bioconductor: phyloseq | Projects

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 7 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 7 years ago

10.3389/fnut.2019.00045

What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study
Cited by: 135
Author(s): Kimberly A. Lackey, Janet E. Williams, Courtney L. Meehan, Jessica A. Zachek, Elizabeth D. Benda, William J. Price, James A. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Linda J. Kvist, Gloria E. Otoo, Cristina García-Carral, Esther Jiménez, Lorena Ruíz, Juan M. Rodríguez, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Michelle K. McGuire
Software Mentions: 6
Published: over 7 years ago

10.3390/insects11040217

Host Plants Influence the Symbiont Diversity of Eriosomatinae (Hemiptera: Aphididae)
Cited by: 14
Author(s): Tingting Xu, Li‐Yun Jiang, Jing Chen, Ge‐Xia Qiao
Software Mentions: 6
Published: over 6 years ago

10.1186/s13073-021-00844-8

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries
Cited by: 21
Author(s): Caroline Young, Henry M. Wood, Ramakrishnan Ayloor Seshadri, Pham Van Nang, Carlos Vaccaro, Luis Contreras Melendez, Mayilvahanan Bose, Mai Van Doi, Tamara Alejandra Piñero, Camilo Tapia Valladares, Julieta Argüero, Alba Fuentes Balaguer, Kelsey N. Thompson, Yan Yan, Curtis Huttenhower, Philip Quirke
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-018-0586-6

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
Cited by: 96
Author(s): Vanessa L. Hale, Patricio Jeraldo, Jun Chen, Michael B. Mundy, Jingwen Yao, Sambhawa Priya, Gary Keeney, Kelly Lyke, Jason M. Ridlon, Bryan A. White, Amy J. French, Stephen N. Thibodeau, Christian Diener, Osbaldo Reséndis-Antonio, Jaime Gransee, Tumpa Dutta, Xuan Mai Petterson, Jaeyun Sung, Ran Blekhman, Lisa A. Boardman, David W. Larson, Heidi Nelson, Nicholas Chia
Software Mentions: 6
Published: about 8 years ago

10.12688/f1000research.16680.1

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
Cited by: 105
Author(s): Gaurav S. Kandlikar, Zachary Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan J. B. Kraft, Jordan Moberg Parker, Joshua Sprague, David J. Kushner, Emily Curd
Software Mentions: 6
Published: about 8 years ago

10.1093/femsec/fiz108

Diversity of tryptophan halogenases in sponges of the genus Aplysina
Cited by: 9
Author(s): Johanna Gutleben, Jasper J. Koehorst, Kyle McPherson, Shirley A. Pomponi, René H. Wijffels, Hauke Smidt, Detmer Sipkema
Software Mentions: 6
Published: over 7 years ago

10.3390/nu13030807

Transient Effect of Infant Formula Supplementation on the Intestinal Microbiota
Cited by: 6
Author(s): Ning Chin, Gema Méndez-Lagares, Diana H. Taft, Victoria Laleau, Hung T. Kieu, Narayan Nicole, Susan B. Roberts, David A. Mills, Dennis J. Hartigan-O’Connor, Valerie J. Flaherman
Software Mentions: 6
Published: over 5 years ago

10.1093/femsec/fiaa205

Effects of simulated drought on biological soil quality, microbial diversity and yields under long-term conventional and organic agriculture
Cited by: 23
Author(s): Dominika Kundel, Natacha Bodenhausen, Helene Bracht Jørgensen, Jaak Truu, Klaus Birkhofer, Katarina Hedlund, Paul Mäder, Andreas Fließbach
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-020-80557-x

Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)
Cited by: 33
Author(s): Esteban Góngora, Kyle H. Elliott, Lyle G. Whyte
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2021.647977

Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae
Cited by: 12
Author(s): Orlando Vargas, María Soledad Gutiérrez, Mario Caruffo, Benjamín Valderrama, Daniel A. Medina, Katherine García, Angélica Reyes-Jara, Mauricio Toro, Carmen G. Feijóo, Paola Navarrete
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2019.00717

Disentangling the Influence of Environment, Host Specificity and Thallus Differentiation on Bacterial Communities in Siphonous Green Seaweeds
Cited by: 23
Author(s): Kathryn Lee Morrissey, Levent Çavaş, Anne Willems, Olivier De Clerck
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2020.00966

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus
Cited by: 21
Author(s): Kristina Ulrich, Regina Becker, Undine Behrendt, Michael Kube, Andreas Ulrich
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-019-1831-z

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity
Cited by: 83
Author(s): Robert C. Kaplan, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Álvarez, Martha L. Daviglus, Neil Schneiderman, Gregory A. Talavera, Marc D. Gellman, Bharat Thyagarajan, Jee Young Moon, Yoshiki Vázquez-Baeza, Daniel McDonald, Jessica Williams-Nguyen, Michael C. Wu, Kari E. North, Justin P. Shaffer, Christopher C. Sollecito, Qibin Qi, Carmen R. Isasi, Tao Wang, Rob Knight, Robert D. Burk
Software Mentions: 5
Published: about 7 years ago

10.3389/fvets.2020.00255

Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces
Cited by: 24
Author(s): Nicole Ricker, Julian Trachsel, Phillip Colgan, Jennifer Jones, Jinlyung Choi, Jaejin Lee, Johann F. Coetzee, Adina Howe, Susan L. Brockmeier, Crystal L. Loving, Heather K. Allen
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2019.02738

Microbial Composition and Variability of Natural Marine Planktonic and Biofouling Communities From the Bay of Bengal
Cited by: 12
Author(s): Angelina Angelova, Gregory A. Ellis, H. W. Wijesekera, Gary J. Vora
Software Mentions: 5
Published: almost 7 years ago

10.3389/fpls.2021.694727

The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance
Cited by: 3
Author(s): Laxmi S. Mishra, Sanatkumar Mishra, Daniel Caddell, Devin Coleman‐Derr, Christiane Funk
Software Mentions: 5
Published: over 5 years ago

10.3390/nu8100660

Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study
Cited by: 92
Author(s): Andrea Quagliariello, Irene Aloisio, Nicole Bozzi Cionci, Donata Luiselli, Giuseppe D’Auria, Llúcia Martínez-Priego, David Pérez-Villarroya, Tomaž Langerholc, Maša Primec, Dušanka Mičetić-Turk, Diana Di Gioia
Software Mentions: 5
Published: about 10 years ago

10.12688/f1000research.20660.2

microbiomeDASim: Simulating longitudinal differential abundance for microbiome data
Cited by: 6
Author(s): Justin Williams, Héctor Corrada Bravo, Jennifer Tom, Joseph N. Paulson
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-57798-x

Impact of the early-life skin microbiota on the development of canine atopic dermatitis in a high-risk breed birth cohort
Cited by: 8
Author(s): Sabrina Rodriguez‐Campos, Ana Rostaher, Lena Zwickl, Nina Fischer, Isabelle Brodard, Sara Vidal, Bernd W. Brandt, Claude Favrot, Vincent Perreten
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2021.659179

Investigation of Spaceflight Induced Changes to Astronaut Microbiomes
Cited by: 25
Author(s): Michael D. Morrison, James B. Thissen, Fathi Karouia, Satish K. Mehta, Camilla Urbaniak, Kasthuri Venkateswaran, David J. Smith, Crystal Jaing
Software Mentions: 5
Published: over 5 years ago

10.1186/s40793-021-00381-2

Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome
Cited by: 17
Author(s): Samuel M. M. Prudence, Jake T. Newitt, Sarah F. Worsley, Michael C. Macey, J. Colin Murrell, Laura E. Lehtovirta-Morley, Matthew I. Hutchings
Software Mentions: 5
Published: over 5 years ago

10.3390/nu13093289

Analyzing Type 2 Diabetes Associations with the Gut Microbiome in Individuals from Two Ethnic Backgrounds Living in the Same Geographic Area
Cited by: 13
Author(s): Manon Balvers, Mélanie Deschasaux, Bert‐Jan H. van den Born, Koos Zwinderman, Max Nieuwdorp, Evgeni Levin
Software Mentions: 5
Published: about 5 years ago

10.1111/ele.13082

Linking phytoplankton community metabolism to the individual size distribution
Cited by: 20
Author(s): Daniel Padfield, Angus Buckling, Ruth Warfield, Chris D. Lowe, Gabriel Yvon‐Durocher
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-021-83524-2

Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures
Cited by: 37
Author(s): Shashank Gupta, Malini Shariff, Gaura Chaturvedi, Arpit Sharma, Nitin Goel, Monika Yadav, Martin Steen Mortensen, Søren J. Sørensen, Mitali Mukerji, Nar Singh Chauhan
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.7434

Tree diversity and functional leaf traits drive herbivore‐associated microbiomes in subtropical China
Cited by: 1
Author(s): Yang Li, Douglas Chesters, Ming‐Qiang Wang, Tesfaye Wubet, Andreas Schuldt, Perttu Anttonen, Pengfei Guo, Jing‐Ting Chen, Qianxiong Zhou, Nai‐Li Zhang, Keping Ma, Helge Bruelheide, Chunsheng Wu, Chao‐Dong Zhu
Software Mentions: 5
Published: over 5 years ago

10.3390/nu11020313

Sex-Specific Changes in Gut Microbiome Composition following Blueberry Consumption in C57BL/6J Mice
Cited by: 28
Author(s): Umesh D. Wankhade, Ying Zhang, Oxana P. Lazarenko, Sree V. Chintapalli, Brian D. Piccolo, Jin‐Ran Chen, Kartik Shankar
Software Mentions: 5
Published: almost 8 years ago

10.3389/fmicb.2020.590944

Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus
Cited by: 21
Author(s): Regina Becker, Kristina Ulrich, Undine Behrendt, Michael Kube, Andreas Ulrich
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-019-53623-2

A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome
Cited by: 41
Author(s): Shijie Deng, Heidi M.-L. Wipf, Grady Pierroz, Theodore K. Raab, Rajnish Khanna, Devin Coleman‐Derr
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-021-84497-y

Gut microbiota resilience in horse athletes following holidays out to pasture
Cited by: 15
Author(s): Núria Mach, Léa Lansade, David Bars-Cortina, Sophie Dhorne–Pollet, Aline Foury, Marie‐Pierre Moisan, Alice Ruet
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2017.00655

Lactobacillus johnsonii N6.2 Modulates the Host Immune Responses: A Double-Blind, Randomized Trial in Healthy Adults
Cited by: 66
Author(s): Guillermo Marcial, Amanda Ford, Michael J. Haller, Salvador A. Gezan, Natalie A. Harrison, David Cai, Julie Meyer, Daniel J. Perry, Mark A. Atkinson, Clive Wasserfall, Timothy J. Garrett, Claudio F. González, Todd M. Brusko, Wendy J. Dahl, Graciela L. Lorca
Software Mentions: 5
Published: over 9 years ago

10.3389/fcimb.2019.00339

Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses
Cited by: 17
Author(s): Allison R. Kolbe, Eduardo Castro-Nallar, Diego Preciado, Marcos Pérez‐Losada
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-021-02401-3

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

10.3389/fneur.2020.528056

Oral Health, Oral Microbiota, and Incidence of Stroke-Associated Pneumonia—A Prospective Observational Study
Cited by: 14
Author(s): Fabian Cieplik, Alma Maria Wiedenhofer, Verena Pietsch, Karl‐Anton Hiller, Andreas Hiergeist, Andrea Wagner, Dobri Baldaranov, Ralf A. Linker, Jonathan Jantsch, Wolfgang Buchalla, Felix Schlachetzki, André Gessner
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-021-94761-w

Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica
Cited by: 3
Author(s): Lavinia Iancu, Iulia Roxana Angelescu, Victoria Ioana Paun, Carlos Henríquez‐Castillo, Paris Lavín, Cristina Purcărea
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giy054

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

10.3389/fcimb.2018.00301

Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies
Cited by: 105
Author(s): Zheng Wang, Christine P. Zolnik, Yunping Qiu, Mykhaylo Usyk, Tao Wang, Howard D. Strickler, Carmen R. Isasi, Robert C. Kaplan, Irwin J. Kurland, Qibin Qi, Robert D. Burk
Software Mentions: 5
Published: about 8 years ago

10.1007/s10096-020-04049-6

The vaginal microbiota in the course of bacterial vaginosis treatment
Cited by: 7
Author(s): Romy D. Zwittink, Ellen H A van den Munckhof, Maurine A. Leverstein–van Hall, Kim E. Boers, Anco Molijn, Cornelis W. Knetsch, Ed J. Kuijper
Software Mentions: 5
Published: about 6 years ago

10.1111/jvim.15671

Effects of nebulized dexamethasone on the respiratory microbiota and mycobiota and relative equine herpesvirus‐1, 2, 4, 5 in an equine model of asthma
Cited by: 8
Author(s): Stephanie L. Bond, Matthew L. Workentine, Jana Hundt, James R. Gilkerson, Renaud Léguillette
Software Mentions: 5
Published: almost 7 years ago

10.1128/mBio.00311-19

Gut Microbiota and Phytoestrogen-Associated Infertility in Southern White Rhinoceros
Cited by: 32
Author(s): Candace L. Williams, Alexis R. Ybarra, Ashley N. Meredith, Barbara S. Durrant, Christopher W. Tubbs
Software Mentions: 5
Published: over 7 years ago

10.1002/ece3.5789

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species ( Sciurus aberti and S. niger ) living in sympatry
Cited by: 5
Author(s): Andrew Joseph Reed, Jon C. Pigage, Helen K. Pigage, Cody Glickman, Jeremy M. Bono
Software Mentions: 5
Published: almost 7 years ago

10.1186/s40635-021-00398-4

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

10.3389/fonc.2021.650026

Fecal Microbiota and Gut Microbe-Derived Extracellular Vesicles in Colorectal Cancer
Cited by: 33
Author(s): Jihye Park, Nam-Eun Kim, Hyuk Yoon, Cheol Min Shin, Nayoung Kim, Dong Hoon Lee, Jae Yong Park, Chang Hwan Choi, Jae Gyu Kim, Eui Chong Kim, Tae-Seop Shin, Jinho Yang, Young Soo Park
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-97619-3

Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)
Cited by: 13
Author(s): Kleopatra Leontidou, Despoina Vokou, Anna Sandionigi, Antonia Bruno, Maria Lazarina, Johannes De Groeve, Mingai Li, Claudio Varotto, Matteo Girardi, Andrea Galimberti, Alessandro Cristofori
Software Mentions: 5
Published: about 5 years ago

10.3390/nu11102348

Specific Wheat Fractions Influence Hepatic Fat Metabolism in Diet-Induced Obese Mice
Cited by: 6
Author(s): Daniela Gräf, Karolin Weitkunat, Andreas Dötsch, Gerhard Liebisch, Maik Döring, Ralf Krüger, Elisabeth Vatareck, Elena von Coburg, Gunnar Loh, Bernhard Watzl
Software Mentions: 5
Published: about 7 years ago

10.3390/nu13093013

Composition of the Gut Microbiome Influences Production of Sulforaphane-Nitrile and Iberin-Nitrile from Glucosinolates in Broccoli Sprouts
Cited by: 11
Author(s): John A. Bouranis, Laura M. Beaver, Jaewoo Choi, Carmen P. Wong, Duo Jiang, Thomas J. Sharpton, Jan F. Stevens, Emily Ho
Software Mentions: 5
Published: about 5 years ago

10.1002/ece3.5228

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats
Cited by: 51
Author(s): Melissa R. Ingala, Daniel J. Becker, Jacob Bak Holm, Karsten Kristiansen, Nancy B. Simmons
Software Mentions: 5
Published: over 7 years ago

10.3390/insects10110391

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

10.3389/fpls.2020.575861

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization
Cited by: 29
Author(s): María Illescas, M. Belén Rubio, Víctor Hernández-Ruiz, María E. Morán-Diez, Ángel Emilio Martínez de Alba, Carlos Nicolás, Enrique Monte, Rosa Hermosa
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-70249-x

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study
Cited by: 5
Author(s): Tereza Matějková, Petra Hájková, Romana Stopková, Michał Stanko, Jean‐François Martin, Jakub Kreisinger, Pavel Stopka
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-69317-z

Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis
Cited by: 46
Author(s): Osvaldo Bogado Pascottini, Sabrina J. Van Schyndel, J. F. W. Sprícigo, Joyce D. Rousseau, J. Scott Weese, S.J. LeBlanc
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-98549-w

Effect of functional oils or probiotics on performance and microbiota profile of newly weaned piglets
Cited by: 4
Author(s): Alexandre Maciel Vieira, Amanda Pires Sessin, Tatiany Aparecida Teixeira Soratto, Paula Gabriela da Silva Pires, Kátia Maria Cardinal, Glauber Wagner, Lucélia Hauptli, André Luís Ferreira Lima, Fabiano Dahlke, Diego Peres Netto, Priscila de Oliveira Moraes
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2018.01561

A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations
Cited by: 16
Author(s): Even Sannes Riiser, Thomas Haverkamp, Ørnulf Borgan, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Software Mentions: 5
Published: over 8 years ago

10.3389/fcimb.2019.00216

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis
Cited by: 78
Author(s): Anna Lundmark, Yue Hu, Mikael Huss, Gunnar Johannsen, Anders F. Andersson, Tülay Yucel‐Lindberg
Software Mentions: 5
Published: over 7 years ago

10.1053/j.gastro.2020.08.007

Alterations in Intestinal Microbiota of Children With Celiac Disease at the Time of Diagnosis and on a Gluten-free Diet
Cited by: 44
Author(s): Konstantina Zafeiropoulou, Ben Nichols, Mary Mackinder, Olga Biskou, Eleni Rizou, Antonia Karanikolou, Caspar Clark, Evan G. Buchanan, Tracey Cardigan, H. J. Duncan, David Wands, Julie A. Russell, Richard Hansen, Richard K. Russell, Paraic McGrogan, Christine Edwards, Umer Zeeshan Ijaz, Konstantinos Gerasimidis
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2019.01427

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
Cited by: 11
Author(s): Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe‐Fadrosh, Paul Dijkstra, Brian P. Hedlund
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-020-68933-z

Size resolved characteristics of urban and suburban bacterial bioaerosols in Japan as assessed by 16S rRNA amplicon sequencing
Cited by: 14
Author(s): Daisuke Tanaka, So Fujiyoshi, Fumito Maruyama, Motoshi Goto, Shinichi Koyama, Jun-ichi Kanatani, Junko Isobe, Masanori Watahiki, Akihiro Sakatoku, Shigehiro Kagaya, Shōgo Nakamura
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2020.00203

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar
Cited by: 19
Author(s): Andrea Firrincieli, Mahsa Khorasani, A. Carolin Frank, Sharon L. Doty
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2018.02382

Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing
Cited by: 23
Author(s): Blaire Steven, Jayne Belnap, Cheryl R. Kuske
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-020-66178-4

Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis
Cited by: 5
Author(s): Shoichi Fukui, Shimpei Morimoto, Kunihiro Ichinose, Shota Nakashima, Hiroshi Ishimoto, Atsuko Hara, Tomoyuki Kakugawa, Noriho Sakamoto, Yoshika Tsuji, Toshiyuki Aramaki, Tomohiro Koga, Shin‐ya Kawashiri, Naoki Iwamoto, Mami Tamai, Hideki Nakamura, Tomoki Origuchi, Yukitaka Ueki, Shino Suzuki, Hiroshi Mukae, Atsushi Kawakami
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-66028-3

Sward type alters the relative abundance of members of the rumen microbial ecosystem in dairy cows
Cited by: 7
Author(s): Pamela M. Smith, Daniel Enríquez-Hidalgo, Deirdre Hennessy, Matthew S. McCabe, David A. Kenny, A. K. Kelly, Sinéad M. Waters
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.01735

Great Tit (Parus major) Uropygial Gland Microbiomes and Their Potential Defensive Roles
Cited by: 13
Author(s): Kasun H. Bodawatta, Signe K. Schierbech, Nanna R. Petersen, Kateřina Sam, Nick Bos, Knud A. Jønsson, Michael Poulsen
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-65329-x

Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase
Cited by: 9
Author(s): Max‐Bernhard Ballhausen, Rebecca E. Hewitt, Matthias C. Rillig
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-64393-7

Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study
Cited by: 13
Author(s): Manuela de Oliveira Ramalho, Christophe Duplais, Jérôme Orivel, Alain Déjean, Joshua C. Gibson, Andrew V. Suarez, Corrie S. Moreau
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.595555

Antibiotic Treatment for Chronic Rhinosinusitis: Prescription Patterns and Associations With Patient Outcome and the Sinus Microbiota
Cited by: 16
Author(s): Christian A Lux, Brett Wagner Mackenzie, James Johnston, Melissa Zoing, Kristi Biswas, Michael W. Taylor, Richard Douglas
Software Mentions: 5
Published: almost 6 years ago

10.1186/s40793-021-00382-1

Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed
Cited by: 5
Author(s): Leena Malayil, Suhana Chattopadhyay, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 5
Published: over 5 years ago

10.3390/toxics9090215

Subacute Exposure to an Environmentally Relevant Dose of Di-(2-ethylhexyl) Phthalate during Gestation Alters the Cecal Microbiome, but Not Pregnancy Outcomes in Mice
Cited by: 4
Author(s): Karen Chiu, Shah Tauseef Bashir, Lei Gao, Jessica Gutiérrez, María R C de Godoy, Jenny Drnevich, Christopher J. Fields, Isaac Cann, Jodi A. Flaws, Romana A. Nowak
Software Mentions: 5
Published: about 5 years ago

10.1093/bioinformatics/btw311

PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances
Cited by: 94
Author(s): Zheng-Zheng Tang, Guanhua Chen, Alexander V. Alekseyenko
Software Mentions: 5
Published: over 10 years ago

10.1186/s40168-017-0334-y

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome
Cited by: 144
Author(s): Virginie Lemieux-Labonté, Anouk Simard, Craig K. R. Willis, François‐Joseph Lapointe
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pntd.0007361

Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya
Cited by: 3
Author(s): David P. Tchouassi, Ephantus J. Muturi, Samwel O. Arum, Chang‐Hyun Kim, Christopher J. Fields, Baldwyn Torto
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1008640

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa
Cited by: 7
Author(s): Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R. Holmes, Gloria Rendon, Sumir Panji, Christopher J. Fields, Nicola Mulder
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-021-01134-6

SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities
Cited by: 4
Author(s): Raminta Kazlauskaite, Bachar Cheaib, Chloe Heys, Umer Ijaz, Stephanie Connelly, William T. Sloan, Julie Russel, Laura Rubio, John Sweetman, Alex Kitts, Philip McGinnity, Philip Lyons, Martin S. Llewellyn
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2021.596517

Fungal Communities on Standing Litter Are Structured by Moisture Type and Constrain Decomposition in a Hyper-Arid Grassland
Cited by: 11
Author(s): Jim Logan, Kathryn M. Jacobson, Peter J. Jacobson, Sarah E. Evans
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-017-0297-z

Formula diet driven microbiota shifts tryptophan metabolism from serotonin to tryptamine in neonatal porcine colon
Cited by: 69
Author(s): Manish Kumar Saraf, Brian D. Piccolo, Anne K. Bowlin, Kelly E. Mercer, Tanya LeRoith, Sree V. Chintapalli, Kartik Shankar, Thomas M. Badger, Laxmi Yeruva
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0238764

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes
Cited by: 24
Author(s): Sahar Radwan, Darby Gilfillan, Bridget Eklund, Hend M. Radwan, Nagwan Galal El Menofy, Justin Lee, Marylee Kapuscinski, Zaid Abdo
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2020.00749

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact
Cited by: 16
Author(s): Jean de Dieu Habiyaremye, Kezia Goldmann, Thomas Reitz, Sylvie Herrmann, François Buscot
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.02032

Berry Polyphenols and Fibers Modulate Distinct Microbial Metabolic Functions and Gut Microbiota Enterotype-Like Clustering in Obese Mice
Cited by: 75
Author(s): Maria Carolina Rodríguez-Daza, Marcela Roquim, Stéphanie Dudonné, Geneviève Pilon, Émile Lévy, André Marette, Denis Roy, Yves Desjardins
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2016.00606

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria
Cited by: 28
Author(s): Vincent J. Denef, Masanori Fujimoto, Michelle A. Berry, Marian L. Schmidt
Software Mentions: 5
Published: over 10 years ago

10.7717/peerj.9235

Bacterial communities associated with cell phones and shoes
Cited by: 5
Author(s): David A. Coil, Russell Y. Neches, Jenna M. Lang, Guillaume Jospin, Wendy E. Brown, Darlene Cavalier, Jarrad Hampton-Marcell, Jack A. Gilbert, Jonathan A. Eisen
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.11836

Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay
Cited by: 4
Author(s): Fumiaki Mori, Yu Umezawa, Ryou Kondo, Gregory N. Nishihara, Mitsuru Wada
Software Mentions: 5
Published: about 5 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: about 5 years ago

10.7717/peerj.3246

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge
Cited by: 77
Author(s): Cassandra L. Ettinger, Sofie E. Voerman, Jenna M. Lang, John J. Stachowicz, Jonathan A. Eisen
Software Mentions: 5
Published: over 9 years ago

10.3389/fmicb.2018.00675

Gut Microbiota Profiling and Gut–Brain Crosstalk in Children Affected by Pediatric Acute-Onset Neuropsychiatric Syndrome and Pediatric Autoimmune Neuropsychiatric Disorders Associated With Streptococcal Infections
Cited by: 76
Author(s): Andrea Quagliariello, Federica Del Chierico, Alessandra Russo, Sofia Reddel, Giulia Conte, Loris Riccardo Lopetuso, Gianluca Ianiro, Bruno Dallapiccola, Francesco Cardona, Antonio Gasbarrini, Lorenza Putignani
Software Mentions: 5
Published: over 8 years ago

10.1186/s40168-018-0543-z

Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies
Cited by: 40
Author(s): Jeffrey M. Bender, Fan Li, Helty Adisetiyo, David Lee, Sara Zabih, Long Hung, Thomas A. Wilkinson, Pia S. Pannaraj, Rosemary C. She, Jennifer Dien Bard, Nicole H. Tobin, Grace M. Aldrovandi
Software Mentions: 5
Published: about 8 years ago

10.1186/s40168-021-01052-7

Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome
Cited by: 54
Author(s): Jordi Mayneris‐Perxachs, Marina Cardellini, Lesley Hoyles, Jéssica Latorre, Francesca Davato, José María Moreno-Navarrete, María Arnoriaga-Rodríguez, Matteo Sérino, James Abbott, Richard H. Barton, Josep Puig, Xavier Fernández-Real, Wifredo Ricart, Christopher Tomlinson, Mark Woodbridge, Paolo Gentileschi, Sarah Butcher, Elaine Holmes, Jeremy K. Nicholson, Vicente Pérez‐Brocal, Andrés Moya, Donald Mc Clain, Rémy Burcelin, Marc Dumas, Massimo Federici, José‐Manuel Fernández‐Real
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.9205

Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns
Cited by: 27
Author(s): Karina Corona-Cervantes, Igrid García-González, Loan Edel Villalobos-Flores, Fernando Hernández-Quiroz, Alberto Piña-Escobedo, Carlos Hoyo‐Vadillo, Martín Noé Rangel-Calvillo, Jaime García‐Mena
Software Mentions: 5
Published: over 6 years ago

10.1186/s12903-021-01439-w

Microbiological findings in early and late implant loss: an observational clinical case-controlled study
Cited by: 12
Author(s): Michael Korsch, Silke‐Mareike Marten, Dominic A. Stoll, Christopher Prechtl, Andreas Dötsch
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-020-00925-7

Early-life gut dysbiosis linked to juvenile mortality in ostriches
Cited by: 28
Author(s): Elin Videvall, Se Jin Song, Hanna M. Bensch, Maria Strandh, Anel Engelbrecht, Naomi Serfontein, Olof Hellgren, Adriaan Olivier, S.W.P. Cloete, Rob Knight, Charlie K. Cornwallis
Software Mentions: 5
Published: about 6 years ago

10.18632/aging.103399

Changes of saliva microbiota in the onset and after the treatment of diabetes in patients with periodontitis
Cited by: 27
Author(s): Yang Ying, Shili Liu, Yihua Wang, Zhibin Wang, Wei Ding, Xiaoyuan Sun, Kunlun He, Qiang Feng, Xiandang Zhang
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-018-0458-8

Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation
Cited by: 16
Author(s): Kymberleigh A. Romano, Kimberly A. Dill‐McFarland, Kazuyuki Kasahara, Robert L. Kerby, Eugenio I. Vivas, Daniel Amador‐Noguez, Pamela Herd, Federico E. Rey
Software Mentions: 5
Published: over 8 years ago

10.7717/peerj.10424

Ixodes scapularis microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing
Cited by: 14
Author(s): Joshua C Gil, Zeinab H. Helal, Guillermo R. Risatti, Sarah M. Hird
Software Mentions: 5
Published: almost 6 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 5 years ago

10.1371/journal.pone.0215497

Gut microbiota features associated with Clostridioides difficile colonization in puppies
Cited by: 15
Author(s): Alexander S. F. Berry, Brendan J Kelly, Denise Barnhart, Douglas G. Kelly, Daniel P. Beiting, Robert N. Baldassano, Laurel E. Redding
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0227860

Fungal diversity in canopy soil of silver beech, Nothofagus menziesii (Nothofagaceae)
Cited by: 4
Author(s): Andy R. Nilsen, Suliana Teasdale, P. L. Guy, Tina C. Summerfield, David A. Orlovich
Software Mentions: 5
Published: almost 7 years ago

10.1186/s40168-018-0555-8

The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch
Cited by: 54
Author(s): Alice Michel, Lewis M. Ward, Shana K. Goffredi, Katherine S. Dawson, Daniel T. Baldassarre, Alec Brenner, Kiyoko M. Gotanda, John E. McCormack, Sean W. Mullin, Ariel O’Neill, Gabrielle S. Tender, J. Albert C. Uy, Kristie Yu, Victoria J. Orphan, Jaime A. Chaves
Software Mentions: 5
Published: about 8 years ago

10.7717/peerj.8172

Exploring profile and potential influencers of vaginal microbiome among asymptomatic pregnant Chinese women
Cited by: 10
Author(s): Yining He, Yun Huang, Zhengyin Zhang, Fei Yu, Yuejie Zheng
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2018.01138

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada
Cited by: 43
Author(s): Matti O. Ruuskanen, Kyra A. St. Pierre, Vincent L. St. Louis, Stéphane Aris‐Brosou, Alexandre J. Poulain
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2019.01486

Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia
Cited by: 39
Author(s): Flora Jane Mary O'Brien, Maya Almaraz, Melissa A. Foster, A. F. Hill, David P. Huber, Elizabeth King, Harry Langford, Mary-Anne Lowe, Bede S. Mickan, Valerie S. Miller, Oliver Moore, Falko Mathes, Deirdre Gleeson, Matthias Leopold
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2020.01075

Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System
Cited by: 18
Author(s): Linta Reji, Bradley B. Tolar, Francisco P. Chávez, Christopher A. Francis
Software Mentions: 5
Published: over 6 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702