bioconductor: phyloseq | Projects

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 6 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 6 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: almost 7 years ago

10.1186/s13059-021-02401-3

Detection of cell-free microbial DNA using a contaminant-controlled analysis framework
Cited by: 18
Author(s): Enrique Zozaya‐Valdés, Stephen Q. Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T. Papenfuss, Shahneen Sandhu, Mark A. Dawson, Sarah‐Jane Dawson
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giy054

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
Cited by: 82
Author(s): Alexandre Almeida, Alex L. Mitchell, Aleksandra Tarkowska, Alex Bateman
Software Mentions: 5
Published: over 8 years ago

10.3390/insects10110391

Do Host Plant and Associated Ant Species Affect Microbial Communities in Myrmecophytes?
Cited by: 5
Author(s): Mario X. Ruiz-González, Céline Leroy, Alain Déjean, Hervé Gryta, Patricia Jargeat, Angelo D. Armijos Carrión, Jérôme Orivel
Software Mentions: 5
Published: almost 7 years ago

10.1186/s40635-021-00398-4

Pulmonary and intestinal microbiota dynamics during Gram-negative pneumonia-derived sepsis
Cited by: 8
Author(s): Nora S. Wolff, Max C. Jacobs, W. Joost Wiersinga, Floor Hugenholtz
Software Mentions: 5
Published: over 5 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 6 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 9 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 5 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 9 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 9 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 8 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: almost 8 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: almost 7 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 6 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 6 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 6 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 5 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: about 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 5 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 6 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 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: over 5 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 5 years ago

10.3390/ijms21093262

Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations
Cited by: 5
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00290-19

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments
Cited by: 149
Author(s): Lisa Karstens, Mark Asquith, Sean Davin, Damien A. Fair, W. Thomas Gregory, Alan J. Wolfe, Jonathan Braun, Shannon K. McWeeney
Software Mentions: 4
Published: about 7 years ago

10.3389/fcimb.2020.00174

Longitudinal Associations of the Cystic Fibrosis Airway Microbiome and Volatile Metabolites: A Case Study
Cited by: 13
Author(s): Andrea Hahn, Katrine Whiteson, Thomas J. Davis, Joann Phan, Iman Sami, Anastassios C. Koumbourlis, Robert J. Freishtat, Keith A. Crandall, Heather D. Bean
Software Mentions: 4
Published: over 6 years ago

10.3389/fphys.2016.00606

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Cited by: 30
Author(s): Alejandra Contreras, Benjamin Cocom-Chan, Georgina Hernández-Montes, Tobías Portillo-Bobadilla, Osbaldo Resendis‐Antonio
Software Mentions: 4
Published: almost 10 years ago

10.1128/mSystems.00133-16

SSUnique: Detecting Sequence Novelty in Microbiome Surveys
Cited by: 4
Author(s): Michael D. J. Lynch, Josh D. Neufeld
Software Mentions: 4
Published: almost 10 years ago

10.3389/fcimb.2019.00271

Successional Dynamics in the Gut Microbiome Determine the Success of Clostridium difficile Infection in Adult Pig Models
Cited by: 4
Author(s): Stephanie D. Jurburg, Jan J. B. W. J. Cornelissen, Paulo de Boer, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 4
Published: about 7 years ago

10.1128/mSphere.00083-21

Exposure to Parasitic Protists and Helminths Changes the Intestinal Community Structure of Bacterial Communities in a Cohort of Mother-Child Binomials from a Semirural Setting in Mexico
Cited by: 8
Author(s): Oswaldo Partida-Rodríguez, Miriam Nieves-Ramı́rez, Isabelle Laforest‐Lapointe, Eric Brown, Laura Wegener Parfrey, A Valadez-Salazar, Lisa Thorson, Patricia Morán, Enrique González, E. Ortiz Rascón, Ulises Magaña, E. Hernández, Liliana Rojas-Velázquez, Javier Torres, Marie Claire Arrieta, Cecilia Ximénez, B. Brett Finlay
Software Mentions: 4
Published: about 5 years ago

10.1128/mSphere.00936-20

Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients
Cited by: 18
Author(s): Skye Fishbein, Tiffany Hink, Kimberly A. Reske, Candice Cass, Emily Struttmann, Zainab Hassan Iqbal, Sondra Seiler, Jennie H. Kwon, Carey‐Ann D. Burnham, Gautam Dantas, Erik R. Dubberke
Software Mentions: 4
Published: over 5 years ago

10.3389/fvets.2020.00438

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats
Cited by: 2
Author(s): Andrea Balboni, Giovanni Franzo, Luca Bano, Stefano Arcangeli, Alessia Rizzardi, Lorenza Urbani, Sofia Segatore, Federica Serafini, Francesco Dondi, Mara Battilani
Software Mentions: 4
Published: about 6 years ago

10.3389/fnut.2020.00083

Vitamin B12 Deficiency Alters the Gut Microbiota in a Murine Model of Colitis
Cited by: 37
Author(s): Eberhard Lurz, Rachael Horne, Pekka Määttänen, Richard Wu, Steven R. Botts, Bo Li, Laura Rossi, Kathene C. Johnson‐Henry, Agostino Pierro, Michael G. Surette, Philip M. Sherman
Software Mentions: 4
Published: over 6 years ago

10.3389/fnut.2021.640100

Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome
Cited by: 7
Author(s): Jason W. Arnold, Hunter D. Whittington, Sue F. Dagher, Jeffery Roach, M. Andrea Azcárate-Peril, José M. Bruno-Bárcena
Software Mentions: 4
Published: over 5 years ago

10.1128/mSphere.01237-20

Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity
Cited by: 16
Author(s): Jialin Hu, Virginia L. Jin, Julie Y. M. Konkel, Sean M. Schaeffer, Liesel G Schneider, Jennifer M. DeBruyn
Software Mentions: 4
Published: over 5 years ago

10.3389/fcimb.2020.00073

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota
Cited by: 29
Author(s): Ashley E. Kates, Omar Jarrett, Joseph H. Skarlupka, Ajay K. Sethi, Megan Duster, Lauren Watson, Garret Suen, Keith P. Poulsen, Nasia Safdar
Software Mentions: 4
Published: over 6 years ago

10.1128/mSphere.00730-19

Gut Microbiomes of the Eastern Oyster ( Crassostrea virginica ) and the Blue Mussel ( Mytilus edulis ): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities
Cited by: 43
Author(s): Melissa L. Pierce, J. Evan Ward
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.67740

Bacterial–fungal interactions in the neonatal gut influence asthma outcomes later in life
Cited by: 16
Author(s): Rozlyn C.T. Boutin, Charisse Petersen, Sarah E. Woodward, Antonio Serapio-Palacios, Tahereh Bozorgmehr, Rachelle Loo, Alina Chalanuchpong, Mihai Cirstea, Bernard C. Lo, Kelsey E. Huus, Weronika Barcik, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Kelly M. McNagny, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.54792

Gut Helicobacter presentation by multiple dendritic cell subsets enables context-specific regulatory T cell generation
Cited by: 18
Author(s): Emilie V. Russler-Germain, Jaeu Yi, Shannon Young, Katherine Nutsch, Ho-Lun Wong, Teresa L. Ai, Jiani N. Chai, Vivek Durai, Daniel H. Kaplan, Ronald N. Germain, Kenneth M. Murphy, Chyi-Song Hsieh
Software Mentions: 4
Published: over 5 years ago

10.1128/mSphere.00626-18

Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity
Cited by: 15
Author(s): Sarahi L. Garcia, Anna J. Székely, Christoffer Bergvall, Martha Schattenhofer, Sari Peura
Software Mentions: 4
Published: over 7 years ago

10.1016/j.jaci.2017.08.041

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting
Cited by: 159
Author(s): Marie‐Claire Arrieta, Andrea Arévalo, Leah T. Stiemsma, Pedro A. Dimitriu, Martha Chico, Sofia Loor, Maritza Vaca, Rozlyn C.T. Boutin, Evan Morien, Mingliang Jin, Stuart E. Turvey, Jens Walter, Laura Wegener Parfrey, Philip J. Cooper, B. Brett Finlay
Software Mentions: 4
Published: about 8 years ago

10.1128/mSphere.00382-18

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
Cited by: 22
Author(s): Sarah M. Hird, Holly H. Ganz, Jonathan A. Eisen, Walter M. Boyce
Software Mentions: 4
Published: almost 8 years ago

10.1093/jas/skaa181

The effect of maternal antibiotic use in sows on intestinal development in offspring
Cited by: 10
Author(s): Astrid de Greeff, Dirkjan Schokker, Petra Roubos-van den Hil, P. Ramaekers, S.A. Vastenhouw, Frank Harders, Alex Bossers, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.36741

Convergence between the microcosms of Southeast Asian and North American pitcher plants
Cited by: 26
Author(s): Leonora S. Bittleston, Charles J. Wolock, Bakhtiar Effendi Yahya, Xin Yue Chan, Kok Gan Chan, Naomi E. Pierce, Anne Pringle
Software Mentions: 4
Published: about 8 years ago

10.3389/fcimb.2020.00173

Cystic Fibrosis Patients Infected With Epidemic Pseudomonas aeruginosa Strains Have Unique Microbial Communities
Cited by: 7
Author(s): Nicole Acosta, Barbara Waddell, Alya Heirali, Ranjani Somayaji, Michael G. Surette, Matthew L. Workentine, Harvey Rabin, Michael D. Parkins
Software Mentions: 4
Published: over 6 years ago

10.3389/fendo.2020.606530

Gastrointestinal Helminth Infection Improves Insulin Sensitivity, Decreases Systemic Inflammation, and Alters the Composition of Gut Microbiota in Distinct Mouse Models of Type 2 Diabetes
Cited by: 15
Author(s): Zainab Khudhair, Rafid Alhallaf, Ramon M. Eichenberger, Jen Whan, Andreas Kupz, Matthew A. Field, Lutz Krause, David T. Wilson, Norelle L. Daly, Paul Giacomin, Javier Sotillo, Alex Loukas
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.491425

Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems
Cited by: 5
Author(s): Erin Jones, Natasha A. Griffin, Julia E. Kelso, Gregory T. Carling, Michelle A. Baker, Zachary T. Aanderud
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSphere.00226-16

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City
Cited by: 22
Author(s): Holly M. Bik, Julia M. Maritz, Albert Luong, Hakdong Shin, Maria Gloria Domínguez-Bello, Jane M. Carlton
Software Mentions: 4
Published: almost 10 years ago

10.3389/fmicb.2019.01206

Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem
Cited by: 70
Author(s): Racha El Hage, Emma Hernandez-Sanabria, Marta Calatayud, Ruben Props, Tom Van de Wiele
Software Mentions: 4
Published: over 7 years ago

10.3390/ijerph18126348

Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test
Cited by: 4
Author(s): Francesco Spennati, Salvatore La China, G. Siracusa, Simona Di Gregorio, A. Bardi, Valeria Tigini, Greg Mori, David Gabriel, Giulio Munz
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.00824-21

Drosophila Antimicrobial Peptides and Lysozymes Regulate Gut Microbiota Composition and Abundance
Cited by: 52
Author(s): Alice Marra, Mark A. Hanson, Shu Kondo, Berra Erkoşar, Bruno Lemaître
Software Mentions: 4
Published: about 5 years ago

10.3390/jof5040095

9th Trends in Medical Mycology Held on 11–14 October 2019, Nice, France, Organized under the Auspices of EORTC-IDG and ECMM
Cited by: 14
Author(s): Jean Pierre Gangneux, Olivier Lortholary, Oliver A. Cornely, Livio Pagano
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2020.00993

Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition?
Cited by: 14
Author(s): Zhiguang Qiu, Juntao Wang, Manuel Delgado‐Baquerizo, Pankaj Trivedi, Eleonora Egidi, Yi-Min Chen, Haiyang Zhang, Brajesh K. Singh
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.3133

Transcriptomic differentiation underlying marine‐to‐freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)
Cited by: 17
Author(s): Lily C. Hughes, Gustavo M. Somoza, Bryan Nguyen, James P. Bernot, Mariano González‐Castro, Juan Martín Díaz de Astarloa, Guillermo Ortı́
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2019.02874

Lifestyle-Induced Microbial Gradients: An Indian Perspective
Cited by: 6
Author(s): Rashmi Singh, Mohammed Monzoorul Haque, Sharmila S. Mande
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40793-020-00364-9

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato
Cited by: 12
Author(s): Peter Kusstatscher, Wisnu Adi Wicaksono, Alessandro Bergna, Tomislav Cernava, Nick Bergau, Alain Tissier, Bettina Hause, Gabriele Berg
Software Mentions: 4
Published: about 6 years ago

10.1038/s41396-021-00988-w

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem
Cited by: 68
Author(s): Ya Jou Chen, Pok Man Leung, Jennifer L. Wood, Sean K. Bay, Philip Hugenholtz, Adam J. Kessler, Guy Shelley, David W. Waite, Ashley E. Franks, Perran L. M. Cook, Chris Greening
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2020.572741

Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine (Lupinus angustifolius)
Cited by: 15
Author(s): Ana A. Robles-Aguilar, Oliver Grunert, Emma Hernandez-Sanabria, Mohamed Mysara, Erik Meers, Nico Boon, Nicolai David Jablonowski
Software Mentions: 4
Published: almost 6 years ago

10.1093/femsec/fiab054

Relative contributions of egg-associated and substrate-associated microorganisms to black soldier fly larval performance and microbiota
Cited by: 12
Author(s): Stijn J. J. Schreven, Hugo de Vries, Gerben D. A. Hermes, Hauke Smidt, Marcel Dicke, J.J.A. van Loon
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2019.01697

Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management
Cited by: 19
Author(s): Paula Harkes, Joris J.M. van Steenbrugge, S.J.J. van den Elsen, Afnan Khalil Ahmad Suleiman, J.J. de Haan, M.H.M. Holterman, J. Helder
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13073-021-00843-9

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
Cited by: 42
Author(s): Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 4
Published: over 5 years ago

10.1186/s13073-021-00856-4

Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India
Cited by: 29
Author(s): Camila Alvarez-Silva, Alireza Kashani, Torben Hansen, Nishal Kumar Pinna, Ranjit Mohan Anjana, Anirban Dutta, Shruti Saxena, Julie Støy, Ulla Kampmann, Trine Nielsen, Torben Jørgensen, Visvanathan Gnanaprakash, Rameshkumar Gnanavadivel, Sukumaran Aswath, Coimbatore Subramanian Shanthi Rani, Kristine Færch, Venkatesan Radha, Muthuswamy Balasubramanyam, G. Balakrish Nair, Bhabatosh Das, Henrik Vestergaard, Torben Hansen, Sharmila S. Mande, Viswanathan Mohan, Manimozhiyan Arumugam, Oluf Pedersen
Software Mentions: 4
Published: over 5 years ago

10.1093/femsec/fiaa128

The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community
Cited by: 25
Author(s): Martijn Callens, Luc De Meester, Koenraad Muylaert, Shinjini Mukherjee, Ellen Decaestecker
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.00457

Core Microbiota and Metabolome of Vitis vinifera L. cv. Corvina Grapes and Musts
Cited by: 19
Author(s): Irene Stefanini, Silvia Carlin, Noemi Tocci, Davide Albanese, Claudio Donati, Pietro Franceschi, Michele Paris, Alberto Zenato, Silvano Tempesta, Alberto Bronzato, Urška Vrhovšek, Fulvio Mattivi, Duccio Cavalieri
Software Mentions: 4
Published: over 9 years ago

10.1093/femsec/fiz128

Biogeographical patterns in soil bacterial communities across the Arctic region
Cited by: 49
Author(s): Lucie Malard, Muhammad Zohaib Anwar, Carsten Suhr Jacobsen, David A. Pearce
Software Mentions: 4
Published: about 7 years ago

10.1093/femsec/fix126

Community structure of rare methanogenic archaea: insight from a single functional group
Cited by: 15
Author(s): Shuai Yang, Matthias Winkel, Dirk Wagner, Susanne Liebner
Software Mentions: 4
Published: about 9 years ago

10.1038/s41396-020-0686-3

Ecological succession in the vaginal microbiota during pregnancy and birth
Cited by: 39
Author(s): Morten Arendt Rasmussen, Jonathan Thorsen, Maria Gloria Domínguez-Bello, Martin J. Blaser, Martin Steen Mortensen, Asker Brejnrod, Samir A. Shah, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Urvish Trivedi, Hans Bisgaard, Søren J. Sørensen, Jakob Stokholm
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.02682

Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP
Cited by: 29
Author(s): Anne E. Dekas, Alma E. Parada, Xavier Mayali, Jed A. Fuhrman, Jessica Wollard, Peter K. Weber, Jennifer Pett‐Ridge
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41396-019-0568-8

Gut microbiota structure differs between honeybees in winter and summer
Cited by: 157
Author(s): Lucie Kešnerová, Olivier Emery, Michaël Troilo, Joanito Liberti, Berra Erkoşar, Philipp Engel
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmed.2021.646710

Dietary and Pharmacologic Manipulations of Host Lipids and Their Interaction With the Gut Microbiome in Non-human Primates
Cited by: 3
Author(s): Jennifer M. Lang, Leslie R. Sedgeman, Lei Cai, Joseph D. Layne, Zhen Wang, Calvin Pan, Richard Lee, Ryan E. Temel, Aldons J. Lusis
Software Mentions: 4
Published: about 5 years ago

10.3389/fmed.2019.00201

Vaginal Microbiome Signature Is Associated With Spontaneous Preterm Delivery
Cited by: 50
Author(s): Keli Hočevar, Aleš Maver, Marijana Šimić, Alenka Hodžić, Alexander G. Haslberger, Tanja Premru Seršen, Borut Peterlin
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2013.00279

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter
Cited by: 59
Author(s): C. Ryan Penton, Timothy A. Johnson, John F. Quensen, Shoko Iwai, James R. Cole, James M. Tiedje
Software Mentions: 4
Published: almost 14 years ago

10.3390/ijerph18073742

Do Rural Second Homes Shape Commensal Microbiota of Urban Dwellers? A Pilot Study among Urban Elderly in Finland
Cited by: 4
Author(s): Mika Saarenpää, Marja I. Roslund, Riikka Puhakka, Mira Grönroos, Nan Hui, Noora Nurminen, Olli H. Laitinen, Heikki Hyöty, Ondřej Cinek, Aki Sinkkonen
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2018.00182

Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota
Cited by: 160
Author(s): Helen Groves, Leah Cuthbertson, Phillip James, Miriam F. Moffatt, Michael J. Cox, John S. Tregoning
Software Mentions: 4
Published: over 8 years ago

10.3389/fvets.2020.00616

An Assessment of the Stability of the Canine Oral Microbiota After Probiotic Administration in Healthy Dogs Over Time
Cited by: 10
Author(s): Sara E. Bell, Andrea K. Nash, Brian M. Zanghi, Cynthia M. Otto, Erin Perry
Software Mentions: 4
Published: about 6 years ago

10.1080/19490976.2021.1875797

Early life environmental exposures have a minor impact on the gut ecosystem following a natural birth
Cited by: 6
Author(s): Nishat Tasnim, Candice Quin, S K Gill, Chunping Dai, Miranda M. Hart, Deanna L. Gibson
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.00319-21

Facial Skin Microbiota-Mediated Host Response to Pollution Stress Revealed by Microbiome Networks of Individual
Cited by: 7
Author(s): Lu Wang, Yining Xu, Chung-Ching Chu, Zehua Jing, Yabin Chen, Jingsong Zhang, Mingming Pu, Tingyan Mi, Yaping Du, Zong-Qi Liang, Chandraprabha Doraiswamy, Tao Zeng, Jiarui Wu, Luonan Chen
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.01114-20

Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese
Cited by: 7
Author(s): Zhengyao Xue, Jason T. Brooks, Zachary Quart, Eric Stevens, Mary E. Kable, J. Heidenreich, J. W. McLeod, Maria L. Marco
Software Mentions: 4
Published: over 5 years ago

10.1080/19490976.2021.1897209

The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome
Cited by: 6
Author(s): John P. Haran, Doyle V. Ward, Shakti Bhattarai, Ethan Loew, Protiva Dutta, Amanda Higgins, Beth A. McCormick, Vanni Bucci
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2020.573158

Significant and Conflicting Correlation of IL-9 With Prevotella and Bacteroides in Human Colorectal Cancer
Cited by: 31
Author(s): Elena Niccolai, Edda Russo, Simone Baldi, Francesca Ricci, Giulia Nannini, Matteo Pedone, Francesco C. Stingo, Antonio Taddei, Maria Novella Ringressi, Paolo Bechi, Alessio Mengoni, Renato Fani, Giovanni Bacci, Camilla Fagorzi, Carolina Chiellini, Domenico Prisco, Matteo Ramazzotti, Amedeo Amedei
Software Mentions: 4
Published: almost 6 years ago

10.7448/IAS.18.5.20479

8th IAS Conference on HIV Pathogenesis, Treatment & Prevention 19-22 July 2015, Vancouver, Canada
Cited by: 9
Author(s):
Software Mentions: 4
Published: over 11 years ago

10.1128/mSystems.00640-20

Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes
Cited by: 34
Author(s): Chengying Shi, Lu Zhao, Evans Atoni, Weihua Zeng, Xiaomin Hu, Jelle Matthijnssens, Zhiming Yuan, Han Xia
Software Mentions: 4
Published: almost 6 years ago

10.3389/fphys.2021.668645

A Holistic Assessment of Polyethylene Fiber Ingestion in Larval and Juvenile Japanese Medaka Fish
Cited by: 4
Author(s): Elizabeth DiBona, Lee J. Pinnell, Annika Heising-Huang, Simon Joscha Geist, John Turner, Frauke Seemann
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.572706

Influence of Season and Soil Properties on Fungal Communities of Neighboring Climax Forests (Carpinus cordata and Fraxinus rhynchophylla)
Cited by: 10
Author(s): Ki Hyeong Park, Seung‐Yoon Oh, Shinnam Yoo, Jonathan J. Fong, Changsun Kim, Jong Won Jo, Young Woon Lim
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.00334-20

Human Milk Oligosaccharides Modulate the Risk for Preterm Birth in a Microbiome-Dependent and -Independent Manner
Cited by: 9
Author(s): Manuela-Raluca Pausan, V Kolovetsiou-Kreiner, Gesa Richter, Tobias Madl, Elisabeth Giselbrecht, Barbara Obermayer‐Pietsch, Eva-Christine Weiss, Evelyn Jantscher-Krenn, Christine Moissl-Eichinger
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2020.570484

Fine Particulate Matter Exposure Alters Pulmonary Microbiota Composition and Aggravates Pneumococcus-Induced Lung Pathogenesis
Cited by: 18
Author(s): Yu Wen Chen, Shiao Wen Li, Chia Der Lin, Mei Huang, Hwai Jeng Lin, Chia Yin Chin, Yi Ru Lai, Cheng Hsun Chiu, Chia Yu Yang, Chih Ho Lai
Software Mentions: 4
Published: almost 6 years ago

10.1080/19490976.2021.1936378

Effect of COVID-19 precautions on the gut microbiota and nosocomial infections
Cited by: 9
Author(s): Armin Rashidi, Maryam Ebadi, Tauseef Ur Rehman, Heba Elhusseini, Harika Nalluri, Thomas Kaiser, Shernan G. Holtan, Alexander Khoruts, Daniel J. Weisdorf, Christopher Staley
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.00547-19

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
Cited by: 31
Author(s): Quinten R Ducarmon, Bastian Hornung, A. R. Geelen, E. Kuijper, Romy D. Zwittink
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00566-19

Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands
Cited by: 22
Author(s): Nana Liu, Huifeng Hu, Wenqi Ma, Ye Deng, Yuqing Liu, Baihui Hao, Xinying Zhang, Dimitar Dimitrov, Xiaojuan Feng, Zhiheng Wang
Software Mentions: 4
Published: almost 7 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

10.1186/s42523-021-00076-6

Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets
Cited by: 23
Author(s): Kasun H. Bodawatta, Inga Freiberga, Kateřina Pužejová, Kateřina Sam, Michael Poulsen, Knud A. Jønsson
Software Mentions: 4
Published: over 5 years ago

10.3390/ani9121063

Effect of Supplementing Hydrolysable Tannins to a Grower–Finisher Diet Containing Divergent PUFA Levels on Growth Performance, Boar Taint Levels in Back Fat and Intestinal Microbiota of Entire Males
Cited by: 24
Author(s): M. Tretola, Federica Maghin, Paolo Silacci, S. Ampuero, Giuseppe Bee
Software Mentions: 4
Published: almost 7 years ago

10.3390/ani11051372

Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs
Cited by: 0
Author(s): Emily Van Syoc, Natália Carrillo Gaeta, Erika Ganda
Software Mentions: 4
Published: over 5 years ago

10.3390/ani11092705

Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF
Cited by: 2
Author(s): Gercino Ferreira Virgínio Júnior, Ana Paula da Silva, Ariany Faria de Toledo, Milaine Poczynek, Amanda Moelemberg Cezar, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 4
Published: about 5 years ago

10.3390/ani10040577

Improvement of Cecal Commensal Microbiome Following the Insect Additive into Chicken Diet
Cited by: 30
Author(s): Agata Józefiak, Abdelbasset Benzertiha, Bartosz Kierończyk, Anna Łukomska, Izabela Wesołowska, Mateusz Rawski
Software Mentions: 4
Published: over 6 years ago

10.1128/AEM.01336-19

Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction
Cited by: 11
Author(s): Maria Fernanda Campa, Stephen M. Techtmann, Mallory P. Ladd, Jun Yan, Megan Patterson, Amanda Garcia de Matos Amaral, Kimberly E. Carter, Nikea Ulrich, Christopher J. Grant, Robert L. Hettich, Regina Lamendella, Terry C. Hazen
Software Mentions: 4
Published: almost 7 years ago

10.1128/AEM.02658-18

Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile
Cited by: 5
Author(s): Urse Scheel Krüger, Arnaud Dechesne, Friedhelm Bak, Nora Badawi, Ole Nybroe, Jens Aamand
Software Mentions: 4
Published: over 7 years ago

10.1089/ast.2018.1870

A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars
Cited by: 18
Author(s): Charles S. Cockell, Jesse Patrick Harrison, Adam H. Stevens, Samuel J. Payler, S. S. Hughes, S. E. Kobs Nawotniak, A. L. Brady, R. C. Elphic, C. W. Haberle, A. Sehlke, K. Beaton, Andrew F. J. Abercromby, Petra Schwendner, Jennifer Wadsworth, Hanna Landenmark, Rosie Cane, Andrew W. Dickinson, Natasha Nicholson, Liam Perera, D. S. S. Lim
Software Mentions: 4
Published: over 7 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702