bioconductor: phyloseq | Projects

10.7717/peerj.6687

A longitudinal study of the faecal microbiome and metabolome of periparturient mares
Cited by: 11
Author(s): Shebl E. Salem, Rachael Hough, Chris Probert, Thomas W. Maddox, Philipp Antczak, Julian M. Ketley, Nicola Williams, Sarah J. Stoneham, Debra Archer
Software Mentions: 7
Published: over 5 years ago

10.3390/microorganisms6040096

Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
Cited by: 37
Author(s): Prashant Singh, Sylvain Santoni, Patrice This, Jean‐Pierre Péros
Software Mentions: 7
Published: about 6 years ago

10.12688/f1000research.18866.2

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data
Cited by: 12
Author(s): Mike W.C. Thang, Xin-Yi Chua, Gareth Price, D. Gorse, Matthew A. Field
Software Mentions: 7
Published: about 5 years ago

10.7717/peerj.10836

Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry
Cited by: 9
Author(s): Kerri L. Steenwerth, Ian Arthur Morelan, Ruby J. Stahel, Rosa Figueroa‐Balderas, Dario Cantu, Jungmin Lee, Ron C. Runnebaum, Amisha T. Poret-Peterson
Software Mentions: 7
Published: almost 4 years ago

10.1007/s00248-019-01426-3

Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes
Cited by: 45
Author(s): Edward C. Rojas, Rumakanta Sapkota, Birgit Jensen, Henning Jørgensen, Tina Henriksson, Lise Nistrup Jørgensen, Mogens Nicolaisen, David B. Collinge
Software Mentions: 7
Published: about 5 years ago

10.1007/s00248-018-1209-x

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition
Cited by: 35
Author(s): Marcin Gołębiewski, Agata Tarasek, Marcin Sikora, Edyta Deja-Sikora, Andrzej Tretyn, Maria Niklińska
Software Mentions: 7
Published: over 6 years ago

10.12688/f1000research.9618.2

biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
Cited by: 2
Author(s): Markus J. Ankenbrand, Niklas Terhoeven, Sonja Hohlfeld, Frank Förster, Alexander Keller
Software Mentions: 7
Published: almost 8 years ago

10.1186/s13059-020-02144-7

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding
Cited by: 32
Author(s): Toby Wilkinson, Daniel Korir, Moses Ogugo, Robert D. Stewart, Mick Watson, Edith Paxton, John P. Goopy, Christelle Robert
Software Mentions: 7
Published: about 4 years ago

10.1186/s40793-020-00365-8

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond
Cited by: 14
Author(s): Jessica Chopyk, Daniel J. Nasko, Sarah Allard, Anthony Bui, Mihai Pop, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 7
Published: about 4 years ago

10.1080/19490976.2021.1921927

Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells <i>in vitro</i>
Cited by: 7
Author(s): Dušan Radojević, Sergej Tomić, Dušan Mihajlović, Maja Tolinački, Bojan Pavlović, Dragana Vučević, Svetlana Bojić, Nataša Golić, Miodrag Čolić, Jelena Đokić
Software Mentions: 7
Published: almost 4 years ago

10.3390/pathogens10050603

Altered Nasal Microbiota Composition Associated with Development of Polyserositis by Mycoplasma hyorhinis
Cited by: 9
Author(s): Miguel Blanco-Fuertes, Florencia Correa‐Fiz, Lorenzo Fraile, Marina Sibila, Virginia Aragón
Software Mentions: 7
Published: over 3 years ago

10.1111/gcb.15302

Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewater
Cited by: 44
Author(s): Francis J. Burdon, Yaohui Bai, Marta Reyes, Manu Tamminen, Philipp Staudacher, Simon Mangold, Heinz Singer, Katja Räsänen, Adriano Joss, Scott D. Tiegs, Jukka Jokela, Rik I.L. Eggen, Christian Stamm
Software Mentions: 7
Published: about 4 years ago

10.7717/peerj.11985

Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields
Cited by: 14
Author(s): Ademir Durrer, Thiago Gumière, Maurício Rumenos Guidetti Zagatto, Henrique Petry Feiler, Antônio Marcos Miranda Silva, Rodrigo Henriques Longaresi, Sérgio Kenji Homma, Elke Jurandy Bran Nogueira Cardoso
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pone.0250344

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome
Cited by: 13
Author(s): Arnon Gal, Patrick C. Barko, Patrick J. Biggs, Kristene Gedye, Anne C. Midwinter, David A. Williams, Richard K. Burchell, P. Pazzi
Software Mentions: 7
Published: over 3 years ago

10.1186/s40168-020-00869-y

Topography of the respiratory tract bacterial microbiota in cattle
Cited by: 36
Author(s): Christopher McMullen, Trevor W. Alexander, Renaud Léguillette, Matthew L. Workentine, Edouard Timsit
Software Mentions: 7
Published: over 4 years ago

10.1111/1751-7915.13640

Synthetic community with six <i>Pseudomonas</i> strains screened from garlic rhizosphere microbiome promotes plant growth
Cited by: 55
Author(s): Lubo Zhuang, Yán Li, Zhenshuo Wang, Yue Yu, Nan Zhang, Chang Yeol Yang, Qingchao Zeng, Qi Wang
Software Mentions: 7
Published: over 4 years ago

10.3389/fpls.2020.602645

Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products
Cited by: 11
Author(s): Vinício Oliosi Favero, Rita Hilário de Carvalho, Victória Monteiro da Motta, Ana Beatriz Carneiro Leite, Márcia Reed Rodrigues Coelho, Gustavo Ribeiro Xavier, Norma Gouvêa Rumjanek, Segundo Urquiaga
Software Mentions: 7
Published: almost 4 years ago

10.1002/ece3.5476

Plant‐driven changes in soil microbial communities influence seed germination through negative feedbacks
Cited by: 20
Author(s): E. C. Miller, Gabriel G. Perron, Cathy D. Collins
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2019.01246

Temporal Dynamics of the Sap Microbiome of Grapevine Under High Pierce’s Disease Pressure
Cited by: 43
Author(s): Elizabeth Deyett, Philippe E. Rolshausen
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0227289

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach
Cited by: 27
Author(s): Aashish R. Jha, Justin Shmalberg, Jirayu Tanprasertsuk, Lee Ann M. Perry, Dan Massey, Ryan W. Honaker
Software Mentions: 7
Published: almost 5 years ago

10.3389/fpls.2019.01313

A Bioinformatics Guide to Plant Microbiome Analysis
Cited by: 45
Author(s): Rares Calin Lucaciu, Claus Pelikan, Samuel M. Gerner, Christos Zioutis, Stephan Köstlbacher, Harald Marx, Craig W. Herbold, Hannes Schmidt, Thomas Rattei
Software Mentions: 7
Published: about 5 years ago

10.3390/microorganisms8101592

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes
Cited by: 12
Author(s): Andrés Sánchez-Quinto, Daniel Cerqueda‐García, Luisa I. Falcón, Osiris Gaona, Santiago Martínez-Correa, Javier Nieto, Isaac González‐Santoyo
Software Mentions: 7
Published: about 4 years ago

10.1053/j.gastro.2017.10.007

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
Cited by: 199
Author(s): Kate J. Howell, Judith Kraiczy, Komal Nayak, Marco Gasparetto, Alex Ross, Claire Lee, Tim N. Mak, Bon–Kyoung Koo, Nitin Kumar, Trevor D. Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Software Mentions: 7
Published: almost 7 years ago

10.3389/fpls.2019.01405

Fungicides and the Grapevine Wood Mycobiome: A Case Study on Tracheomycotic Ascomycete Phaeomoniella chlamydospora Reveals Potential for Two Novel Control Strategies
Cited by: 16
Author(s): Giovanni Del Frari, Alex Gobbi, Marie Rønne Aggerbeck, Helena Oliveira, Lars Hestbjerg Hansen, Ricardo B. Ferreira
Software Mentions: 7
Published: about 5 years ago

10.3390/life10090185

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists
Cited by: 3
Author(s): Hamza Mbareche, Nathan Dumont-Leblond, Guillaume J. Bilodeau, Caroline Duchaine
Software Mentions: 7
Published: about 4 years ago

10.3390/microorganisms9071368

Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)
Cited by: 0
Author(s): Qianqian Li, Rebecca E. Cooper, Carl‐Eric Wegner, Martin Taubert, Nico Jehmlich, Martin von Bergen, Kirsten Küsel
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2020.00669

Patterns in Microbial Assemblages Exported From the Meltwater of Arctic and Sub-Arctic Glaciers
Cited by: 20
Author(s): Tyler J. Kohler, Petra Vinšová, Lukáš Falteisek, Jakub D. Žárský, Jacob C. Yde, Jade E. Hatton, Jon R. Hawkings, Guillaume Lamarche-Gagnon, Eran Hood, Karen A. Cameron, Marek Stibal
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0219235

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data
Cited by: 17
Author(s): Stephen Woloszynek, Joshua Chang Mell, Zhengqiao Zhao, Gideon Simpson, Michael O’Connor, Gail Rosen
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12931-020-01392-2

Characterisation of microbiota in saliva, bronchoalveolar lavage fluid, non-malignant, peritumoural and tumour tissue in non-small cell lung cancer patients: a cross-sectional clinical trial
Cited by: 27
Author(s): Rea Bingula, Edith Filaire, Ioana Molnar, Eve Delmas, Jean‐Yves Berthon, Marie‐Paule Vasson, Annick Bernalier-Donadille, Marc Filaire
Software Mentions: 7
Published: over 4 years ago

10.3390/genes10070484

Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback
Cited by: 25
Author(s): Robert A Steury, Mark Currey, William A. Cresko, Brendan J. M. Bohannan
Software Mentions: 7
Published: over 5 years ago

10.1038/srep45369

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for
Cited by: 12
Author(s): Rachel Kaminsky, Blandine Trouche, Sergio E. Morales
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0240512

Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community
Cited by: 19
Author(s): Anne Eriksen, Tue Kjærgaard Nielsen, Henning Matthiesen, Christian Carøe, Lars Hestbjerg Hansen, David Gregory, Gordon Turner‐Walker, Matthew J. Collins, M. Thomas P. Gilbert
Software Mentions: 7
Published: about 4 years ago

10.1186/s42523-021-00117-0

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels
Cited by: 3
Author(s): Kirsten Grond, Courtney C. Kurtz, Jasmine J. Hatton, Michelle M. Sonsalla, Khrystyne N. Duddleston
Software Mentions: 7
Published: over 3 years ago

10.3389/fmolb.2021.656204

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse
Cited by: 12
Author(s): Núria Mach, Marco Moroldo, Andrea Rau, Jérôme Lecardonnel, Laurence Le Moyec, Céline Robert, Éric Barrey
Software Mentions: 7
Published: over 3 years ago

10.1186/s40168-019-0677-7

Maize synthesized benzoxazinoids affect the host associated microbiome
Cited by: 160
Author(s): Enoch Narh Kudjordjie, Rumakanta Sapkota, Stine K. Steffensen, Inge S. Fomsgaard, Mogens Nicolaisen
Software Mentions: 7
Published: over 5 years ago

10.1007/s00253-021-11475-9

Do initial concentration and activated sludge seasonality affect pharmaceutical biotransformation rate constants?
Cited by: 10
Author(s): Tamara J. H. M. van Bergen, Ana B. Rios‐Miguel, Tom M. Nolte, A.M.J. Ragas, Rosalie van Zelm, Martien H.F. Graumans, Paul T.J. Scheepers, Mike S. M. Jetten, A. Jan Hendriks, Cornelia U. Welte
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2021.658116

Endophytic Fungal Community of Tobacco Leaves and Their Potential Role in the Formation of “Cherry-Red” Tobacco
Cited by: 4
Author(s): Yonglei Jiang, Xing Chen, Gaokun Zhao, Jiahong Liu, Yan Xie, Yong Li, Huaguo Gu, Congming Zou
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0200729

The murine female intestinal microbiota does not shift throughout the estrous cycle
Cited by: 18
Author(s): Jessica G. Wallace, Ryan Potts, Jake C. Szamosi, Michael G. Surette, Deborah M. Sloboda
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2021.685937

Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota
Cited by: 10
Author(s): Martı́n Aluja, Jesús Alejandro Zamora‐Briseño, Vicente Pérez‐Brocal, Alma Altúzar-Molina, Larissa Guillén, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Enrique Ibarra-Laclette, Alexandro Alonso-Sánchez, Andrés Moya
Software Mentions: 7
Published: over 3 years ago

10.1128/mBio.00764-17

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes
Cited by: 278
Author(s): Christian Santos‐Medellín, Joseph Edwards, Zachary Liechty, Bao‐Anh Thi Nguyen, Venkatesan Sundaresan
Software Mentions: 7
Published: about 7 years ago

10.1038/s42003-021-02315-7

Human encroachment into wildlife gut microbiomes
Cited by: 29
Author(s): Gloria Fackelmann, Mark A. F. Gillingham, Julian Schmid, Alexander Christoph Heni, Kerstin Wilhelm, Nina Schwensow, Simone Sommer
Software Mentions: 7
Published: over 3 years ago

10.3390/microorganisms8060961

The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia
Cited by: 10
Author(s): Aldian Irma Amaruddin, Firdaus Hamid, J. Koopman, Munawir Muhammad, Eric A. T. Brienen, Lisette van Lieshout, A. R. Geelen, Sitti Wahyuni, Ed J. Kuijper, Erliyani Sartono, Maria Yazdanbakhsh, Romy D. Zwittink
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2021.569791

Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem
Cited by: 15
Author(s): Yaqi You, Ken Aho, Kathleen A. Lohse, Stacy G. Schwabedissen, Rhesa N. Ledbetter, Timothy S. Magnuson
Software Mentions: 7
Published: over 3 years ago

10.3390/microorganisms9030557

The Composition and Diversity of the Gut Microbiota in Children Is Modifiable by the Household Dogs: Impact of a Canine-Specific Probiotic
Cited by: 10
Author(s): Carlos Gómez-Gallego, Mira Forsgren, Marta Selma‐Royo, Merja Nermes, María Carmen Collado, Seppo Salminen, Shea Beasley, Erika Isolauri
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2020.00789

Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach
Cited by: 18
Author(s): Nico Salmaso, Bruno Adriano, Massimo Pindo
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-021-92513-4

High-throughput 16S rRNA gene sequencing of the microbial community associated with palm oil mill effluents of two oil processing systems
Cited by: 2
Author(s): Benedicte Ella Zranseu Aka, Theodore N. Djéni, Simon Laurent Tiemele Amoikon, Jan Kannengießer, Naaila Ouazzani, Marcellin Koffi Djè
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2018.01073

Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function
Cited by: 28
Author(s): Jacob W. Bledsoe, Geoffrey C. Waldbieser, Kelly S. Swanson, Brian Peterson, Brian C. Small
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-021-93918-x

Probiotic supplementation reduces inflammatory profiles but does not prevent oral immune perturbations during SIV infection
Cited by: 4
Author(s): Rhianna Jones, Kyle Kroll, Courtney Broedlow, Luca Schifanella, Scott Smith, Brady Hueber, Spandan V. Shah, Daniel R. Ram, Cordelia Manickam, Valerie Varner, Nichole R. Klatt, R. Keith Reeves
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2017.00358

Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions
Cited by: 38
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 7
Published: over 7 years ago

10.7717/peerj.8056

Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral
Cited by: 18
Author(s): Mallory M. Rice, Rebecca L. Maher, Rebecca Vega Thurber, Deron E. Burkepile
Software Mentions: 7
Published: about 5 years ago

10.1186/s42523-021-00092-6

Metatranscriptomic analyses reveal ruminal pH regulates fiber degradation and fermentation by shifting the microbial community and gene expression of carbohydrate-active enzymes
Cited by: 15
Author(s): Meng M. Li, Robin R. White, Le Luo Guan, Laura Harthan, M.D. Hanigan
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-85855-6

Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches
Cited by: 29
Author(s): Jana Batovska, Alexander M. Piper, Isabel Valenzuela, John Paul Cunningham, Mark J. Blacket
Software Mentions: 7
Published: over 3 years ago

10.1007/s11274-019-2737-3

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization
Cited by: 15
Author(s): Priscila Caroline Thiago Dobbler, Volker Mai, Renato S. Procianoy, Rita de Cássia dos Santos Silveira, Andrea Corso, Luiz Fernando Würdig Roesch
Software Mentions: 7
Published: about 5 years ago

10.1186/s40168-019-0684-8

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Cited by: 38
Author(s): Luís Pedro Coelho, Renato Alves, Paulo P. Monteiro, Jaime Huerta-Cepas, Ana T. Freitas, Peer Bork
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2019.02037

Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon
Cited by: 41
Author(s): S. R. Gupta, Jep Lokesh, Yousri Abdelhafiz, Prabhugouda Siriyappagouder, Ronan Pierre, Mette Sørensen, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-021-93645-3

Tree-aggregated predictive modeling of microbiome data
Cited by: 14
Author(s): Jacob Bien, Xiaohan Yan, Léo Simpson, Christian L. Müller
Software Mentions: 7
Published: over 3 years ago

10.3390/plants9121801

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil
Cited by: 10
Author(s): Andrey A. Belimov, А. И. Шапошников, D. S. Syrova, Arina Kichko, Polina Guro, O. S. Yuzikhin, T. S. Azarova, Anna L Sazanova, E. A. Sekste, Vladimir A Litvinskiy, Vladimir V. Nosikov, А. А. Завалин, E. E. Andronov, Vera I. Safronova
Software Mentions: 6
Published: almost 4 years ago

10.1128/AEM.02555-20

Microbial Community Shifts Reflect Losses of Native Soil Carbon with Pyrogenic and Fresh Organic Matter Additions and Are Greatest in Low-Carbon Soils
Cited by: 6
Author(s): Thea Whitman, Silene DeCiucies, Kelly Hanley, Akio Enders, Jamie Woolet, Johannes Lehmann
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-021-01053-6

Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues
Cited by: 60
Author(s): Talisa Doering, Marlene Wall, Lalita Putchim, Tipwimon Rattanawongwan, Roman Schroeder, Ute Hentschel, Anna Krystyna Roik
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-60929-z

Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reef
Cited by: 11
Author(s): Danielle C. Claar, Kristina L. Tietjen, Kieran Cox, Ruth D. Gates, Julia K. Baum
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-017-0314-2

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis
Cited by: 61
Author(s): Fiona Whelan, Michael G. Surette
Software Mentions: 6
Published: over 7 years ago

10.1186/s12917-019-2205-1

Acute changes in the colonic microbiota are associated with large intestinal forms of surgical colic
Cited by: 8
Author(s): Shebl E. Salem, Thomas W. Maddox, Philipp Antczak, Julian M. Ketley, Nicola Williams, Debra Archer
Software Mentions: 6
Published: almost 5 years ago

10.1186/s40168-019-0639-0

Rare gut microbiota associated with breeding success, hormone metabolites and ovarian cycle phase in the critically endangered eastern black rhino
Cited by: 61
Author(s): Rachael E. Antwis, Katie L. Edwards, Bryony Unwin, Susan L. Walker, Susanne Shultz
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12887-020-02067-z

Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment
Cited by: 15
Author(s): Romy D. Zwittink, Diny van Zoeren‐Grobben, Ingrid B. Renes, Richard A. van Lingen, Obbe F. Norbruis, Rocı́o Martı́n, Liesbeth J. Groot Jebbink, Jan Knol, Clara Belzer
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-019-52148-y

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil
Cited by: 64
Author(s): Vanessa Brisson, Jennifer E. Schmidt, Trent Northen, John P. Vogel, Amélie C. M. Gaudin
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-019-50839-0

Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures
Cited by: 36
Author(s): Prashant Singh, Sylvain Santoni, Audrey Weber, Patrice This, Jean‐Pierre Péros
Software Mentions: 6
Published: about 5 years ago

10.1186/s12882-020-01773-1

The urinary microbiome shows different bacterial genera in renal transplant recipients and non-transplant patients at time of acute kidney injury – a pilot study
Cited by: 10
Author(s): Daniela Gerges, Peter Pichler, Alexander Zimprich, Christoph Hotzy, Wolfgang Barousch, Rita Lang, Elisabeth Lobmeyr, Sabina Baumgartner‐Parzer, Ludwig Wagner, Wolfgang Winnicki
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2020.01528

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation
Cited by: 7
Author(s): Nicholas C. Dove, Timothy J. Rogers, Christy Leppanen, Daniel Simberloff, James A. Fordyce, Veronica A. Brown, Anthony V. LeBude, Thomas G. Ranney, Melissa Cregger
Software Mentions: 6
Published: over 4 years ago

10.1098/rstb.2019.0242

Phylogenetic conservation of soil bacterial responses to simulated global changes
Cited by: 41
Author(s): Kazuo Isobe, Nicholas J. Bouskill, Eoin L. Brodie, Erika A. Sudderth, Jennifer B. H. Martiny
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2021.659918

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species
Cited by: 12
Author(s): Alice Risely, Mark A. F. Gillingham, Arnaud Béchet, Stefan Dominik Brändel, Alexander Christoph Heni, Marco Heurich, Sebastian Menke, Marta B. Manser, Marco Tschapka, . Wasimuddin, Simone Sommer
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-54098-x

Obesity during pregnancy results in maternal intestinal inflammation, placental hypoxia, and alters fetal glucose metabolism at mid-gestation
Cited by: 48
Author(s): Jessica G. Wallace, Christian J. Bellissimo, Erica Yeo, Yu Xia, Jim Petrik, Michael G. Surette, Dawn M. E. Bowdish, Deborah M. Sloboda
Software Mentions: 6
Published: almost 5 years ago

10.1186/s40168-019-0734-2

Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics
Cited by: 94
Author(s): Chengying Shi, Leen Beller, Ward Deboutte, Kwe Claude Yinda, Leen Delang, Anubis Vega-Rúa, Anna‐Bella Failloux, Jelle Matthijnssens
Software Mentions: 6
Published: about 5 years ago

10.1186/s40168-015-0069-6

Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure
Cited by: 108
Author(s): Adrienne B. Narrowe, Munira Albuthi-Lantz, Erin P. Smith, Kimberly J Bower, Timberley M. Roane, Alan M. Vajda, Christopher S. Miller
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0237272

Passenger-surface microbiome interactions in the subway of Mexico City
Cited by: 10
Author(s): Daniela Vargas-Robles, Carolina Gonzalez-Cedillo, Apolinar M. Hernández, Luis David Alcaraz, Mariana Peimbert
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-018-29277-x

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model
Cited by: 50
Author(s): Jonathan B. Clayton, Gabriel A. Al‐Ghalith, Ha Thang Long, Bui Van Tuan, Francis Cabana, Hu Huang, Pajau Vangay, Tonya Ward, Vo Van Minh, Nguyen Ai Tam, Nguyen Tat Dat, Dominic A. Travis, Michael P. Murtaugh, Herbert H. Covert, Kenneth E. Glander, Tilo Nadler, Barbara Toddes, John Chih Mun Sha, Randy Singer, Dan Knights, Timothy J. Johnson
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-018-25927-2

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses
Cited by: 24
Author(s): Zhongming Ge, Alexander Sheh, Yan Feng, Sureshkumar Muthupalani, Lili Ge, Chuanwu Wang, Susanna Kurnick, Anthony Mannion, Mark T. Whary, James G. Fox
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2021.642197

Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life
Cited by: 25
Author(s): Modupe Coker, Hannah E. Laue, Anne G. Hoen, Margaret Hilliard, Erika Dade, Zhigang Li, Thomas J. Palys, Hilary G. Morrison, Emily Baker, Margaret R. Karagas, Juliette C. Madan
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2021.645362

Larval Diet Abundance Influences Size and Composition of the Midgut Microbiota of Aedes aegypti Mosquitoes
Cited by: 13
Author(s): Hannah J. MacLeod, George Dimopoulos, Sarah M. Short
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-021-01031-y

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals
Cited by: 25
Author(s): Tina Keller‐Costa, Asunción Lago‐Lestón, J. Saraiva, Rodolfo Brizola Toscan, Sandra Godinho Silva, Jorge M. S. Gonçalves, Cymon J. Cox, Nikos C. Kyrpides, Ulisses Nunes da Rocha, Rodrigo Costa
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-020-00943-5

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species
Cited by: 26
Author(s): Antonio Suppa, Jouni Kvist, Xiaojing Li, Vignesh Dhandapani, Hanan Almulla, Antoine Y. Tian, Stephen Kissane, Jian Zhou, Alessio Perotti, Hayley Mangelson, Kyle W. Langford, Valeria Rossi, James B. Brown, Luisa Orsini
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0235159

Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding
Cited by: 13
Author(s): Kathleen J. Pitz, Jinchen Guo, Shannon B. Johnson, Tracy L. Campbell, Haibin Zhang, Robert C. Vrijenhoek, Francisco P. Chávez, Jonathan B. Geller
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-019-0686-6

Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets
Cited by: 32
Author(s): Anukriti Sharma, Miles Richardson, Lauren Cralle, Christopher E. Stamper, Juan P. Maestre, Kelly A. Stearns‐Yoder, Teodor T. Postolache, Katherine L Bates, Kerry A. Kinney, Lisa A. Brenner, Christopher A. Lowry, Jack A. Gilbert, Andrew J. Hoisington
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-019-0705-7

Microbial indicators of environmental perturbations in coral reef ecosystems
Cited by: 109
Author(s): Bettina Glasl, David G. Bourne, Pedro R. Frade, Torsten Thomas, Britta Schaffelke, Nicole S. Webster
Software Mentions: 6
Published: over 5 years ago

10.3390/ani11092597

Effect of a Low-Methane Diet on Performance and Microbiome in Lactating Dairy Cows Accounting for Individual Pre-Trial Methane Emissions
Cited by: 3
Author(s): Juana Catarina Cariri Chagas, Mohammad Ramin, Ruth Gómez Expósito, Hauke Smidt, S.J. Krizsan
Software Mentions: 6
Published: about 3 years ago

10.7717/peerj.10237

Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species
Cited by: 4
Author(s): Benjamin D. Gallo, John M. Farrell, Brian F. Leydet
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0250401

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru
Cited by: 5
Author(s): Pedro E. Romero, Erika Calla-Quispe, Camila Castillo-Vilcahuaman, Mateo Yokoo, Hammerly Lino Fuentes-Rivera, Jorge L. Ramírez, André Ampuero, Alfredo J. Ibáñez, Paolo Wong
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2021.717990

Resistance and Vulnerability of Honeybee (Apis mellifera) Gut Bacteria to Commonly Used Pesticides
Cited by: 15
Author(s): Ana Cuesta-Maté, Justinn Renelies‐Hamilton, Per Kryger, Annette Bruun Jensen, Veronica M. Sinotte, Michael Poulsen
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0169339

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA
Cited by: 51
Author(s): Kathleen H. Lavoie, Ara S. Winter, Kaitlyn J. H. Read, Evan M. Hughes, M. Spilde, Diana E. Northup
Software Mentions: 6
Published: almost 8 years ago

10.3389/fmicb.2018.00792

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations
Cited by: 25
Author(s): Jessica Chopyk, Sarah Allard, Daniel J. Nasko, Anthony Bui, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 6
Published: over 6 years ago

10.1126/sciadv.abg5016

High-salt diet mediates interplay between NK cells and gut microbiota to induce potent tumor immunity
Cited by: 48
Author(s): Zaigham Abbas Rizvi, Rajdeep Dalal, Srikanth Sadhu, Yashwant Kumar, Sunil Kumar, Sonu Kumar Gupta, Manas Ranjan Tripathy, Deepak Kumar Rathore, Amit Awasthi
Software Mentions: 6
Published: about 3 years ago

10.3390/ph14070635

Probiotic Bacteria with High Alpha-Gal Content Protect Zebrafish against Mycobacteriosis
Cited by: 10
Author(s): Iván Pacheco, Sandra Díaz-Sánchez, Marinela Contreras, Margarita Villar, Alejandro Cabezas-Cruz, Christian Gortázar, José de la Fuente
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0251136

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study
Cited by: 7
Author(s): Martijn G H Sanders, Tamar Nijsten, Joost Verlouw, Robert Kraaij, Luba M. Pardo
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-018-0449-9

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool
Cited by: 113
Author(s): Jo De Vrieze, Ameet J. Pinto, William T. Sloan, Umer Zeeshan Ijaz
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0204317

Association of metformin administration with gut microbiome dysbiosis in healthy volunteers
Cited by: 85
Author(s): Ilze Elbere, Ineta Kalniņa, Ivars Silamiķelis, Ilze Konrāde, Linda Zaharenko, Kristine Sekace, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Dita Gudrā, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 6
Published: about 6 years ago

10.3389/fmicb.2020.586437

Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen
Cited by: 13
Author(s): Mohamed Kamal Abdelhamid, Narciso M. Quijada, Monika Dzieciol, Tamas Hatfaludi, Ivana Bilić, Evelyne Selberherr, Dieter Liebhart, Claudia Heß, Michael Heß, Surya Paudel
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-017-15554-8

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women
Cited by: 7
Author(s): Supriya D. Mehta, Ashish Pradhan, Stefan J. Green, Ankur Naqib, Elijah Odoyo-June, Charlotte A. Gaydos, Sheila M. Barry, Alan Landay, Robert C. Bailey
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-020-80568-8

Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula
Cited by: 15
Author(s): Nicole Trefault, Rodrigo De la Iglesia, Mario Moreno-Pino, Adriana Lopes dos Santos, Catherine Gérikas Ribeiro, Génesis Parada-Pozo, Antonia Cristi, Dominique Marie, Daniel Vaulot
Software Mentions: 6
Published: almost 4 years ago

10.3389/fmicb.2020.00954

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

10.7717/peerj.12135

Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics
Cited by: 9
Author(s): Ashley K. Coons, Kathrin Busch, Mark Lenz, Ute Hentschel, Erik Borchert
Software Mentions: 6
Published: about 3 years ago

10.1186/s40104-021-00580-4

Convergence of the turkey gut microbiota following cohabitation under commercial settings
Cited by: 1
Author(s): Elizabeth A. Miller, Brittanie Winfield, Bonnie Weber, Cristian Flores-Figueroa, Jeannette Muñoz-Aguayo, Jared Huisinga, Timothy J. Johnson
Software Mentions: 6
Published: over 3 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702