bioconductor: phyloseq | Projects

10.1128/mSystems.00629-19

Intranasal Bacterial Therapeutics Reduce Colonization by the Respiratory Pathogen Mannheimia haemolytica in Dairy Calves
Cited by: 32
Author(s): Samat Amat, Trevor W. Alexander, Devin B. Holman, Timothy Schwinghamer, Edouard Timsit
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2015.00348

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

10.1371/journal.pone.0219982

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae
Cited by: 12
Author(s): Osiris Gaona, Selene Gómez-Acata, Daniel Cerqueda‐García, Carla Ximena Neri-Barrios, Luisa I. Falcón
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2020.00838

IL-22 Paucity in APECED Is Associated With Mucosal and Microbial Alterations in Oral Cavity
Cited by: 13
Author(s): Epp Kaleviste, Malte Rühlemann, Jaanika Kärner, Liis Haljasmägi, Liina Tserel, Elin Org, Katarina Trebušak Podkrajšek, Tadej Battelino, Corinna Bang, André Franke, Pärt Peterson, Kai Kisand
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2017.01914

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

10.3389/fmed.2021.586875

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

10.1186/s12866-020-01759-x

The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection
Cited by: 23
Author(s): Harris Onywera, Anna‐Lise Williamson, Luca Cozzuto, Sarah Bonnin, Zizipho Z. A. Mbulawa, David Coetzee, Julia Ponomarenko, Tracy L. Meiring
Software Mentions: 3
Published: over 4 years ago

10.1128/mSystems.00317-20

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin
Cited by: 21
Author(s): Damien J. Cabral, Jenna I. Wurster, Benjamin J. Korry, Swathi Penumutchu, Peter Belenky
Software Mentions: 3
Published: about 4 years ago

10.1128/mSystems.00668-20

Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways
Cited by: 9
Author(s): Shawn M. Doyle, Genmei Lin, Maya Morales‐McDevitt, Terry L. Wade, Antonietta Quigg, Jason B. Sylvan
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0237262

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet
Cited by: 11
Author(s): F. Albonico, Claudia Barelli, Davide Albanese, Mattia Manica, Erika Partel, Fausta Rosso, Silvia Ripellino, Massimo Pindo, Claudio Donati, A. Zecconi, Michele Mortarino, Heidi C. Hauffe
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0232699

Azolla filiculoides L. as a source of metal-tolerant microorganisms
Cited by: 22
Author(s): Artur Banach, Agnieszka Kuźniar, Jarosław Grządziel, Agnieszka Woliñska
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0215918

Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses
Cited by: 15
Author(s): Michelle Coleman, Canaan Whitfield-Cargile, Rodolfo Madrigal, Noah D. Cohen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0242108

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

10.3389/fmicb.2021.676880

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

10.1371/journal.pone.0178755

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

10.1371/journal.pone.0217296

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

10.1371/journal.pone.0174890

Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers
Cited by: 33
Author(s): Jason T. Payne, Justin Millar, Colin R. Jackson, Clifford A. Ochs
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0215872

Incubation and grazing effects on spirotrich ciliate diversity inferred from molecular analyses of microcosm experiments
Cited by: 6
Author(s): Jean‐David Grattepanche, Doris L. Juarez, Cameah Corin Wood, George B. McManus, Laura A. Katz
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2021.694406

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

10.1371/journal.pone.0204629

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing
Cited by: 64
Author(s): Simon Poirier, Olivier Rué, R. Peguilhan, Gwendoline Coeuret, Monique Zagorec, Marie‐Christine Champomier‐Vergès, Valentin Loux, Stéphane Chaillou
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0112763

Bacterial Endophytic Communities in the Grapevine Depend on Pest Management
Cited by: 101
Author(s): A. Campisano, Livio Antonielli, Michael Pancher, Sohail Yousaf, Massimo Pindo, I. Pertot
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0231942

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

10.3390/nu10081069

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice
Cited by: 28
Author(s): Simon Ghaly, Nadeem O. Kaakoush, Frances Lloyd, Lavinia Gordon, Cynthia Forest, Ian C. Lawrance, Prue H. Hart
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2020.596156

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

10.1371/journal.pone.0183716

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

10.1371/journal.pone.0181964

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

10.3389/fmicb.2017.00431

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment
Cited by: 22
Author(s): Pauliina Rajala, Malin Bomberg
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2019.02368

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

10.1186/s12866-021-02139-9

Identification of cutaneous fungi and mites in adult atopic dermatitis: analysis by targeted 18S rRNA amplicon sequencing
Cited by: 8
Author(s): Sofie Marie Edslev, Paal Skytt Andersen, Tove Agner, Ditte Marie Lindhardt Saunte, Anna Cäcilia Ingham, Thor Bech Johannesen, Maja‐Lisa Clausen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0116704

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice
Cited by: 241
Author(s): Aaron C. Ericsson, J. Wade Davis, William G. Spollen, Nathan J. Bivens, Scott A. Givan, Catherine E. Hagan, Mark A. McIntosh, Craig L. Franklin
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0199291

Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil
Cited by: 25
Author(s): Pilar Truchado, María I. Gil, Trevor Suslow, Ana Allende
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0224658

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia
Cited by: 15
Author(s): Heng Choon Cheong, Polly Soo Xi Yap, Chun Wie Chong, Yi Ying Cheok, Chalystha Yie Qin Lee, Guan Huat Tan, Sofiah Sulaiman, Jamiyah Hassan, Negar Shafiei Sabet, Chung Yeng Looi, Rishein Gupta, Bernard P. Arulanandam, Sazaly AbuBakar, Cindy Shuan Ju Teh, Li Chang, Won Fen Wong
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0142603

Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities
Cited by: 33
Author(s): Jamie A. FitzGerald, Eoin Allen, David Wall, Stephen A. Jackson, Jerry D. Murphy, Alan D. W. Dobson
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0207985

Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest
Cited by: 40
Author(s): Jose E. Pietri, Connor R. Tiffany, Dangsheng Liang
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0208018

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

10.1186/s40413-015-0074-z

The microbiome of the human lower airways: a next generation sequencing perspective
Cited by: 34
Author(s): Velma Aho, Pedro Pereira, Tari Haahtela, Ruby Pawankar, Petri Auvinen, Kaisa Koskinen
Software Mentions: 2
Published: almost 10 years ago

10.3390/biology10030180

The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)
Cited by: 17
Author(s): Negash Kabtimer Bereded, Getachew Beneberu, Solomon Workneh Fanta, Manuel Curto, Herwig Waidbacher, Harald Meimberg, Konrad J. Domig
Software Mentions: 2
Published: over 3 years ago

10.3390/jcm8020164

Fecal Microbiota Analysis in Patients Going through a Depressive Episode during Treatment in a Psychiatric Hospital Setting
Cited by: 26
Author(s): Paweł Liśkiewicz, Justyna Pełka-Wysiecka, Mariusz Kaczmarczyk, Igor Łoniewski, Michał Wroński, Agata Bąba-Kubiś, Karolina Skonieczna-Żydecka, Wojciech Marlicz, Błażej Misiak, Jerzy Samochowiec
Software Mentions: 2
Published: almost 6 years ago

10.3390/jcm8050630

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis
Cited by: 60
Author(s): Kaja Eriksson, Guo-Zhong Fei, Anna Lundmark, Daniel Benchimol, Linkiat Lee, Yue Hu, Anna Kats, Saedís Saevarsdóttir, Anca I. Catrina, Björn Klinge, Anders F. Andersson, Lars Klareskog, Karin Lundberg, Leif Jansson, Tülay Yucel‐Lindberg
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2019.00957

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes
Cited by: 7
Author(s): Jiarong Guo, John F. Quensen, Yanni Sun, Qiong Wang, C. Titus Brown, James R. Cole, James M. Tiedje
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0222470

Investigating the dispersal of antibiotic resistance associated genes from manure application to soil and drainage waters in simulated agricultural farmland systems
Cited by: 19
Author(s): Schuyler D. Smith, Phillip Colgan, Fan Yang, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Heather K. Allen, Adina Howe
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.609644

Prevotella histicola Protects From Arthritis by Expansion of Allobaculum and Augmenting Butyrate Production in Humanized Mice
Cited by: 41
Author(s): Baskar Balakrishnan, David Luckey, Rahul Bodhke, Jun Chen, Eric Marietta, Patricio Jeraldo, Joseph A. Murray, Veena Taneja
Software Mentions: 2
Published: over 3 years ago

10.3390/jcm9113700

Amoebae in Chronic, Polymicrobial Endodontic Infections Are Associated with Altered Microbial Communities of Increased Virulence
Cited by: 3
Author(s): Garrit Koller, Federico Foschi, Philip Mitchell, Elizabeth A. Witherden, Kenneth D. Bruce, Francesco Mannocci
Software Mentions: 2
Published: about 4 years ago

10.1038/s41396-020-0722-3

Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations
Cited by: 20
Author(s): Eleonora Chiri, Chris Greening, Rachael Lappan, David W. Waite, Thanavit Jirapanjawat, Xiyang Dong, Stefan K. Arndt, Philipp A. Nauer
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-32583-z

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells
Cited by: 23
Author(s): Alessia Butera, Monica Di Paola, Lorenzo Pavarini, Francesco Strati, Massimo Pindo, Massimo Sanchez, Duccio Cavalieri, Monica Boirivant, Carlotta De Filippo
Software Mentions: 2
Published: about 6 years ago

10.1093/femsec/fiaa102

Enhanced microbial degradation of irradiated cellulose under hyperalkaline conditions
Cited by: 7
Author(s): Naji M. Bassil, Joe S. Small, Jonathan R. Lloyd
Software Mentions: 2
Published: over 4 years ago

10.14814/phy2.13649

Fecal <i>Enterobacteriales</i> enrichment is associated with increased in vivo intestinal permeability in humans
Cited by: 24
Author(s): Christian Fischer Pedersen, Umer Zeeshan Ijaz, Edith Gallagher, Felicity Horton, Richard J. Ellis, Etana Joy Jaiyeola, Thibaut Duparc, David Russell‐Jones, Paul Hinton, Patrice D. Cani, Roberto M. La Ragione, M. Denise Robertson
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0237561

Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment
Cited by: 6
Author(s): Magdalena L Warren, Karin E. Kram, Kathryn Theiss
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-019-3021-0

VOLARE: visual analysis of disease-associated microbiome-immune system interplay
Cited by: 5
Author(s): Janet Siebert, C. Preston Neff, Jennifer M. Schneider, Emilie Regner, Neha Ohri, Kristine A. Kuhn, Brent E. Palmer, Catherine Lozupone, Carsten Görg
Software Mentions: 2
Published: over 5 years ago

10.1007/s00203-019-01661-9

Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan
Cited by: 15
Author(s): Kimiho Omae, Yuto Fukuyama, Hisato Yasuda, Kenta Mise, Takashi Yoshida, Yoshihiko Sako
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22041649

Gut Microbiota Profile in Children with IgE-Mediated Cow’s Milk Allergy and Cow’s Milk Sensitization and Probiotic Intestinal Persistence Evaluation
Cited by: 10
Author(s): Maurizio Mennini, Sofia Reddel, Federica Del Chierico, Simone Gardini, Andrea Quagliariello, Pamela Vernocchi, Rocco Valluzzi, Vincenzo Fierro, Carla Riccardi, Tania Napolitano, Alessandro Fiocchi, Lorenza Putignani
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-018-37321-z

Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita
Cited by: 24
Author(s): Nancy Weiland‐Bräuer, Martin Fischer, Nicole Pinnow, Ruth A. Schmitz
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.01031

Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System
Cited by: 38
Author(s): Nancy Merino, Mikihiko Kawai, Eric S. Boyd, Daniel R. Colman, Shawn E. McGlynn, Kenneth H. Nealson, Ken Kurokawa, Yuichi Hongoh
Software Mentions: 2
Published: over 4 years ago

10.1017/S1751731120001299

Transient effect of single or repeated acute deoxynivalenol and zearalenone dietary challenge on fecal microbiota composition in female finishing pigs
Cited by: 10
Author(s): M. Le Sciellour, Olivier Zemb, Aira Maye Serviento, David Renaudeau
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0249571

Distinct community structures of soil nematodes from three ecologically different sites revealed by high-throughput amplicon sequencing of four 18S ribosomal RNA gene regions
Cited by: 5
Author(s): Harutaro Kenmotsu, Masahiro Ishikawa, Tomokazu Nitta, Yuu Hirose, Toshihiko Eki
Software Mentions: 2
Published: over 3 years ago

10.1002/mbo3.456

The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors
Cited by: 28
Author(s): Shelesh Agrawal, Søren Michael Karst, Eva M. Gilbert, Harald Horn, Per Halkjær Nielsen, Susanne Lackner
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.6414

Evaluation of DESS as a storage medium for microbial community analysis
Cited by: 17
Author(s): Kevin M Lee, Madison Adams, Jonathan L. Klassen
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.4989

Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater
Cited by: 10
Author(s): Christophe Paul, Zhanna Bayrychenko, Thomas Junier, Sevasti Filippidou, Karin Beck, Matthieu Bueche, Gilbert Greub, Helmut Bürgmann, Pilar Junier
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.01583

Highly Diverse Aquatic Microbial Communities Separated by Permafrost in Greenland Show Distinct Features According to Environmental Niches
Cited by: 10
Author(s): Malin Bomberg, Lillemor Claesson Liljedahl, Tiina Lamminmäki, Anne Kontula
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.11075

Limited influence of marine sediment lyophilization on prokaryotic community structure assessed via amplicon sequencing: an example from environmentally contrasted sediment layers in Toulon harbor (France)
Cited by: 0
Author(s): Benjamin Misson, Cédric Garnier, Alexandre J. Poulain
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.4671

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing
Cited by: 4
Author(s): Lauren M. O’Connell, Song Gao, Donald McCorquodale, Jay M. Fleisher, Jose V. Lopez
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-38984-y

Changes in microbiome diversity following beta-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis
Cited by: 15
Author(s): Andrea Hahn, Hani Fanous, Caroline Jensen, Hollis Chaney, Iman Sami, Geovanny F. Pérez, Anastassios C. Koumbourlis, Stan G. Louie, James E. Bost, John N. van den Anker, Robert J. Freishtat, Edith T. Zemanick, Keith A. Crandall
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.00353

Petroleum Depletion Property and Microbial Community Shift After Bioremediation Using Bacillus halotolerans T-04 and Bacillus cereus 1-1
Cited by: 13
Author(s): Zhili Deng, Yingying Jiang, Kaikai Chen, Fei Gao, Xiaodong Liu
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.6316

Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms
Cited by: 12
Author(s): Mikko Pyysalo, Pashupati P. Mishra, Kati Sundström, Terho Lehtimäki, Pekka J. Karhunen, Tanja Pessi
Software Mentions: 2
Published: almost 6 years ago

10.1128/AEM.01171-18

Metabolic Capability and Phylogenetic Diversity of Mono Lake during a Bloom of the Eukaryotic Phototroph Picocystis sp. Strain ML
Cited by: 7
Author(s): Blake W. Stamps, Heather S. Nunn, Victoria A. Petryshyn, Ronald S. Oremland, Laurence G. Miller, Michael R. Rosen, Kohen W. Bauer, Katherine Jenny Thompson, Elise M. Tookmanian, Anna R. Waldeck, S. J. Loyd, Hope A. Johnson, Bradley S. Stevenson, William M. Berelson, Frank A. Corsetti, John R. Spear
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.4197

A historical legacy of antibiotic utilization on bacterial seed banks in sediments
Cited by: 8
Author(s): Laura Madueño, Christophe Paul, Thomas Junier, Zhanna Bayrychenko, Sevasti Filippidou, Karin Beck, Gilbert Greub, Helmut Bürgmann, Pilar Junier
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-41195-0

Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria
Cited by: 37
Author(s): Ida Nordang Kieler, Melania Osto, Leoni Hugentobler, Lara Puetz, M. Thomas P. Gilbert, Torben Hansen, Oluf Pedersen, Claudia E Reusch, Eric Zini, Thomas Lutz, Charlotte Reinhard Bjørnvad
Software Mentions: 2
Published: over 5 years ago

10.3389/fcvm.2017.00017

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in a Pediatric Heart Transplant Patient
Cited by: 25
Author(s): Kyle L. Flannigan, Taylor Rajbar, Andrew Moffat, L McKenzie, Frank Dicke, Kevin P. Rioux, Matthew L. Workentine, Thomas Louie, Simon A. Hirota, Steven C. Greenway
Software Mentions: 2
Published: over 7 years ago

10.1186/s13568-018-0607-2

The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses
Cited by: 13
Author(s): Martine A. R. Kox, Sanni L. Aalto, Timo Penttilä, Katharina F. Ettwig, Mike S. M. Jetten, Maartje A. H. J. van Kessel
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.11532

Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species
Cited by: 7
Author(s): Bárbara Santos, Molly C. Bletz, Joana Sabino‐Pinto, Walter Cocca, Jean Francois Solofoniaina Fidy, Karen Freeman, Sven Kuenzel, Serge H. Ndriantsoa, Jean Noël, Tsanta Rakotonanahary, Miguel Vences, Angelica Crottini
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0221868

Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal
Cited by: 11
Author(s): Dibesh Karmacharya, Prajwol Manandhar, Sulochana Manandhar, Adarsh Man Sherchan, Ajay Sharma, Jyoti Joshi, Manisha Bista, Shailendra Bajracharya, Nagendra Awasthi, Netra Prasad Sharma, Bronwyn Llewellyn, Lisette P. Waits, Kanchan Thapa, Marcella J. Kelly, Momchilo Vuyisich, Shawn R. Starkenburg, Jean‐Marc Hero, Jane Hughes, Claudia Wultsch, Laura D. Bertola, Nicholas M. Fountain-Jones, Amit Kumar Sinha
Software Mentions: 2
Published: about 5 years ago

10.3389/fnut.2021.707763

In vitro Colon Fermentation of Soluble Arabinoxylan Is Modified Through Milling and Extrusion
Cited by: 9
Author(s): Teresa Demuth, Veronica Edwards, Lea Bircher, Christophe Lacroix, Laura Nyström, Annelies Geirnaert
Software Mentions: 2
Published: about 3 years ago

10.3390/antibiotics9090631

Antimicrobial Resistance, an Update from the Ward: Increased Incidence of New Potential Pathogens and Site of Infection-Specific Antibacterial Resistances
Cited by: 4
Author(s): Irene Stefanini, Martina Boni, Paola Silvaplana, Paola Lovera, Stefania Pelassa, Giuseppe De Renzi, Barbara Mognetti
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-43814-2

High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly in peri-Alpine lakes
Cited by: 17
Author(s): Marie‐Ève Monchamp, Piet Spaak, Francesco Pomati
Software Mentions: 2
Published: over 5 years ago

10.3389/fnut.2020.566950

Evolution of Fructans in Aguamiel (Agave Sap) During the Plant Production Lifetime
Cited by: 12
Author(s): Ibeth Peralta-García, Fernando González-Muñoz, Rodríguez-Alegría María Elena, Alejandro Sánchez-Flores, Agustín López Munguía
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0182924

Bile microbiota in primary sclerosing cholangitis: Impact on disease progression and development of biliary dysplasia
Cited by: 62
Author(s): Pedro Pereira, Velma Aho, Johanna Arola, Sonja Boyd, Kalle Jokelainen, Lars Paulín, Petri Auvinen, Martti Färkkilä
Software Mentions: 2
Published: over 7 years ago

10.1111/1751-7915.13837

Effect of concentration and hydraulic reaction time on the removal of pharmaceutical compounds in a membrane bioreactor inoculated with activated sludge
Cited by: 12
Author(s): Ana B. Rios‐Miguel, Mike S. M. Jetten, Cornelia U. Welte
Software Mentions: 2
Published: over 3 years ago

10.3389/fphar.2021.706703

Spontaneous and Naloxone-Precipitated Withdrawal Behaviors From Chronic Opiates are Accompanied by Changes in N-Oleoylglycine and N-Oleoylalanine Levels in the Brain and Ameliorated by Treatment With These Mediators
Cited by: 8
Author(s): Samantha M. Ayoub, Fabiana Piscitelli, Cristoforo Silvestri, Cheryl L. Limebeer, Erin M. Rock, Reem Smoum, Mathew Farag, Hannah de Almeida, Megan T. Sullivan, Sébastien Lacroix, Besma Boubertakh, Nayudu Nallabelli, Aron H. Lichtman, Francesco Leri, Raphael Mechoulam, Vincenzo Di Marzo, Linda A. Parker
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2020.00862

The Cultivable Bacterial Microbiota Associated to the Medicinal Plant Origanum vulgare L.: From Antibiotic Resistance to Growth-Inhibitory Properties
Cited by: 16
Author(s): Lara Mitia Castronovo, Carmela Calonico, Roberta Ascrizzi, Sara Del Duca, Vania Delfino, Sofia Chioccioli, Alberto Vassallo, Iolanda Strozza, Marinella De Leo, Sauro Biffi, Giovanni Bacci, Patrizia Bogani, Valentina Maggini, Alessio Mengoni, Luisa Pistelli, Antonella Lo Nostro, Fabio Firenzuoli, Renato Fani
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-45066-6

Association between the pig genome and its gut microbiota composition
Cited by: 54
Author(s): Daniel Crespo-Piazuelo, Lourdes Migura-García, Jordi Estellé, Lourdes Criado-Mesas, Manuel Revilla, Anna Castelló, María Muñoz, Juan García‐Casco, Ana Fernández, María Ballester, Josep María Folch
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2018.01662

Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation
Cited by: 60
Author(s): Julien P. Guyonnet, Martin Guillemet, Audrey Dubost, Laurent Simon, Philippe Ortet, Mohamed Barakat, Thierry Heulin, Wafa Achouak, Feth el Zahar Haichar
Software Mentions: 2
Published: about 6 years ago

10.1111/1751-7915.13482

Air‐side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome
Cited by: 19
Author(s): Nuria Fernandez‐Gonzalez, Chiara Pedizzi, Juan M. Lema, Marta Carballa
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2016.00314

454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems
Cited by: 20
Author(s): Elham A. Kazeeroni, Abdullah M. Al-Sadi
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0194272

Behaviour during transportation predicts stress response and lower airway contamination in horses
Cited by: 30
Author(s): Barbara Padalino, Sharanne Raidal, Peter Knight, Pietro Celi, L. B. Jeffcott, Gary Muscatello
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-46904-3

Co-cultivation of the marine sponge Halichondria panicea and its associated microorganisms
Cited by: 16
Author(s): Stephen Knobloch, Ragnar Jóhannsson, V. Marteinsson
Software Mentions: 2
Published: over 5 years ago

10.3390/md19040183

Effect of Supplementing Seaweed Extracts to Pigs until d35 Post-Weaning on Performance and Aspects of Intestinal Health
Cited by: 12
Author(s): Stafford Vigors, John V. O’Doherty, Ruth Rattigan, T. Sweeney
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0244763

Modeling dysbiosis of human NASH in mice: Loss of gut microbiome diversity and overgrowth of Erysipelotrichales
Cited by: 24
Author(s): James K. Carter, Dipankar Bhattacharya, Joshua N. Borgerding, Maria Isabel Fiel, Jeremiah J. Faith, Scott L. Friedman
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.11753

Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning
Cited by: 3
Author(s): Maslin Osathanunkul, Nipitpong Sawongta, Panagiotis Madesis, Nikolaos Pechlivanis, Fotis Psomopoulos, Panagiotis Madesis
Software Mentions: 2
Published: over 3 years ago

10.3390/pathogens10050504

Drift of the Subgingival Periodontal Microbiome during Chronic Periodontitis in Type 2 Diabetes Mellitus Patients
Cited by: 14
Author(s): И П Балмасова, Evgenii I. Olekhnovich, Ksenia M. Klimina, Anna A. Korenkova, Maria T. Vakhitova, Elmar Babaev, Leyla A. Ovchinnikova, Yakov A. Lomakin, Иван Смирнов, В.Н. Царев, А. M. Mkrtumyan, Alexey A. Belogurov, Alexander G. Gabibov, Elena Ilina, С Д Арутюнов
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-49893-5

Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production
Cited by: 28
Author(s): Daniéla Oliveira Magro, Andrey dos Santos, Dioze Guadagnini, Flavia Moreira de Godoy, Sylvia Helena Monteiro Silva, Wilson José Fernandes Lemos, Nicola Vitulo, Sandra Torriani, Lílian Vital Pinheiro, Carlos Augusto Real Martinez, Mário José Abdalla Saad, Cláudio Saddy Rodrigues Coy
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-49832-4

Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances
Cited by: 19
Author(s): Giulia Gionchetta, Anna M. Romaní, Francesc Oliva, Joan Artigas
Software Mentions: 2
Published: about 5 years ago

10.3389/fvets.2020.570074

Characterization of Rumen Microbiota of Two Sheep Breeds Supplemented With Direct-Fed Lactic Acid Bacteria
Cited by: 15
Author(s): Sinalo Mani, Olayinka Ayobami Aiyegoro, Matthew Adekunle Adeleke
Software Mentions: 2
Published: almost 4 years ago

10.3390/pathogens10080941

A Pilot Study on the Microbiome of Amblyomma hebraeum Tick Stages Infected and Non-Infected with Rickettsia africae
Cited by: 3
Author(s): Dalicia Kisten, Jory Brinkerhoff, Selaelo Ivy Tshilwane, Samson Mukaratirwa
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-49966-5

The diversity and ecological roles of Penicillium in intertidal zones
Cited by: 25
Author(s): Myung Soo Park, Seung‐Yoon Oh, Jonathan J. Fong, Jos Houbraken, Young Woon Lim
Software Mentions: 2
Published: about 5 years ago

10.3389/fvets.2021.644738

Effect of Dried Distillers Grains With Solubles and Red Osier Dogwood Extract on Fermentation Pattern and Microbial Profiles of a High-Grain Diet in an Artificial Rumen System
Cited by: 2
Author(s): Walaa M.S. Gomaa, A.M. Saleem, Ran Tao, Long Jin, Mohamed Samir, E. J. McGeough, Kim Ominski, Lingyun Chen, Wenzhu Yang
Software Mentions: 2
Published: over 3 years ago

10.1186/s13071-018-3036-9

Mosquito microbiota cluster by host sampling location
Cited by: 52
Author(s): Ephantus J. Muturi, Doris Lagos‐Kutz, Christopher A. Dunlap, José L. Ramirez, Alejandro P. Rooney, G. L. Hartman, Christopher J. Fields, Gloria Rendon, Chang‐Hyun Kim
Software Mentions: 2
Published: over 6 years ago

10.1186/s13071-020-04408-4

Culex pipiens and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues
Cited by: 2
Author(s): Elijah O. Juma, Chang‐Hyun Kim, Christopher A. Dunlap, Brian F. Allan, Chris Stone
Software Mentions: 2
Published: about 4 years ago

10.1186/s13071-020-04565-6

Morphological identification of ticks and molecular detection of tick-borne pathogens from bare-nosed wombats (Vombatus ursinus)
Cited by: 6
Author(s): Danielle Beard, Hayley J. Stannard, Julie M. Old
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13071-020-04491-7

Relative contributions of various endogenous and exogenous factors to the mosquito microbiota
Cited by: 7
Author(s): Haikel N. Bogale, Matthew Cannon, Kalil Keita, Denka Camara, Yaya Barry, Moussa Keïta, Drissa Coulibaly, Abdoulaye K. Koné, Ogobara K. Doumbo, Mahamadou A. Théra, Christopher V. Plowe, Mark A. Travassos, Seth R. Irish, David Serre
Software Mentions: 2
Published: almost 4 years ago

10.3164/jcbn.18-105

Dietary supplementation with partially hydrolyzed guar gum helps improve constipation and gut dysbiosis symptoms and behavioral irritability in children with autism spectrum disorder
Cited by: 42
Author(s): Ryo Inoüe, Yuko Sakaue, Yuki Kawada, Ryuji Tamaki, Zenta Yasukawa, Makoto Ozeki, Satoko Ueba, Chihiro Sawai, Kazuo Nonomura, Takamitsu Tsukahara, Yuji Naito
Software Mentions: 2
Published: almost 6 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702