bioconductor: phyloseq | Projects

10.3389/fmicb.2020.00380

Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities
Cited by: 32
Author(s): Emilie Macke, Martijn Callens, François Massol, Isabel Vanoverberghe, Luc De Meester, Ellen Decaestecker
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.6377

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis
Cited by: 50
Author(s): Bettina Glasl, Caitlin E. Smith, David G. Bourne, Nicole S. Webster
Software Mentions: 4
Published: over 7 years ago

10.3390/microorganisms9091842

The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire
Cited by: 5
Author(s): Sara Laetitia Elphège Gnangui, Romain Kouakou Fossou, Anicet Ebou, Chiguié Estelle Raïssa Amon, Dominique Koua, Claude Ghislaine Kouadjo, Don A. Cowan, Adolphe Zézé
Software Mentions: 4
Published: about 5 years ago

10.3390/md19080442

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India
Cited by: 4
Author(s): Jamseel Moopantakath, Madangchanok Imchen, Ranjith Kumavath, Rosa María Martínez‐Espinosa
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.10231

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture
Cited by: 22
Author(s): John K. Pearman, Nigel Keeley, Susanna A. Wood, Olivier Laroche, Anastasija Zaiko, Georgia Thomson‐Laing, Laura Biessy, Javier Atalah, Xavier Pochon
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41390-021-01419-4

Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids
Cited by: 12
Author(s): Erin Felton, A. Millie Burrell, Hollis Chaney, Iman Sami, Anastassios C. Koumbourlis, Robert J. Freishtat, Keith A. Crandall, Andrea Hahn
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.02926

Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios
Cited by: 25
Author(s): Juanjo Rodríguez, Christine Gallampois, Sari Timonen, Agneta Andersson, Hanna Sinkko, Peter Haglund, Åsa M. M. Berglund, Mátyás Ripszám, Daniela Figueroa, Mats Tysklind, Owen Rowe
Software Mentions: 4
Published: almost 8 years ago

10.3390/microorganisms9030530

The Adult Phenylketonuria (PKU) Gut Microbiome
Cited by: 16
Author(s): Viviana J. Mancilla, Allison E. Mann, Yan Zhang, Michael S. Allen
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.4017

5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro.
Cited by: 7
Author(s): Eline Vanlancker, Barbara Vanhoecke, Andrea M. Stringer, Tom Van de Wiele
Software Mentions: 4
Published: almost 10 years ago

10.3390/jof5040095

9th Trends in Medical Mycology Held on 11–14 October 2019, Nice, France, Organized under the Auspices of EORTC-IDG and ECMM
Cited by: 14
Author(s): Jean Pierre Gangneux, Olivier Lortholary, Oliver A. Cornely, Livio Pagano
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-021-81507-x

Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus
Cited by: 6
Author(s): Hua Zha, Fengping Liu, Zongxin Ling, Kevin Chang, Jiezuan Yang, Lanjuan Li
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.7552

Oceanographic habitat and the coral microbiomes of urban-impacted reefs
Cited by: 4
Author(s): Stephanie M. Rosales, Christopher D. Sinigalliano, Maribeth L. Gidley, Paul R. Jones, Lewis J. Gramer
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2021.703014

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds
Cited by: 14
Author(s): Flavia Tarquinio, Océane Attlan, Mathew A. Vanderklift, Oliver Berry, Andrew Bissett
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms8101506

Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health
Cited by: 16
Author(s): Peter Kusstatscher, Wisnu Adi Wicaksono, Dhivya Priya Thenappan, Eveline Adam, Henry Müller, Gabriele Berg
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms9061157

Does the Composition of the Gut Bacteriome Change during the Growth of Tuna?
Cited by: 5
Author(s): Elsa Gadoin, Lucile Durand, Aurélie Guillou, Sandrine Crochemore, Thierry Bouvier, Emmanuelle Roque, Laurent Dagorn, Jean‐Christophe Auguet, Antoinette Adingra, Christelle Desnues, Yvan Bettarel
Software Mentions: 4
Published: over 5 years ago

10.1080/19490976.2021.1875797

Early life environmental exposures have a minor impact on the gut ecosystem following a natural birth
Cited by: 6
Author(s): Nishat Tasnim, Candice Quin, S K Gill, Chunping Dai, Miranda M. Hart, Deanna L. Gibson
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms9071378

Effects of Wine and Its Microbial-Derived Metabolites on Intestinal Permeability Using Simulated Gastrointestinal Digestion/Colonic Fermentation and Caco-2 Intestinal Cell Models
Cited by: 11
Author(s): Irene Zorraquín‐Peña, Diego Taladrid, Alba Tamargo, Mariana Silva, Natalia Molinero, Dolores González de Llano, Begoňa Bartolomé, M. Victoria Moreno‐Arribas
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.01686

Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts
Cited by: 11
Author(s): Noemi Procopio, Stefano Ghignone, Samuele Voyron, Marco Chiapello, Anna Williams, Andrew Chamberlain, Antonietta Mello, Michael Buckley
Software Mentions: 4
Published: about 6 years ago

10.1093/conphys/coaa040

A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders
Cited by: 3
Author(s): Erin K. Kenison, Obed Hernández‐Gómez, Rod N. Williams
Software Mentions: 4
Published: almost 7 years ago

10.3390/microorganisms8010030

Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines
Cited by: 20
Author(s): Susanne Jacksch, Dominik Kaiser, Severin Weis, Mirko Weide, Stefan Ratering, Sylvia Schnell, Markus Egert
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40168-018-0603-4

A comparative study of the gut microbiota in immune-mediated inflammatory diseases—does a common dysbiosis exist?
Cited by: 238
Author(s): Jessica D. Forbes, Chih-Yu Chen, Natalie Knox, Ruth Ann Marrie, Hani El-Gabalawy, Teresa de Kievit, Michelle J. Alfa, Çharles N. Bernstein, Gary Van Domselaar
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13054-021-03623-4

Staphylococcus aureus ventilator-associated pneumonia in patients with COVID-19: clinical features and potential inference with lung dysbiosis
Cited by: 36
Author(s): Gennaro De Pascale, Flavio De Maio, Simone Carelli, Giulia De Angelis, Margherita Cacaci, Luca Montini, Giuseppe Bello, Salvatore Lucio Cutuli, Gabriele Pintaudi, Eloisa Sofia Tanzarella, Rikardo Xhemalaj, Domenico Luca Grieco, Mario Tumbarello, Maurizio Sanguinetti, Brunella Posteraro, Massimo Antonelli
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9326

Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea
Cited by: 2
Author(s): Yukino Mizutani, Tetsushi Mori, Taeko Miyazaki, Satoshi Fukuzaki, Reiji Tanaka
Software Mentions: 4
Published: over 6 years ago

10.3390/ijerph18126348

Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test
Cited by: 4
Author(s): Francesco Spennati, Salvatore La China, G. Siracusa, Simona Di Gregorio, A. Bardi, Valeria Tigini, Greg Mori, David Gabriel, Giulio Munz
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00566-19

Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands
Cited by: 22
Author(s): Nana Liu, Huifeng Hu, Wenqi Ma, Ye Deng, Yuqing Liu, Baihui Hao, Xinying Zhang, Dimitar Dimitrov, Xiaojuan Feng, Zhiheng Wang
Software Mentions: 4
Published: almost 7 years ago

10.1093/cdn/nzaa165

Pomegranate Metabolites Impact Tryptophan Metabolism in Humans and Mice
Cited by: 10
Author(s): Jieping Yang, Yuanqiang Guo, Ru-Po Lee, Susanne M. Henning, Jing Wang, Yajing Pan, Tianyu Qing, Mark Hsu, Alex Nguyen, Prabha Siddarth, Rashi Ojha, Gary W. Small, David Heber, Zhaoping Li
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.00867

Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility
Cited by: 10
Author(s): Benjamin Schwan, Christian Abendroth, Adriel Latorre‐Pérez, Manuel Porcar, Cristina Vilanova, Christina Dornack
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-54855-y

Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays
Cited by: 51
Author(s): Stephanie M. Rosales, Margaret W. Miller, Dana E. Williams, Nikki Traylor-Knowles, Benjamin Young, Xaymara M. Serrano
Software Mentions: 4
Published: almost 7 years ago

10.1128/AEM.01336-19

Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction
Cited by: 11
Author(s): Maria Fernanda Campa, Stephen M. Techtmann, Mallory P. Ladd, Jun Yan, Megan Patterson, Amanda Garcia de Matos Amaral, Kimberly E. Carter, Nikea Ulrich, Christopher J. Grant, Robert L. Hettich, Regina Lamendella, Terry C. Hazen
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2021.718727

Soil Fungal Community in Grazed Inner Mongolian Grassland Adjacent to Coal-Mining Activity
Cited by: 2
Author(s): Liji Xie, Yinli Bi, Xianglei Li, Kun Wang, Peter Christie
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-018-0400-0

Effects of predation stress and food ration on perch gut microbiota
Cited by: 47
Author(s): Yinghua Zha, Alexander Eiler, Frank Johansson, Richard Svanbäck
Software Mentions: 4
Published: over 8 years ago

10.14814/phy2.14199

Oral vancomycin treatment does not alter markers of postprandial inflammation in lean and obese subjects
Cited by: 10
Author(s): Guido J. Bakker, Johan G. Schnitzler, Siroon Bekkering, Nicolien C. de Clercq, Annefleur M. Koopen, Annick V. Hartstra, Emma C. E. Meessen, Torsten P. M. Scheithauer, Maaike Winkelmeijer, Geesje M. Dallinga‐Thie, Patrice D. Cani, E. Marleen Kemper, Maarten R. Soeters, Jeffrey Kroon, Albert K. Groen, Daniël H. van Raalte, Hilde Herrema, Max Nieuwdorp
Software Mentions: 4
Published: about 7 years ago

10.1038/s41396-020-0686-3

Ecological succession in the vaginal microbiota during pregnancy and birth
Cited by: 39
Author(s): Morten Arendt Rasmussen, Jonathan Thorsen, Maria Gloria Domínguez-Bello, Martin J. Blaser, Martin Steen Mortensen, Asker Brejnrod, Samir A. Shah, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Urvish Trivedi, Hans Bisgaard, Søren J. Sørensen, Jakob Stokholm
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.00006

Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment
Cited by: 38
Author(s): Jarosław Grządziel, Anna Gałązka
Software Mentions: 4
Published: over 7 years ago

10.1007/s12975-020-00863-4

Disruptions of Anaerobic Gut Bacteria Are Associated with Stroke and Post-stroke Infection: a Prospective Case–Control Study
Cited by: 60
Author(s): Bastiaan W. Haak, Willeke F. Westendorp, Tjitske S. R. van Engelen, Xanthe Brands, Matthijs C. Brouwer, Jan-Dirk Vermeij, Floor Hugenholtz, Aswin Verhoeven, Rico Derks, Martin Giera, Paul J. Nederkoorn, Willem M. de Vos, Diederik van de Beek, W. Joost Wiersinga
Software Mentions: 4
Published: about 6 years ago

10.3390/ijerph18073742

Do Rural Second Homes Shape Commensal Microbiota of Urban Dwellers? A Pilot Study among Urban Elderly in Finland
Cited by: 4
Author(s): Mika Saarenpää, Marja I. Roslund, Riikka Puhakka, Mira Grönroos, Nan Hui, Noora Nurminen, Olli H. Laitinen, Heikki Hyöty, Ondřej Cinek, Aki Sinkkonen
Software Mentions: 4
Published: over 5 years ago

10.3390/ani10040577

Improvement of Cecal Commensal Microbiome Following the Insect Additive into Chicken Diet
Cited by: 30
Author(s): Agata Józefiak, Abdelbasset Benzertiha, Bartosz Kierończyk, Anna Łukomska, Izabela Wesołowska, Mateusz Rawski
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-80444-5

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt
Cited by: 23
Author(s): Adrienn Tóth, István Csabai, Gergely Maróti, Ákos Jerzsele, Attila Dubecz, Árpád V. Patai, Maura Fiona Judge, Sára Ágnes Nagy, László Makrai, Krisztián Bànyai, G. Szita, Norbert Solymosi
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.00547-19

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
Cited by: 31
Author(s): Quinten R Ducarmon, Bastian Hornung, A. R. Geelen, E. Kuijper, Romy D. Zwittink
Software Mentions: 4
Published: over 6 years ago

10.3390/diagnostics11091622

Alteration in Nasopharyngeal Microbiota Profile in Aged Patients with COVID-19
Cited by: 9
Author(s): Ravindra Kolhe, Nikhil Sahajpal, Sagar Vyavahare, Akhilesh S. Dhanani, Satish Adusumilli, Sudha Ananth, Ashis Mondal, Gregory Taylor Patterson, Sandeep Kumar, Amyn M. Rojiani, Carlos M. Isales, Sadanand Fulzele
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.584699

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom
Cited by: 8
Author(s): Keith Mitchell, Jiem R. Ronas, Christopher Dao, Amanda C. Freise, Serghei Mangul, Casey Shapiro, Jordan Moberg Parker
Software Mentions: 4
Published: about 6 years ago

10.1186/s13550-017-0318-8

Gut microbiota and physiologic bowel 18F-FDG uptake
Cited by: 16
Author(s): Ji Yeon Kang, Han Na Kim, Yoosoo Chang, Yeojun Yun, Seungho Ryu, Hocheol Shin, Hyung Lae Kim
Software Mentions: 4
Published: about 9 years ago

10.15252/emmm.201707882

Household triclosan and triclocarban effects on the infant and maternal microbiome
Cited by: 67
Author(s): Jessica V. Ribado, Catherine Ley, Thomas D. Haggerty, Е. И. Ткаченко, Ami S. Bhatt, Julie Parsonnet
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-020-79055-x

Simultaneous allergic traits in dogs and their owners are associated with living environment, lifestyle and microbial exposures
Cited by: 13
Author(s): Jenni Lehtimäki, Hanna Sinkko, Anna Hielm‐Björkman, Tiina Laatikainen, Lasse Ruokolainen, Hannes Lohi
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.00133-16

SSUnique: Detecting Sequence Novelty in Microbiome Surveys
Cited by: 4
Author(s): Michael D. J. Lynch, Josh D. Neufeld
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pntd.0009597

Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections
Cited by: 8
Author(s): Katharina Stracke, Poom Adisakwattana, Suparat Phuanukoonnon, Tippayarat Yoonuan, Akkarin Poodeepiyasawat, Paron Dekumyoy, Kittipong Chaisiri, Alexandra Roth Schulze, Stephen Wilcox, Harin Karunajeewa, Rebecca J. Traub, Aaron R. Jex
Software Mentions: 4
Published: about 5 years ago

10.3390/toxins13010025

Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?
Cited by: 16
Author(s): Farhad Jalili, Hana Trigui, Juan Maldonado, Sarah Dorner, Arash Zamyadi, Ben Shapiro, Yves Terrat, Nathalie Fortin, Sébastien Sauvé, Michèle Prévost
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-016-0214-x

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants
Cited by: 140
Author(s): Katherine E. Gregory, Buck S. Samuel, Pearl Houghteling, Shan Guru, Frederick M. Ausubel, Ruslan I. Sadreyev, W. Allan Walker
Software Mentions: 4
Published: almost 10 years ago

10.1002/ece3.4742

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding
Cited by: 45
Author(s): Natalie A. Sawaya, Anni Djurhuus, Collin J. Closek, Megan Hepner, Emily Olesin, Lindsey A. Visser, Christopher R. Kelble, Katherine A. Hubbard, Mya Breitbart
Software Mentions: 4
Published: over 7 years ago

10.1186/s40168-019-0695-5

Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area
Cited by: 27
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Julian Gordon, Prasanthi Gandhi, Rachel Reboulet, Jarrad Hampton-Marcell
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.3777

Evolution of a key trait greatly affects underground community assembly process through habitat adaptation in earthworms
Cited by: 9
Author(s): Hiroshi Ikeda, Kayoko Fukumori, Etsuko Shoda‐Kagaya, Masamichi Takahashi, Masamichi Ito, Yoshimi Sakai, Kazuma Matsumoto
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0168573

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil
Cited by: 33
Author(s): Seung‐Yoon Oh, Jonathan J. Fong, Myung Soo Park, Young Woon Lim
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0231238

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources
Cited by: 5
Author(s): Sergi Compte-Port, Mireia Fillol, Frédéric Gich, Carles M. Borrego
Software Mentions: 4
Published: over 6 years ago

10.3390/ani11092705

Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF
Cited by: 2
Author(s): Gercino Ferreira Virgínio Júnior, Ana Paula da Silva, Ariany Faria de Toledo, Milaine Poczynek, Amanda Moelemberg Cezar, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21093262

Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations
Cited by: 5
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0252086

Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation
Cited by: 9
Author(s): Kerry McNally, Charles J. Innis, Adam Kennedy, Jennifer L. Bowen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0159289

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris
Cited by: 352
Author(s): Sonja Oberbeckmann, A. Mark Osborn, Melissa B. Duhaime
Software Mentions: 4
Published: about 10 years ago

10.1186/s40168-017-0370-7

The Inuit gut microbiome is dynamic over time and shaped by traditional foods
Cited by: 43
Author(s): Geneviève Dubois, Catherine Girard, François‐Joseph Lapointe, B. Jesse Shapiro
Software Mentions: 4
Published: almost 9 years ago

10.1002/ece3.3248

Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia
Cited by: 5
Author(s): Keith A. Christian, Mirjam Kaestli, Karen S. Gibb
Software Mentions: 4
Published: about 9 years ago

10.1038/s41396-019-0568-8

Gut microbiota structure differs between honeybees in winter and summer
Cited by: 157
Author(s): Lucie Kešnerová, Olivier Emery, Michaël Troilo, Joanito Liberti, Berra Erkoşar, Philipp Engel
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-78525-6

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia
Cited by: 11
Author(s): Katrina West, Zoe T. Richards, Euan S. Harvey, Robert Susac, Alicia Grealy, Michael Bunce
Software Mentions: 4
Published: almost 6 years ago

10.1080/19490976.2021.1897209

The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome
Cited by: 6
Author(s): John P. Haran, Doyle V. Ward, Shakti Bhattarai, Ethan Loew, Protiva Dutta, Amanda Higgins, Beth A. McCormick, Vanni Bucci
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0250514

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea
Cited by: 8
Author(s): Grażyna Płaza, Łukasz Jałowiecki, Dominika Głowacka, Jakub Hubeny, Monika Harnisz, Ewa Korzeniewska
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-99127-w

Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
Cited by: 10
Author(s): Tanweer Goolam Mahomed, Rph Peters, Mushal Allam, Arshad Ismail, Senzo Mtshali, Akhter Goolam Mahomed, Veronica Ueckermann, Marleen M. Kock, M.M. Ehlers
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-61092-1

Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning
Cited by: 35
Author(s): Miguel de Celis, Ignacio Belda, Rüdiger Ortiz‐Álvarez, Lucía Arregui, Domingo Marquina, Susana Serrano, Andrés de la Oliva Santos
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.01979

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy
Cited by: 177
Author(s): Carlotta De Filippo, Monica Di Paola, Matteo Ramazzotti, Davide Albanese, Giuseppe Pieraccini, Elena Banci, Franco Miglietta, Duccio Cavalieri, Paolo Lionetti
Software Mentions: 4
Published: about 9 years ago

10.3390/microorganisms9040751

Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene
Cited by: 10
Author(s): Jiangwei Li, Anyi Hu, Shaoping Bai, Xiaoyang Yang, Qian Sun, Xu Liao, Chang‐Ping Yu
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.00809

Conditionally Rare Taxa Contribute but Do Not Account for Changes in Soil Prokaryotic Community Structure
Cited by: 12
Author(s): Rachel Kaminsky, Sergio E. Morales
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.54792

Gut Helicobacter presentation by multiple dendritic cell subsets enables context-specific regulatory T cell generation
Cited by: 18
Author(s): Emilie V. Russler-Germain, Jaeu Yi, Shannon Young, Katherine Nutsch, Ho-Lun Wong, Teresa L. Ai, Jiani N. Chai, Vivek Durai, Daniel H. Kaplan, Ronald N. Germain, Kenneth M. Murphy, Chyi-Song Hsieh
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00133

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun
Cited by: 15
Author(s): Vandana R. Prabhu, . Wasimuddin, Ranganathan Kamalakkannan, Moolamkudy Suresh Arjun, Muniyandi Nagarajan
Software Mentions: 4
Published: over 6 years ago

10.1128/mSphere.00083-21

Exposure to Parasitic Protists and Helminths Changes the Intestinal Community Structure of Bacterial Communities in a Cohort of Mother-Child Binomials from a Semirural Setting in Mexico
Cited by: 8
Author(s): Oswaldo Partida-Rodríguez, Miriam Nieves-Ramı́rez, Isabelle Laforest‐Lapointe, Eric Brown, Laura Wegener Parfrey, A Valadez-Salazar, Lisa Thorson, Patricia Morán, Enrique González, E. Ortiz Rascón, Ulises Magaña, E. Hernández, Liliana Rojas-Velázquez, Javier Torres, Marie Claire Arrieta, Cecilia Ximénez, B. Brett Finlay
Software Mentions: 4
Published: about 5 years ago

10.1186/s13071-021-04859-3

Blastocystis in the faeces of children from six distant countries: prevalence, quantity, subtypes and the relation to the gut bacteriome
Cited by: 11
Author(s): Ondřej Cinek, Katerina Polackova, Rasha Odeh, Abeer Alassaf, Lenka Kramná, Mary Ann Ugochi Ibekwe, Edna Majaliwa, Gunduz Ahmadov, Bashir Mukhtar Elwasila Elmahi, Hanan Mekki, Sami Oikarinen, Jan Lebl, Mohammed A. Abdullah
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-73515-0

Preliminary insights into the impact of primary radiochemotherapy on the salivary microbiome in head and neck squamous cell carcinoma
Cited by: 15
Author(s): Christina Kumpitsch, Christine Moissl-Eichinger, Jakob Pock, Dietmar Thurnher, Axel Wolf
Software Mentions: 4
Published: about 6 years ago

10.1186/s40168-020-00803-2

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection
Cited by: 38
Author(s): Lingdi Zhang, Christian V. Forst, Aubree Gordon, Gabrielle Gussin, Adam Geber, Porfirio J. Fernandez, Tao Ding, Lauren Lashua, Minghui Wang, Ángel Balmaseda, Richard Bonneau, Bin Zhang, Elodie Ghedin
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.01647

Tucumã Oil Shifted Ruminal Fermentation, Reducing Methane Production and Altering the Microbiome but Decreased Substrate Digestibility Within a RUSITEC Fed a Mixed Hay – Concentrate Diet
Cited by: 29
Author(s): Aline Maria Pereira Cruz Ramos, Stephanie A. Terry, Devin B. Holman, Gerhard Breves, L. G. R. Pereira, André G. M. Silva, A. V. Chaves
Software Mentions: 4
Published: about 8 years ago

10.1128/mSystems.00334-20

Human Milk Oligosaccharides Modulate the Risk for Preterm Birth in a Microbiome-Dependent and -Independent Manner
Cited by: 9
Author(s): Manuela-Raluca Pausan, V Kolovetsiou-Kreiner, Gesa Richter, Tobias Madl, Elisabeth Giselbrecht, Barbara Obermayer‐Pietsch, Eva-Christine Weiss, Evelyn Jantscher-Krenn, Christine Moissl-Eichinger
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.01756

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage
Cited by: 78
Author(s): Victoria Mesa, José Luis Gallego, Ricardo González-Gil, Béatrice Lauga, Jesús Sánchez, Celia Méndez–García
Software Mentions: 4
Published: about 9 years ago

10.1128/mSphere.00730-19

Gut Microbiomes of the Eastern Oyster ( Crassostrea virginica ) and the Blue Mussel ( Mytilus edulis ): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities
Cited by: 43
Author(s): Melissa L. Pierce, J. Evan Ward
Software Mentions: 4
Published: almost 7 years ago

10.1128/MRA.00968-20

16S rRNA Gene Diversity of Bacterial Endophytes in Parasitic Cuscuta campestris and Its Helianthus annuus Host
Cited by: 0
Author(s): Adam T. Avila, Tricia A. Van Laar, John V. H. Constable, Katherine Waselkov
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSphere.00626-18

Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity
Cited by: 15
Author(s): Sarahi L. Garcia, Anna J. Székely, Christoffer Bergvall, Martha Schattenhofer, Sari Peura
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.540404

The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra
Cited by: 10
Author(s): Ingeborg J. Klarenberg, Christoph Keuschnig, Denis Warshan, Ingibjörg S. Jónsdóttir, Oddur Vilhelmsson
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2021.684233

Maternal Antibiotic Treatment Disrupts the Intestinal Microbiota and Intestinal Development in Neonatal Mice
Cited by: 8
Author(s): Chung-Ming Chen, Hsiu Chu Chou, Yu Yang
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00993

The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets
Cited by: 71
Author(s): Thomas Klammsteiner, Andreas Walter, Tajda Bogataj, Carina Desirée Heussler, Blaž Stres, Florian M. Steiner, Birgit C. Schlick‐Steiner, Wolfgang Arthofer, Heribert Insam
Software Mentions: 4
Published: over 6 years ago

10.1186/s12866-017-1092-5

Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone
Cited by: 43
Author(s): Stephanie L. Bond, Edouard Timsit, Matthew L. Workentine, Trevor W. Alexander, Renaud Léguillette
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-021-97337-w

DNA metabarcoding reveals the dietary composition in the endangered black-faced spoonbill
Cited by: 3
Author(s): Pei‐Yu Huang, Emily Shui Kei Poon, Anson Tsz Chun Wong, Ivy Wai Yan So, Yik-Hei Sung, Simon Yung Wa Sin
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-97790-7

Glycosaminoglycan biosynthesis pathway in host genome is associated with Helicobacter pylori infection
Cited by: 0
Author(s): Dingxue Hu, Yueqi Lu, Daoming Wang, Chao Nie, Yan Li
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-018-0537-x

Root exudates drive the soil-borne legacy of aboveground pathogen infection
Cited by: 294
Author(s): Jun Yuan, Jun Zhao, Teng Wen, Mingwen Zhao, Rong Li, Pim Goossens, Qiwei Huang, Yang Bai, Jorge M. Vivanco, George A. Kowalchuk, Roeland L. Berendsen
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2020.580397

Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability
Cited by: 10
Author(s): Shuting Liu, Nicholas Baetge, Jacqueline Comstock, Keri Opalk, Rachel Parsons, Elisa R. Halewood, Chance English, Stephen J. Giovannoni, Luis M. Bolaños, Craig E. Nelson, Kevin L. Vergin, Craig A. Carlson
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2019.01361

Biochar Amendment Stimulates Utilization of Plant-Derived Carbon by Soil Bacteria in an Intercropping System
Cited by: 33
Author(s): Hongkai Liao, Yaying Li, Huaiying Yao
Software Mentions: 4
Published: over 7 years ago

10.1089/ast.2018.1870

A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars
Cited by: 18
Author(s): Charles S. Cockell, Jesse Patrick Harrison, Adam H. Stevens, Samuel J. Payler, S. S. Hughes, S. E. Kobs Nawotniak, A. L. Brady, R. C. Elphic, C. W. Haberle, A. Sehlke, K. Beaton, Andrew F. J. Abercromby, Petra Schwendner, Jennifer Wadsworth, Hanna Landenmark, Rosie Cane, Andrew W. Dickinson, Natasha Nicholson, Liam Perera, D. S. S. Lim
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2021.649312

Characterising Post-mortem Bacterial Translocation Under Clinical Conditions Using 16S rRNA Gene Sequencing in Two Animal Models
Cited by: 2
Author(s): Lily Gates, Nigel Klein, Neil J. Sebire, Dagmar Alber
Software Mentions: 4
Published: over 5 years ago

10.1128/mSphere.00382-18

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
Cited by: 22
Author(s): Sarah M. Hird, Holly H. Ganz, Jonathan A. Eisen, Walter M. Boyce
Software Mentions: 4
Published: almost 8 years ago

10.3390/ani11051372

Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs
Cited by: 0
Author(s): Emily Van Syoc, Natália Carrillo Gaeta, Erika Ganda
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2019.00347

Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches
Cited by: 49
Author(s): Logan M. Peoples, Eleanna Grammatopoulou, Michelle Pombrol, Xu Xin, Oladayo Osuntokun, Jessica M. Blanton, Eric E. Allen, Clifton C. Nunnally, Jeffrey C. Drazen, Daniel J. Mayor, Douglas H. Bartlett
Software Mentions: 4
Published: over 7 years ago

10.1128/mSystems.00640-20

Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes
Cited by: 34
Author(s): Chengying Shi, Lu Zhao, Evans Atoni, Weihua Zeng, Xiaomin Hu, Jelle Matthijnssens, Zhiming Yuan, Han Xia
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0236944

Impact of time and temperature on gut microbiota and SCFA composition in stool samples
Cited by: 9
Author(s): Janet L. Cunningham, Ludvig Bramstång, Abhijeet Singh, Shishanthi Jayarathna, Annica J. Rasmusson, Ali A. Moazzami, Bettina Müller
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.602404

Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking
Cited by: 7
Author(s): Lucie Rault, Pierre-Alexandre Lévêque, Sarah Barbey, Frédéric Launay, Hélène Larroque, Yves Le Loir, Pierre Germon, Jocelyne Guinard-Flament, Sergine Even
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-021-01071-4

A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota
Cited by: 60
Author(s): Yusook Chung, Yongku Ryu, Byung Chull An, Yeo-Sang Yoon, Oksik Choi, Tai Yeub Kim, Jae Kyung Yoon, Jun Young Ahn, Ho Jin Park, Soon-Kyeong Kwon, Jihyun F. Kim, Myung Jun Chung
Software Mentions: 4
Published: over 5 years ago

10.1186/s12866-021-02119-z

Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane
Cited by: 7
Author(s): Vincent Stevens, Sofie Thijs, Jaco Vangronsveld
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2019.00346

Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera
Cited by: 56
Author(s): Brooke L. Weigel, Catherine A. Pfister
Software Mentions: 4
Published: over 7 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702