bioconductor: phyloseq | Projects

10.1186/s40104-020-00498-3

Dietary Bacillus spp. enhanced growth and disease resistance of weaned pigs by modulating intestinal microbiota and systemic immunity
Cited by: 34
Author(s): Yijie He, Cynthia Jinno, Kwang‐Wook Kim, Zhaohai Wu, Bin Tan, Xunde Li, Rose Whelan, Yanhong Liu
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-34453-0

Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice
Cited by: 64
Author(s): Umesh D. Wankhade, Ying Zhang, Ping Kang, Maria P. Alfaro, Sree V. Chintapalli, Brian D. Piccolo, Kelly E. Mercer, Aline Andres, Keshari Thakali, Kartik Shankar
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-018-34640-z

Reduced diversity of gut microbiota in two Aedes mosquitoes species in areas of recent invasion
Cited by: 30
Author(s): Fausta Rosso, Valentina Tagliapietra, Davide Albanese, Massimo Pindo, Frédéric Baldacchino, Daniele Arnoldi, Claudio Donati, Annapaola Rizzoli
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-018-29971-w

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs
Cited by: 28
Author(s): Marion Lemaire, Samir Dou, Armelle Cahu, Michèle Formal, Laurence Le Normand, Véronique Rome, Isabelle Nogret, Stéphanie Ferret‐Bernard, Moez Rhimi, Isabelle Cuinet, Cécile Canlet, Marie Tremblay-Franco, Pascale Le Ruyet, Charlotte Baudry, Philippe Gérard, Isabelle Le Huërou‐Luron, Sophie Blat
Software Mentions: 4
Published: about 8 years ago

10.1038/srep18837

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems
Cited by: 49
Author(s): Oliver Grunert, Emma Hernandez-Sanabria, Ramiro Vílchez-Vargas, Ruy Jáuregui, Dietmar H. Pieper, Maaike Perneel, Marie-Christine Van Labeke, Dirk Reheul, Nico Boon
Software Mentions: 4
Published: almost 11 years ago

10.3390/nu13010205

Parenteral Fish-Oil Containing Lipid Emulsions Limit Initial Lipopolysaccharide-Induced Host Immune Responses in Preterm Pigs
Cited by: 5
Author(s): William Yakah, David Ramiro-Cortijo, Pratibha Singh, J. Howard Brown, Barbara J. Stoll, Madhulika Kulkarni, Berthe C Oosterloo, Doug Burrin, Krishna Rao Maddipati, Raina N. Fichorova, Steven D. Freedman, Camilia R. Martin
Software Mentions: 4
Published: over 5 years ago

10.3390/nu12113557

High Fat-High Fructose Diet-Induced Changes in the Gut Microbiota Associated with Dyslipidemia in Syrian Hamsters
Cited by: 29
Author(s): Rachael Horne, Yifan Yu, Rianna Zhang, Nyan Abdalqadir, Laura Rossi, Michael G. Surette, Philip M. Sherman, Khosrow Adeli
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.ppat.1008236

The cervicovaginal mucus barrier to HIV-1 is diminished in bacterial vaginosis
Cited by: 45
Author(s): Thuy Hoang, Emily Toler, Kevin DeLong, Nomfuneko A. Mafunda, Seth M. Bloom, Hannah C. Zierden, Thomas R. Moench, Jenell S. Coleman, Justin Hanes, Douglas S. Kwon, Samuel K. Lai, Richard A. Cone, Laura M. Ensign
Software Mentions: 4
Published: over 6 years ago

10.3390/nu13072467

Gastrointestinal Digestion of a Grape Pomace Extract: Impact on Intestinal Barrier Permeability and Interaction with Gut Microbiome
Cited by: 11
Author(s): Diego Taladrid, Dolores González de Llano, Irene Zorraquín‐Peña, Alba Tamargo, Mariana Silva, Natalia Molinero, M. Victoria Moreno‐Arribas, Begoňa Bartolomé
Software Mentions: 4
Published: about 5 years ago

10.1186/s12986-017-0170-x

High-cholesterol diet does not alter gut microbiota composition in mice
Cited by: 31
Author(s): Lidiya G. Dimova, Nikola Zlatkov, Henkjan J. Verkade, Bernt Eric Uhlin, Uwe J. F. Tietge
Software Mentions: 4
Published: over 9 years ago

10.3390/nu13062069

Timing of Tributyrin Supplementation Differentially Modulates Gastrointestinal Inflammation and Gut Microbial Recolonization Following Murine Ileocecal Resection
Cited by: 1
Author(s): Valentin Mocanu, Heekuk Park, Jerry Dang, Naomi Hotte, Aducio Thiesen, Michael Laffin, Haili Wang, Daniel W. Birch, Karen Madsen
Software Mentions: 4
Published: over 5 years ago

10.1038/s41597-019-0141-3

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot
Cited by: 8
Author(s): Antônio Pedro Camargo, Rafael Soares Correa de Souza, Patrícia de Britto Costa, Isabel Rodrigues Gerhardt, Ricardo A. Dante, Grazielle Sales Teodoro, Anna Abrahão, Hans Lambers, Marcelo Falsarella Carazzolle, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishna Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I. Min A. Chen, Natalia Ivanova, Nikos C. Kyrpides, Christa Pennacchio, Emiley A. Eloe‐Fadrosh, Paulo Arruda, Rafael S. Oliveira
Software Mentions: 4
Published: about 7 years ago

10.3390/nu11123006

Effect of Low-Protein Diet and Inulin on Microbiota and Clinical Parameters in Patients with Chronic Kidney Disease
Cited by: 38
Author(s): Silvia Lai, Alessio Molfino, Massimo Testorio, Adolfo Perrotta, Annachiara Currado, G Pintus, Daniele Pietrucci, Valeria Unida, Davide La Rocca, Silvia Biocca, Alessandro Desideri
Software Mentions: 3
Published: almost 7 years ago

10.3164/jcbn.18-84

Effect of storage and DNA extraction method on 16S rRNA-profiled fecal microbiota in Japanese adults
Cited by: 19
Author(s): Yuki Kawada, Yuji Naito, Akira Andoh, Motoyuki Ozeki, Ryo Inoüe
Software Mentions: 3
Published: almost 8 years ago

10.1210/clinem/dgaa382

Effect of Gut Microbiota and <i>PNPLA3</i> rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth
Cited by: 39
Author(s): Ayesha Monga Kravetz, Todd Testerman, Brittany Galuppo, Joerg Graf, Bridget Pierpont, Stephan Siebel, Richard Feinn, Nicola Santoro
Software Mentions: 3
Published: over 6 years ago

10.3390/jcm9061882

Transient and Persistent Gastric Microbiome: Adherence of Bacteria in Gastric Cancer and Dyspeptic Patient Biopsies after Washing
Cited by: 19
Author(s): Malene Roed Spiegelhauer, Juozas Kupčinskas, Thor Bech Johannesen, Mindaugas Urba, Jurgita Skiecevičienė, Laimas Virginijus Jonaitis, Tove Havnhøj Frandsen, Limas Kupčinskas, Kurt Fuursted, Leif Percival Andersen
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1007672

Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection
Cited by: 34
Author(s): Tiffany Hensley-McBain, Michael C. Wu, Jennifer A. Manuzak, Ryan Cheu, Andrew T. Gustin, Connor B. Driscoll, Alexander S. Zevin, Charlene Miller, Ernesto Coronado, Eric E. Smith, Jean Chang, Michael Gale, Ma Somsouk, Adam Burgener, Peter W. Hunt, Thomas J. Hope, Ann C. Collier, Nichole R. Klatt
Software Mentions: 3
Published: over 7 years ago

10.1098/rsos.170033

Microbe biogeography tracks water masses in a dynamic oceanic frontal system
Cited by: 26
Author(s): Anni Djurhuus, Philipp H. Boersch‐Supan, Svein‐Ole Mikalsen, Alex D. Rogers
Software Mentions: 3
Published: over 9 years ago

10.1186/s12931-019-1080-4

Chronic obstructive pulmonary disease upper airway microbiota alpha diversity is associated with exacerbation phenotype: a case-control observational study
Cited by: 29
Author(s): Alexa A. Pragman, Katherine A. Knutson, Trevor Gould, Richard E. Isaacson, Cavan Reilly, Christine Wendt
Software Mentions: 3
Published: over 7 years ago

10.1038/srep23680

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland
Cited by: 102
Author(s): Noriko A. Cassman, Márcio Fernandes Alves Leite, Yao Pan, Mattias de Hollander, Johannes A. van Veen, Eiko E. Kuramae
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-017-03476-4

Gut microbiota of liver transplantation recipients
Cited by: 37
Author(s): Li‐Ying Sun, Yunsheng Yang, Wei Qu, Zhi‐Jun Zhu, Wei Lin, Zhi‐Sheng Ye, Jian-Rui Zhang, Xuguo Sun, Zhili Zeng
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-06928-z

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence
Cited by: 44
Author(s): John K. Pearman, Joanne I. Ellis, Xabier Irigoien, Y.V.B. Sarma, Burton H. Jones, Susana Carvalho
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-11427-2

The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization
Cited by: 29
Author(s): Damien J. Cabral, Jenna I. Wurster, Myrto Eleni Flokas, Michail Alevizakos, Michelle A. Zabat, Benjamin J. Korry, Aislinn D. Rowan, William H. Sano, Nikolaos Andreatos, Robert Ducharme, Philip A. Chan, Eleftherios Mylonakis, Beth Burgwyn Fuchs, Peter Belenky
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-11552-y

Bacterial communities 16S rDNA fingerprinting as a potential tracing tool for cultured seabass Dicentrarchus labrax
Cited by: 34
Author(s): Tânia Pimentel, Joana Marcelino, Fernando Ricardo, Amadeu M.V.M. Soares, Ricardo Calado
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-11644-9

Can intestinal microbiota be associated with non-intestinal cancers?
Cited by: 18
Author(s): Camille M. Jacqueline, Lionel Brazier, Dominique Faugère, François Renaud, Frédéric Thomas, Benjamín Roche
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-15377-7

Mitochondrial gene polymorphism is associated with gut microbial communities in mice
Cited by: 47
Author(s): Misa Hirose, Axel Künstner, Paul Schilf, Annika Sünderhauf, Jan Rupp, Olaf Jöhren, Markus Schwaninger, Christian Sina, John F. Baines, Saleh M. Ibrahim
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-018-25081-9

Diversity, structure and sources of bacterial communities in earthworm cocoons
Cited by: 19
Author(s): Manuel Aira, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-26641-9

Exploring the diversity-stability paradigm using sponge microbial communities
Cited by: 36
Author(s): Bettina Glasl, Caitlin E. Smith, David G. Bourne, Nicole S. Webster
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-27100-1

Spatial and Environmental Variation of the Human Hair Microbiota
Cited by: 24
Author(s): Lauren Brinkac, Thomas H. Clarke, Harinder Singh, Chris Greco, Andrés Gómez, Manolito Torralba, Bryan Frank, Karen E. Nelson
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-29443-1

Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients
Cited by: 32
Author(s): Laura Iaffaldano, Ilaria Granata, Chiara Pagliuca, Maria Valeria Esposito, Giorgio Casaburi, Giuliana Salerno, Roberta Colicchio, Marina Piccirillo, Carolina Ciacci, Giovanna Del Vecchio Blanco, Mario Rosario Guarracino, Paola Salvatore, Francesco Salvatore, Valeria D’Argenio, Lucia Sacchetti
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-29759-y

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis
Cited by: 36
Author(s): Simon Ghaly, Nadeem O. Kaakoush, Frances Lloyd, Terence McGonigle, D. Mok, Angela Baird, Borut Klopcic, Lavinia Gordon, Shelley Gorman, Cynthia Forest, Roger Bouillon, Ian C. Lawrance, Prue H. Hart
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-30179-1

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing
Cited by: 40
Author(s): Francisco J. A. Nascimento, Delphine Lallias, Holly M. Bik, Simon Creer
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-32925-x

Oleoylethanolamide treatment affects gut microbiota composition and the expression of intestinal cytokines in Peyer’s patches of mice
Cited by: 35
Author(s): Monica Di Paola, Elena Bonechi, Gustavo Provensi, Alessia Costa, Gerard Clarke, Clara Ballerini, Carlotta De Filippo, Maria Beatrice Passani
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-36364-6

Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation
Cited by: 88
Author(s): Chee Y. Ooi, Saad Syed, Laura Rossi, Millie Garg, Bronwen Needham, Julie Avolio, Kelsey Young, Michael G. Surette, Tanja Gonska
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-38489-8

Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome
Cited by: 39
Author(s): Megha Singhal, Benjamin A. Turturice, Christopher R. Manzella, Ravi Ranjan, Ahmed A. Metwally, Juliana Theorell, Yue Huang, Waddah A. Alrefai, Pradeep K. Dudeja, Patricia W. Finn, David L. Perkins, Ravinder K. Gill
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39586-4

Temporal variability of diazotroph community composition in the upwelling region off NW Iberia
Cited by: 17
Author(s): Víctor Moreira-Coello, Beatriz Mouriño‐Carballido, Emilio Marañón, Ana Fernández-Carrera, Antonio Bode, Eva Sintes, Jonathan P. Zehr, Kendra A. Turk‐Kubo, Marta M. Varela
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42862-y

A longitudinal characterization of the Non-Cystic Fibrosis Bronchiectasis airway microbiome
Cited by: 29
Author(s): Taylor E Woo, Rachel Lim, Alya Heirali, Nicole Acosta, Harvey Rabin, Christopher H. Mody, Ranjani Somayaji, Michael G. Surette, Christopher D. Sibley, Douglas G. Storey, Michael D. Parkins
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43517-8

Chemosynthetic ectosymbionts associated with a shallow-water marine nematode
Cited by: 14
Author(s): Laure Bellec, Marie-Anne Cambon-Bonavita, Stéphane Hourdez, Mohamed Jebbar, Aurélie Tasiemski, Lucile Durand, Nicolas Gayet, Daniela Zeppilli
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-46087-x

Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages
Cited by: 48
Author(s): George Tetz, Stuart M. Brown, Yuhan Hao, Victor Tetz
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-46535-8

Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma
Cited by: 70
Author(s): Jennifer N. Walker, Blake Hanson, Chloe L. Pinkner, Shelby Simar, Jerome S. Pinkner, Rohan Parikh, Mark W. Clemens, Scott J. Hultgren, Terence M. Myckatyn
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-48784-z

Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice
Cited by: 29
Author(s): Raúl Cabrera‐Rubio, Angela Patterson, Paul D. Cotter, Naiara Beraza
Software Mentions: 3
Published: about 7 years ago

10.3390/nu13051673

Infant Gut Microbiota Associated with Fine Motor Skills
Cited by: 13
Author(s): Inmaculada Acuña, Tomás Cerdó, Alberto Matarán Ruiz, Francisco J. Torres-Espínola, Ana López‐Moreno, Margarita Aguilera, Antonio Suárez, Cristina Campoy
Software Mentions: 3
Published: over 5 years ago

10.3390/nu12051532

Human Milk Oligosaccharide Supplementation Affects Intestinal Barrier Function and Microbial Composition in the Gastrointestinal Tract of Young Sprague Dawley Rats
Cited by: 19
Author(s): Faye Chleilat, Teja Klančič, Kyle Ma, Alana Schick, Jodi E. Nettleton, Raylene A. Reimer
Software Mentions: 3
Published: over 6 years ago

10.3390/nu10122009

Gut Microbiota and Endothelial Dysfunction Markers in Obese Mexican Children and Adolescents
Cited by: 80
Author(s): Khemlal Nirmalkar, Selvasankar Murugesan, María Luisa Pizano-Zárate, Loan Edel Villalobos-Flores, Cristina García-González, Rosa María Morales-Hernández, Jorge A. Núñez-Hernández, Fernando Hernández-Quiroz, María del Socorro Romero Figueroa, César Hernández‐Guerrero, Carlos Hoyo‐Vadillo, Jaime García‐Mena
Software Mentions: 3
Published: almost 8 years ago

10.3390/nu12020290

Long-Term Blackcurrant Supplementation Modified Gut Microbiome Profiles in Mice in an Age-Dependent Manner: An Exploratory Study
Cited by: 13
Author(s): Lei Cao, Sang Gil Lee, Melissa M. Melough, Junichi Sakaki, Kendra Maas, Sung I. Koo
Software Mentions: 3
Published: over 6 years ago

10.3390/nu11051063

Tart Cherry Concentrate Does Not Alter the Gut Microbiome, Glycaemic Control or Systemic Inflammation in a Middle-Aged Population
Cited by: 22
Author(s): Rebecca Lear, Mary F. O’Leary, Lee O’Brien Andersen, Corey C. Holt, Christen Rune Stensvold, Mark van der Giezen, Joanna L. Bowtell
Software Mentions: 3
Published: over 7 years ago

10.3390/nu12041122

Saccharin Supplementation Inhibits Bacterial Growth and Reduces Experimental Colitis in Mice
Cited by: 14
Author(s): Annika Sünderhauf, René Pagel, Axel Künstner, Anika E. Wagner, Jan Rupp, Saleh M. Ibrahim, Stefanie Derer, Christian Sina
Software Mentions: 3
Published: over 6 years ago

10.3390/nu10081069

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice
Cited by: 28
Author(s): Simon Ghaly, Nadeem O. Kaakoush, Frances Lloyd, Lavinia Gordon, Cynthia Forest, Ian C. Lawrance, Prue H. Hart
Software Mentions: 3
Published: about 8 years ago

10.3390/nu13030820

Microbiota Changes in Fathers Consuming a High Prebiotic Fiber Diet Have Minimal Effects on Male and Female Offspring in Rats
Cited by: 3
Author(s): Faye Chleilat, Alana Schick, Raylene A. Reimer
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0219070

Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology
Cited by: 14
Author(s): Melissa R. L. Whitaker, Christopher C. M. Baker, Shayla Salzman, Dino J. Martins, Naomi E. Pierce
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2020.541554

An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature
Cited by: 28
Author(s): Caitlin M. Gionfriddo, Ann M. Wymore, Daniel S. Jones, Regina L. Wilpiszeski, Mackenzie M. Lynes, Geoff A. Christensen, Ally Soren, Cynthia C. Gilmour, Mircea Podar, Dwayne A. Elias
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0223128

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia
Cited by: 22
Author(s): Joan T. Price, Bellington Vwalika, Marcia M. Hobbs, Julie A. Nelson, Elizabeth M. Stringer, Fei Zou, Katelyn J. Rittenhouse, Andrea Azcárate-Peril, Margaret P. Kasaro, Jeffrey S. A. Stringer
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0151594

Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions
Cited by: 49
Author(s): Hennersdorf Philipp, Sonja Kleinertz, Stefan Theisen, Muslihudeen A. Abdul-Aziz, Grit Mrotzek, Harry W. Palm, Hans Peter Saluz
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0219982

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae
Cited by: 12
Author(s): Osiris Gaona, Selene Gómez-Acata, Daniel Cerqueda‐García, Carla Ximena Neri-Barrios, Luisa I. Falcón
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0237262

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet
Cited by: 11
Author(s): F. Albonico, Claudia Barelli, Davide Albanese, Mattia Manica, Erika Partel, Fausta Rosso, Silvia Ripellino, Massimo Pindo, Claudio Donati, A. Zecconi, Michele Mortarino, Heidi C. Hauffe
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.02243

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants
Cited by: 60
Author(s): Priscila Caroline Thiago Dobbler, Renato S. Procianoy, Volker Mai, Rita de Cássia dos Santos Silveira, Andrea Corso, Bruna Schafer Rojas, Luiz Fernando Würdig Roesch
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.42866

The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs
Cited by: 36
Author(s): Leah Guthrie, Sarah J. Wolfson, Libusha Kelly
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0232699

Azolla filiculoides L. as a source of metal-tolerant microorganisms
Cited by: 22
Author(s): Artur Banach, Agnieszka Kuźniar, Jarosław Grządziel, Agnieszka Woliñska
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.00121

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology
Cited by: 57
Author(s): Jennifer L. Wood, Caixian Tang, Ashley E. Franks
Software Mentions: 3
Published: over 8 years ago

10.1128/mSystems.00095-16

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
Cited by: 132
Author(s): Berith Elkær Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank Møller Aarestrup, Sünje Johanna Pamp
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0215918

Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses
Cited by: 15
Author(s): Michelle Coleman, Canaan Whitfield-Cargile, Rodolfo Madrigal, Noah D. Cohen
Software Mentions: 3
Published: over 7 years ago

10.1186/s12866-020-01759-x

The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection
Cited by: 23
Author(s): Harris Onywera, Anna‐Lise Williamson, Luca Cozzuto, Sarah Bonnin, Zizipho Z. A. Mbulawa, David Coetzee, Julia Ponomarenko, Tracy L. Meiring
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0242108

Broiler chickens and early life programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects
Cited by: 16
Author(s): Gustavo A. Ramírez, Ella Richardson, Jory Clark, Jitendra Keshri, Yvonne Drechsler, M. E. Berrang, Richard J. Meinersmann, N. A. Cox, Brian B. Oakley
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0178755

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries
Cited by: 29
Author(s): Mikel Aguirre, David Abad, Aitor Albaina, Lauren Cralle, María Soledad Goñi-Urriza, Andone Estonba, Iratxe Zarraonaindia
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0217296

Influence of own mother's milk and different proportions of formula on intestinal microbiota of very preterm newborns
Cited by: 17
Author(s): Adriana Zanella, Rita de Cássia dos Santos Silveira, Luiz Fernando Würdig Roesch, Andrea Corso, Priscila Caroline Thiago Dobbler, Volker Mai, Renato S. Procianoy
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.564408

Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life
Cited by: 10
Author(s): Stephanie D. Jurburg, Alex Bossers
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00119-17

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring
Cited by: 77
Author(s): Amy Apprill, Colin Miller, Michael J. Moore, John W. Durban, Holly Fearnbach, Lance G. Barrett‐Lennard
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2018.00870

Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes
Cited by: 30
Author(s): Ditte V. Vestergaard, Gitte Juel Holst, Ioannis Basinas, Grethe Elholm, Vivi Schlünssen, Allan Linneberg, Tina Šantl-Temkiv, Kai Finster, Torben Sigsgaard, Ian P. G. Marshall
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0174890

Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers
Cited by: 33
Author(s): Jason T. Payne, Justin Millar, Colin R. Jackson, Clifford A. Ochs
Software Mentions: 3
Published: over 9 years ago

10.1186/s12866-021-02139-9

Identification of cutaneous fungi and mites in adult atopic dermatitis: analysis by targeted 18S rRNA amplicon sequencing
Cited by: 8
Author(s): Sofie Marie Edslev, Paal Skytt Andersen, Tove Agner, Ditte Marie Lindhardt Saunte, Anna Cäcilia Ingham, Thor Bech Johannesen, Maja‐Lisa Clausen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12866-021-02156-8

Microbial predation accelerates granulation and modulates microbial community composition
Cited by: 7
Author(s): Siew Herng Chan, Muhammad Hafiz Ismail, Chuan Hao Tan, Scott A. Rice, Diane McDougald
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0215872

Incubation and grazing effects on spirotrich ciliate diversity inferred from molecular analyses of microcosm experiments
Cited by: 6
Author(s): Jean‐David Grattepanche, Doris L. Juarez, Cameah Corin Wood, George B. McManus, Laura A. Katz
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0204629

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing
Cited by: 64
Author(s): Simon Poirier, Olivier Rué, R. Peguilhan, Gwendoline Coeuret, Monique Zagorec, Marie‐Christine Champomier‐Vergès, Valentin Loux, Stéphane Chaillou
Software Mentions: 3
Published: about 8 years ago

10.1186/s12866-021-02288-x

Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome
Cited by: 2
Author(s): Tanweer Goolam Mahomed, Rph Peters, Ghj Pretorius, Akhter Goolam Mahomed, Veronica Ueckermann, Marleen M. Kock, M.M. Ehlers
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2021.567961

Tree Species Richness and Neighborhood Effects on Ectomycorrhizal Fungal Richness and Community Structure in Boreal Forest
Cited by: 11
Author(s): Eveli Otsing, Sten Anslan, Elia Ambrosio, Julia Koricheva, Leho Tedersoo
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0112763

Bacterial Endophytic Communities in the Grapevine Depend on Pest Management
Cited by: 101
Author(s): A. Campisano, Livio Antonielli, Michael Pancher, Sohail Yousaf, Massimo Pindo, I. Pertot
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12866-018-1367-5

Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study
Cited by: 13
Author(s): Martin Steen Mortensen, Bo Jensen, Jeanne V.A. Williams, Asker Brejnrod, Lee O’Brien Andersen, Dennis Röser, Bente Utoft Andreassen, Andreas Munk Petersen, Christen Rune Stensvold, Søren J. Sørensen, Karen A. Krogfelt
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12866-019-1586-4

Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes
Cited by: 14
Author(s): Samuel Verbanic, Colin Y. Kim, John M. Deacon, Irene Chen
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0231942

Putting the microbiota to work: Epigenetic effects of early life antibiotic treatment are associated with immune-related pathways and reduced epithelial necrosis following Salmonella Typhimurium challenge in vitro
Cited by: 4
Author(s): Matheus O. Costa, Janelle M Fouhse, Ana Paula P. Silva, Benjamin P. Willing, John C. S. Harding
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.02361

Bacterial Associates of a Gregarious Riparian Beetle With Explosive Defensive Chemistry
Cited by: 18
Author(s): Reilly McManus, Alison Ravenscraft, Wendy Moore
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2021.637834

Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia
Cited by: 18
Author(s): R. M. Costa, Anny Cárdenas, Céline Loussert, Gaëlle Toullec, A. Meibom, Christian R. Voolstra
Software Mentions: 3
Published: over 5 years ago

10.1186/s12866-020-01724-8

The influence of blood on the human gut microbiome
Cited by: 23
Author(s): Thierry Chénard, Mandy Malick, Jean Dubé, Éric Massé
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2020.01093

Taxon Appearance From Extraction and Amplification Steps Demonstrates the Value of Multiple Controls in Tick Microbiota Analysis
Cited by: 24
Author(s): Emilie Lejal, Agustı́n Estrada-Peña, Maud Marsot, Jean-François Cosson, Olivier Rué, Mahendra Mariadassou, Cédric Midoux, Muriel Vayssier‐Taussat, Thomas V. Pollet
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0183716

Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen
Cited by: 93
Author(s): Nadja Danner, Alexander Keller, Stephan Härtel, Ingolf Steffan‐Dewenter
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0181964

Regulation of type 1 diabetes development and B-cell activation in nonobese diabetic mice by early life exposure to a diabetogenic environment
Cited by: 15
Author(s): Alessandra Riva, Maja Wållberg, Francesca Ronchi, Richard M. R. Coulson, Andrew P. Sage, Lucy Thorne, Ian Goodfellow, Kathleen McCoy, Miyuki Azuma, Anne Cooke, Robert Busch
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0116704

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice
Cited by: 241
Author(s): Aaron C. Ericsson, J. Wade Davis, William G. Spollen, Nathan J. Bivens, Scott A. Givan, Catherine E. Hagan, Mark A. McIntosh, Craig L. Franklin
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0199291

Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil
Cited by: 25
Author(s): Pilar Truchado, María I. Gil, Trevor Suslow, Ana Allende
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0224658

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia
Cited by: 15
Author(s): Heng Choon Cheong, Polly Soo Xi Yap, Chun Wie Chong, Yi Ying Cheok, Chalystha Yie Qin Lee, Guan Huat Tan, Sofiah Sulaiman, Jamiyah Hassan, Negar Shafiei Sabet, Chung Yeng Looi, Rishein Gupta, Bernard P. Arulanandam, Sazaly AbuBakar, Cindy Shuan Ju Teh, Li Chang, Won Fen Wong
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2021.640469

Mycoplankton Biome Structure and Assemblage Processes Differ Along a Transect From the Elbe River Down to the River Plume and the Adjacent Marine Waters
Cited by: 7
Author(s): Yanyan Yang, Stefanos Banos, Gunnar Gerdts, Antje Wichels, M. Reich
Software Mentions: 3
Published: over 5 years ago

10.1080/20002297.2018.1536182

Preliminary study of the oral mycobiome of children with and without dental caries
Cited by: 27
Author(s): Jacquelyn M. Fechney, Gina V. Browne, Neeta Prabhu, László Irinyi, Wieland Meyer, Toby Hughes, Michelle Bockmann, Grant Townsend, Hanieh Salehi, Christina Adler
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0142603

Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities
Cited by: 33
Author(s): Jamie A. FitzGerald, Eoin Allen, David Wall, Stephen A. Jackson, Jerry D. Murphy, Alan D. W. Dobson
Software Mentions: 3
Published: almost 11 years ago

10.3389/fmicb.2019.02103

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages
Cited by: 16
Author(s): Madangchanok Imchen, Ranjith Kumavath, Aline B. M. Vaz, Aristóteles Goés-Neto, Debmalya Barh, Preetam Ghosh, Natalia Kozyrovska, Olga Podolich, Vasco Azevedo
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2020.541972

Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products
Cited by: 11
Author(s): Enrique Doster, K. Thomas, Margaret D. Weinroth, Jennifer Parker, K.K. Crone, Terrance M. Arthur, J. W. Schmidt, T. L. Wheeler, K. E. Belk, Paul S. Morley
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2020.576750

Variability of the Atmospheric PM10 Microbiome in Three Climatic Regions of France
Cited by: 6
Author(s): Abdoulaye Samaké, Jean M.F. Martins, Aurélie Bonin, Gaëlle Uzu, Pierre Taberlet, Sébastien Conil, Olivier Favez, Alexandre Thomasson, Benjamin Chazeau, Nicolas Marchand, Jean-Luc Jaffrezo
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2021.735022

Shifts in Soil Structure, Biological, and Functional Diversity Under Long-Term Carbon Deprivation
Cited by: 4
Author(s): Paul B. L. George, David B. Fidler, Joy D. Van Nostrand, Jonathan A. Atkinson, Sacha J. Mooney, Simon Creer, Robert I. Griffiths, James E. McDonald, David A. Robinson, Davey L. Jones
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2016.01884

Diazotroph Diversity in the Sea Ice, Melt Ponds, and Surface Waters of the Eurasian Basin of the Central Arctic Ocean
Cited by: 31
Author(s): Mar Fernández‐Méndez, Kendra A. Turk‐Kubo, Pier Luigi Buttigieg, Josephine Z. Rapp, Thomas Krumpen, Jonathan P. Zehr, Antje Boetius
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0207985

Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest
Cited by: 40
Author(s): Jose E. Pietri, Connor R. Tiffany, Dangsheng Liang
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2016.00893

Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome
Cited by: 16
Author(s): Julie Meyer, J. Michael Rodgers, Brian A. Dillard, Valerie J. Paul, Max Teplitski
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0208018

Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease
Cited by: 12
Author(s): Steven Cowman, Phillip James, Robert Wilson, William Cookson, Miriam F. Moffatt, Michael R. Loebinger
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0179945

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major)
Cited by: 21
Author(s): Lucie Kropáčková, Hana Pechmanová, Michal Vinkler, Jana Svobodová, Hana Velová, Martin Těšičký, Jean‐François Martin, Jakub Kreisinger
Software Mentions: 3
Published: over 9 years ago

Projects: bioconductor: phyloseq

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Papers Mentioning phyloseq 1,702