bioconductor: phyloseq | Projects

10.3389/fnbeh.2020.581296

A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats
Cited by: 6
Author(s): Valérie Daugé, Catherine Philippe, Mahendra Mariadassou, Olivier Rué, Jean‐Charles Martin, Marie Rossignol, Nathalie Dourmap, Ljubica Svilar, Franck Tourniaire, Magali Monnoye, Déborah Jardet, Marie Bangratz, Sophie Holowacz, Sylvie Rabot, Laurent Naudon
Software Mentions: 6
Published: about 4 years ago

10.1002/ece3.3638

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)
Cited by: 54
Author(s): Michael S. Robeson, Kamil Khanipov, George Golovko, Samantha M. Wisely, Michael D. White, Michael J. Bodenchuck, Timothy J. Smyser, Yuriy Fofanov, Noah Fierer, Antoinette J. Piaggio
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41396-021-00987-x

Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria
Cited by: 14
Author(s): François Thomas, Nolwen Le Duff, Ting-Di Wu, Aurélie Cébron, Stéphane Uroz, Pascal Riera, Cédric Leroux, Gwenn Tanguy, Erwan Legeay, Jean‐Luc Guerquin‐Kern
Software Mentions: 6
Published: over 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

10.1038/s41396-020-00844-3

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles
Cited by: 45
Author(s): Annelein Meisner, L. Basten Snoek, Joseph Nesme, Elizabeth Dent, Samuel Jacquiod, Aimée T. Classen, Anders Priemé
Software Mentions: 6
Published: almost 4 years ago

10.3389/fmicb.2017.01379

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis)
Cited by: 25
Author(s): Obed Hernández‐Gómez, Jason T. Hoverman, Rod N. Williams
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2018.00674

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop
Cited by: 38
Author(s): Késia Silva Lourenço, Noriko A. Cassman, Agata Pijl, Johannes A. van Veen, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2020.00954

Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite
Cited by: 22
Author(s): Fátima Jorge, Nolwenn M. Dheilly, Robert Poulin
Software Mentions: 6
Published: over 4 years ago

10.1128/mSystems.00003-19

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil
Cited by: 39
Author(s): Alan W. Bowsher, Patrick J. Kearns, Ashley Shade
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22115981

Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract
Cited by: 8
Author(s): Adrian Low, Melissa Soh, Sou Miyake, Vanessa Zhi Jie Aw, Jian Feng, Adeline Wong, Henning Seedorf
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2016.00606

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria
Cited by: 28
Author(s): Vincent J. Denef, Masanori Fujimoto, Michelle A. Berry, Marian L. Schmidt
Software Mentions: 5
Published: over 8 years ago

10.1128/mBio.02637-20

Seed-Derived Microbial Colonization of Wild Emmer and Domesticated Bread Wheat ( Triticum dicoccoides and T. aestivum ) Seedlings Shows Pronounced Differences in Overall Diversity and Composition
Cited by: 34
Author(s): Ezgi Özkurt, M. Amine Hassani, Uğur Sesiz, Sven Künzel, Tal Dagan, Hakan Özkan, Eva H. Stukenbrock
Software Mentions: 5
Published: almost 4 years ago

10.1038/srep17084

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures
Cited by: 22
Author(s): Laetitia G. E. Wilkins, Aude Rogivue, Frédéric Schütz, Luca Fumagalli, Claus Wedekind
Software Mentions: 5
Published: almost 9 years ago

10.1038/srep30349

Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil
Cited by: 92
Author(s): Johnny R. Soares, Noriko A. Cassman, Anna M. Kielak, Agata Pijl, Janaína Braga do Carmo, Késia Silva Lourenço, Hendrikus J. Laanbroek, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-019-45368-9

Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity
Cited by: 23
Author(s): Corinne Celestina, Jennifer L. Wood, James B. Manson, Xiaojuan Wang, P. W. G. Sale, Caixian Tang, Ashley E. Franks
Software Mentions: 5
Published: over 5 years ago

10.3390/ijerph18062832

Impact of Covid-19 Lockdown on Availability of Drinking Water in the Arsenic-Affected Ganges River Basin
Cited by: 17
Author(s): Srimanti Duttagupta, Soumendra N. Bhanja, Avishek Dutta, S. Sarkar, M. Chakraborty, Ashok Ghosh, Debapriya Mondal, Abhijit Mukherjee
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-43907-y

Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño
Cited by: 31
Author(s): Allison R. Kolbe, Manuel Aira, María Gómez-Brandòn, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.7434

Tree diversity and functional leaf traits drive herbivore‐associated microbiomes in subtropical China
Cited by: 1
Author(s): Yang Li, Douglas Chesters, Ming‐Qiang Wang, Tesfaye Wubet, Andreas Schuldt, Perttu Anttonen, Pengfei Guo, Jing‐Ting Chen, Qianxiong Zhou, Nai‐Li Zhang, Keping Ma, Helge Bruelheide, Chunsheng Wu, Chao‐Dong Zhu
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-017-18668-1

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems
Cited by: 12
Author(s): Elham Ehsani, Emma Hernandez-Sanabria, Frederiek‐Maarten Kerckhof, Ruben Props, Ramiro Vílchez-Vargas, Marius Vital, Dietmar H. Pieper, Nico Boon
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-019-40496-8

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline
Cited by: 41
Author(s): Mahdi Ghanbari, Viviana Klose, Fiona Crispie, Paul D. Cotter
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-24931-w

Exposure to toxic metals triggers unique responses from the rat gut microbiota
Cited by: 85
Author(s): Joshua B. Richardson, Blair C. R. Dancy, Cassandra L. Horton, Young S. Lee, Michael S. Madejczyk, Zhenjiang Zech Xu, Gail Ackermann, Gregory Humphrey, Gustavo Palacios, Rob Knight, John A. Lewis
Software Mentions: 5
Published: over 6 years ago

10.3389/fcimb.2019.00216

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis
Cited by: 78
Author(s): Anna Lundmark, Yue Hu, Mikael Huss, Gunnar Johannsen, Anders F. Andersson, Tülay Yucel‐Lindberg
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-28720-3

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus
Cited by: 9
Author(s): Inga Reich, Umer Zeeshan Ijaz, Michael J. Gormally, Cindy J. Smith
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-018-29320-x

Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection
Cited by: 35
Author(s): Christina Balle, Katie Lennard, Smritee Dabee, Shaun Barnabas, Shameem Z. Jaumdally, Melanie A. Gasper, Venessa Maseko, Zizipho Z. A. Mbulawa, Anna‐Lise Williamson, Linda‐Gail Bekker, David A. Lewis, Jo‐Ann S. Passmore, Heather B. Jaspan
Software Mentions: 5
Published: over 6 years ago

10.1002/ece3.5789

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species ( Sciurus aberti and S. niger ) living in sympatry
Cited by: 5
Author(s): Andrew Joseph Reed, Jon C. Pigage, Helen K. Pigage, Cody Glickman, Jeremy M. Bono
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-36709-1

Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents
Cited by: 27
Author(s): Olumide Ajibola, Aislinn D. Rowan, Clement O. Ogedengbe, Mari B. Mshelia, Damien J. Cabral, Anthonius A. Eze, Stephen K. Obaro, Peter Belenky
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcimb.2018.00301

Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies
Cited by: 105
Author(s): Zheng Wang, Christine P. Zolnik, Yunping Qiu, Mykhaylo Usyk, Tao Wang, Howard D. Strickler, Carmen R. Isasi, Robert C. Kaplan, Irwin J. Kurland, Qibin Qi, Robert D. Burk
Software Mentions: 5
Published: about 6 years ago

10.3390/jof7010045

Metabarcoding of Soil Fungal Communities Associated with Alpine Field-Grown Saffron (Crocus sativus L.) Inoculated with AM Fungi
Cited by: 13
Author(s): Íris Marisa Maxaieie Victorino, Samuele Voyron, Matteo Caser, Alberto Orgiazzi, Sonia Demasi, Andrea Berruti, Valentina Scariot, Valeria Bianciotto
Software Mentions: 5
Published: almost 4 years ago

10.3389/fcimb.2019.00339

Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses
Cited by: 17
Author(s): Allison R. Kolbe, Eduardo Castro-Nallar, Diego Preciado, Marcos Pérez‐Losada
Software Mentions: 5
Published: about 5 years ago

10.1111/ele.13082

Linking phytoplankton community metabolism to the individual size distribution
Cited by: 20
Author(s): Daniel Padfield, Angus Buckling, Ruth Warfield, Chris D. Lowe, Gabriel Yvon‐Durocher
Software Mentions: 5
Published: over 6 years ago

10.1038/s41396-021-00920-2

Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi
Cited by: 72
Author(s): Bryan D. Emmett, Veronique Levesque‐Tremblay, Maria J. Harrison
Software Mentions: 5
Published: over 3 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/fmicb.2020.00966

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus
Cited by: 21
Author(s): Kristina Ulrich, Regina Becker, Undine Behrendt, Michael Kube, Andreas Ulrich
Software Mentions: 5
Published: over 4 years ago

10.1038/s41396-020-00735-7

Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought
Cited by: 35
Author(s): Joana Séneca, Petra Pjevac, Alberto Canarini, Craig W. Herbold, Christos Zioutis, Marlies Dietrich, Eva Simon, Judith Prommer, Michael Bahn, E. M. Pötsch, Michael Wagner, Wolfgang Wanek, Andreas Richter
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.595555

Antibiotic Treatment for Chronic Rhinosinusitis: Prescription Patterns and Associations With Patient Outcome and the Sinus Microbiota
Cited by: 16
Author(s): Christian A Lux, Brett Wagner Mackenzie, James Johnston, Melissa Zoing, Kristi Biswas, Michael W. Taylor, Richard Douglas
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2019.01427

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
Cited by: 11
Author(s): Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe‐Fadrosh, Paul Dijkstra, Brian P. Hedlund
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms22041778

Association of Maternal Microbiota and Diet in Cord Blood Cytokine and Immunoglobulin Profiles
Cited by: 11
Author(s): Karla Rio-Aigé, Ignasi Azagra-Boronat, Malén Massot-Cladera, Marta Selma‐Royo, Anna Parra-Llorca, Sonia González, Izaskun García-Mantrana, Cristina Castellote, María J. Rodríguez-Lagunas, María Carmen Collado, Francisco J. Pérez-Cano
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2018.01561

A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations
Cited by: 16
Author(s): Even Sannes Riiser, Thomas Haverkamp, Ørnulf Borgan, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Software Mentions: 5
Published: over 6 years ago

10.1186/s40793-021-00382-1

Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed
Cited by: 5
Author(s): Leena Malayil, Suhana Chattopadhyay, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2018.02382

Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing
Cited by: 23
Author(s): Blaire Steven, Jayne Belnap, Cheryl R. Kuske
Software Mentions: 5
Published: about 6 years ago

10.1186/s40793-021-00381-2

Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome
Cited by: 17
Author(s): Samuel M. M. Prudence, Jake T. Newitt, Sarah F. Worsley, Michael C. Macey, J. Colin Murrell, Laura E. Lehtovirta-Morley, Matthew I. Hutchings
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2020.01735

Great Tit (Parus major) Uropygial Gland Microbiomes and Their Potential Defensive Roles
Cited by: 13
Author(s): Kasun H. Bodawatta, Signe K. Schierbech, Nanna R. Petersen, Kateřina Sam, Nick Bos, Knud A. Jønsson, Michael Poulsen
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.00582

Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes
Cited by: 12
Author(s): Sainur Samad, Hyo‐Jung Lee, Sławek Cerbin, Marion Meima-Franke, Paul L. E. Bodelier
Software Mentions: 5
Published: over 4 years ago

10.1007/s10096-020-04049-6

The vaginal microbiota in the course of bacterial vaginosis treatment
Cited by: 7
Author(s): Romy D. Zwittink, Ellen H A van den Munckhof, Maurine A. Leverstein–van Hall, Kim E. Boers, Anco Molijn, Cornelis W. Knetsch, Ed J. Kuijper
Software Mentions: 5
Published: about 4 years ago

10.1128/mSystems.01196-20

Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations
Cited by: 6
Author(s): Sarahi L. Garcia, Maliheh Mehrshad, Moritz Buck, Jackson M. Tsuji, Josh D. Neufeld, Katherine D. McMahon, Stefan Bertilsson, Chris Greening, Sari Peura
Software Mentions: 5
Published: over 3 years ago

10.1128/mSystems.00954-20

Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater
Cited by: 4
Author(s): Elizabeth A. Monaghan, Kelle C. Freel, Michael S. Rappé
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2021.683685

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries
Cited by: 13
Author(s): Vivianne Cruz de Jesus, Mohd Wasif Khan, Betty-Anne Mittermuller, Kangmin Duan, Pingzhao Hu, Robert J Schroth, Prashen Chelikani
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.00481

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype
Cited by: 40
Author(s): Gregory Bonito, Gian Maria Niccolò Benucci, Khalid Hameed, Deborah Weighill, Piet Jones, Ko‐Hsuan Chen, Daniel Jacobson, Christopher W. Schadt, Rytas Vilgalys
Software Mentions: 5
Published: over 5 years ago

10.12688/f1000research.20660.2

microbiomeDASim: Simulating longitudinal differential abundance for microbiome data
Cited by: 6
Author(s): Justin Williams, Héctor Corrada Bravo, Jennifer Tom, Joseph N. Paulson
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2018.00031

Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes
Cited by: 37
Author(s): Kevin D’hoe, Lorenza Conterno, Francesca Fava, Gwen Falony, Sara Vieira-Silva, Joan Vermeiren, Kieran Tuohy, Jeroen Raes
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2019.00256

Soil Macroinvertebrate Presence Alters Microbial Community Composition and Activity in the Rhizosphere
Cited by: 25
Author(s): Natalie Bray, Jenny Kao‐Kniffin, Serita D. Frey, Timothy J. Fahey, Kyle Wickings
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.00377-20

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
Cited by: 21
Author(s): Alexander Zaborin, Beatriz Peñalver Bernabé, Robert Keskey, Naseer Sangwan, Sanjiv Hyoju, Neil Gottel, Jack A. Gilbert, Olga Zaborina, John C. Alverdy
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00061-20

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance
Cited by: 35
Author(s): Claudia Barelli, Davide Albanese, Rebecca M. Stumpf, Abigail E. Asangba, Claudio Donati, Francesco Rovero, Heidi C. Hauffe
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.01614

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)
Cited by: 7
Author(s): Pamela M. Smith, Sinéad M. Waters, David A. Kenny, T. M. Boland, J. S. Heffernan, A. K. Kelly
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00093-19

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry
Cited by: 14
Author(s): Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon, Willem Waegeman, Vincent J. Denef
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2020.01075

Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System
Cited by: 18
Author(s): Linta Reji, Bradley B. Tolar, Francisco P. Chávez, Christopher A. Francis
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2021.703693

Identification of an Intestinal Microbiota Signature Associated With the Severity of Necrotic Enteritis
Cited by: 14
Author(s): Qing Yang, Jing Liu, Xiaofan Wang, Kelsy Robinson, Melanie A. Whitmore, Sydney Stewart, Jiangchao Zhao, Guolong Zhang
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.01486

Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia
Cited by: 39
Author(s): Flora Jane Mary O'Brien, Maya Almaraz, Melissa A. Foster, A. F. Hill, David P. Huber, Elizabeth King, Harry Langford, Mary-Anne Lowe, Bede S. Mickan, Valerie S. Miller, Oliver Moore, Falko Mathes, Deirdre Gleeson, Matthias Leopold
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.5228

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats
Cited by: 51
Author(s): Melissa R. Ingala, Daniel J. Becker, Jacob Bak Holm, Karsten Kristiansen, Nancy B. Simmons
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.00094-18

Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers
Cited by: 77
Author(s): Leen Boesmans, Mireia Vallès-Colomer, Jun Wang, Venessa Eeckhaut, Gwen Falony, Richard Ducatelle, Filip Van Immerseel, Jeroen Raes, Kristin Verbeke
Software Mentions: 5
Published: about 6 years ago

10.1128/mSystems.00007-18

Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns
Cited by: 86
Author(s): Miriam Nieves-Ramı́rez, Oswaldo Partida-Rodríguez, Isabelle Laforest‐Lapointe, Lisa A. Reynolds, Eric Brown, A. Valdez-Salazar, P. Morán-Silva, Liliana Rojas-Velázquez, Evan Morien, Laura Wegener Parfrey, Mingliang Jin, Jens Walter, Javier Torres, Marie‐Claire Arrieta, C. Ximénez-García, B. Brett Finlay
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2021.738129

Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China
Cited by: 3
Author(s): Jun Zhang, Pengcheng Xing, Mengyu Niu, Gehong Wei, Peng Shi
Software Mentions: 5
Published: about 3 years ago

10.3389/fmicb.2018.00675

Gut Microbiota Profiling and Gut–Brain Crosstalk in Children Affected by Pediatric Acute-Onset Neuropsychiatric Syndrome and Pediatric Autoimmune Neuropsychiatric Disorders Associated With Streptococcal Infections
Cited by: 76
Author(s): Andrea Quagliariello, Federica Del Chierico, Alessandra Russo, Sofia Reddel, Giulia Conte, Loris Riccardo Lopetuso, Gianluca Ianiro, Bruno Dallapiccola, Francesco Cardona, Antonio Gasbarrini, Lorenza Putignani
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.02032

Berry Polyphenols and Fibers Modulate Distinct Microbial Metabolic Functions and Gut Microbiota Enterotype-Like Clustering in Obese Mice
Cited by: 75
Author(s): Maria Carolina Rodríguez-Daza, Marcela Roquim, Stéphanie Dudonné, Geneviève Pilon, Émile Lévy, André Marette, Denis Roy, Yves Desjardins
Software Mentions: 5
Published: about 4 years ago

10.1128/mSystems.00087-17

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity
Cited by: 43
Author(s): Isabelle Laforest‐Lapointe, Christian Messier, Steven W. Kembel
Software Mentions: 5
Published: almost 7 years ago

10.1128/mSystems.00132-17

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
Cited by: 18
Author(s): Elin Videvall, Maria Strandh, Anel Engelbrecht, S.W.P. Cloete, Charlie K. Cornwallis
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2020.00749

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact
Cited by: 16
Author(s): Jean de Dieu Habiyaremye, Kezia Goldmann, Thomas Reitz, Sylvie Herrmann, François Buscot
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2021.596517

Fungal Communities on Standing Litter Are Structured by Moisture Type and Constrain Decomposition in a Hyper-Arid Grassland
Cited by: 11
Author(s): Jim Logan, Kathryn M. Jacobson, Peter J. Jacobson, Sarah E. Evans
Software Mentions: 5
Published: over 3 years ago

10.1128/mSphere.00308-21

Covariation of the Fecal Microbiome with Diet in Nonpasserine Birds
Cited by: 17
Author(s): Kangpeng Xiao, Yutan Fan, Zhipeng Zhang, Xuejuan Shen, Xiaobing Li, Xianghui Liang, Ran Bi, Yuling Wu, Junqiong Zhai, Jun-Wei Dai, David M. Irwin, Chen Wu, Yongyi Shen
Software Mentions: 5
Published: over 3 years ago

10.1186/s40104-020-00542-2

Linkage between the intestinal microbiota and residual feed intake in broiler chickens
Cited by: 26
Author(s): Jing Liu, Sydney Stewart, Kelsy Robinson, Qing Yang, Wentao Lyu, Melanie A. Whitmore, Guolong Zhang
Software Mentions: 5
Published: almost 4 years ago

10.1128/mSphere.00189-17

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder
Cited by: 11
Author(s): Vincent J. Denef, Hunter J. Carrick, Joann F. Cavaletto, Edna Chiang, Thomas H. Johengen, Henry A. Vanderploeg
Software Mentions: 5
Published: over 7 years ago

10.1098/rspb.2018.2697

Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome
Cited by: 38
Author(s): Susana Carvalho, Eva Aylagas, Rodrigo Villalobos, Yasser Kattan, Michael L. Berumen, John K. Pearman
Software Mentions: 5
Published: almost 6 years ago

10.3390/ijms22189930

Comparative Evaluation of Sucrosomial Iron and Iron Oxide Nanoparticles as Oral Supplements in Iron Deficiency Anemia in Piglets
Cited by: 7
Author(s): Rafał Mazgaj, Paweł Lipiński, Mateusz Szudzik, Aneta Jończy, Z Kopeć, Adrian Stankiewicz, M. Kamyczek, Dorine W. Swinkels, Beata Żelazowska, Rafał R. Starzyński
Software Mentions: 5
Published: about 3 years ago

10.1002/mbo3.1133

A low‐cost pipeline for soil microbiome profiling
Cited by: 5
Author(s): Anita Bollmann‐Giolai, Michael Giolai, Darren Heavens, Iain C. Macaulay, Jacob G. Malone, Matt Clark
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2018.00922

Enrichment of Bacteria From Eastern Mediterranean Sea Involved in Lignin Degradation via the Phenylacetyl-CoA Pathway
Cited by: 20
Author(s): Hyun-Joo Woo, Terry C. Hazen
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2016.01703

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status
Cited by: 53
Author(s): Monica Di Paola, Duccio Cavalieri, Davide Albanese, M. Sordo, Massimo Pindo, Claudio Donati, Ilaria Pagnini, Teresa Giani, Gabriele Simonini, Alessia Paladini, Paolo Lionetti, Carlotta De Filippo, Rolando Cimaz
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2020.01757

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation
Cited by: 9
Author(s): Taejung Chung, Daniel Weller, Jasna Kovač
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2018.01138

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada
Cited by: 43
Author(s): Matti O. Ruuskanen, Kyra A. St. Pierre, Vincent L. St. Louis, Stéphane Aris‐Brosou, Alexandre J. Poulain
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2021.660190

Relationships Between the Microbial Composition and the Geochemistry and Mineralogy of the Cobalt-Bearing Legacy Mine Tailings in Northeastern Ontario
Cited by: 5
Author(s): Brittaney Courchesne, Michael Schindler, Nadia Mykytczuk
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-019-1831-z

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity
Cited by: 83
Author(s): Robert C. Kaplan, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Álvarez, Martha L. Daviglus, Neil Schneiderman, Gregory A. Talavera, Marc D. Gellman, Bharat Thyagarajan, Jee Young Moon, Yoshiki Vázquez-Baeza, Daniel McDonald, Jessica Williams-Nguyen, Michael C. Wu, Kari E. North, Justin P. Shaffer, Christopher C. Sollecito, Qibin Qi, Carmen R. Isasi, Tao Wang, Rob Knight, Robert D. Burk
Software Mentions: 5
Published: about 5 years ago

10.3390/life11030246

Postoperative Complications Are Associated with Long-Term Changes in the Gut Microbiota Following Colorectal Cancer Surgery
Cited by: 7
Author(s): Felix C. F. Schmitt, Martin Schneider, William Mathejczyk, Markus A. Weigand, Jane C. Figueiredo, Christopher I. Li, David Shibata, Erin M. Siegel, Adetunji T. Toriola, Cornelia M. Ulrich, Alexis Ulrich, Sébastien Boutin, Biljana Gigic
Software Mentions: 5
Published: over 3 years ago

10.1053/j.gastro.2020.08.007

Alterations in Intestinal Microbiota of Children With Celiac Disease at the Time of Diagnosis and on a Gluten-free Diet
Cited by: 44
Author(s): Konstantina Zafeiropoulou, Ben Nichols, Mary Mackinder, Olga Biskou, Eleni Rizou, Antonia Karanikolou, Caspar Clark, Evan G. Buchanan, Tracey Cardigan, H. J. Duncan, David Wands, Julie A. Russell, Richard Hansen, Richard K. Russell, Paraic McGrogan, Christine Edwards, Umer Zeeshan Ijaz, Konstantinos Gerasimidis
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12936-021-03624-2

Development of a new barcode-based, multiplex-PCR, next-generation-sequencing assay and data processing and analytical pipeline for multiplicity of infection detection of Plasmodium falciparum
Cited by: 2
Author(s): Rebecca Mitchell, Zhansong Zhou, Mili Sheth, Sheila B. Sergent, Michael Frace, Vishal Nayak, Bin Hu, John E. Gimnig, Feiko ter Kuile, Kim A. Lindblade, Laurence Slutsker, Mary J. Hamel, Meghna Desai, Kephas Otieno, Simon Kariuki, Ýmir Vigfússon, Ya Ping Shi
Software Mentions: 5
Published: almost 4 years ago

10.1093/ajcn/nqab077

Associations of healthy food choices with gut microbiota profiles
Cited by: 33
Author(s): Kari K. Koponen, Aaro Salosensaari, Matti O. Ruuskanen, Aki S. Havulinna, Satu Männistö, Pekka Jousilahti, Joonatan Palmu, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Jon G. Sanders, Guillaume Méric, Susan Cheng, Michael Inouye, Mohit Jain, Teemu J. Niiranen, Liisa Valsta, Rob Knight, Veikko Salomaa
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.647861

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed
Cited by: 4
Author(s): Alyssa A. Carrell, Grace E. Schwartz, Melissa Cregger, Caitlin M. Gionfriddo, Dwayne A. Elias, Regina L. Wilpiszeski, Dawn M. Klingeman, Ann M. Wymore, Katherine A. Muller, Scott C. Brooks
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.02118

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)
Cited by: 20
Author(s): Elizabeth M. Reinhart, Benjamin J. Korry, Aislinn D. Rowan-Nash, Peter Belenky
Software Mentions: 5
Published: about 5 years ago

10.3389/fvets.2020.00255

Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces
Cited by: 24
Author(s): Nicole Ricker, Julian Trachsel, Phillip Colgan, Jennifer Jones, Jinlyung Choi, Jaejin Lee, Johann F. Coetzee, Adina Howe, Susan L. Brockmeier, Crystal L. Loving, Heather K. Allen
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-98549-w

Effect of functional oils or probiotics on performance and microbiota profile of newly weaned piglets
Cited by: 4
Author(s): Alexandre Maciel Vieira, Amanda Pires Sessin, Tatiany Aparecida Teixeira Soratto, Paula Gabriela da Silva Pires, Kátia Maria Cardinal, Glauber Wagner, Lucélia Hauptli, André Luís Ferreira Lima, Fabiano Dahlke, Diego Peres Netto, Priscila de Oliveira Moraes
Software Mentions: 5
Published: about 3 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/fmicb.2019.02944

Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi
Cited by: 12
Author(s): Gian Maria Niccolò Benucci, Delaney Burnard, Lara D. Shepherd, Gregory Bonito, Andrew B. Munkacsi
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpls.2021.694727

The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance
Cited by: 3
Author(s): Laxmi S. Mishra, Sanatkumar Mishra, Daniel Caddell, Devin Coleman‐Derr, Christiane Funk
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2020.01541

Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida)
Cited by: 15
Author(s): Justyna J. Hampel, Mark J. McCarthy, Sanni L. Aalto, Silvia E. Newell
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2021.629449

Diversity of Weissella confusa in Pozol and Its Carbohydrate Metabolism
Cited by: 5
Author(s): Diana Hernández-Oaxaca, Rafael López-Sánchez, Luis Lozano, Carmen Wacher, Lorenzo Segovia, Agustín López Munguía
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.02244

Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract
Cited by: 115
Author(s): Julie Meyer, Jessy Castellanos-Gell, Greta S. Aeby, Claudia C. Häse, Blake Ushijima, Valerie J. Paul
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-97619-3

Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)
Cited by: 13
Author(s): Kleopatra Leontidou, Despoina Vokou, Anna Sandionigi, Antonia Bruno, Maria Lazarina, Johannes De Groeve, Mingai Li, Claudio Varotto, Matteo Girardi, Andrea Galimberti, Alessandro Cristofori
Software Mentions: 5
Published: about 3 years ago

10.3389/fmicb.2018.02121

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils
Cited by: 48
Author(s): Miguel Semedo, Bongkeun Song, Tavis Sparrer, R. Phillips
Software Mentions: 5
Published: about 6 years ago

10.3389/fpls.2020.00203

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar
Cited by: 19
Author(s): Andrea Firrincieli, Mahsa Khorasani, A. Carolin Frank, Sharon L. Doty
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.548618

Microbiome in Healthy Women Between Two Districts With Different Air Quality Index
Cited by: 8
Author(s): Yinhua Wu, Zujin Wang, Yu Zhang, Li-Ming Ruan, Ang Li, Xiaoyan Liu
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2019.00496

Temperature-Dependent Network Modules of Soil Methanogenic Bacterial and Archaeal Communities
Cited by: 6
Author(s): Pengfei Liu, Melanie Klose, Ralf Conrad
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2021.631244

Unravelling the Importance of Diazotrophy in Corals – Combined Assessment of Nitrogen Assimilation, Diazotrophic Community and Natural Stable Isotope Signatures
Cited by: 6
Author(s): Vanessa N. Bednarz, Jeroen A. J. M. van de Water, Renaud Grover, Jean‐François Maguer, Maoz Fine, Christine Ferrier‐Pagès
Software Mentions: 5
Published: over 3 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702