks
Cited by: 21
Author(s): Jenni Inkinen, Balamuralikrishna Jayaprakash, Sallamaari Siponen, Anna-Maria Hokajärvi, Anna Pursiainen, Jenni Ikonen, Ivan Ryzhikov, Martin Täubel, Ari Kauppinen, Jussi Paananen, Ilkka T. Miettinen, Eila Torvinen, Mikko Kolehmainen, Tarja Pitkänen
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2015.01087

Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog
Cited by: 81
Author(s): Stuart E. Denman, Gonzalo Martínez Fernández, Takumi Shinkai, Makoto Mitsumori, Christopher S. McSweeney
Software Mentions: 4
Published: about 9 years ago

10.7717/peerj.9367

Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis
Cited by: 7
Author(s): Paula Lado, Bo Liu, Michelle E. J. Allerdice, Christopher D. Paddock, Sandor E. Karpathy, Hans Klompen
Software Mentions: 4
Published: over 4 years ago

10.1186/s12918-018-0566-x

KF-finder: identification of key factors from host-microbial networks in cervical cancer
Cited by: 15
Author(s): Jialu Hu, Yiqun Gao, Yanyan Zheng, Xuequn Shang
Software Mentions: 4
Published: over 6 years ago

10.1186/2049-2618-2-7

Bacterial communities on classroom surfaces vary with human contact
Cited by: 121
Author(s): James F. Meadow, Adam E. Altrichter, Steven W. Kembel, Maxwell Moriyama, Timothy K. O’Connor, A. M. Womack, Glen Brown, Jessica L. Green, B. J. M. Bohannan
Software Mentions: 4
Published: over 10 years ago

10.1002/ajpa.23763

The efficacy of whole human genome capture on ancient dental calculus and dentin
Cited by: 21
Author(s): Kirsten A. Ziesemer, Jazmín Ramos‐Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno L. P. Hoogland, Courtney A. Hofman, Domingo C. Salazar‐García, Bruno Fröhlich, George R. Milner, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner, Hannes Schroeder
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2017.00351

The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function
Cited by: 68
Author(s): Sachia J. Traving, Owen Rowe, Nina Munkholt Jakobsen, Helle Sørensen, Julie Dinasquet, Colin A. Stedmon, Agneta Andersson, Lasse Riemann
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-13-S13-S11

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
Cited by: 37
Author(s): Kevin Riehle, Cristian Coarfa, Andrew Jackson, Jun Ma, Arpit Tandon, Sameer Paithankar, Sriram Raghuraman, Toni Ann Mistretta, Delphine M. Saulnier, Sabeen Raza, M.A. Valdovinos Díaz, Robert J. Shulman, Kjersti M. Aagaard, James Versalovic, Aleksandar Milosavljevic
Software Mentions: 4
Published: over 12 years ago

10.1186/s40168-018-0470-z

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Cited by: 2,605
Author(s): Nicholas A. Bokulich, Benjamin Kaehler, Jai Ram Rideout, Matthew R. Dillon, Evan Bolyen, Rob Knight, Gavin A. Huttley, J. Gregory Caporaso
Software Mentions: 4
Published: over 6 years ago

10.1186/s13104-016-2064-9

DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses
Cited by: 40
Author(s): Marie Lisandra Zepeda Mendoza, Kristine Bohmann, Aldo Carmona Baez, M. Thomas P. Gilbert
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0154514

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host
Cited by: 85
Author(s): Heike Staudacher, Martin Kaltenpoth, Johannes A. J. Breeuwer, Steph B. J. Menken, David G. Heckel, Astrid T. Groot
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2021.639997

Identifying the Specific Root Microbiome of the Hyperaccumulator Noccaea brachypetala Growing in Non-metalliferous Soils
Cited by: 0
Author(s): Soledad Martos, John Danku, Laura Pérez‐Martín, Mercè Llugany, Catalina Cabot, Charlotte Poschenrieder
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-64801-y

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels
Cited by: 7
Author(s): Po‐Yu Liu, An-Chi Cheng, Shu‐Mei Huang, Hsiao Pei Lu, Tatsuo Oshida, Wenhua Liu, Hongjun Yu
Software Mentions: 4
Published: over 4 years ago

10.1002/mbo3.375

Ectomycorrhizal and saprotrophic fungi respond differently to long‐term experimentally increased snow depth in the High Arctic
Cited by: 28
Author(s): Sunil Mundra, Rune Halvorsen, Håvard Kauserud, Mohammad Bahram, Leho Tedersoo, Bo Elberling, Elisabeth J. Cooper, Pernille Bronken Eidesen
Software Mentions: 3
Published: over 8 years ago

10.3390/ani9090599

Effects of Land Transport Stress on Variations in Ruminal Microbe Diversity and Immune Functions in Different Breeds of Cattle
Cited by: 20
Author(s): Fengpeng Li, Ali Mujtaba Shah, Zhisheng Wang, Quanhui Peng, Rui Hu, Huawei Zou, Cui Tan, Xiangfei Zhang, Yupeng Liao, Yongjie Wang, Xueying Wang, Lingping Zeng, Bai Xue, Lizhi Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2021.715241

Synbiotics Containing Nanoprebiotics: A Novel Therapeutic Strategy to Restore Gut Dysbiosis
Cited by: 2
Author(s): Liang Hong, Sang-Mok Lee, Whee‐Soo Kim, Yun‐Jaie Choi, Seo-Ho Oh, Yuling Li, Sun-Hye Choi, Chung‐Chih Wu, Eunkyoung Jung, Seoung-Hun Kang, Chong‐Su Cho
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2017.00796

Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome
Cited by: 33
Author(s): Christina A. Kellogg, Dawn B. Goldsmith, Michael A. Gray
Software Mentions: 3
Published: over 7 years ago

Projects: cran: uclust

Papers Mentioning uclust 454