bioconductor: phyloseq | Projects

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 4 years ago

10.1186/s42523-021-00084-6

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis
Cited by: 5
Author(s): Adrian Muwonge, Anbu K. Karuppannan, Tanja Opriessnig
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms9040845

Impact of Chronic Exposure to Sublethal Doses of Glyphosate on Honey Bee Immunity, Gut Microbiota and Infection by Pathogens
Cited by: 29
Author(s): Loreley Castelli, Sofía Balbuena, Belén Branchiccela, Pablo Zunino, Joanito Liberti, Philipp Engel, Karina Antúnez
Software Mentions: 5
Published: over 3 years ago

10.1002/mbo3.1231

Marine biofilms on different fouling control coating types reveal differences in microbial community composition and abundance
Cited by: 16
Author(s): Maria Papadatou, Samuel Robson, Sergey Dobretsov, Joy E. M. Watts, Jennifer Longyear, Maria Salta
Software Mentions: 5
Published: over 3 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 3 years ago

10.1002/mbo3.1133

A low‐cost pipeline for soil microbiome profiling
Cited by: 5
Author(s): Anita Bollmann‐Giolai, Michael Giolai, Darren Heavens, Iain C. Macaulay, Jacob G. Malone, Matt Clark
Software Mentions: 5
Published: about 4 years ago

10.1002/mbo3.681

Do composition and diversity of bacterial communities and abiotic conditions of spring water reflect characteristics of groundwater ecosystems exposed to different agricultural activities?
Cited by: 4
Author(s): Karsten Karczewski, Patricia Göbel, Elisabeth I. Meyer
Software Mentions: 5
Published: over 6 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: about 5 years ago

10.3390/microorganisms7120598

Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China
Cited by: 24
Author(s): Anyi Hu, Hongjie Wang, Meixian Cao, Abbas Rashid, Mingfeng Li, Chang‐Ping Yu
Software Mentions: 5
Published: about 5 years ago

10.3390/microorganisms7080233

Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon
Cited by: 35
Author(s): S. R. Gupta, Jorge M.O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: over 5 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 3 years ago

10.1264/jsme2.ME20153

Inoculation of Mimosa Pudica with Paraburkholderia phymatum Results in Changes to the Rhizoplane Microbial Community Structure
Cited by: 5
Author(s): Shashini U. Welmillage, Qian Zhang, Virinchipuram S. Sreevidya, Michael J. Sadowsky, Prasad Gyaneshwar
Software Mentions: 5
Published: almost 4 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 4 years ago

10.3390/microorganisms8060944

Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple
Cited by: 48
Author(s): Ahmed Abdelfattah, Susan R. Whitehead, Dumitru Macarisin, Jia Liu, Erik Burchard, Shiri Freilich, Christopher Dardick, Samir Droby, Michael Wisniewski
Software Mentions: 5
Published: over 4 years ago

10.3390/ani9110970

Enzymatically Digested Food Waste Altered Fecal Microbiota But Not Meat Quality and Carcass Characteristics of Growing-Finishing Pigs
Cited by: 2
Author(s): Cynthia Jinno, Perot Saelao, Elizabeth A. Maga, Arthur S. King, Dan Morash, Steven M. Zicari, Xiang Yang, Yanhong Liu
Software Mentions: 5
Published: about 5 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 7 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 4 years ago

10.1038/s42003-020-01477-0

Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models
Cited by: 9
Author(s): Nirosh D. Aluthge, Wesley A Tom, Alison Bartenslager, Thomas E. Burkey, Phillip S. Miller, Kelly D. Heath, Craig Kreikemeier-Bower, Hatem Kittana, Robert Schmaltz, Amanda E. Ramer‐Tait, Samodha C. Fernando
Software Mentions: 5
Published: almost 4 years ago

10.1038/s42003-021-01690-5

Development of a robust protocol for the characterization of the pulmonary microbiota
Cited by: 6
Author(s): Nathan Dumont-Leblond, Marc Veillette, Christine Racine, Philippe Joubert, Caroline Duchaine
Software Mentions: 5
Published: almost 4 years ago

10.3390/microorganisms8030404

Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica
Cited by: 13
Author(s): Maria Monteiro, Mafalda S. Baptista, Joana Séneca, Luı́s Torgo, Charles K. Lee, S. Craig Cary, Catarina Magalhães
Software Mentions: 5
Published: over 4 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 3 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 4 years ago

10.1038/s42003-021-02372-y

Function-adaptive clustered nanoparticles reverse Streptococcus mutans dental biofilm and maintain microbiota balance
Cited by: 9
Author(s): Fatemeh Ostadhossein, Parikshit Moitra, Esra Altun, Debapriya Dutta, Dinabandhu Sar, Indu Tripathi, Shih Hsuan Hsiao, Valeriya Kravchuk, Shuming Nie, Dipanjan Pan
Software Mentions: 5
Published: over 3 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 4 years ago

10.3390/microorganisms9030641

A Mouse Model Suggests That Heart Failure and Its Common Comorbidity Sleep Fragmentation Have No Synergistic Impacts on the Gut Microbiome
Cited by: 4
Author(s): Olfat Khannous-Lleiffe, Jesse R. Willis, Ester Saus, Ignacio Cabrera-Aguilera, Isaac Almendros, Ramón Farré, David Gozal, Núria Farré, Toni Gabaldón
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms8071073

Maturational Changes Alter Effects of Dietary Phytase Supplementation on the Fecal Microbiome in Fattening Pigs
Cited by: 7
Author(s): Barbara U. Metzler‐Zebeli, Jutamat Klinsoda, Julia Vötterl, Doris Verhovsek
Software Mentions: 5
Published: over 4 years ago

10.1016/j.cmet.2020.03.003

Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory B Cells
Cited by: 247
Author(s): Elizabeth C. Rosser, Christopher Piper, Diana E. Matei, Paul A. Blair, André F. Rendeiro, Michael Orford, Dagmar Alber, Thomas Krausgruber, Diego Catalán, Nigel Klein, Jessica Manson, Ignat Drozdov, Christoph Bock, Lucy R. Wedderburn, Simon Eaton, Claudia Mauri
Software Mentions: 5
Published: over 4 years ago

10.1186/s42523-021-00080-w

The skin microbiome of Xenopus laevis and the effects of husbandry conditions
Cited by: 7
Author(s): Maya Z. Piccinni, Joy E. M. Watts, Marie Fourny, Matthew Guille, Samuel Robson
Software Mentions: 5
Published: almost 4 years ago

10.3390/cancers12030628

tRNA Queuosine Modification Enzyme Modulates the Growth and Microbiome Recruitment to Breast Tumors
Cited by: 35
Author(s): Jilei Zhang, Rong Lü, Yongguo Zhang, Żaneta Matuszek, Wen Zhang, Yinglin Xia, Tao Pan, Jun Sun
Software Mentions: 5
Published: over 4 years ago

10.1007/s00248-019-01412-9

Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature
Cited by: 32
Author(s): Jonas Frankel-Bricker, Michael Song, Maia J. Benner, Sarah Schaack
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 3 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 5 years ago

10.1371/journal.pone.0243609

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data
Cited by: 6
Author(s): Yi An Chen, Jonguk Park, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Attayeb Mohsen, Koji Hosomi, Kumpei Tanisawa, Harumi Ohno, Kana Konishi, Haruka Murakami, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi
Software Mentions: 5
Published: almost 4 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 8 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 3 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 3 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 6 years ago

10.3390/ijms22041778

Association of Maternal Microbiota and Diet in Cord Blood Cytokine and Immunoglobulin Profiles
Cited by: 11
Author(s): Karla Rio-Aigé, Ignasi Azagra-Boronat, Malén Massot-Cladera, Marta Selma‐Royo, Anna Parra-Llorca, Sonia González, Izaskun García-Mantrana, Cristina Castellote, María J. Rodríguez-Lagunas, María Carmen Collado, Francisco J. Pérez-Cano
Software Mentions: 5
Published: almost 4 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 7 years ago

10.3390/ijerph18062832

Impact of Covid-19 Lockdown on Availability of Drinking Water in the Arsenic-Affected Ganges River Basin
Cited by: 17
Author(s): Srimanti Duttagupta, Soumendra N. Bhanja, Avishek Dutta, S. Sarkar, M. Chakraborty, Ashok Ghosh, Debapriya Mondal, Abhijit Mukherjee
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22189930

Comparative Evaluation of Sucrosomial Iron and Iron Oxide Nanoparticles as Oral Supplements in Iron Deficiency Anemia in Piglets
Cited by: 7
Author(s): Rafał Mazgaj, Paweł Lipiński, Mateusz Szudzik, Aneta Jończy, Z Kopeć, Adrian Stankiewicz, M. Kamyczek, Dorine W. Swinkels, Beata Żelazowska, Rafał R. Starzyński
Software Mentions: 5
Published: about 3 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 4 years ago

10.3390/microorganisms9071374

The Microbiome Associated with the Reef Builder Neogoniolithon sp. in the Eastern Mediterranean
Cited by: 2
Author(s): Shany Gefen-Treves, Alexander Bartholomäus, Fabian Horn, Adam Boleslaw Zaborowski, Dan Tchernov, Dirk Wagner, Aharon Oren, Aaron Kaplan
Software Mentions: 5
Published: over 3 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 4 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 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 5 years ago

10.3390/microorganisms9081711

Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts
Cited by: 6
Author(s): Marie-Charlotte Cheutin, Sébastien Villéger, Christina C. Hicks, James P. W. Robinson, Nicholas A. J. Graham, Clémence Marconnet, Claudia Ximena Ortiz Restrepo, Yvan Bettarel, Thierry Bouvier, Jean‐Christophe Auguet
Software Mentions: 5
Published: over 3 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 5 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 5 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 5 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 4 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 5 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 3 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 3 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 8 years ago

10.1186/s12859-020-03838-2

Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference
Cited by: 3
Author(s): Robert J. Moore, Michael Barnathan, Brian Fristensky, Yán Li, Greg Knowles, Paul Gardner-Stephen, Angelo Bueti, Peter Anderson, Jianguang Qin, Andrew S. Ball
Software Mentions: 5
Published: almost 4 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 5 years ago

10.1038/s41396-021-00920-2

Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi
Cited by: 72
Author(s): Bryan D. Emmett, Veronique Levesque‐Tremblay, Maria J. Harrison
Software Mentions: 5
Published: over 3 years ago

10.1038/s41396-020-00735-7

Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought
Cited by: 35
Author(s): Joana Séneca, Petra Pjevac, Alberto Canarini, Craig W. Herbold, Christos Zioutis, Marlies Dietrich, Eva Simon, Judith Prommer, Michael Bahn, E. M. Pötsch, Michael Wagner, Wolfgang Wanek, Andreas Richter
Software Mentions: 5
Published: over 4 years ago

10.3390/microorganisms8060906

Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature
Cited by: 23
Author(s): Francisco Luis Massello, Chia Sing Chan, Kok Gan Chan, Kian Mau Goh, Edgardo R. Donati, María Sofía Urbieta
Software Mentions: 5
Published: over 4 years ago

10.1093/ajcn/nqab077

Associations of healthy food choices with gut microbiota profiles
Cited by: 33
Author(s): Kari K. Koponen, Aaro Salosensaari, Matti O. Ruuskanen, Aki S. Havulinna, Satu Männistö, Pekka Jousilahti, Joonatan Palmu, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Jon G. Sanders, Guillaume Méric, Susan Cheng, Michael Inouye, Mohit Jain, Teemu J. Niiranen, Liisa Valsta, Rob Knight, Veikko Salomaa
Software Mentions: 5
Published: over 3 years ago

10.1128/mSystems.01196-20

Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations
Cited by: 6
Author(s): Sarahi L. Garcia, Maliheh Mehrshad, Moritz Buck, Jackson M. Tsuji, Josh D. Neufeld, Katherine D. McMahon, Stefan Bertilsson, Chris Greening, Sari Peura
Software Mentions: 5
Published: over 3 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: almost 4 years ago

10.3390/jof7010045

Metabarcoding of Soil Fungal Communities Associated with Alpine Field-Grown Saffron (Crocus sativus L.) Inoculated with AM Fungi
Cited by: 13
Author(s): Íris Marisa Maxaieie Victorino, Samuele Voyron, Matteo Caser, Alberto Orgiazzi, Sonia Demasi, Andrea Berruti, Valentina Scariot, Valeria Bianciotto
Software Mentions: 5
Published: almost 4 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 4 years ago

10.1186/s12936-021-03624-2

Development of a new barcode-based, multiplex-PCR, next-generation-sequencing assay and data processing and analytical pipeline for multiplicity of infection detection of Plasmodium falciparum
Cited by: 2
Author(s): Rebecca Mitchell, Zhansong Zhou, Mili Sheth, Sheila B. Sergent, Michael Frace, Vishal Nayak, Bin Hu, John E. Gimnig, Feiko ter Kuile, Kim A. Lindblade, Laurence Slutsker, Mary J. Hamel, Meghna Desai, Kephas Otieno, Simon Kariuki, Ýmir Vigfússon, Ya Ping Shi
Software Mentions: 5
Published: almost 4 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 4 years ago

10.1186/s42523-020-00058-0

Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides
Cited by: 1
Author(s): Bianca R. P. Brown, Joaquin C. B. Nunez, David M. Rand
Software Mentions: 5
Published: about 4 years ago

10.1128/mSystems.00377-20

Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics
Cited by: 21
Author(s): Alexander Zaborin, Beatriz Peñalver Bernabé, Robert Keskey, Naseer Sangwan, Sanjiv Hyoju, Neil Gottel, Jack A. Gilbert, Olga Zaborina, John C. Alverdy
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00093-19

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry
Cited by: 14
Author(s): Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon, Willem Waegeman, Vincent J. Denef
Software Mentions: 5
Published: about 5 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 6 years ago

10.3389/fmicb.2021.738129

Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China
Cited by: 3
Author(s): Jun Zhang, Pengcheng Xing, Mengyu Niu, Gehong Wei, Peng Shi
Software Mentions: 5
Published: about 3 years ago

10.3390/life11030246

Postoperative Complications Are Associated with Long-Term Changes in the Gut Microbiota Following Colorectal Cancer Surgery
Cited by: 7
Author(s): Felix C. F. Schmitt, Martin Schneider, William Mathejczyk, Markus A. Weigand, Jane C. Figueiredo, Christopher I. Li, David Shibata, Erin M. Siegel, Adetunji T. Toriola, Cornelia M. Ulrich, Alexis Ulrich, Sébastien Boutin, Biljana Gigic
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-021-04106-7

EzMAP: Easy Microbiome Analysis Platform
Cited by: 0
Author(s): Gnanendra Shanmugam, Song Hee Lee, Junhyun Jeon
Software Mentions: 5
Published: over 3 years ago

10.1128/mSystems.00061-20

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance
Cited by: 35
Author(s): Claudia Barelli, Davide Albanese, Rebecca M. Stumpf, Abigail E. Asangba, Claudio Donati, Francesco Rovero, Heidi C. Hauffe
Software Mentions: 5
Published: over 4 years ago

10.3390/microorganisms8020308

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems
Cited by: 206
Author(s): Jesse R. Willis, Toni Gabaldón
Software Mentions: 5
Published: almost 5 years ago

10.1128/mSystems.00007-18

Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns
Cited by: 86
Author(s): Miriam Nieves-Ramı́rez, Oswaldo Partida-Rodríguez, Isabelle Laforest‐Lapointe, Lisa A. Reynolds, Eric Brown, A. Valdez-Salazar, P. Morán-Silva, Liliana Rojas-Velázquez, Evan Morien, Laura Wegener Parfrey, Mingliang Jin, Jens Walter, Javier Torres, Marie‐Claire Arrieta, C. Ximénez-García, B. Brett Finlay
Software Mentions: 5
Published: over 6 years ago

10.1128/mSystems.00087-17

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity
Cited by: 43
Author(s): Isabelle Laforest‐Lapointe, Christian Messier, Steven W. Kembel
Software Mentions: 5
Published: almost 7 years ago

10.1128/mSystems.00094-18

Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers
Cited by: 77
Author(s): Leen Boesmans, Mireia Vallès-Colomer, Jun Wang, Venessa Eeckhaut, Gwen Falony, Richard Ducatelle, Filip Van Immerseel, Jeroen Raes, Kristin Verbeke
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0194131

Instar- and host-associated differentiation of bacterial communities in the Mediterranean fruit fly Ceratitis capitata
Cited by: 55
Author(s): Antonino Malacrinò, Orlando Campolo, Raúl F. Medina, Vincenzo Palmeri
Software Mentions: 5
Published: over 6 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: over 3 years ago

10.1371/journal.pone.0243395

The applicability of forensic time since death estimation methods for buried bodies in advanced decomposition stages
Cited by: 21
Author(s): Stefan Pittner, Valentina Bugelli, M. Eric Benbow, Bianca Ehrenfellner, Angela Zissler, Carlo Pietro Campobasso, Roelof‐Jan Oostra, Maurice C. G. Aalders, Richard Zehner, Lena Lutz, Fabio Monticelli, Christian Staufer, Katharina Helm, Vilma Pinchi, Joseph P. Receveur, Janine Geißenberger, Peter Steinbacher, Jens Amendt
Software Mentions: 5
Published: almost 4 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 6 years ago

10.1128/mSystems.00132-17

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
Cited by: 18
Author(s): Elin Videvall, Maria Strandh, Anel Engelbrecht, S.W.P. Cloete, Charlie K. Cornwallis
Software Mentions: 5
Published: almost 7 years ago

10.1128/mSystems.00954-20

Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater
Cited by: 4
Author(s): Elizabeth A. Monaghan, Kelle C. Freel, Michael S. Rappé
Software Mentions: 5
Published: almost 4 years ago

10.3390/microorganisms8060905

First Detection of Paralytic Shellfish Toxins from Alexandrium pacificum above the Regulatory Limit in Blue Mussels (Mytilus galloprovincialis) in New South Wales, Australia
Cited by: 8
Author(s): Abanti Barua, Penelope Ajani, Rendy Ruvindy, H. Farrell, A. Zammit, Steve Brett, David R. Hill, Chowdhury Sarowar, Mona Hoppenrath, Shauna A. Murray
Software Mentions: 5
Published: over 4 years ago

10.1186/s13068-016-0652-5

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
Cited by: 56
Author(s): Jo De Vrieze, Leticia Regueiro, Ruben Props, Ramiro Vílchez-Vargas, Ruy Jáuregui, Dietmar H. Pieper, Juan M. Lema, Marta Carballa
Software Mentions: 5
Published: about 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 5 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 4 years ago

10.3389/fmicb.2021.703693

Identification of an Intestinal Microbiota Signature Associated With the Severity of Necrotic Enteritis
Cited by: 14
Author(s): Qing Yang, Jing Liu, Xiaofan Wang, Kelsy Robinson, Melanie A. Whitmore, Sydney Stewart, Jiangchao Zhao, Guolong Zhang
Software Mentions: 5
Published: over 3 years ago

10.1002/ece3.4518

Ecological patterns in the skin microbiota of frogs from tropical Australia
Cited by: 15
Author(s): Keith A. Christian, Chava L. Weitzman, Alea Rose, Mirjam Kaestli, Karen S. Gibb
Software Mentions: 5
Published: about 6 years ago

10.1186/s40478-020-00988-5

Different effects of constitutive and induced microbiota modulation on microglia in a mouse model of Alzheimer’s disease
Cited by: 64
Author(s): Charlotte Mezö, Nikolaos Dokalis, Omar Mossad, Ori Staszewski, Jana Neuber, Bahtiyar Yılmaz, Daniel Schnepf, Mercedes Gomez de Agüero, Stephanie C. Ganal‐Vonarburg, Andrew J. Macpherson, Melanie Meyer‐Luehmann, Peter Staeheli, Thomas Blank, Marco Prinz, Daniel Erny
Software Mentions: 5
Published: over 4 years ago

10.1128/mSphere.00189-17

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder
Cited by: 11
Author(s): Vincent J. Denef, Hunter J. Carrick, Joann F. Cavaletto, Edna Chiang, Thomas H. Johengen, Henry A. Vanderploeg
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2020.01614

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)
Cited by: 7
Author(s): Pamela M. Smith, Sinéad M. Waters, David A. Kenny, T. M. Boland, J. S. Heffernan, A. K. Kelly
Software Mentions: 5
Published: over 4 years ago

10.1128/mBio.02637-20

Seed-Derived Microbial Colonization of Wild Emmer and Domesticated Bread Wheat ( Triticum dicoccoides and T. aestivum ) Seedlings Shows Pronounced Differences in Overall Diversity and Composition
Cited by: 34
Author(s): Ezgi Özkurt, M. Amine Hassani, Uğur Sesiz, Sven Künzel, Tal Dagan, Hakan Özkan, Eva H. Stukenbrock
Software Mentions: 5
Published: almost 4 years ago

10.1128/AEM.02969-19

Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil
Cited by: 12
Author(s): Yuan Zhang, Xiuli Hao, Adriana M. García-Lemos, Inês Nunes, Mette Haubjerg Nicolaisen, Ole Nybroe
Software Mentions: 5
Published: over 4 years ago

10.3390/brainsci11081085

Maternal Immune Activation Causes Social Behavior Deficits and Hypomyelination in Male Rat Offspring with an Autism-Like Microbiota Profile
Cited by: 29
Author(s): Gilbert Lee, Yen Kuang Lin, Jing Lai, Yu Chun Lo, Yu Yang, Syuan You Ye, Chia-Jung Lee, Ching Chiung Wang, Yung Hsiao Chiang, Sung Hui Tseng
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-43907-y

Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño
Cited by: 31
Author(s): Allison R. Kolbe, Manuel Aira, María Gómez-Brandòn, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-45368-9

Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity
Cited by: 23
Author(s): Corinne Celestina, Jennifer L. Wood, James B. Manson, Xiaojuan Wang, P. W. G. Sale, Caixian Tang, Ashley E. Franks
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms8060868

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig
Cited by: 34
Author(s): Ann M. Arfken, Juli Foster Frey, Katie Lynn Summers
Software Mentions: 5
Published: over 4 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702