bioconductor: phyloseq | Projects

10.1371/journal.pcbi.1006242

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 5 years ago

10.3390/s20247188

Which Are the Central Aspects of Infant Sleep? The Dynamics of Sleep Composites across Infancy
Cited by: 17
Author(s): Sarah F. Schoch, Reto Huber, Malcolm Kohler, Salomé Kurth
Software Mentions: 26
Published: over 3 years ago

10.3389/fvets.2020.547181

Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec
Cited by: 9
Author(s): Catherine Turcotte, Alexandre Thibodeau, Sylvain Quessy, Edward Topp, Guy Beauchamp, Philippe Fravalo, Marie Archambault, Marie-Lou Gaucher
Software Mentions: 23
Published: over 3 years ago

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: over 3 years ago

10.7717/peerj.2836

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
Cited by: 273
Author(s): Ilias Lagkouvardos, Sandra E. Fischer, Neeraj Kumar, Thomas Clavel
Software Mentions: 20
Published: over 7 years ago

10.1186/s12866-021-02282-3

Associations between the gut microbiome and metabolome in early life
Cited by: 14
Author(s): Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal Pathmasiri, Susan McRitche, Susan Sumner, H. Robert Frost, Anne G. Hoen
Software Mentions: 19
Published: over 2 years ago

10.1371/journal.pone.0061217

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Cited by: 11,386
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 19
Published: about 11 years ago

10.3390/microorganisms7110547

Linking Soil Fungal Generality to Tree Richness in Young Subtropical Chinese Forests
Cited by: 9
Author(s): Christina Weißbecker, Anna Heintz‐Buschart, Helge Bruelheide, François Buscot, Tesfaye Wubet
Software Mentions: 19
Published: over 4 years ago

10.1186/s40168-019-0702-x

Understanding microbial community dynamics to improve optimal microbiome selection
Cited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: almost 5 years ago

10.1186/s40168-021-01100-2

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Cited by: 31
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Hanne Mordhorst, Marianne Ifversen, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 18
Published: almost 3 years ago

10.1128/mBio.01054-19

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures
Cited by: 28
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Simon Lax
Software Mentions: 18
Published: over 4 years ago

10.1371/journal.pone.0194899

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali
Cited by: 34
Author(s): Benjamin J Krajacich, Diana L. Huestis, Adama Dao, Alpha Seydou Yaro, Moussa Diallo, Asha Krishna, Jianchu Xu, Tovi Lehmann
Software Mentions: 18
Published: about 6 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: about 10 years ago

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: almost 4 years ago

10.1186/s13059-020-02020-4

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians
Cited by: 43
Author(s): Meagan A Rubel, Arwa Abbas, Louis J. Taylor, Andrew Jesse Connell, Ceylan Tanes, Kyle Bittinger, Valantine Ngum Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 16
Published: almost 4 years ago

10.1038/s41598-017-11514-4

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles
Cited by: 121
Author(s): Lindsay A. Parnell, Catherine Briggs, Bin Cao, Omar Delannoy-Bruno, Andrew E. Schrieffer, Indira U. Mysorekar
Software Mentions: 16
Published: over 6 years ago

10.1186/s40168-019-0725-3

Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host
Cited by: 43
Author(s): Aonghus Lavelle, Thomas Hoffmann, Hang-Phuong Pham, Philippe Langella, Éric Guédon, Harry Sokol
Software Mentions: 16
Published: almost 5 years ago

10.12688/f1000research.27268.1

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: over 3 years ago

10.1371/journal.pone.0195112

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats
Cited by: 43
Author(s): Edna Chiang, Marian L. Schmidt, Michelle A. Berry, Bopaiah A. Biddanda, Ashley M. Burtner, Thomas H. Johengen, Danna Palladino, Vincent J. Denef
Software Mentions: 16
Published: about 6 years ago

10.1098/rsos.191609

Spatial heterogeneity of the shorebird gastrointestinal microbiome
Cited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: over 4 years ago

10.3390/cells10061292

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background
Cited by: 1
Author(s): Axel Künstner, Rédouane Aherrahrou, Misa Hirose, Petra Bruse, Saleh M. Ibrahim, Hauke Busch, Jeanette Erdmann, Zouhair Aherrahrou
Software Mentions: 15
Published: almost 3 years ago

10.1186/s40168-020-00961-3

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Cited by: 30
Author(s): Wang Ya, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Software Mentions: 15
Published: over 3 years ago

10.3390/microorganisms9051050

Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum
Cited by: 5
Author(s): Jing Zhu, Xiang Sun, Zhidong Zhang, Qi-Yong Tang, Minghong Gu, Lijuan Zhang, Min Hou, Amir Sharon, Hongli Yuan
Software Mentions: 15
Published: almost 3 years ago

10.1128/mSphere.01023-20

Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly
Cited by: 15
Author(s): Justinn Renelies‐Hamilton, Kristjan Germer, David Sillam‐Dussès, Kasun H. Bodawatta, Michael Poulsen
Software Mentions: 15
Published: about 3 years ago

10.3389/fmicb.2015.00104

Long-term forest soil warming alters microbial communities in temperate forest soils
Cited by: 237
Author(s): Kristen M. DeAngelis, Grace Pold, Begüm D. Topçuoğlu, Linda T. A. van Diepen, Rebecca Varney, Jeffrey L. Blanchard, Jerry M. Melillo, Serita D. Frey
Software Mentions: 15
Published: about 9 years ago

10.3389/fmicb.2019.01775

Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect Seasonality
Cited by: 23
Author(s): Hannah E. Epstein, Hillary A. Smith, Neal E. Cantin, Véronique J. L. Mocellin, Gergely Torda, Madeleine J. H. van Oppen
Software Mentions: 14
Published: over 4 years ago

10.1038/s41396-020-00798-6

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations
Cited by: 48
Author(s): Kali M. Pruss, Ángela Marcobal, Audrey Southwick, Dylan Dahan, Sam Smits, Jessica A. Ferreyra, Steven K. Higginbottom, Erica D. Sonnenburg, Purna C. Kashyap, Biswa Choudhury, Lars Bode, Justin L. Sonnenburg
Software Mentions: 14
Published: over 3 years ago

10.1186/s42523-020-00027-7

Domesticated equine species and their derived hybrids differ in their fecal microbiota
Cited by: 18
Author(s): Joan E. Edwards, A. Schennink, Faith Burden, Stuart A. Long, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Edoardo Saccenti, Hauke Smidt
Software Mentions: 14
Published: about 4 years ago

10.1186/s12859-021-04193-6

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Cited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: almost 3 years ago

10.1371/journal.pone.0237368

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities?
Cited by: 9
Author(s): Gian Maria Niccolò Benucci, Bryan Rennick, Gregory Bonito
Software Mentions: 14
Published: over 3 years ago

10.1038/s41598-020-59849-9

Response of the human gut and saliva microbiome to urbanization in Cameroon
Cited by: 25
Author(s): Ana Lokmer, Sophie Aflalo, Norbert Amougou, Sophie Lafosse, Alain Froment, Francis Ekwin Tabe, Mathilde Poyet, Mathieu Groussin, Rihlat Saïd-Mohamed, Laure Ségurel
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.pone.0242060

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types
Cited by: 3
Author(s): Elizaveta V. Evdokimova, Grigory Gladkov, Natalya I. Kuzina, Е. А. Иванова, Anastasiia K. Kimeklis, Aleksei Zverev, Arina Kichko, Tatyana S. Aksenova, А. Г. Пинаев, Evgeny Andronov
Software Mentions: 14
Published: over 3 years ago

10.1038/s41598-021-97071-3

Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions
Cited by: 10
Author(s): Ankit T. Hinsu, Ketankumar Panchal, Ramesh Pandit, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 14
Published: over 2 years ago

10.1186/s40168-020-00914-w

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
Cited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: over 3 years ago

10.3390/microorganisms9061222

Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study
Cited by: 5
Author(s): Hend Alqaderi, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla
Software Mentions: 14
Published: almost 3 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: almost 3 years ago

10.3390/cancers12051142

Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer
Cited by: 55
Author(s): Marc Clos-García, Koldo Garcia, Cristina Alonso, Marta Iruarrizaga‐Lejarreta, Mauro D’Amato, Anais Crespo, Águeda Iglesias, Joaquín Cubiella, Luís Bujanda, Juan Manuel Falcón‐Pérez
Software Mentions: 14
Published: about 4 years ago

10.3389/fmicb.2021.709611

Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System
Cited by: 2
Author(s): Yousri Abdelhafiz, Jorge M. O. Fernandes, Simone Larger, Davide Albanese, Claudio Donati, Omid Jafari, Artem Nedoluzhko, Viswanath Kiron
Software Mentions: 14
Published: over 2 years ago

10.7717/peerj.3472

Using high-throughput sequencing of ITS2 to describe <i>Symbiodinium</i> metacommunities in St. John, US Virgin Islands
Cited by: 50
Author(s): Ross Cunning, Ruth D. Gates, Peter J. Edmunds
Software Mentions: 14
Published: almost 7 years ago

10.1080/19490976.2021.1888673

Links between gut microbiome composition and fatty liver disease in a large population sample
Cited by: 31
Author(s): Matti O. Ruuskanen, Fredrik Åberg, Ville Männistö, Aki S. Havulinna, Guillaume Méric, Yang Liu, Rohit Loomba, Yoshiki Vázquez-Baeza, Anupriya Tripathi, Liisa Valsta, Michael Inouye, Pekka Jousilahti, Veikko Salomaa, Mohit Jain, Rob Knight, Leo Lahti, Teemu J. Niiranen
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0248185

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis
Cited by: 15
Author(s): Laura Vega, Giovanny Herrera, Marina Muñoz, Manuel A. Patarroyo, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 14
Published: about 3 years ago

10.1098/rspb.2021.0552

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome
Cited by: 9
Author(s): Xavier A. Harrison, Allan D. McDevitt, Jenny C. Dunn, Sarah M. Griffiths, Chiara Benvenuto, Richard Birtles, Jean P. Boubli, Kevin Bown, Calum Bridson, Darren R. Brooks, Samuel S. Browett, Ruth F. Carden, Julian Chantrey, Friederike Clever, Ilaria Coscia, Katie L. Edwards, Nicolas Ferry, Ian Goodhead, Andrew Highlands, Jane Hopper, Joseph A. Jackson, Robert Jehle, Mariane da Cruz Kaizer, Tony King, Jessica M. D. Lea, Jessica L Lenka, Alexandra McCubbin, Jack McKenzie, Bárbara Lins Caldas de Moraes, Denise O'Meara, Poppy Pescod, Richard F. Preziosi, Jennifer K. Rowntree, Susanne Shultz, Matthew J. Silk, Jennifer E. Stockdale, William O. C. Symondson, Mariana Villalba de la Peña, Susan L. Walker, Michael D. Wood, Rachael E. Antwis
Software Mentions: 14
Published: over 2 years ago

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: almost 4 years ago

10.1128/AEM.01225-21

Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek
Cited by: 7
Author(s): Anna Cäcilia Ingham, Tinna Ravnholt Urth, Raphael N. Sieber, Marc Stegger, Sofie Marie Edslev, Øystein Angen, Anders Rhod Larsen
Software Mentions: 13
Published: over 2 years ago

10.1186/s42523-020-0023-1

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species
Cited by: 31
Author(s): Joan E. Edwards, Sudarshan A. Shetty, Pim van den Berg, Faith Burden, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Hauke Smidt
Software Mentions: 13
Published: about 4 years ago

10.3389/fmicb.2020.02028

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn’s Disease and Ulcerative Colitis
Cited by: 8
Author(s): Jake C. Szamosi, Jessica D. Forbes, John W. Copeland, Natalie Knox, Shahrokh Shekarriz, Laura Rossi, Morag Graham, Christine Bonner, David S. Guttman, Gary Van Domselaar, Michael G. Surette, Çharles N. Bernstein
Software Mentions: 13
Published: over 3 years ago

10.1186/s40168-018-0569-2

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
Cited by: 107
Author(s): Joshua P. Earl, Nithin D. Adappa, Jarosław Król, Archana Bhat, Sergey Balashov, Rachel Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich, Joshua Chang Mell
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: over 7 years ago

10.3389/fmicb.2019.00665

Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front
Cited by: 31
Author(s): Gilda Varliero, Christina Bienhold, Florian Schmid, Antje Boetius, Massimiliano Molari
Software Mentions: 13
Published: about 5 years ago

10.3390/microorganisms9010092

Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems
Cited by: 23
Author(s): Joel F. Swift, Megan E. Hall, Zachary N. Harris, Misha T. Kwasniewski, Allison J. Miller
Software Mentions: 13
Published: over 3 years ago

10.3389/fmicb.2020.01116

Crop Management Impacts the Soybean (Glycine max) Microbiome
Cited by: 41
Author(s): Reid Longley, Zachary A Noel, Gian Maria Niccolò Benucci, Martin I. Chilvers, Frances Trail, Gregory Bonito
Software Mentions: 12
Published: almost 4 years ago

10.1128/mBio.02782-18

Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing Selection
Cited by: 21
Author(s): Milton T. Drott, Tracy Debenport, Steven A. Higgins, Daniel H. Buckley, Michael G. Milgroom
Software Mentions: 12
Published: about 5 years ago

10.1371/journal.pone.0236135

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina
Cited by: 25
Author(s): Cassandra L. Ettinger, Jonathan A. Eisen
Software Mentions: 12
Published: almost 4 years ago

10.1371/journal.pone.0236305

Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance
Cited by: 7
Author(s): David J. Bradshaw, Nicholas J. Dickens, John H. Trefry, Peter J. McCarthy
Software Mentions: 12
Published: over 3 years ago

10.3389/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: about 5 years ago

10.1111/1462-2920.14621

Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes
Cited by: 22
Author(s): Pavla Debeljak, Ève Toulza, Sara Beier, Stéphane Blain, Ingrid Obernosterer
Software Mentions: 12
Published: about 5 years ago

10.12688/f1000research.14013.2

Taxa: An R package implementing data standards and methods for taxonomic data
Cited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: over 5 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: about 3 years ago

10.1093/conphys/coaa047

Changes in physiology and microbial diversity in larval ornate chorus frogs are associated with habitat quality
Cited by: 9
Author(s): Cory B. Goff, Susan C. Walls, David Rodríguez, Caitlin R. Gabor
Software Mentions: 12
Published: over 4 years ago

10.3390/microorganisms9071526

Exploring the Individual Bacterial Microbiota of Questing Ixodes ricinus Nymphs
Cited by: 2
Author(s): Aurélien Alafaci, Alexandre Crépin, Sabine Beaubert, Jean‐Marc Berjeaud, Vincent Delafont, Julien Verdon
Software Mentions: 12
Published: almost 3 years ago

10.1371/journal.pcbi.1005404

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: about 7 years ago

10.3390/nu13082639

Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts
Cited by: 18
Author(s): Chiara-Maria Homann, Connor A J Rossel, Sara Dizzell, Liene Bervoets, Julia Simioni, Jenifer Li, Elizabeth Gunn, Michael G. Surette, Russell J. de Souza, Monique Mommers, Eileen K. Hutton, Katherine M. Morrison, John Penders, Niels van Best, Jennifer C. Stearns
Software Mentions: 12
Published: almost 3 years ago

10.1128/mSystems.00903-19

manta: a Clustering Algorithm for Weighted Ecological Networks
Cited by: 7
Author(s): Lisa Röttjers, Karoline Faust
Software Mentions: 12
Published: about 4 years ago

10.1038/s41396-018-0251-5

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals
Cited by: 56
Author(s): Amanda C. Perofsky, Rebecca J. Lewis, Lauren Ancel Meyers
Software Mentions: 12
Published: over 5 years ago

10.1128/mSystems.00750-21

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies
Cited by: 11
Author(s): Christoph Ammer‐Herrmenau, Nina Pfisterer, T. van den Berg, Ivana Gavrilova, Ahmad Amanzada, Shiv K. Singh, Alaa Mohamed, Rohia Alili, Eugeni Belda, Karine Clément, Ahmed Abd El Wahed, ElSagad Eltayeb Gady, Martin Haubrock, Tim Beißbarth, Volker Ellenrieder, Albrecht Neeße
Software Mentions: 12
Published: over 2 years ago

10.3389/fmicb.2018.02312

Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests
Cited by: 26
Author(s): Christina Weißbecker, Tesfaye Wubet, Guillaume Lentendu, Peter Kühn, Thomas Scholten, Helge Bruelheide, François Buscot
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2019.02291

Reduced Gut Microbiome Diversity and Metabolome Differences in Rhinoceros Species at Risk for Iron Overload Disorder
Cited by: 25
Author(s): Terri L. Roth, Alexandra D. Switzer, Miki Watanabe-Chailland, Elisabeth M. Bik, David A. Relman, Lindsey E. Romick-Rosendale, Nicholas J. Ollberding
Software Mentions: 11
Published: over 4 years ago

10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: about 3 years ago

10.3389/fmicb.2020.619226

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island
Cited by: 4
Author(s): Ahmed Taïbi, Ronan Rivallan, Véronique Broussolle, Dominique Pallet, Sylvie Lortal, Jean-Christophe Meile, Florentin Constancias
Software Mentions: 11
Published: over 3 years ago

10.1128/mSphere.00481-19

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities
Cited by: 15
Author(s): Ryan B. Ghannam, Laura G. Schaerer, Timothy Butler, Stephen M. Techtmann
Software Mentions: 11
Published: about 4 years ago

10.3390/microorganisms8040550

Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering
Cited by: 22
Author(s): Micha Weil, Haitao Wang, Mia M. Bengtsson, Daniel Köhn, Anke Günther, Gerald Jurasinski, John Couwenberg, Wakene Negassa, Dominik Zak, Tim Urich
Software Mentions: 11
Published: about 4 years ago

10.3390/microorganisms8101619

Salt Marsh Elevation Drives Root Microbial Composition of the Native Invasive Grass Elytrigia atherica
Cited by: 6
Author(s): Edisa García Hernández, Elena Baraza, Christian Smit, Matty P. Berg, Joana Falcão Salles
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-021-86396-8

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Cited by: 15
Author(s): Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard‐Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud‐Haond, Daniela Zeppilli
Software Mentions: 11
Published: about 3 years ago

10.3389/fmicb.2020.570985

Differently Pre-treated Rapeseed Meals Affect in vitro Swine Gut Microbiota Composition
Cited by: 8
Author(s): Long Cheng, S. de Vries, Koen Venema
Software Mentions: 11
Published: over 3 years ago

10.3389/fmicb.2021.633659

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast
Cited by: 14
Author(s): Maria Luis de Vilar Correia Brito Bôto, Catarina Magalhães, Rafaela Perdigão, Diogo A. M. Alexandrino, Joana P. Fernandes, Ana M. Bernabéu, Sandra Ramos, Maria F. Carvalho, Miguel Semedo, Julie LaRoche, C. Marisa R. Almeida, Ana P. Mucha
Software Mentions: 11
Published: about 3 years ago

10.3389/fmicb.2018.02301

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach
Cited by: 38
Author(s): Wen Chen, Graham Wilkes, Izhar U. H. Khan, Katarina Pintar, Joseph P. Thomas, C. André Lévesque, Julie T. Chapados, Edward Topp, David R. Lapen
Software Mentions: 11
Published: over 5 years ago

10.12688/f1000research.26669.2

TreeSummarizedExperiment: a S4 class for data with hierarchical structure
Cited by: 14
Author(s): Ronald Huang, Charlotte Soneson, Felix G.M. Ernst, Kévin Rue-Albrecht, Yu Guo, Stephanie C. Hicks, Mark D. Robinson
Software Mentions: 11
Published: about 3 years ago

10.1186/s42523-020-00045-5

Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)
Cited by: 4
Author(s): Emily Dodd, Melissa L. Pierce, Jonathan S. F. Lee, Rachel Poretsky
Software Mentions: 11
Published: almost 4 years ago

10.1371/journal.pone.0132783

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities
Cited by: 388
Author(s): Mads Albertsen, Søren Michael Karst, Anja Ziegler, Rasmus Hansen Kirkegaard, Per Halkjær Nielsen
Software Mentions: 11
Published: almost 9 years ago

10.1038/s42003-020-01166-y

Spatial patterns of microbial communities across surface waters of the Great Barrier Reef
Cited by: 28
Author(s): Pedro R. Frade, Bettina Glasl, Samuel A. Matthews, Camille Mellin, Ester Á. Serrão, Kennedy Wolfe, Peter J. Mumby, Nicole S. Webster, David G. Bourne
Software Mentions: 11
Published: over 3 years ago

10.1186/s40168-019-0714-6

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments
Cited by: 78
Author(s): Jiarui Chen, Shelby E. McIlroy, Anand Asundi, David M. Baker, Gianni Panagiotou
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0220961

Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data
Cited by: 4
Author(s): Amanda H. Pendegraft, Boyi Guo, Nengjun Yi
Software Mentions: 11
Published: over 4 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: about 4 years ago

10.1186/s42523-020-00066-0

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary
Cited by: 16
Author(s): Rebecca J. Stevick, Anton F. Post, Marta Gómez-Chiarri
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-020-71663-x

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: almost 3 years ago

10.1038/s41598-020-79875-x

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models
Cited by: 23
Author(s): Marta Relvas, Alba Regueira-Iglesias, Carlos Balsa-Castro, Filomena Salazar, José Júlio Pacheco, Cristina Cabral, Corsina Velazco de Henriques, Inmaculada Tomás
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2020.597745

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce
Cited by: 15
Author(s): Saskia Windisch, Loreen Sommermann, Doreen Babin, Soumitra Paul Chowdhury, Rita Grosch, Narges Moradtalab, Frank Walker, Birgit Höglinger, Abbas El‐Hasan, Wolfgang Armbruster, Joseph Nesme, Søren J. Sørensen, Ingo Schellenberg, Joerg Geistlinger, Kornelia Smalla, Michael Rothballer, Uwe Ludewig, Günter Neumann
Software Mentions: 10
Published: over 3 years ago

10.1186/s42523-021-00094-4

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales
Cited by: 23
Author(s): Connie A. Rojas, Santiago Ramírez‐Barahona, Kay E. Holekamp, Kevin R. Theis
Software Mentions: 10
Published: about 3 years ago

10.3389/fmicb.2021.706214

Dietary Exposure of Pacific Oyster (Crassostrea gigas) Larvae to Compromised Microalgae Results in Impaired Fitness and Microbiome Shift
Cited by: 5
Author(s): Julien Vignier, Olivier Laroche, Anne Rolton, Pandora Wadsworth, K. Kumanan, Branwen Trochel, Xavier Pochon, Nathan King
Software Mentions: 10
Published: over 2 years ago

10.1111/mec.15179

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem
Cited by: 25
Author(s): Elias Broman, Caroline Raymond, Christian Sommer, Jonas S. Gunnarsson, Simon Creer, Francisco J. A. Nascimento
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41598-017-09303-0

The impact of immigration on microbial community composition in full-scale anaerobic digesters
Cited by: 111
Author(s): Rasmus Hansen Kirkegaard, Simon Jon McIlroy, Jannie Munk Kristensen, Marta Nierychlo, Søren Michael Karst, Morten Simonsen Dueholm, Mads Albertsen, Per Halkjær Nielsen
Software Mentions: 10
Published: over 6 years ago

10.3390/microorganisms9071487

Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
Cited by: 20
Author(s): Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja‐Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman‐Yassky, Tove Agner
Software Mentions: 10
Published: almost 3 years ago

10.3389/fmicb.2021.657508

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas
Cited by: 3
Author(s): Fernando Igne Rocha, Thiago Gonçalves Ribeiro, Marcelo Antoniol Fontes, Stefan Schwab, Márcia Reed Rodrigues Coelho, J. F. Lumbreras, P. E. F. da Motta, W. G. Teixeira, James R. Cole, Ana Carolina Borsanelli, Iveraldo S. Dutra, Adina Howe, Aline Pacobahyba de Oliveira, Ederson da Conceição Jesus
Software Mentions: 10
Published: about 3 years ago

10.3390/microorganisms8121887

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function
Cited by: 13
Author(s): Laurin Christopher Gierse, Alexander Meene, Daniel Schultz, Theresa Schwaiger, Claudia Karte, Charlotte Schröder, Haitao Wang, Christine Wünsche, Karen Methling, Bernd Kreikemeyer, Stephan Fuchs, Jörg Bernhardt, Dörte Becher, Michael Lalk, Tim Urich, Katharina Riedel
Software Mentions: 10
Published: over 3 years ago

10.1186/s42523-019-0007-1

Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice
Cited by: 15
Author(s): Alireza Kashani, Asker Brejnrod, Chunyu Jin, Timo Kern, Andreas Nygaard Madsen, Louise Holm, Georg K. Gerber, Jens-Christian Holm, Torben Hansen, Birgitte Holst, Manimozhiyan Arumugam
Software Mentions: 10
Published: over 4 years ago

10.3390/jcm9051572

Eye-Catching Microbes—Polyphasic Analysis of the Microbiota on Microscope Oculars Verifies Their Role as Fomites
Cited by: 3
Author(s): Birgit Fritz, Karin Schäfer, Melanie März, Siegfried Wahl, Focke Ziemssen, Markus Egert
Software Mentions: 10
Published: almost 4 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: over 4 years ago

10.1186/s42523-020-00039-3

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata
Cited by: 20
Author(s): H. Pieter J. van Veelen, Joana Falcão Salles, Kevin D. Matson, Marco van der Velde, B. Irene Tieleman
Software Mentions: 10
Published: almost 4 years ago

10.1002/ece3.5599

Linking pollen foraging of megachilid bees to their nest bacterial microbiota
Cited by: 29
Author(s): Anna Voulgari‐Kokota, Markus J. Ankenbrand, Gudrun Grimmer, Ingolf Steffan‐Dewenter, Alexander Keller
Software Mentions: 10
Published: over 4 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702