bioconductor: phyloseq | Projects

10.1371/journal.pone.0159289

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris
Cited by: 352
Author(s): Sonja Oberbeckmann, A. Mark Osborn, Melissa B. Duhaime
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0250514

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea
Cited by: 8
Author(s): Grażyna Płaza, Łukasz Jałowiecki, Dominika Głowacka, Jakub Hubeny, Monika Harnisz, Ewa Korzeniewska
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0236944

Impact of time and temperature on gut microbiota and SCFA composition in stool samples
Cited by: 9
Author(s): Janet L. Cunningham, Ludvig Bramstång, Abhijeet Singh, Shishanthi Jayarathna, Annica J. Rasmusson, Ali A. Moazzami, Bettina Müller
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0238385

Replicable simulation of distal hot water premise plumbing using convectively-mixed pipe reactors
Cited by: 3
Author(s): Maryellen Spencer, Abraham C. Cullom, William J. Rhoads, Amy Pruden, Marc Edwards
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0215767

Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities
Cited by: 11
Author(s): François Thomas, James T. Morris, Cathleen Wigand, Stefan M. Sievert
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0199664

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients
Cited by: 32
Author(s): Bahtiyar Yılmaz, Marianne R. Spalinger, Luc Biedermann, Yannick Franc, Nicolas Fournier, Jean‐Benoît Rossel, Pascal Juillerat, Gerhard Rogler, Andrew J. Macpherson, Michael Scharl
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0219633

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve
Cited by: 72
Author(s): Kattayoun Kordy, Thaidra Gaufin, Martin Mwangi, Ли Фан, Chiara Cerini, Dong Hoon Lee, Helty Adisetiyo, Cora L. Woodward, Pia S. Pannaraj, Nicole H. Tobin, Grace M. Aldrovandi
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0212949

The nasal and oropharyngeal microbiomes of healthy livestock workers
Cited by: 15
Author(s): Ashley E. Kates, Mark Dalman, James C. Torner, Tara C. Smith
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0176669

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study
Cited by: 33
Author(s): Mohan Pammi, Jacqueline O’Brien, Nadim J. Ajami, Matthew C. Wong, James Versalovic, Joseph F. Petrosino
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0245314

Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment
Cited by: 16
Author(s): Taylor Ely, Paul H. Barber, Lauren Man, Zachary Gold
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0226128

Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats
Cited by: 70
Author(s): Emma K.A. Schmidt, Abel Torres-Espín, Pamela Raposo, Karen Madsen, Kristina A. Kigerl, Phillip G. Popovich, Keith K. Fenrich, Karim Fouad
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0245243

Potential role of the skin and gut microbiota in premenarchal vulvar lichen sclerosus: A pilot case-control study
Cited by: 13
Author(s): Suhana Chattopadhyay, Justin D. Arnold, Leena Malayil, Lauren E. Hittle, Emmanuel F. Mongodin, Kalyani Marathe, Veronica Gómez-Lobo, Amy R. Sapkota
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0255323

Gut microbiota alterations in response to sleep length among African-origin adults
Cited by: 13
Author(s): Na Fei, Candice Choo-Kang, Sirimon Reutrakul, Stephanie J. Crowley, Dale E. Rae, Kweku Bedu-Addo, Jacob Plange‐Rhule, Terrence Forrester, Estelle V. Lambert, Pascal Bovet, Walter Riesen, Wolfgang Korte, Amy Luke, Brian T. Layden, Jack A. Gilbert, Lara R. Dugas
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0211705

Little cigars and cigarillos harbor diverse bacterial communities that differ between the tobacco and the wrapper
Cited by: 11
Author(s): Suhana Chattopadhyay, Eoghan M. Smyth, Prachi Kulkarni, Kelsey R. Babik, Molly C. Reid, Lauren E. Hittle, Pamela I. Clark, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0098115

Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities
Cited by: 44
Author(s): Yong Xu, Éric Dugat-Bony, Rahat Zaheer, L.B. Selinger, Ruth Barbieri, Krysty Munns, Tim A. McAllister, L. Brent Selinger
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0234050

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors
Cited by: 4
Author(s): Rebecca A. McCabe, Joseph P. Receveur, Jennifer L. Houtz, Kayli L. Thomas, M. Eric Benbow, Jennifer L. Pechal, John R. Wallace
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0226835

Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation
Cited by: 21
Author(s): Josefine Hantschel, Severin Weis, Karl‐Herbert Schäfer, Michael D. Menger, Matthias Kohl, Markus Egert, Matthias W. Laschke
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0234860

BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline
Cited by: 18
Author(s): Amirhossein Shamsaddini, Kimia Dadkhah, Patrick M. Gillevet
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0238632

Meconium microbiome and its relation to neonatal growth and head circumference catch-up in preterm infants
Cited by: 13
Author(s): Ana Carolina Terrazzan Nutricionist, Renato S. Procianoy, Luiz Fernando Würdig Roesch, Andrea Corso, Priscila Caroline Thiago Dobbler, Rita de Cássia dos Santos Silveira
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0247378

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling
Cited by: 11
Author(s): José Diógenes Jaimes, Andrea Slavíčková, Jakub Hurych, Ondřej Cinek, Ben Nichols, Lucie Vodolánová, K. Černý, Jaroslav Havlík
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0232437

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations
Cited by: 3
Author(s): Regina L. Wilpiszeski, Caitlin M. Gionfriddo, Ann M. Wymore, Ji Won Moon, Kenneth A. Lowe, Mircea Podar, Sa’ad Rafie, Matthew W. Fields, Terry C. Hazen, Xiaoxuan Ge, Farris L. Poole, Michael W. W. Adams, Romy Chakraborty, Yuhang Fan, Joy D. Van Nostrand, Jizhong Zhou, Adam P. Arkin, Dwayne A. Elias
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0229745

Changes in the gut microbiota of mice orally exposed to methylimidazolium ionic liquids
Cited by: 9
Author(s): Gregory R. Young, Tarek M. Abdelghany, Alistair C. Leitch, Michael Dunn, Peter G. Blain, Clare Lanyon, Matthew C. Wright
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0231838

Crewmember microbiome may influence microbial composition of ISS habitable surfaces
Cited by: 47
Author(s): Aram Avila-Herrera, James B. Thissen, Camilla Urbaniak, Nicholas A. Be, David J. Smith, Fathi Karouia, Satish K. Mehta, Kasthuri Venkateswaran, Crystal Jaing
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers13184687

Bacteria-Derived Extracellular Vesicles in Urine as a Novel Biomarker for Gastric Cancer: Integration of Liquid Biopsy and Metagenome Analysis
Cited by: 7
Author(s): Jae Yong Park, Chil Sung Kang, Ho Chan Seo, Jin Chul Shin, Sung Min Kym, Young Soo Park, Tae Seop Shin, Jae Gyu Kim, Yoon Keun Kim
Software Mentions: 4
Published: about 3 years ago

10.1093/cid/ciz906

Gut Microbiota Features Associated With Campylobacter Burden and Postnatal Linear Growth Deficits in a Peruvian Birth Cohort
Cited by: 19
Author(s): Saba Rouhani, Nicholas W. Griffin, Pablo Peñataro Yori, Maribel Paredes Olórtegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H. Moulton, Eric R. Houpt, Michael J. Barratt, Margaret Kosek, Jeffrey I. Gordon
Software Mentions: 4
Published: about 5 years ago

10.1093/conphys/coaa040

A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders
Cited by: 3
Author(s): Erin K. Kenison, Obed Hernández‐Gómez, Rod N. Williams
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13054-021-03623-4

Staphylococcus aureus ventilator-associated pneumonia in patients with COVID-19: clinical features and potential inference with lung dysbiosis
Cited by: 36
Author(s): Gennaro De Pascale, Flavio De Maio, Simone Carelli, Giulia De Angelis, Margherita Cacaci, Luca Montini, Giuseppe Bello, Salvatore Lucio Cutuli, Gabriele Pintaudi, Eloisa Sofia Tanzarella, Rikardo Xhemalaj, Domenico Luca Grieco, Mario Tumbarello, Maurizio Sanguinetti, Brunella Posteraro, Massimo Antonelli
Software Mentions: 4
Published: over 3 years ago

10.1093/cdn/nzaa165

Pomegranate Metabolites Impact Tryptophan Metabolism in Humans and Mice
Cited by: 10
Author(s): Jieping Yang, Yuanqiang Guo, Ru-Po Lee, Susanne M. Henning, Jing Wang, Yajing Pan, Tianyu Qing, Mark Hsu, Alex Nguyen, Prabha Siddarth, Rashi Ojha, Gary W. Small, David Heber, Zhaoping Li
Software Mentions: 4
Published: about 4 years ago

10.3390/diagnostics11091622

Alteration in Nasopharyngeal Microbiota Profile in Aged Patients with COVID-19
Cited by: 9
Author(s): Ravindra Kolhe, Nikhil Sahajpal, Sagar Vyavahare, Akhilesh S. Dhanani, Satish Adusumilli, Sudha Ananth, Ashis Mondal, Gregory Taylor Patterson, Sandeep Kumar, Amyn M. Rojiani, Carlos M. Isales, Sadanand Fulzele
Software Mentions: 4
Published: about 3 years ago

10.1186/s13550-017-0318-8

Gut microbiota and physiologic bowel 18F-FDG uptake
Cited by: 16
Author(s): Ji Yeon Kang, Han Na Kim, Yoosoo Chang, Yeojun Yun, Seungho Ryu, Hocheol Shin, Hyung Lae Kim
Software Mentions: 4
Published: about 7 years ago

10.15252/emmm.201707882

Household triclosan and triclocarban effects on the infant and maternal microbiome
Cited by: 67
Author(s): Jessica V. Ribado, Catherine Ley, Thomas D. Haggerty, Е. И. Ткаченко, Ami S. Bhatt, Julie Parsonnet
Software Mentions: 4
Published: about 7 years ago

10.1002/ece3.4742

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding
Cited by: 45
Author(s): Natalie A. Sawaya, Anni Djurhuus, Collin J. Closek, Megan Hepner, Emily Olesin, Lindsey A. Visser, Christopher R. Kelble, Katherine A. Hubbard, Mya Breitbart
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.3777

Evolution of a key trait greatly affects underground community assembly process through habitat adaptation in earthworms
Cited by: 9
Author(s): Hiroshi Ikeda, Kayoko Fukumori, Etsuko Shoda‐Kagaya, Masamichi Takahashi, Masamichi Ito, Yoshimi Sakai, Kazuma Matsumoto
Software Mentions: 4
Published: almost 7 years ago

10.1002/ece3.3248

Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia
Cited by: 5
Author(s): Keith A. Christian, Mirjam Kaestli, Karen S. Gibb
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.3133

Transcriptomic differentiation underlying marine‐to‐freshwater transitions in the South American silversides <i>Odontesthes argentinensis</i> and <i>O. bonariensis</i> (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 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 4 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 3 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 4 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: over 5 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 7 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: about 4 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 4 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: 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 4 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 4 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: almost 4 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 4 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: almost 7 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 5 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: over 3 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 5 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 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: about 4 years ago

10.3389/fmicb.2018.01647

Tucumã Oil Shifted Ruminal Fermentation, Reducing Methane Production and Altering the Microbiome but Decreased Substrate Digestibility Within a RUSITEC Fed a Mixed Hay – Concentrate Diet
Cited by: 29
Author(s): Aline Maria Pereira Cruz Ramos, Stephanie A. Terry, Devin B. Holman, Gerhard Breves, L. G. R. Pereira, André G. M. Silva, A. V. Chaves
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.01756

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage
Cited by: 78
Author(s): Victoria Mesa, José Luis Gallego, Ricardo González-Gil, Béatrice Lauga, Jesús Sánchez, Celia Méndez–García
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2020.580397

Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability
Cited by: 10
Author(s): Shuting Liu, Nicholas Baetge, Jacqueline Comstock, Keri Opalk, Rachel Parsons, Elisa R. Halewood, Chance English, Stephen J. Giovannoni, Luis M. Bolaños, Craig E. Nelson, Kevin L. Vergin, Craig A. Carlson
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2020.602404

Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking
Cited by: 7
Author(s): Lucie Rault, Pierre-Alexandre Lévêque, Sarah Barbey, Frédéric Launay, Hélène Larroque, Yves Le Loir, Pierre Germon, Jocelyne Guinard-Flament, Sergine Even
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2019.00346

Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera
Cited by: 56
Author(s): Brooke L. Weigel, Catherine A. Pfister
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00129

Broad and Fine Scale Variability in Bacterial Diversity and Cyanotoxin Quotas in Benthic Cyanobacterial Mats
Cited by: 8
Author(s): Georgia Thomson‐Laing, Jonathan Puddick, Olivier Laroche, Samantha Fulton, Konstanze Steiner, Mark W. Heath, Susanna A. Wood
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.01305

Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic Interactions
Cited by: 21
Author(s): Stefanos Banos, Deisy Morselli Gysi, Tim Richter-Heitmann, Frank Oliver Glöckner, Maarten Boersma, Karen Helen Wiltshire, Gunnar Gerdts, Antje Wichels, M. Reich
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2018.00297

Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks
Cited by: 10
Author(s): Tatiana V. Karpinets, Vancheswaran Gopalakrishnan, Jennifer A. Wargo, Andrew Futreal, Christopher W. Schadt, Jianhua Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.01245

Outbreaks of an Emerging Viral Disease Covary With Differences in the Composition of the Skin Microbiome of a Wild United Kingdom Amphibian
Cited by: 23
Author(s): Lewis J. Campbell, Trenton W. J. Garner, Kevin Hopkins, Amber Gieselle Firefly Griffiths, Xavier A. Harrison
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2017.00050

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird
Cited by: 52
Author(s): Jakub Kreisinger, Lucie Kropáčková, Adéla Petrželková, Marie Kotasová Adámková, Oldřich Tomášek, Jean‐François Martin, Romana Michálková, Tomáš Albrecht
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2019.00599

Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs
Cited by: 11
Author(s): Benjamin Zwirzitz, Beate Pinior, Barbara U. Metzler‐Zebeli, Monika Handler, Kristina Gense, Christian Knecht, Andrea Ladinig, Monika Dzieciol, Stefanie U. Wetzels, Martin Wagner, Stephan Schmitz‐Esser, Evelyne Mann
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.01249

Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration
Cited by: 12
Author(s): Laura Zinke, Brandi Kiel Reese, James McManus, C. G. Wheat, Beth N. Orcutt, Jan P. Amend
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.03203

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity
Cited by: 61
Author(s): Nicola Vitulo, Wilson José Fernandes Lemos, Matteo Calgaro, Marco Confalone, Giovanna E. Felis, Giacomo Zapparoli, Tiziana Nardi
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2018.03344

Long Term Diversity and Distribution of Non-photosynthetic Cyanobacteria in Peri-Alpine Lakes
Cited by: 36
Author(s): Marie‐Ève Monchamp, Piet Spaak, Francesco Pomati
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2018.02878

Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea
Cited by: 51
Author(s): Kosuke Yamamoto, Yuh Shiwa, Taichiro Ishige, Hikaru Sakamoto, Keisuke Tanaka, Makoto Uchino, Naoto Tanaka, Suguru Oguri, Hiromasa Saitoh, Seiya Tsushima
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2021.703014

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds
Cited by: 14
Author(s): Flavia Tarquinio, Océane Attlan, Mathew A. Vanderklift, Oliver Berry, Andrew Bissett
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2020.00867

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

10.3389/fmicb.2019.01850

Disease Specific Bacterial Communities in a Coralline Algae of the Northwestern Mediterranean Sea: A Combined Culture Dependent and -Independent Approach
Cited by: 13
Author(s): Gaëlle Quéré, Laurent Intertaglia, Claude Payri, Pierre E. Galand
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00380

Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities
Cited by: 32
Author(s): Emilie Macke, Martijn Callens, François Massol, Isabel Vanoverberghe, Luc De Meester, Ellen Decaestecker
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2021.718727

Soil Fungal Community in Grazed Inner Mongolian Grassland Adjacent to Coal-Mining Activity
Cited by: 2
Author(s): Liji Xie, Yinli Bi, Xianglei Li, Kun Wang, Peter Christie
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2021.627539

Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies
Cited by: 10
Author(s): Gertrude Wegl, Nikolaus Grabner, Andreas Köstelbauer, Viviana Klose, Mahdi Ghanbari
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2018.01534

Jellyfish Life Stages Shape Associated Microbial Communities, While a Core Microbiome Is Maintained Across All
Cited by: 24
Author(s): Michael D. Lee, Joshua D. Kling, Rubén Araya, Janja Ceh
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.01069

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity
Cited by: 6
Author(s): Andrea Hahn, Matthew L. Bendall, Keylie M. Gibson, Hollis Chaney, Iman Sami, Geovanny F. Pérez, Anastassios C. Koumbourlis, Timothy A. McCaffrey, Robert J. Freishtat, Keith A. Crandall
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.02558

Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments
Cited by: 14
Author(s): Claus Pelikan, Marion Jaussi, Kenneth Wasmund, Marit‐Solveig Seidenkrantz, Christof Pearce, Zou Zou A. Kuzyk, Craig W. Herbold, Hans Røy, Kasper Urup Kjeldsen, Alexander Loy
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2018.02094

Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique
Cited by: 27
Author(s): Melanie Eger, Michael Graz, Susanne Riede, Gerhard Breves
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2018.01363

Persistence of Cellulolytic Bacteria Fibrobacter and Treponema After Short-Term Corn Stover-Based Dietary Intervention Reveals the Potential to Improve Rumen Fibrolytic Function
Cited by: 66
Author(s): Xiao Xie, Chunlei Yang, Le Luo Guan, Jiakun Wang, Mingyuan Xue, Jian X. Liu
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.00322

Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut Microbiota
Cited by: 11
Author(s): Benjamin J. Korry, Damien J. Cabral, Peter Belenky
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2015.00891

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland
Cited by: 85
Author(s): Rebecca C. Mueller, Jayne Belnap, Cheryl R. Kuske
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2018.02926

Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios
Cited by: 25
Author(s): Juanjo Rodríguez, Christine Gallampois, Sari Timonen, Agneta Andersson, Hanna Sinkko, Peter Haglund, Åsa M. M. Berglund, Mátyás Ripszám, Daniela Figueroa, Mats Tysklind, Owen Rowe
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.584699

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom
Cited by: 8
Author(s): Keith Mitchell, Jiem R. Ronas, Christopher Dao, Amanda C. Freise, Serghei Mangul, Casey Shapiro, Jordan Moberg Parker
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2021.720513

DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data
Cited by: 8
Author(s): Daniel Loos, Lu Zhang, Christine Beemelmanns, Oliver Kurzai, Gianni Panagiotou
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.01636

Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications
Cited by: 12
Author(s): Magdalena N. Georgieva, Sergi Taboada, Ana Riesgo, Cristina Díez‐Vives, Fabio C. De Leo, Rachel M. Jeffreys, Jonathan T. Copley, Crispin T. S. Little, Pilar Ríos, Javier Cristobo, Jon Thomassen Hestetun, Adrian G. Glover
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2020.01686

Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts
Cited by: 11
Author(s): Noemi Procopio, Stefano Ghignone, Samuele Voyron, Marco Chiapello, Anna Williams, Andrew Chamberlain, Antonietta Mello, Michael Buckley
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2020.01981

Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency
Cited by: 62
Author(s): Steven McLoughlin, Charles Spillane, Noel A. Claffey, Pamela M. Smith, Tommy O’Rourke, M.G. Diskin, Sinéad M. Waters
Software Mentions: 4
Published: over 4 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 4 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 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 12 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 5 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 3 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 4 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 8 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: over 3 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 5 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 4 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: about 4 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 4 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: over 4 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702