bioconductor: phyloseq | Projects

10.3389/fcimb.2021.595554

Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort
Cited by: 4
Author(s): Milkessa HaileMariam, Yu Yoshida, Harinder Singh, Takele Teklu, Biniam Wondale, Adane Worku, Aboma Zewude, Stephanie Mounaud, Tamara Tsitrin, Mengistu Legesse, Gobena Ameni, Rembert Pieper
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-87017-0

The larval environment strongly influences the bacterial communities of Aedes triseriatus and Aedes japonicus (Diptera: Culicidae)
Cited by: 6
Author(s): Elijah O. Juma, Brian F. Allan, Chang‐Hyun Kim, Chris Stone, Christopher A. Dunlap, Ephantus J. Muturi
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2015.00348

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
Cited by: 223
Author(s): Alejandra Escobar‐Zepeda, Arturo Vera‐Ponce de León, Alejandro Sánchez-Flores
Software Mentions: 3
Published: about 9 years ago

10.20411/pai.v4i1.269

Microbiomes of Inflammatory Thoracic Aortic Aneurysms Due to Giant Cell Arteritis and Clinically Isolated Aortitis Differ From Those of Non-Inflammatory Aneurysms
Cited by: 18
Author(s): Ted M. Getz, Gary S. Hoffman, Roshan Padmanabhan, Alexandra Villa‐Forte, Eric E. Roselli, Eugene H. Blackstone, Douglas R. Johnston, Gösta Pettersson, Edward G. Soltesz, Lars Svensson, Leonard H. Calabrese, Alison Clifford, Charis Eng
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-85990-0

Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process
Cited by: 8
Author(s): Camilo Quiroga-González, Luis Alberto Chica Cárdenas, Mónica A. Ramírez, Alejandro Reyes, Camila González, Pablo R. Stevenson
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0217296

Influence of own mother's milk and different proportions of formula on intestinal microbiota of very preterm newborns
Cited by: 17
Author(s): Adriana Zanella, Rita de Cássia dos Santos Silveira, Luiz Fernando Würdig Roesch, Andrea Corso, Priscila Caroline Thiago Dobbler, Volker Mai, Renato S. Procianoy
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-94468-y

Comparative analysis of the bronchoalveolar microbiome in Portuguese patients with different chronic lung disorders
Cited by: 5
Author(s): Susana Seixas, Allison R. Kolbe, Sílvia Cristina Vieira Gomes, Maria Sucena, Catarina Sousa, Luís Rodrigues, Gilberto Teixeira, Paula Pinto, Tiago Abreu, Cristina Bárbara, Júlio Semedo, Leonor Mota, Ana Sofía Carvalho, Rune Matthiesen, Patrícia Marques, Marcos Pérez‐Losada
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0208018

Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease
Cited by: 12
Author(s): Steven Cowman, Phillip James, Robert Wilson, William Cookson, Miriam F. Moffatt, Michael R. Loebinger
Software Mentions: 3
Published: about 6 years ago

10.3390/cancers12123702

Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank
Cited by: 15
Author(s): Ulrike Wirth, Debora Garzetti, Lara Jochum, Stefanie Spriewald, Florian Kühn, Matthias Ilmer, Serene M. L. Lee, Hanno Nieß, Alexandr V. Bazhin, Joachim Andrassy, Jens Werner, Bärbel Stecher, Tobias S. Schiergens
Software Mentions: 3
Published: about 4 years ago

10.3389/fimmu.2020.00838

IL-22 Paucity in APECED Is Associated With Mucosal and Microbial Alterations in Oral Cavity
Cited by: 13
Author(s): Epp Kaleviste, Malte Rühlemann, Jaanika Kärner, Liis Haljasmägi, Liina Tserel, Elin Org, Katarina Trebušak Podkrajšek, Tadej Battelino, Corinna Bang, André Franke, Pärt Peterson, Kai Kisand
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2017.01914

Feeding Immunity: Physiological and Behavioral Responses to Infection and Resource Limitation
Cited by: 27
Author(s): Sarah A. Budischak, Christina Hansen, Quentin Caudron, Romain Garnier, Tyler R. Kartzinel, István Pelczer, Clayton E. Cressler, Anieke van Leeuwen, Andrea L. Graham
Software Mentions: 3
Published: about 7 years ago

10.3389/fmed.2021.586875

Impact on the Gut Microbiota of Intensive and Prolonged Antimicrobial Therapy in Patients With Bone and Joint Infection
Cited by: 7
Author(s): Benoît Levast, Nicolas Benech, Cyrielle Gasc, Cécile Batailler, Éric Senneville, Sébastien Lustig, Cécile Pouderoux, David Boutoille, Lilia Boucinha, Frédéric‐Antoine Dauchy, Valérie Zeller, Marianne Maynard, Charles Cazanave, Thanh-Thuy Thi, Jérôme Josse, Joël Doré, Frédéric Laurent, Tristan Ferry
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.8147

Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community
Cited by: 6
Author(s): Samantha Velazquez, Chenyang Bi, Jeff Kline, Susie Nunez, Rich Corsi, Ying Xu, Suzanne L. Ishaq
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0215872

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

10.1371/journal.pone.0179945

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major)
Cited by: 21
Author(s): Lucie Kropáčková, Hana Pechmanová, Michal Vinkler, Jana Svobodová, Hana Velová, Martin Těšičký, Jean‐François Martin, Jakub Kreisinger
Software Mentions: 3
Published: over 7 years ago

10.3390/nu10122009

Gut Microbiota and Endothelial Dysfunction Markers in Obese Mexican Children and Adolescents
Cited by: 80
Author(s): Khemlal Nirmalkar, Selvasankar Murugesan, María Luisa Pizano-Zárate, Loan Edel Villalobos-Flores, Cristina García-González, Rosa María Morales-Hernández, Jorge A. Núñez-Hernández, Fernando Hernández-Quiroz, María del Socorro Romero Figueroa, César Hernández‐Guerrero, Carlos Hoyo‐Vadillo, Jaime García‐Mena
Software Mentions: 3
Published: about 6 years ago

10.3390/microorganisms8050638

Intestinal Microbiota of Fattening Pigs Offered Non-Fermented and Fermented Liquid Feed with and without the Supplementation of Non-Fermented Coarse Cereals
Cited by: 14
Author(s): Sebastian Bunte, Richard Grone, Birgit Keller, Christoph A. Keller, Eric Galvez, Till Strowig, Josef Kamphues, Julia Hankel
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-95099-z

Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge
Cited by: 27
Author(s): Jorge Domínguez, Manuel Aira, Keith A. Crandall, Marcos Pérez‐Losada
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8121861

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community
Cited by: 3
Author(s): Claudia Sala, Hanne Mordhorst, Josephine Grützke, Annika Brinkmann, Thomas Nordahl Petersen, Casper Sahl Poulsen, Paul D. Cotter, Fiona Crispie, Richard J. Ellis, Gastone Castellani, Clara Amid, Mikhayil Hakhverdyan, Soizick Le Guyader, Gerardo Manfreda, Joël Mossong, Andreas Nitsche, Catherine Ragimbeau, Julien Schaeffer, Jørgen Schlundt, Moon Y. F. Tay, Frank Møller Aarestrup, René S. Hendriksen, Sünje Johanna Pamp, Alessandra De Cesare
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2021.676880

Outbreaks of Root Rot Disease in Different Aged American Ginseng Plants Are Associated With Field Microbial Dynamics
Cited by: 16
Author(s): Ji Li, Fahad Nasir, Lei Tian, Jingjing Chang, Yu Sun, Jianfeng Zhang, Xiujun Li, Chunjie Tian
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0231942

Putting the microbiota to work: Epigenetic effects of early life antibiotic treatment are associated with immune-related pathways and reduced epithelial necrosis following Salmonella Typhimurium challenge in vitro
Cited by: 4
Author(s): Matheus O. Costa, Janelle M Fouhse, Ana Paula P. Silva, Benjamin P. Willing, John C. S. Harding
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0202054

Enteric virome of Ethiopian children participating in a clean water intervention trial
Cited by: 29
Author(s): Eda Altan, Kristen Aiemjoy, Tung Gia Phan, Xutao Deng, Solomon Aragie, Zerihun Tadesse, Kelly Callahan, Jeremy D. Keenan, Eric Delwart
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.694406

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera
Cited by: 2
Author(s): I. Salonen, Panagiota-Myrsini Chronopoulou, Hidetaka Nomaki, Dewi Langlet, Masashi Tsuchiya, Karoliina A. Koho
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8101482

Seasonal Variations in Soil Microbiota Profile of Termite (Syntermes wheeleri) Mounds in the Brazilian Tropical Savanna
Cited by: 9
Author(s): Helena Ipe Pinheiro Guimaraes, Renata Henrique Santana, Rafaella Silveira Sousa, Otávio Henrique Bezerra Pinto, Betânia Ferraz Quirino, Cristine Chaves Barreto, Mercedes Maria da Cunha Bustamante
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.596156

Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms
Cited by: 1
Author(s): Wen Qin, Frederik Hammes
Software Mentions: 3
Published: about 4 years ago

10.3390/microorganisms9010113

Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA
Cited by: 7
Author(s): Tanvi Govil, Manasi Paste, Dipayan Samanta, Aditi David, Kian Mau Goh, Xiangkai Li, David R. Salem, Rajesh K. Sani
Software Mentions: 3
Published: about 4 years ago

10.1093/cid/ciz905

Diarrhea as a Potential Cause and Consequence of Reduced Gut Microbial Diversity Among Undernourished Children in Peru
Cited by: 32
Author(s): Saba Rouhani, Nicholas W. Griffin, Pablo Peñataro Yori, Jeanette L. Gehrig, 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: 3
Published: over 5 years ago

10.3389/fmicb.2017.00431

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment
Cited by: 22
Author(s): Pauliina Rajala, Malin Bomberg
Software Mentions: 3
Published: almost 8 years ago

10.3390/nu12020290

Long-Term Blackcurrant Supplementation Modified Gut Microbiome Profiles in Mice in an Age-Dependent Manner: An Exploratory Study
Cited by: 13
Author(s): Lei Cao, Sang Gil Lee, Melissa M. Melough, Junichi Sakaki, Kendra Maas, Sung I. Koo
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2019.02368

Microbial Communities in Bioswale Soils and Their Relationships to Soil Properties, Plant Species, and Plant Physiology
Cited by: 8
Author(s): Olivia L Brodsky, Katherine L. Shek, Devin Dinwiddie, Sarah G. Bruner, Amanjit Gill, Jessica M. K. Hoch, Matthew I. Palmer, Krista L. McGuire
Software Mentions: 3
Published: about 5 years ago

10.3390/microorganisms9081752

Modulation of the Mucosa-Associated Microbiome Linked to the PTPN2 Risk Gene in Patients with Primary Sclerosing Cholangitis and Ulcerative Colitis
Cited by: 6
Author(s): Luisa Denoth, Pascal Juillerat, Andreas E. Kremer, Gerhard Rogler, Michael Scharl, Bahtiyar Yılmaz, Sena Bluemel
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-98119-0

The importance of environmental microbes for Drosophila melanogaster during seasonal macronutrient variability
Cited by: 4
Author(s): Lucy Rebecca Davies, Volker Loeschcke, Mads Fristrup Schou, Andreas Schramm, Torsten Nygård Kristensen
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8122022

Comparative Microbiome and Metabolome Analyses of the Marine Tunicate Ciona intestinalis from Native and Invaded Habitats
Cited by: 15
Author(s): Caroline Utermann, Martina Blümel, Kathrin Busch, Larissa Buedenbender, Ya‐Ping Lin, Brad Haltli, Russell G. Kerr, Elizabeta Briski, Ute Hentschel, Deniz Taşdemir
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0169753

Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms
Cited by: 65
Author(s): Simon Bahrndorff, Nadieh de Jonge, Henrik Skovgård, Jeppe Lund Nielsen
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2018.01410

Humic Substances Alter Ammonia Production and the Microbial Populations Within a RUSITEC Fed a Mixed Hay – Concentrate Diet
Cited by: 18
Author(s): Stephanie A. Terry, Aline Maria Pereira Cruz Ramos, Devin B. Holman, Tim A. McAllister, Gerhard Breves, A. V. Chaves
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms8121941

Impacts of Wet Market Modernization Levels and Hygiene Practices on the Microbiome and Microbial Safety of Wooden Cutting Boards in Hong Kong
Cited by: 11
Author(s): Wing Yui Ngan, Subramanya Rao, Long Chung Chan, Patrick T. Sekoai, Yunfeng Pu, Yuan Yao, Aster Hei Yiu Fung, Olivier Habimana
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-98519-2

Changes in microbial community phylogeny and metabolic activity along the water column uncouple at near sediment aphotic layers in fjords
Cited by: 2
Author(s): Sven P. Tobias-Hünefeldt, Stephen R. Wing, Federico Baltar, Sergio E. Morales
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2019.00461

Spatial Variability of Antarctic Surface Snow Bacterial Communities
Cited by: 19
Author(s): Lucie Malard, Marie Šabacká, Iordanis Magiopoulos, Matthew C. Mowlem, Andy Hodson, Martyn Tranter, Martín J. Siegert, David A. Pearce
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2016.00476

Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin
Cited by: 76
Author(s): Francesco Paolo Mancuso, Sofie D’hondt, Anne Willems, Laura Airoldi, Olivier De Clerck
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.2430

Environment and host species shape the skin microbiome of captive neotropical bats
Cited by: 46
Author(s): Virginie Lemieux-Labonté, Nicolas Tromas, B. Jesse Shapiro, François‐Joseph Lapointe
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.6090

Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the<i>Firmicutes</i>phylum
Cited by: 34
Author(s): Craig Anderson, Michelle E. Peterson, Rebekah A. Frampton, Simon Bulman, Sandi Keenan, D. Curtin
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2018.01998

Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F)
Cited by: 14
Author(s): Margaret Mars Brisbin, Lisa Y. Mesrop, Mary M. Grossmann, Satoshi Mitarai
Software Mentions: 3
Published: over 6 years ago

10.3390/ani11010084

A Single Dose of Synbiotics and Vitamins at Birth Affects Piglet Microbiota before Weaning and Modifies Post-Weaning Performance
Cited by: 5
Author(s): Marion Girard, M. Tretola, Giuseppe Bee
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0249521

Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem
Cited by: 9
Author(s): Claire E. Couch, Benjamin L. Wise, Brandon M. Scurlock, Jared D. Rogerson, Rebecca K. Fuda, Eric K. Cole, Kimberly E. Szcodronski, Adam J. Sepulveda, Patrick R. Hutchins, Paul C. Cross
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0178755

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries
Cited by: 29
Author(s): Mikel Aguirre, David Abad, Aitor Albaina, Lauren Cralle, María Soledad Goñi-Urriza, Andone Estonba, Iratxe Zarraonaindia
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.674556

Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping
Cited by: 13
Author(s): Barbara Pivato, Amélie Semblat, Thibault Guégan, Samuel Jacquiod, Juliette Martin, Florence Deau, Nathalie Moutier, Christophe Lecomte, Judith Burstin, Philippe Lemanceau
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2017.02096

Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition
Cited by: 52
Author(s): Gulnaz T. Javan, Sheree J. Finley, Tasia M. Smith, Joselyn Miller, Jeremy E. Wilkinson
Software Mentions: 3
Published: over 7 years ago

10.3390/microorganisms9010021

Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions
Cited by: 8
Author(s): Abdul Ghafar, Anson V. Koehler, Ross S. Hall, Charles G. Gauci, Robin B. Gasser, Abdul Jabbar
Software Mentions: 3
Published: about 4 years ago

10.1038/s42003-020-01582-0

Curbing gastrointestinal infections by defensin fragment modifications without harming commensal microbiota
Cited by: 4
Author(s): Louis Koeninger, Lisa Osbelt, Anne Berscheid, Judith Wendler, Jürgen Berger, Katharina Hipp, Till Robin Lesker, Marina C. Pils, Nisar P. Malek, Benjamin Anderschou Holbech Jensen, Heike Brötz‐Oesterhelt, Till Strowig, Jan Wehkamp
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2015.00729

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability
Cited by: 16
Author(s): Kathleen Merritt Brannen-Donnelly, Annette Summers Engel
Software Mentions: 3
Published: over 9 years ago

10.3390/microorganisms8060872

Arbuscular Mycorrhizal Fungal Communities of Native Plant Species under High Petroleum Hydrocarbon Contamination Highlights Rhizophagus as a Key Tolerant Genus
Cited by: 10
Author(s): Soon‐Jae Lee, Mengxuan Kong, Marc St‐Arnaud, Mohamed Hijri
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.593401

The Microbiome of Leonardo da Vinci’s Drawings: A Bio-Archive of Their History
Cited by: 20
Author(s): Güadalupe Piñar, Maria Carla Sclocchi, Flavia Pinzari, Piero Colaizzi, Alexandra B. Graf, Maria Letizia Sebastiani, Katja Sterflinger
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0183716

Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen
Cited by: 93
Author(s): Nadja Danner, Alexander Keller, Stephan Härtel, Ingolf Steffan‐Dewenter
Software Mentions: 3
Published: over 7 years ago

10.3390/microorganisms7090282

Differential Impact of Subtherapeutic Antibiotics and Ionophores on Intestinal Microbiota of Broilers
Cited by: 31
Author(s): Kelsy Robinson, Sage Becker, Yingping Xiao, Wentao Lyu, Qing Yang, Huiling Zhu, Hua Yang, Jiangchao Zhao, Guolong Zhang
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms8101582

Bioaminergic Responses in an In Vitro System Studying Human Gut Microbiota–Kiwifruit Interactions
Cited by: 4
Author(s): Shanthi G. Parkar, Carel M. H. Jobsis, Tania Trower, Janine M. Cooney, Duncan Hedderley, Kerry L. Bentley‐Hewitt
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2019.01743

Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter–Gatherer Group
Cited by: 27
Author(s): Liliane Costa Conteville, Joseli Oliveira-Ferreira, Ana Carolina Paulo Vicente
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-99028-y

The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes
Cited by: 10
Author(s): María Velasco-Galilea, M. Piles, Yuliaxis Ramayo-Caldas, Juan Pablo Sánchez
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0210679

Fecal microbiota dysbiosis in macaques and humans within a shared environment
Cited by: 9
Author(s): Erica T. Grant, Randall C. Kyes, Pensri Kyes, Pauline Trinh, Vickie Ramirez, Tawatchai Tanee, Porntip Pinlaor, Rungtiwa Dangtakot, Peter Rabinowitz
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2018.02662

Plant Litter Type Dictates Microbial Communities Responsible for Greenhouse Gas Production in Amended Lake Sediments
Cited by: 15
Author(s): Kurt M. Yakimovich, Erik J. S. Emilson, M. A. Carson, Andrew J. Tanentzap, Nathan Basiliko, Nadia Mykytczuk
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0257207

Nasopharyngeal microbiome composition associated with Streptococcus pneumoniae colonization suggests a protective role of Corynebacterium in young children
Cited by: 9
Author(s): Lei Xu, Joshua P. Earl, Michael E. Pichichero
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.635772

Comprehensive Ecological and Geographic Characterization of Eukaryotic and Prokaryotic Microbiomes in African Anopheles
Cited by: 5
Author(s): Eugeni Belda, Boubacar Coulibaly, Tullu Bukhari, Karin Eiglmeier, Raymond Kone, Mamadou B. Coulibaly, Soumanaba Zongo, Megan Barry, Awa Gnémé, Wamdaogo Moussa Guelbéogo, Abdoul Habib Béavogui, Sékou F. Traorè, N’Falé Sagnon, Kenneth D. Vernick, Michelle M. Riehle
Software Mentions: 3
Published: almost 4 years ago

10.3390/microorganisms8040497

Investigating Algal Communities in Lacustrine and Hydro-Terrestrial Environments of East Antarctica Using Deep Amplicon Sequencing
Cited by: 6
Author(s): Yuu Hirose, Takuhei Shiozaki, Midori Õtani, Sakae Kudoh, Satoru Imura, Toshihiko Eki, Naomi Harada
Software Mentions: 3
Published: almost 5 years ago

10.3390/microorganisms9020272

Dynamics of the Apple Fruit Microbiome after Harvest and Implications for Fruit Quality
Cited by: 18
Author(s): Yvonne Bösch, E. Britt, Sarah Perren, Andreas Naef, Jürg E. Frey, Andreas Bühlmann
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0227561

Parasites modulate the gut-microbiome in insects: A proof-of-concept study
Cited by: 39
Author(s): Brian L. Fredensborg, Inga Fossdal í Kálvalíð, Thor Bech Johannesen, Christen Rune Stensvold, Henrik Vedel Nielsen, Christian M. O. Kapel
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0158768

Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning
Cited by: 8
Author(s): Chunlei Yang, Lan Mi, Xianqiao Hu, Jianxin Liu, Jiakun Wang
Software Mentions: 3
Published: over 8 years ago

10.1186/s42523-020-00034-8

Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history
Cited by: 23
Author(s): T. Franciscus Scheelings, Robert J. Moore, Thi Thu Hao Van, Marcel Klaassen, Richard D. Reina
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2021.643945

Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems
Cited by: 2
Author(s): Kavita Kumari, Malay Naskar, Md. Aftabuddin, Soma Das Sarkar, Bandana Das Ghosh, Uttam Kumar Sarkar, Subir Nag, Chayna Jana, Basanta Kumar Das
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2020.00069

Oral Administration of Heat-Treated Lactobacilli Modifies the Murine Microbiome and Reduces Citrobacter Induced Colitis
Cited by: 18
Author(s): Alicja K. Warda, Pedro H. de Almeida Bettio, Cara M. Hueston, Giulio Di Benedetto, Adam G. Clooney, Colin Hill
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2020.541554

An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature
Cited by: 28
Author(s): Caitlin M. Gionfriddo, Ann M. Wymore, Daniel S. Jones, Regina L. Wilpiszeski, Mackenzie M. Lynes, Geoff A. Christensen, Ally Soren, Cynthia C. Gilmour, Mircea Podar, Dwayne A. Elias
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-019-0672-z

Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center
Cited by: 27
Author(s): Aaron J. Prussin, Pedro J. Torres, John Shimashita, Steven R. Head, Kyle Bibby, Scott T. Kelley, Linsey C. Marr
Software Mentions: 3
Published: almost 6 years ago

10.1186/s40168-018-0455-y

Use of dietary indices to control for diet in human gut microbiota studies
Cited by: 80
Author(s): Ruth C E Bowyer, Matthew A. Jackson, Tess Pallister, Jane Skinner, Tim D. Spector, Ailsa Welch, Claire J. Steves
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.10959

Diversity structure of the microbial communities in the guts of four neotropical termite species
Cited by: 8
Author(s): Surendra Vikram, Joel D. Arneodo, Javier Á. Calcagno, Maximiliano Ortiz, María Laura Mon, Clara Etcheverry, Don A. Cowan, Paola Talia
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40168-015-0106-5

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)
Cited by: 100
Author(s): Jennifer M. Auchtung, Catherine D. Robinson, Robert A. Britton
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0242108

Broiler chickens and early life programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects
Cited by: 16
Author(s): Gustavo A. Ramírez, Ella Richardson, Jory Clark, Jitendra Keshri, Yvonne Drechsler, M. E. Berrang, Richard J. Meinersmann, N. A. Cox, Brian B. Oakley
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0157513

Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing
Cited by: 41
Author(s): Felipe Pinheiro de Oliveira, Roberta Hack Mendes, Priscila Caroline Thiago Dobbler, Volker Mai, Victor Satler Pylro, Sheldon Waugh, Filippo Pinto e Vairo, Lı́lia Farret Refosco, Luiz Fernando Würdig Roesch, Ida Vanessa Döederlein Schwartz
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2017.02243

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants
Cited by: 60
Author(s): Priscila Caroline Thiago Dobbler, Renato S. Procianoy, Volker Mai, Rita de Cássia dos Santos Silveira, Andrea Corso, Bruna Schafer Rojas, Luiz Fernando Würdig Roesch
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2018.00121

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology
Cited by: 57
Author(s): Jennifer L. Wood, Caixian Tang, Ashley E. Franks
Software Mentions: 3
Published: about 7 years ago

10.1016/j.dib.2020.106143

An intensive multilocation temporal dataset of fungal and bacterial communities in the root and rhizosphere of Brassica napus
Cited by: 4
Author(s): Navid Bazghaleh, Jennifer K. Bell, Steven D. Mamet, Zayda Piedad Morales Moreira, Zelalem M. Taye, Shanay Williams, Charlotte E. Norris, Tanner Dowhy, Melissa M. Arcand, Eric G. Lamb, Matthew G. Links, Steven J. Shirtliffe, Sally Vail, Steven D. Siciliano, Bobbi L. Helgason
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0181964

Regulation of type 1 diabetes development and B-cell activation in nonobese diabetic mice by early life exposure to a diabetogenic environment
Cited by: 15
Author(s): Alessandra Riva, Maja Wållberg, Francesca Ronchi, Richard M. R. Coulson, Andrew P. Sage, Lucy Thorne, Ian Goodfellow, Kathleen McCoy, Miyuki Azuma, Anne Cooke, Robert Busch
Software Mentions: 3
Published: over 7 years ago

10.1016/j.dib.2020.105467

An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus
Cited by: 3
Author(s): Navid Bazghaleh, Steven D. Mamet, Jennifer K. Bell, Zayda Piedad Morales Moreira, Zelalem M. Taye, Shanay Williams, Melissa M. Arcand, Eric G. Lamb, Steven J. Shirtliffe, Sally Vail, Steven D. Siciliano, Bobbi L. Helgason
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.3536

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment
Cited by: 21
Author(s): Ellen M. Black, Michael S. Chimenti, Craig L. Just
Software Mentions: 3
Published: over 7 years ago

10.1186/s40168-015-0097-2

Humanized microbiota mice as a model of recurrent Clostridium difficile disease
Cited by: 63
Author(s): James W. Collins, Jennifer M. Auchtung, Laura Schaefer, Kathryn A. Eaton, Robert A. Britton
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2021.564408

Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life
Cited by: 10
Author(s): Stephanie D. Jurburg, Alex Bossers
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2018.00870

Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes
Cited by: 30
Author(s): Ditte V. Vestergaard, Gitte Juel Holst, Ioannis Basinas, Grethe Elholm, Vivi Schlünssen, Allan Linneberg, Tina Šantl-Temkiv, Kai Finster, Torben Sigsgaard, Ian P. G. Marshall
Software Mentions: 3
Published: almost 7 years ago

10.3390/nu11051063

Tart Cherry Concentrate Does Not Alter the Gut Microbiome, Glycaemic Control or Systemic Inflammation in a Middle-Aged Population
Cited by: 22
Author(s): Rebecca Lear, Mary F. O’Leary, Lee O’Brien Andersen, Corey C. Holt, Christen Rune Stensvold, Mark van der Giezen, Joanna L. Bowtell
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0240336

Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene
Cited by: 10
Author(s): Harutaro Kenmotsu, Kiichi Uchida, Yuu Hirose, Toshihiko Eki
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-017-0373-4

The gut mycobiome of the Human Microbiome Project healthy cohort
Cited by: 526
Author(s): Andrea K. Nash, Thomas A. Auchtung, Matthew C. Wong, Daniel P. Smith, Jonathan R. Gesell, Matthew C. Ross, Christopher J. Stewart, Ginger Metcalf, Donna M. Muzny, Richard A. Gibbs, Nadim J. Ajami, Joseph F. Petrosino
Software Mentions: 3
Published: about 7 years ago

10.3390/toxins12060349

Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes
Cited by: 8
Author(s): Mario Alberto Martínez-Núñez, Zuemy Rodríguez-Escamilla
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.567961

Tree Species Richness and Neighborhood Effects on Ectomycorrhizal Fungal Richness and Community Structure in Boreal Forest
Cited by: 11
Author(s): Eveli Otsing, Sten Anslan, Elia Ambrosio, Julia Koricheva, Leho Tedersoo
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40168-016-0227-5

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome
Cited by: 54
Author(s): Catherine Igartua, Emily Davenport, Yoav Gilad, Dan L. Nicolae, Jayant M. Pinto, Carole Ober
Software Mentions: 3
Published: about 8 years ago

10.3390/toxins12110728

Diversity Assessment of Toxic Cyanobacterial Blooms during Oxidation
Cited by: 20
Author(s): Saber Moradinejad, Hana Trigui, Juan Maldonado, B. Jesse Shapiro, Yves Terrat, Arash Zamyadi, Sarah Dorner, Michèle Prévost
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2018.02361

Bacterial Associates of a Gregarious Riparian Beetle With Explosive Defensive Chemistry
Cited by: 18
Author(s): Reilly McManus, Alison Ravenscraft, Wendy Moore
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.637834

Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia
Cited by: 18
Author(s): R. M. Costa, Anny Cárdenas, Céline Loussert, Gaëlle Toullec, A. Meibom, Christian R. Voolstra
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0226432

An inter-island comparison of Darwin’s finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome
Cited by: 13
Author(s): Wesley T. Loo, Rachael Y. Dudaniec, Sonia Kleindorfer, Colleen M. Cavanaugh
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2020.01093

Taxon Appearance From Extraction and Amplification Steps Demonstrates the Value of Multiple Controls in Tick Microbiota Analysis
Cited by: 24
Author(s): Emilie Lejal, Agustı́n Estrada-Peña, Maud Marsot, Jean-François Cosson, Olivier Rué, Mahendra Mariadassou, Cédric Midoux, Muriel Vayssier‐Taussat, Thomas V. Pollet
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-85482-1

Benchmarking DNA isolation kits used in analyses of the urinary microbiome
Cited by: 14
Author(s): Lisa Karstens, Nazema Y. Siddiqui, Tamara Zaza, Alecsander Barstad, Cindy L. Amundsen, Tatyana A. Sysoeva
Software Mentions: 3
Published: almost 4 years ago

10.1186/s42523-020-00068-y

Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons)
Cited by: 7
Author(s): Raphael Eisenhofer, Kristofer M. Helgen, David A. Taggart
Software Mentions: 3
Published: about 4 years ago

10.1128/mBio.01343-17

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome
Cited by: 197
Author(s): Tanja Maier, Marianna Lucio, Lang Ho Lee, Nathan C. VerBerkmoes, Colin Brislawn, Jörg Bernhardt, Regina Lamendella, Jason McDermott, Nathalie Bergeron, Silke S. Heinzmann, James T. Morton, Antonio González, Gail Ackermann, Rob Knight, Katharina Riedel, Ronald M. Krauss, Philippe Schmitt‐Kopplin, Janet Jansson
Software Mentions: 3
Published: over 7 years ago

10.3390/v11040347

Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application
Cited by: 15
Author(s): Yuting Li, Hao Sun, Wei Yang, Guanxiong Chen, Xu Hui
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.10695

Local dynamics of a white syndrome outbreak and changes in the microbial community associated with colonies of the scleractinian brain coral <i>Pseudodiploria strigosa</i>
Cited by: 16
Author(s): Patricia E. Thomé, Jacqueline Rivera-Ortega, Jenny Carolina Rodríguez‐Villalobos, Daniel Cerqueda‐García, Edgar O. Guzmán-Urieta, José Q. García-Maldonado, Natalia Carabantes, Eric Jordán-Dahlgren
Software Mentions: 3
Published: about 4 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702