bioconductor: phyloseq | Projects

10.7717/peerj.3098

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests
Cited by: 107
Author(s): Luis E. Castañeda, Olga Barbosa
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.9350

Effects of microbial evolution dominate those of experimental host-mediated indirect selection
Cited by: 19
Author(s): Jigyasa Arora, Margaret A. Mars Brisbin, Alexander S. Mikheyev
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.9644

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters
Cited by: 26
Author(s): Giulia M. Marchioro, Bettina Glasl, Aschwin H. Engelen, Ester Á. Serrão, David G. Bourne, Nicole S. Webster, Pedro R. Frade
Software Mentions: 5
Published: over 4 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

10.1038/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: almost 4 years ago

10.1371/journal.pone.0244341

Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children
Cited by: 9
Author(s): Christine Niemeier‐Walsh, Patrick Ryan, Jarosław Meller, Nicholas J. Ollberding, Atin Adhikari, Tiina Reponen
Software Mentions: 5
Published: over 3 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

10.7717/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 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 7 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

10.7717/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 4 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.2019.00256

Soil Macroinvertebrate Presence Alters Microbial Community Composition and Activity in the Rhizosphere
Cited by: 25
Author(s): Natalie Bray, Jenny Kao‐Kniffin, Serita D. Frey, Timothy J. Fahey, Kyle Wickings
Software Mentions: 5
Published: almost 6 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

10.3389/fmicb.2018.00031

Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes
Cited by: 37
Author(s): Kevin D’hoe, Lorenza Conterno, Francesca Fava, Gwen Falony, Sara Vieira-Silva, Joan Vermeiren, Kieran Tuohy, Jeroen Raes
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12866-021-02099-0

The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice
Cited by: 41
Author(s): Enkhchimeg Lkhagva, Hea-Jong Chung, Jinny Hong, W.H. Wilson Tang, Lee S, Seong‐Tshool Hong, Seungkoo Lee
Software Mentions: 5
Published: almost 4 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 4 years ago

10.3389/fmicb.2019.00481

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype
Cited by: 40
Author(s): Gregory Bonito, Gian Maria Niccolò Benucci, Khalid Hameed, Deborah Weighill, Piet Jones, Ko‐Hsuan Chen, Daniel Jacobson, Christopher W. Schadt, Rytas Vilgalys
Software Mentions: 5
Published: over 5 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/AEM.00149-21

Hyperlocal Variation in Soil Iron and the Rhizosphere Bacterial Community Determines Dollar Spot Development in Amenity Turfgrass
Cited by: 1
Author(s): Ming-Yi Chou, Smita Shrestha, Renée A. Rioux, Paul L. Koch
Software Mentions: 5
Published: over 3 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 3 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

10.3389/fmicb.2021.683685

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries
Cited by: 13
Author(s): Vivianne Cruz de Jesus, Mohd Wasif Khan, Betty-Anne Mittermuller, Kangmin Duan, Pingzhao Hu, Robert J Schroth, Prashen Chelikani
Software Mentions: 5
Published: over 3 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 3 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 7 years ago

10.3390/nu12113557

High Fat-High Fructose Diet-Induced Changes in the Gut Microbiota Associated with Dyslipidemia in Syrian Hamsters
Cited by: 29
Author(s): Rachael Horne, Yifan Yu, Rianna Zhang, Nyan Abdalqadir, Laura Rossi, Michael G. Surette, Philip M. Sherman, Khosrow Adeli
Software Mentions: 4
Published: about 4 years ago

10.1186/s42523-021-00076-6

Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets
Cited by: 23
Author(s): Kasun H. Bodawatta, Inga Freiberga, Kateřina Pužejová, Kateřina Sam, Michael Poulsen, Knud A. Jønsson
Software Mentions: 4
Published: almost 4 years ago

10.3390/ani9121063

Effect of Supplementing Hydrolysable Tannins to a Grower–Finisher Diet Containing Divergent PUFA Levels on Growth Performance, Boar Taint Levels in Back Fat and Intestinal Microbiota of Entire Males
Cited by: 24
Author(s): M. Tretola, Federica Maghin, Paolo Silacci, S. Ampuero, Giuseppe Bee
Software Mentions: 4
Published: almost 5 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 3 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 3 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 4 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: about 5 years ago

10.1128/AEM.02658-18

Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile
Cited by: 5
Author(s): Urse Scheel Krüger, Arnaud Dechesne, Friedhelm Bak, Nora Badawi, Ole Nybroe, Jens Aamand
Software Mentions: 4
Published: over 5 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 5 years ago

10.1186/s12866-020-01979-1

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog
Cited by: 14
Author(s): Randall R. Jiménez, Gilbert Alvarado, José Luís Sandoval, Simone Sommer
Software Mentions: 4
Published: about 4 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: over 7 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 3 years ago

10.1186/s12903-018-0591-6

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach
Cited by: 24
Author(s): Yoshio Nakano, Nao Suzuki, Fumiyuki Kuwata
Software Mentions: 4
Published: over 6 years ago

10.3390/biomedicines9030266

Dysbiosis and Enhanced Beta-Defensin Production in Hair Follicles of Patients with Lichen Planopilaris and Frontal Fibrosing Alopecia
Cited by: 6
Author(s): Andria Constantinou, Katarzyna Polak-Witka, Marios Tomazou, Anastasis Oulas, Varvara Kanti, Rolf Schwarzer, Johannes Helmuth, Anke Edelmann, Ulrike Blume-Peytavi, George M. Spyrou, Annika Vogt
Software Mentions: 4
Published: over 3 years ago

10.3390/biom11091286

Lipocalin 2 Deficiency Restrains Aging-Related Reshaping of Gut Microbiota Structure and Metabolism
Cited by: 2
Author(s): Xing‐Biao Qiu, Chi Chen, Xiaoli Chen
Software Mentions: 4
Published: about 3 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: over 3 years ago

10.1111/1751-7915.12337

Dynamic changes in microbiota and mycobiota during spontaneous ‘<scp>V</scp>ino <scp>S</scp>anto <scp>T</scp>rentino’ fermentation
Cited by: 41
Author(s): Irene Stefanini, Davide Albanese, A. Cavazza, Elena Franciosi, Carlotta De Filippo, Claudio Donati, Duccio Cavalieri
Software Mentions: 4
Published: almost 9 years ago

10.1007/s00248-019-01424-5

Early Colonization of Weathered Polyethylene by Distinct Bacteria in Marine Coastal Seawater
Cited by: 81
Author(s): Gabriel Erni-Cassola, Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 4
Published: about 5 years ago

10.1007/s00248-021-01700-3

Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity
Cited by: 9
Author(s): Florian Caillon, Katharina Besemer, Peter Peduzzi, Jakob Schelker
Software Mentions: 4
Published: almost 4 years ago

10.1264/jsme2.ME18107

Deciphering the Assembly Processes of the Key Ecological Assemblages of Microbial Communities in Thirteen Full-Scale Wastewater Treatment Plants
Cited by: 13
Author(s): Liyuan Hou, Anyi Hu, Shaohua Chen, Kaisong Zhang, Sandi Orlić, Abbas Rashid, Chang-Ping Yu
Software Mentions: 4
Published: almost 6 years ago

10.1002/mbo3.1022

Geographical separation and physiology drive differentiation of microbial communities of two discrete populations of the bat Leptonycteris yerbabuenae
Cited by: 10
Author(s): Osiris Gaona, Daniel Cerqueda‐García, Andrés Moya, Ximena Neri‐Barrios, Luisa I. Falcón
Software Mentions: 4
Published: over 4 years ago

10.1002/mbo3.964

Microbial composition of enigmatic bird parasites: Wolbachia and Spiroplasma are the most important bacterial associates of quill mites (Acariformes: Syringophilidae)
Cited by: 7
Author(s): Eliza Głowska, Zuzanna Karolina Filutowska, Mirosława Dabert, Michael Gerth
Software Mentions: 4
Published: over 4 years ago

10.1128/MRA.01195-19

GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining
Cited by: 7
Author(s): W. M. Tong, Yuen-Yan Chan
Software Mentions: 4
Published: almost 5 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: about 4 years ago

10.1186/s40168-018-0553-x

Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten
Cited by: 23
Author(s): Anders Benteson Nygaard, Colin Charnock
Software Mentions: 4
Published: about 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 3 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 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 4 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: about 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 5 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 8 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: 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 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 3 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 3 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 3 years ago

10.3390/microorganisms8091377

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization
Cited by: 13
Author(s): Martina Kracmarova, Jana Karpíšková, Ondřej Uhlík, Michal Strejcek, Jiřina Száková, J. Balík, Kateřina Demnerova, Hana Stiborová
Software Mentions: 4
Published: about 4 years ago

10.3390/microorganisms9061121

Long-Term Effects of Dietary Supplementation with Olive Oil and Hydrogenated Vegetable Oil on the Rumen Microbiome of Dairy Cows
Cited by: 7
Author(s): Nathaly Cancino‐Padilla, Natalia Catalán, Karen Siu-Ting, Christopher J. Creevey, Sharon Huws, Jaime Romero, Einar Vargas‐Bello‐Pérez
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms9091876

The Terrestrial Plastisphere: Diversity and Polymer-Colonizing Potential of Plastic-Associated Microbial Communities in Soil
Cited by: 21
Author(s): Joana MacLean, Sathish Mayanna, Liane G. Benning, Fabian Horn, Alexander Bartholomäus, Yosri Wiesner, Dirk Wagner, Susanne Liebner
Software Mentions: 4
Published: about 3 years ago

10.3390/microorganisms7030072

Urbanization Altered Bacterial and Archaeal Composition in Tidal Freshwater Wetlands Near Washington DC, USA, and Buenos Aires, Argentina
Cited by: 3
Author(s): Martina Gonzalez Mateu, Cedric Evan Park, Cullen Patrick McAskill, Andrew H. Baldwin, Stephanie A. Yarwood
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms9020221

The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time
Cited by: 9
Author(s): Ilaria Patuzzi, Massimiliano Orsini, Veronica Cibin, Sara Petrin, Eleonora Mastrorilli, Alessia Tiengo, Federica Gobbo, Salvatore Catania, Lisa Barco, Antonia Ricci, Carmen Losasso
Software Mentions: 4
Published: almost 4 years ago

10.3390/microorganisms9040718

Effects of Clinical Wastewater on the Bacterial Community Structure from Sewage to the Environment
Cited by: 5
Author(s): Ilse Verburg, H. Pieter J. van Veelen, Karola Waar, John W. A. Rossen, Alex Friedrich, Lucía Hernández Leal, Silvia García-Cobos, Heike Schmitt
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms8111729

A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes
Cited by: 7
Author(s): Kshitij Tandon, Bayanmunkh Baatar, Pei‐Wen Chiang, Dashdondog Narangarvuu, Bolormaa Oyuntsetseg, Sen‐Lin Tang
Software Mentions: 4
Published: about 4 years ago

10.3390/microorganisms7100441

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale
Cited by: 17
Author(s): Sonia S. Valencia-Agami, Daniel Cerqueda‐García, S. Putzeys, María Magdalena Uribe-Flores, Ulises García-Cruz, Daniel Pech, Jorge A. Herrera-Silveira, M. Leopoldina Aguirre-Macedo, José Q. García-Maldonado
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms8091347

Gut Microbial Changes in Diabetic db/db Mice and Recovery of Microbial Diversity upon Pirfenidone Treatment
Cited by: 17
Author(s): Harinder Singh, Sadaaki Miyamoto, Manjula Darshi, Manolito Torralba, Ki-Ryong Kwon, Kumar Sharma, Rembert Pieper
Software Mentions: 4
Published: about 4 years ago

10.3390/microorganisms9091976

Mussel Mass Mortality and the Microbiome: Evidence for Shifts in the Bacterial Microbiome of a Declining Freshwater Bivalve
Cited by: 15
Author(s): Jordan Richard, Lewis J. Campbell, Eric Leis, Rose E. Agbalog, Chris D. Dunn, Diane L. Waller, Susan Knowles, Joel Putnam, Tony L. Goldberg
Software Mentions: 4
Published: about 3 years ago

10.3390/microorganisms8010094

Characterization of the Gut Microbiota of Individuals at Different T2D Stages Reveals a Complex Relationship with the Host
Cited by: 40
Author(s): Alejandra Chávez-Carbajal, María Luisa Pizano-Zárate, Fernando Hernández-Quiroz, Guillermo Federico Ortíz-Luna, Rosa María Morales-Hernández, Amapola De Sales-Millán, María Hernández‐Trejo, Angelina García-Vite, Luis Beltrán-Lagunés, Carlos Hoyo‐Vadillo, Jaime García‐Mena
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms9040822

Rootstocks Shape Their Microbiome—Bacterial Communities in the Rhizosphere of Different Grapevine Rootstocks
Cited by: 16
Author(s): Leonie Dries, Simone Bussotti, Carlo Pozzi, Robert Kunz, Sylvia Schnell, Otmar Löhnertz, Anne Vortkamp
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms9010030

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

10.3390/microorganisms7010017

Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study
Cited by: 84
Author(s): Ruth C E Bowyer, Matthew A. Jackson, Caroline I. Le Roy, Mary Ní Lochlainn, Timothy D. Spector, Jennifer Beam Dowd, Claire J. Steves
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms9030561

New Insights into Microbial Diversity of the Traditional Packed Table Olives Aloreña de Málaga through Metataxonomic Analysis
Cited by: 10
Author(s): Elio López-García, Antonio Benítez-Cabello, Javier Ramiro-García, Verónica Romero‐Gil, Francisco Rodríguez‐Gómez, Francisco Noé Arroyo‐López
Software Mentions: 4
Published: over 3 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 4 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 3 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 5 years ago

10.1186/s10020-021-00311-5

Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism
Cited by: 27
Author(s): Eder Orlando Méndez-Salazar, Janitzia Vázquez‐Mellado, Carlos S. Casimiro-Soriguer, Joaquín Dopazo, Cankut Çubuk, Yessica Zamudio-Cuevas, Adriana Francisco-Balderas, Karina Martínez-Flores, Javier Fernández‐Torres, Carlos Lozada, Carlos Pineda, Austreberto Sánchez-González, Luis H. Silveira, Ana I. Burguete-García, Citlalli Orbe-Orihuela, Alfredo Lagunas‐Martínez, Alonso Vazquez-Gomez, Alberto López‐Reyes, Berenice Palacios‐González, Gabriela Angélica Martínez‐Nava
Software Mentions: 4
Published: over 3 years ago

10.1093/ve/veab034

Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray–Darling Basin, Australia
Cited by: 21
Author(s): Vincenzo A Costa, Jonathon C O Mifsud, Dean M. Gilligan, Jane E. Williamson, Edward C. Holmes, Jemma L. Geoghegan
Software Mentions: 4
Published: almost 4 years ago

10.3390/v12090922

Impact of Viral Lysis on the Composition of Bacterial Communities and Dissolved Organic Matter in Deep-Sea Sediments
Cited by: 14
Author(s): Mara Elena Heinrichs, Dennis Alexander Tebbe, Bernd Wemheuer, Jutta Niggemann, Bert Engelen
Software Mentions: 4
Published: over 4 years ago

10.1016/j.watres.2019.06.075

Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters
Cited by: 93
Author(s): Marcos Quintela-Baluja, Mohamed Abouelnaga, Jesús L. Romalde, Jian‐Qiang Su, Yongjie Yu, Mariano Gomez-Lopez, Barth F. Smets, Yong‐Guan Zhu, David W. Graham
Software Mentions: 4
Published: about 5 years ago

10.1016/j.wroa.2020.100056

Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households
Cited by: 5
Author(s): Erica R. Fuhrmeister, Ayşe Ercümen, Jessica A. Grembi, Mahfuza Islam, Amy J. Pickering, Kara L. Nelson
Software Mentions: 4
Published: almost 4 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: over 3 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 3 years ago

10.7717/peerj.9367

Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis
Cited by: 7
Author(s): Paula Lado, Bo Liu, Michelle E. J. Allerdice, Christopher D. Paddock, Sandor E. Karpathy, Hans Klompen
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.8492

Influence of host phylogeny, geographical location and seed harvesting diet on the bacterial community of globally distributed Pheidole ants
Cited by: 9
Author(s): Carla Braga Martins, Corrie S. Moreau
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.9307

Succession of bacterial communities on carrion is independent of vertebrate scavengers
Cited by: 8
Author(s): Cody R. Dangerfield, Ethan Frehner, Evan R. Buechley, Çağan H. Şekercioğlu, William J. Brazelton
Software Mentions: 4
Published: over 4 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: almost 6 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: about 4 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 8 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 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 4 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: over 5 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: over 3 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 8 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 4 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 3 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702