bioconductor: decontam | Projects

10.12688/f1000research.27268.1

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: over 3 years ago

10.1098/rsos.191609

Spatial heterogeneity of the shorebird gastrointestinal microbiome
Cited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: over 4 years ago

Reservoirs of antimicrobial resistance genes in retail raw milk
Cited by: 41
Author(s): Jinxin Liu, Yongxu Zhu, Michele Jay-Russell, Danielle G. Lemay, David A. Mills
Software Mentions: 13
Published: about 4 years ago

10.3389/fmicb.2020.01116

Crop Management Impacts the Soybean (Glycine max) Microbiome
Cited by: 41
Author(s): Reid Longley, Zachary A Noel, Gian Maria Niccolò Benucci, Martin I. Chilvers, Frances Trail, Gregory Bonito
Software Mentions: 12
Published: about 4 years ago

10.1038/s41598-021-86396-8

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Cited by: 15
Author(s): Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard‐Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud‐Haond, Daniela Zeppilli
Software Mentions: 11
Published: over 3 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: over 4 years ago

10.3389/fmicb.2019.02476

Characterization of the Mycobiome of the Seagrass, Zostera marina, Reveals Putative Associations With Marine Chytrids
Cited by: 29
Author(s): Cassandra L. Ettinger, Jonathan A. Eisen
Software Mentions: 10
Published: over 4 years ago

10.1186/s40168-020-00895-w

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota
Cited by: 32
Author(s): Shashank Gupta, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Xuanji Li, Martin Steen Mortensen, Jakob Russel, Urvish Trivedi, Morten Arendt Rasmussen, Jakob Stokholm, Hans Bisgaard, Søren J. Sørensen
Software Mentions: 10
Published: almost 4 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: over 4 years ago

10.3390/microorganisms9071487

Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
Cited by: 20
Author(s): Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja‐Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman‐Yassky, Tove Agner
Software Mentions: 10
Published: about 3 years ago

10.1098/rspb.2020.0302

Mating changes the genital microbiome in both sexes of the common bedbug <i>Cimex lectularius</i> across populations
Cited by: 4
Author(s): Sara Bellinvia, Paul R. Johnston, Susan Mbedi, Oliver Otti
Software Mentions: 10
Published: about 4 years ago

10.3390/nu12061779

Maternal Microbiota, Cortisol Concentration, and Post-Partum Weight Recovery Are Dependent on Mode of Delivery
Cited by: 7
Author(s): Marta Selma‐Royo, Izaskun García-Mantrana, Marta Calatayud, Anna Parra-Llorca, Cecilia Martínez‐Costa, María Carmen Collado
Software Mentions: 9
Published: about 4 years ago

10.1002/ece3.7579

Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding
Cited by: 36
Author(s): Melissa R. Ingala, Nancy B. Simmons, Claudia Wultsch, Konstantinos Krampis, Kaiya L. Provost, Susan L. Perkins
Software Mentions: 8
Published: about 3 years ago

10.3389/fmicb.2019.01834

Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome
Cited by: 35
Author(s): Kieran A. Bates, Jennifer Shelton, Victoria L. Mercier, Kevin Hopkins, Xavier A. Harrison, Silviu O. Petrovan, Matthew C. Fisher
Software Mentions: 8
Published: almost 5 years ago

10.3389/fmicb.2021.632935

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events
Cited by: 19
Author(s): Benjamin Zwirzitz, Stefanie U. Wetzels, Emmanuel D. Dixon, Svenja Fleischmann, Evelyne Selberherr, Sarah Thalguter, Narciso M. Quijada, Monika Dzieciol, Martin Wagner, Beatrix Stessl
Software Mentions: 8
Published: over 3 years ago

10.1186/s40168-019-0748-9

Microbial communities of the house fly Musca domestica vary with geographical location and habitat
Cited by: 58
Author(s): Rahel Park, Maria C. Dzialo, Stijn Spaepen, Donat Nsabimana, Kim Gielens, Herman Devriese, Sam Crauwels, Raúl Y. Tito, Jeroen Raes, Bart Lievens, Kevin J. Verstrepen
Software Mentions: 8
Published: over 4 years ago

10.1128/mSystems.00152-21

Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets
Cited by: 2
Author(s): Shriram Patel, Abel A. Vlasblom, Koen M. Verstappen, Aldert Zomer, Ad C. Fluit, Malbert R. C. Rogers, Jaap A. Wagenaar, Marcus J. Claesson, Birgitta Duim
Software Mentions: 8
Published: almost 3 years ago

10.1128/mSystems.01153-20

Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering
Cited by: 8
Author(s): E. Anders Kiledal, Jessica L. Keffer, Julia A. Maresca
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pone.0257471

Deciphering the low abundance microbiota of presumed aseptic hip and knee implants
Cited by: 2
Author(s): Charles Carr, Hannah Wilcox, Jeremy P. Burton, Sharanya Menon, Kait F. Al, David B. O’Gorman, Brent A. Lanting, Edward M. Vasarhelyi, Michael E. Neufeld, Matthew G. Teeter
Software Mentions: 8
Published: almost 3 years ago

10.1002/acn3.51441

Gut microbiome is associated with multiple sclerosis activity in children
Cited by: 18
Author(s): Mary Horton, Kathryn McCauley, Douglas Fadrosh, Kei E. Fujimura, Jennifer Graves, Jayne Ness, Yolanda Wheeler, Mark Gorman, Leslie Benson, Bianca Weinstock‐Guttman, Amy Waldman, Moses Rodriguez, Jan‐Mendelt Tillema, Lauren Krupp, Anita Belman, Soe Mar, Mary Rensel, Tanuja Chitnis, T. Charles Casper, John Rose, Janace Hart, Xiaorong Shao, Helen Tremlett, Susan V. Lynch, Lisa F. Barcellos, Emmanuelle Waubant
Software Mentions: 8
Published: almost 3 years ago

10.3389/fmicb.2021.584676

Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores
Cited by: 0
Author(s): Erica Ewton, Scott Klasek, Erin K. Peck, J. Wiest, Frederick S. Colwell
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2021.644828

The Cheese Production Facility Microbiome Exhibits Temporal and Spatial Variability
Cited by: 12
Author(s): Jared Johnson, Chris Curtin, Joy Waite‐Cusic
Software Mentions: 8
Published: over 3 years ago

10.1128/mSystems.00510-21

Dysbiosis of the Urinary Bladder Microbiome in Cats with Chronic Kidney Disease
Cited by: 5
Author(s): Younjung Kim, Maura Carrai, Marcus H. Y. Leung, Jaime Chin, Jun Li, Patrick K. H. Lee, Julia A. Beatty, Dirk U. Pfeiffer, Vanessa R. Barrs
Software Mentions: 7
Published: almost 3 years ago

10.1080/19490976.2021.1927634

Influence of pig farming on human Gut Microbiota: role of airborne microbial communities
Cited by: 5
Author(s): Julia Moor, Tsering Wüthrich, Suzanne Aebi, Nadezda Mostacci, Gudrun Overesch, Anne Oppliger, Markus Hilty
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2020.607325

Effects of Rare Microbiome Taxa Filtering on Statistical Analysis
Cited by: 53
Author(s): Quy Cao, Xinxin Sun, Karun Rajesh, Naga Chalasani, Kayla Gelow, Barry P. Katz, Vijay H. Shah, Arun J. Sanyal, Ekaterina Smirnova
Software Mentions: 7
Published: over 3 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: about 3 years ago

10.1371/journal.pone.0249832

Non-small cell lung cancer microbiota characterization: Prevalence of enteric and potentially pathogenic bacteria in cancer tissues
Cited by: 14
Author(s): Nathan Dumont-Leblond, Marc Veillette, Christine Racine, Philippe Joubert, Caroline Duchaine
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-52549-z

Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing
Cited by: 29
Author(s): Marta Reyman, Marlies A. van Houten, Kayleigh Arp, Elisabeth A. M. Sanders, Debby Bogaert
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2019.00164

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls
Cited by: 66
Author(s): Rahul Bodkhe, Sudarshan A. Shetty, Dhiraj Dhotre, Anil K. Verma, Khushbo Bhatia, Abhishek Mishra, Gurvinder Kaur, Pranav Pande, Dhinoth Kumar Bangarusamy, Beena P. Santosh, Rajadurai Chinnasamy Perumal, Vineet Ahuja, Yogesh S. Shouche, Govind Makharia
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-020-00962-2

Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions
Cited by: 8
Author(s): Joshua M. Lyte, James Keane, Julia Eckenberger, Nicholas B. Anthony, Sandip Shrestha, Daya Marasini, Karrie M. Daniels, Valentina Caputi, Annie Donoghue, Mark Lyte
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2021.673969

Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals
Cited by: 2
Author(s): Junjie Qin, Shi Xiao-li, Junming Xu, Simin Yuan, Bo Zheng, Enpu Zhang, Guangtao Huang, Li Guo, Ganggang Jiang, Shan Gao, Tian Cheng, Ruochun Guo, Zhicong Fu, Qingru Huang, Rentao Yang, Wenyong Zhang, Shenghui Li, Song Wu
Software Mentions: 6
Published: almost 3 years ago

10.1038/s41396-020-00749-1

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment
Cited by: 37
Author(s): Nicholas J. Reichart, Zackary J. Jay, Viola Krukenberg, Albert E. Parker, Rachel L. Spietz, Roland Hatzenpichler
Software Mentions: 6
Published: almost 4 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: over 3 years ago

10.7717/peerj.10837

Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome
Cited by: 7
Author(s): Stefan Gavriliuc, Mason R. Stothart, Astrid Henry, Jocelyn Poissant
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-019-0766-7

Discordant transmission of bacteria and viruses from mothers to babies at birth
Cited by: 61
Author(s): Rabia Maqsood, Rachel Rodgers, Cynthia Rodríguez, Scott A. Handley, I. Malick Ndao, Phillip I. Tarr, Barbara Warner, Efrem S. Lim, Lori R. Holtz
Software Mentions: 6
Published: over 4 years ago

10.1002/ece3.5361

Drivers and patterns of microbial community assembly in a Lyme disease vector
Cited by: 30
Author(s): Lisa I. Couper, Jessica Y. Kwan, Joyce Ma, Andrea Swei
Software Mentions: 6
Published: about 5 years ago

10.1128/mSystems.00446-21

Transmission of Seed and Soil Microbiota to Seedling
Cited by: 27
Author(s): Aude Rochefort, Marie Simonin, Coralie Marais, Anne‐Yvonne Guillerm‐Erckelboudt, Matthieu Barret, Alain Sarniguet
Software Mentions: 6
Published: about 3 years ago

10.3390/microorganisms9010076

Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics
Cited by: 44
Author(s): Katharina Kesy, Matthias Labrenz, Brittan S. Scales, Bernd Kreikemeyer, Sonja Oberbeckmann
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.12067

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya
Cited by: 2
Author(s): Rehema Liyai, Kimita Gathii, Clement Masakhwe, David Abuom, Beth Mutai, David Miruka Onyango, John N. Waitumbi
Software Mentions: 5
Published: almost 3 years ago

10.1186/s40168-021-01009-w

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques
Cited by: 35
Author(s): Mareike C. Janiak, Michael J. Montague, Catalina I. Villamil, Michala K. Stock, Amber E. Trujillo, Allegra N. DePasquale, Joseph D. Orkin, Samuel E. Bauman Surratt, Olga González, Michael L. Platt, Melween I. Martínez, Susan C. Antón, Maria Gloria Domínguez-Bello, Amanda D. Melin, James P. Higham
Software Mentions: 5
Published: over 3 years ago

10.3389/fvets.2021.654927

Association of Broiler Litter Microbiome Composition and Campylobacter Isolation
Cited by: 7
Author(s): Robert Valeris-Chacín, Maria Pieters, Hyun Seok Hwang, Timothy J. Johnson, Randall S. Singer
Software Mentions: 5
Published: about 3 years ago

10.1186/s12866-020-01795-7

Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens
Cited by: 15
Author(s): Shantelle Claassen-Weitz, Sugnet Gardner-Lubbe, Kilaza Samson Mwaikono, Elloise du Toit, Heather J. Zar, Mark P. Nicol
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2020.572504

Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid
Cited by: 13
Author(s): Montserrat Saladié, José A. Caparrós-Martín, Ana Patrícia, Peter Wark, Stephen M. Stick, Fergal O’Gara
Software Mentions: 5
Published: almost 4 years ago

10.3389/fnut.2019.00058

Integrated Analysis of Human Milk Microbiota With Oligosaccharides and Fatty Acids in the CHILD Cohort
Cited by: 66
Author(s): Shirin Moossavi, Faisal Atakora, Kozeta Miliku, Shadi Sepehri, Bianca Robertson, Qing Duan, Allan B. Becker, Piushkumar J. Mandhane, Stuart E. Turvey, Theo J. Moraes, Diana L. Lefebvre, Malcolm R. Sears, Padmaja Subbarao, Catherine J. Field, Lars Bode, Ehsan Khafipour, Meghan B. Azad
Software Mentions: 5
Published: about 5 years ago

10.1186/s42523-021-00074-8

Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)
Cited by: 10
Author(s): Sesilje Weiss, David A. Taggart, Ian Smith, Kristofer M. Helgen, Raphael Eisenhofer
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms9051054

Microbial Sharing between Pediatric Patients and Therapy Dogs during Hospital Animal-Assisted Intervention Programs
Cited by: 7
Author(s): Kathryn R. Dalton, Kathy Ruble, Laurel E. Redding, Daniel O. Morris, Noel T. Mueller, Roland J. Thorpe, Jacqueline Agnew, Karen C. Carroll, Paul J. Planet, Ronald C. Rubenstein, Allen Chen, Elizabeth A. Grice, Meghan F. Davis
Software Mentions: 5
Published: about 3 years ago

10.7717/peerj.8549

Invasive vegetation affects amphibian skin microbiota and body condition
Cited by: 7
Author(s): Obed Hernández‐Gómez, Allison Q. Byrne, Alex R. Gunderson, Thomas S. Jenkinson, Clay F. Noss, Andrew P. Rothstein, Molly C. Womack, Erica Bree Rosenblum
Software Mentions: 5
Published: over 4 years ago

10.3389/fcimb.2021.622550

Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
Cited by: 7
Author(s): Lorena Ruíz, Claudio Alba, Cristina García-Carral, Esther Jiménez, Kimberly A. Lackey, Michelle K. McGuire, Courtney L. Meehan, James A. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Gloria E. Otoo, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Janet E. Williams, Juan M. Rodríguez
Software Mentions: 4
Published: over 3 years ago

10.1111/1751-7915.13566

Resveratrol affects<i>in vitro</i>rumen fermentation, methane production and prokaryotic community composition in a time‐ and diet‐specific manner
Cited by: 18
Author(s): Ma T, Wei Wu, Tiebin Yan, N. Zhang, Qiyu Diao
Software Mentions: 4
Published: over 4 years ago

10.1186/s40168-021-01082-1

Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching
Cited by: 10
Author(s): David E. Wilkins, Xinzhao Tong, Marcus H. Y. Leung, Christopher E. Mason, Patrick K. H. Lee
Software Mentions: 4
Published: about 3 years ago

10.1186/s40168-020-00940-8

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function
Cited by: 43
Author(s): Marta Selma‐Royo, Marta Calatayud, Izaskun García-Mantrana, Anna Parra-Llorca, Ramón Escuriet, Cecilia Martínez‐Costa, María Carmen Collado
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-020-00998-4

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota
Cited by: 12
Author(s): Shirin Moossavi, Kelsey Fehr, Ehsan Khafipour, Meghan B. Azad
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms9010030

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments
Cited by: 17
Author(s): Marc Cozannet, Guillaume Borrel, Erwan G. Roussel, Yann Moalic, Maxime Allioux, Sanvoisin Amandine, Laurent Toffin, Karine Alain
Software Mentions: 4
Published: over 3 years ago

10.1016/j.ymgmr.2021.100794

Differences in faecal microbiome composition between adult patients with UCD and PKU and healthy control subjects
Cited by: 2
Author(s): Corrie Timmer, Mark Davids, Max Nieuwdorp, J.H.M. Levels, Janneke G. Langendonk, M. Breederveld, Nasrin Mozafari, Mirjam Langeveld
Software Mentions: 4
Published: over 2 years ago

10.1371/journal.pone.0253989

Evaluating extraction methods to study canine urine microbiota
Cited by: 7
Author(s): Ryan Mrofchak, Christopher Madden, Morgan V. Evans, Vanessa L. Hale
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0244643

Characterization of cerebrospinal fluid (CSF) microbiota from patients with CSF shunt infection and reinfection using high throughput sequencing of 16S ribosomal RNAgenes
Cited by: 5
Author(s): Kathryn B. Whitlock, Charles E. Pope, Paul Hodor, Lucas R. Hoffman, David L. Limbrick, Patrick J. McDonald, Jason S. Hauptman, Jeffrey G. Ojemann, Tamara D. Simon
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0217306

Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents
Cited by: 13
Author(s): John E. McGinniss, Ize Imai, Áurea Simón-Soro, Melanie C. Brown, Vincent R. Knecht, Laura Frye, Priyanka M. Ravindran, Marisol I. Dothard, Dylan A. Wadell, Michael B. Sohn, Hongzhe Li, Jason D. Christie, Joshua M. Diamond, Andrew R. Haas, Anthony R. Lanfranco, David M. DiBardino, Frederic D. Bushman, Ronald G. Collman
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2021.670982

Geomicrobiological Heterogeneity of Lithic Habitats in the Extreme Environment of Antarctic Nunataks: A Potential Early Mars Analog
Cited by: 4
Author(s): Miguel Ángel Fernández-Martínez, Miriam García‐Villadangos, Mercedes Moreno‐Paz, Valentin Gangloff, Daniel Carrizo, Yolanda Blanco, Sergi González, Laura Sánchez-García, O. Prieto-Ballesteros, Ianina Altshuler, Lyle G. Whyte, Vı́ctor Parro, Alberto González Fairén
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2021.633396

The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study
Cited by: 8
Author(s): Monica R. Ticlla, Jerry Hella, Hellen Hiza, Mohamed Sasamalo, Francis Mhimbira, Liliana K. Rutaihwa, Sara Droz, Sarah Schaller, Klaus Reither, Markus Hilty, Iñaki Comas, Christian Beisel, Christoph D. Schmid, Lukas Fenner, Sébastien Gagneux
Software Mentions: 4
Published: almost 3 years ago

10.3389/fvets.2021.666887

Replacement of Metaphylactic Antimicrobial Therapy by Oral Administration of Ligilactobacillus salivarius MP100 in a Pig Farm
Cited by: 7
Author(s): Odón J. Sobrino, Claudio Alba, Rebeca Arroyo, Inés Pérez, Lydia Sariego, Susana Delgado, Leónides Fernández, Julián de María, Pilar Fumanal, Antonio J. Fumanal, Juan M. Rodríguez
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-020-73515-0

Preliminary insights into the impact of primary radiochemotherapy on the salivary microbiome in head and neck squamous cell carcinoma
Cited by: 15
Author(s): Christina Kumpitsch, Christine Moissl-Eichinger, Jakob Pock, Dietmar Thurnher, Axel Wolf
Software Mentions: 4
Published: almost 4 years ago

10.1080/19490976.2021.1875109

Compensatory intestinal immunoglobulin response after vancomycin treatment in humans
Cited by: 6
Author(s): Torsten P. M. Scheithauer, Guido J. Bakker, Maaike Winkelmeijer, Mark Davids, Max Nieuwdorp, Daniël H. van Raalte, Hilde Herrema
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-62424-x

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture
Cited by: 17
Author(s): Lisa A. Cummings, Daniel R. Hoogestraat, Sara L. Rassoulian-Barrett, Christopher Rosenthal, Stephen J. Salipante, Brad T. Cookson, Noah G. Hoffman
Software Mentions: 3
Published: over 4 years ago

10.1128/AEM.01047-20

Fungal Signature of Moisture Damage in Buildings: Identification by Targeted and Untargeted Approaches with Mycobiome Data
Cited by: 9
Author(s): Rachel I. Adams, Iman Sylvain, Michal Spilak, John W. Taylor, Michael S. Waring, Mark J. Mendell
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0225636

Airway microbiome composition correlates with lung function and arterial stiffness in an age-dependent manner
Cited by: 22
Author(s): Shuen Yee Lee, Micheál Mac Aogáin, Kai Deng Fam, Kar Ling Chia, Nur A. 'tikah Binte Mohamed Ali, Margaret Mei Chan Yap, E. H. Yap, Sanjay H. Chotirmall, Chin Leong Lim
Software Mentions: 3
Published: over 4 years ago

10.1128/mSystems.00296-20

Parallel Analysis of Cystic Fibrosis Sputum and Saliva Reveals Overlapping Communities and an Opportunity for Sample Decontamination
Cited by: 19
Author(s): Junnan Lu, Lisa A. Carmody, Kristopher Opron, Richard H. Simon, Linda M. Kalikin, Lindsay J. Caverly, John J. LiPuma
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0218257

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination
Cited by: 35
Author(s): Josef Dahlberg, Li Sun, Karin Persson Waller, K. Östensson, Mark A. McGuire, Sigrid Agenäs, Johan Dicksved
Software Mentions: 3
Published: about 5 years ago

10.3390/vision5020027

Ocular Surface Microbiota in Contact Lens Users and Contact-Lens-Associated Bacterial Keratitis
Cited by: 8
Author(s): Jasmine Andersson, Josef Korbinian Vogt, Marlene Danner Dalgaard, Oluf Pedersen, Kim Holmgaard, Steffen Heegaard
Software Mentions: 3
Published: about 3 years ago

10.1186/s40168-021-01059-0

Identifying biases and their potential solutions in human microbiome studies
Cited by: 60
Author(s): Jacob T. Nearing, A. Comeau, Morgan G. I. Langille
Software Mentions: 3
Published: about 3 years ago

10.3389/fcimb.2020.00167

Significant Short-Term Shifts in the Microbiomes of Smokers With Periodontitis After Periodontal Therapy With Amoxicillin & Metronidazole as Revealed by 16S rDNA Amplicon Next Generation Sequencing
Cited by: 5
Author(s): Daniel Hagenfeld, Johannes Matern, Karola Prior, Inga Harks, Peter Eickholz, K. Lorenz, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Dag Harmsen, Benjamin Ehmke
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-78891-1

An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health
Cited by: 26
Author(s): Scott Sugden, D. E. Sanderson, Kyra Ford, Lisa Y. Stein, Colleen Cassady St. Clair
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms20204991

Optimisation and Benchmarking of Targeted Amplicon Sequencing for Mycobiome Analysis of Respiratory Specimens
Cited by: 25
Author(s): Nur A’tikah Binte Mohamed Ali, Micheál Mac Aogáin, Raika Francesca Morales, Pei Yee Tiew, Sanjay H. Chotirmall
Software Mentions: 2
Published: almost 5 years ago

10.1128/mSystems.00186-19

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
Cited by: 119
Author(s): Jeremiah J. Minich, Jon G. Sanders, Amir Almasi‐Hashiani, Greg Humphrey, Jack A. Gilbert, Rob Knight
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40168-018-0605-2

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
Cited by: 1,412
Author(s): Nicole M. Davis, Diana M. Proctor, Susan Holmes, David A. Relman, Benjamin J. Callahan
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00294-21

Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost
Cited by: 3
Author(s): Joshua G. Harrison, Gregg Randolph, C. Alex Buerkle
Software Mentions: 2
Published: almost 3 years ago

10.1186/s40168-020-00949-z

Batch effects account for the main findings of an in utero human intestinal bacterial colonization study
Cited by: 32
Author(s): Marcus C. de Goffau, D. Stephen Charnock‐Jones, Gordon Cs Smith, Julian Parkhill
Software Mentions: 2
Published: over 3 years ago

Projects: bioconductor: decontam

Papers Mentioning decontam 76