bioconductor: phyloseq | Projects

10.1186/s40168-020-00890-1

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study
Cited by: 19
Author(s): Kelsey E. Huus, André Rodriguez-Pozo, Nathalie Kapel, Alison Nestoret, Azimdine Habib, Michel Dédé, Amee R. Manges, Jean-Marc Collard, Philippe J. Sansonetti, Pascale Vonaesch, B. Brett Finlay, Emilson Jean Andriatahirintsoa, Alexandra Bastaraud, Jean-Marc Collard, Maria Doria, Serge Ghislain Djorie, Aurélie Etienne, B. Brett Finlay, Tamara Giles‐Vernick, Jean-Chrysostome Gody, Bolmbaye Privat Godje, Ionela Gouandjika-Vassilache, Francis Allan Hunald, Nathalie Kapel, Jean-Pierre Lombart, Alexandre Manirakiza, Synthia Nazita Nigatoloum, Lisette Raharimalala, Maheninasy Rakotondrainipiana, Rindra Vatosoa Randremanana, Harifetra Mamy Richard Randriamizao, Frédérique Randrianirina, Annick Robinson, Pierre-Alain Rubbo, Philippe J. Sansonetti, Laura Schaeffer, Inès Vigan-Womas, Sonia Sandrine Vondo, Pascale Vonaesch, Laura Wegener-Parfrey
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.00102

Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research
Cited by: 54
Author(s): Sebastian Menke, Mark A. F. Gillingham, Kerstin Wilhelm, Simone Sommer
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2017.02088

Alternative Growth Promoters Modulate Broiler Gut Microbiome and Enhance Body Weight Gain
Cited by: 72
Author(s): Debabrata Biswas, Seon-Woo Kim, Bradd J. Haley, Jo Ann S. Van Kessel, Debabrata Biswas
Software Mentions: 3
Published: almost 9 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: almost 12 years ago

10.1186/s40168-018-0444-1

Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia
Cited by: 63
Author(s): Martijn Callens, Hidenobu Watanabe, Yasuhiko Kato, Jun Miura, Ellen Decaestecker
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2016.01920

Microbial Communities of Lycaenid Butterflies Do Not Correlate with Larval Diet
Cited by: 64
Author(s): Melissa R. L. Whitaker, Shayla Salzman, Jon G. Sanders, Martin Kaltenpoth, Naomi E. Pierce
Software Mentions: 3
Published: almost 10 years ago

10.7717/peerj.9635

Spatial distribution of microbial communities among colonies and genotypes in nursery-reared Acropora cervicornis
Cited by: 14
Author(s): Nicole Miller, Paul Maneval, Carrie Manfrino, Thomas K. Frazer, Julie Meyer
Software Mentions: 3
Published: about 6 years ago

10.1128/mBio.01604-18

Impact of Individual Traits, Saturated Fat, and Protein Source on the Gut Microbiome
Cited by: 67
Author(s): Jennifer M. Lang, Calvin Pan, Rita M. Cantor, W.H. Wilson Tang, Jose Carlos García-García, Ira Kurtz, Stanley L. Hazen, Nathalie Bergeron, Ronald M. Krauss, Aldons J. Lusis
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2014.00526

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level
Cited by: 36
Author(s): Sebastian Menke, . Wasimuddin, Matthias Meier, JÃ¶rg Melzheimer, John K. E. Mfune, Sonja K. Heinrich, Susanne Thalwitzer, Bettina Wachter, Simone Sommer
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0256321

Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California
Cited by: 13
Author(s): Gustavo A. Ramírez, Paraskevi Mara, Taylor R. Sehein, Gunter Wegener, Christopher R. Chambers, Samantha B. Joye, Richard N. Peterson, Aurélie Philippe, Gaëtan Burgaud, Virginia P. Edgcomb, Andreas Teske
Software Mentions: 3
Published: about 5 years ago

10.3389/fnins.2021.595583

Spatial Memory and Gut Microbiota Alterations Are Already Present in Early Adulthood in a Pre-clinical Transgenic Model of Alzheimer’s Disease
Cited by: 25
Author(s): Paola C. Bello-Medina, Fernando Hernández-Quiroz, Marcel Pérez-Morales, Diego A. González-Franco, Guadalupe Cruz-Pauseno, Jaime García‐Mena, Sofía Díaz‐Cintra, Gustavo Pacheco-López
Software Mentions: 3
Published: over 5 years ago

10.3389/fnut.2021.680771

Effects of Probiotic Bacteria Lactobacillaceae on the Gut Microbiota in Children With Celiac Disease Autoimmunity: A Placebo-Controlled and Randomized Clinical Trial
Cited by: 8
Author(s): Elin Oscarsson, Åsa Håkansson, Carin Andrén Aronsson, Göran Molin, Daniel Agardh
Software Mentions: 3
Published: over 5 years ago

10.1186/s40168-020-00921-x

Ontogeny, species identity, and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)
Cited by: 21
Author(s): Joel J. Brown, Sonia M. Rodríguez‐Ruano, Anbu Poosakkannu, Giampiero Batani, Justin O. Schmidt, Walter Roachell, Jan Zima, Václav Hypša, Eva Nováková
Software Mentions: 3
Published: almost 6 years ago

10.3389/fnut.2021.702085

Changes in Intestinal Flora Structure and Metabolites Are Associated With Myocardial Fibrosis in Patients With Persistent Atrial Fibrillation
Cited by: 4
Author(s): Langsha Liu, Juan Su, Rui Li, Fanyan Luo
Software Mentions: 3
Published: about 5 years ago

10.1186/s42523-021-00079-3

Longitudinal assessment of the bovine ocular bacterial community dynamics in calves
Cited by: 14
Author(s): Alison Bartenslager, Nirosh D. Althuge, John Dustin Loy, Matthew M. Hille, Matthew L Spangler, Samodha C. Fernando
Software Mentions: 3
Published: over 5 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 7 years ago

10.3389/fphys.2019.01635

Fermented Animal Source Protein as Substitution of Fishmeal on Intestinal Microbiota, Immune-Related Cytokines and Resistance to Vibrio mimicus in Freshwater Crayfish (Cherax cainii)
Cited by: 20
Author(s): Muhammad A.B. Siddik, Ravi Fotedar, Reaz Chaklader, Javed Foysal, Ashfaqun Nahar, Janet Howieson
Software Mentions: 3
Published: over 6 years ago

10.1186/s13567-019-0633-3

In-feed resin acids reduce matrix metalloproteinase activity in the ileal mucosa of healthy broilers without inducing major effects on the gut microbiota
Cited by: 22
Author(s): Manuel A. Aguirre, Juhani Vuorenmaa, Eija Valkonen, Hannele Kettunen, Chana Callens, Freddy Haesebrouck, Richard Ducatelle, Filip Van Immerseel, Evy Goossens
Software Mentions: 3
Published: over 7 years ago

10.3390/nu12041122

Saccharin Supplementation Inhibits Bacterial Growth and Reduces Experimental Colitis in Mice
Cited by: 14
Author(s): Annika Sünderhauf, René Pagel, Axel Künstner, Anika E. Wagner, Jan Rupp, Saleh M. Ibrahim, Stefanie Derer, Christian Sina
Software Mentions: 3
Published: over 6 years ago

10.1186/s13024-021-00427-6

Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson’s disease
Cited by: 170
Author(s): Velma Aho, Madelyn C. Houser, Pedro Pereira, Jianjun Chang, Knut Rudi, Lars Paulín, Vicki Hertzberg, Petri Auvinen, Malú G. Tansey, Filip Scheperjans
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2018.01239

Bacteria and Competing Herbivores Weaken Top–Down and Bottom–Up Aphid Suppression
Cited by: 16
Author(s): Carmen K. Blubaugh, Lynne Carpenter‐Boggs, John P. Reganold, Robert N. Schaeffer, William E. Snyder
Software Mentions: 3
Published: about 8 years ago

10.1186/s40168-017-0333-z

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants
Cited by: 13
Author(s): Wendy S. W. Wong, Nicole C. Clemency, Elisabeth Klein, Marina Provenzano, Ramaswamy K. Iyer, John E. Niederhuber, Suchitra K. Hourigan
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2017.02022

Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato
Cited by: 72
Author(s): Anastasis Antoniou, Maria-Dimitra Tsolakidou, Ioannis A. Stringlis, Iakovos S. Pantelides
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2017.01834

Root and Rhizosphere Bacterial Phosphatase Activity Varies with Tree Species and Soil Phosphorus Availability in Puerto Rico Tropical Forest
Cited by: 50
Author(s): K. G. M. Cabugao, Collin M. Timm, Alyssa A. Carrell, Joanne Childs, Tse-Yuan S. Lu, Dale A. Pelletier, David J. Weston, R. J. Norby
Software Mentions: 3
Published: almost 9 years ago

10.1002/ece3.6814

Jumping the green wall: The use of PNA‐DNA clamps to enhance microbiome sampling depth in wildlife microbiome research
Cited by: 3
Author(s): Luis Víquez-R, Ramona Fleischer, Kerstin Wilhelm, Marco Tschapka, Simone Sommer
Software Mentions: 3
Published: about 6 years ago

10.1186/s40168-016-0220-z

Deciphering composition and function of the root microbiome of a legume plant
Cited by: 135
Author(s): Kyle Hartman, Marcel G. A. van der Heijden, Valexia Roussely-Provent, Jean‐Claude Walser, Klaus Schlaeppi
Software Mentions: 3
Published: over 9 years ago

10.1002/ece3.7605

Cryptic species and hidden ecological interactions of halictine bees along an elevational gradient
Cited by: 11
Author(s): Antonia V. Mayr, Alexander Keller, Marcell K. Peters, Gudrun Grimmer, Beate Krischke, Mareen Geyer, Thomas Schmitt, Ingolf Steffan‐Dewenter
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.02171-19

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression
Cited by: 21
Author(s): Tonya Ward, Bonnie Weber, Kristelle M. Mendoza, Jessica L. Danzeisen, Katharine Llop, Kevin S. Lang, Jonathan B. Clayton, Elicia D. Grace, J. A. Brannon, Igor Radović, Mai Beauclaire, Timothy Heisel, Dan Knights, Carol J. Cardona, Michael H. Kogut, Casey Johnson, Sally Noll, Ryan J. Arsenault, Kent M. Reed, Timothy J. Johnson
Software Mentions: 3
Published: almost 7 years ago

10.3389/fpls.2020.00633

Rhizospheric Organic Acids as Biostimulants: Monitoring Feedbacks on Soil Microorganisms and Biochemical Properties
Cited by: 78
Author(s): Sandra Macías-Benítez, A.M. García-Martínez, Pablo Caballero Jiménez, Juan M. González, Manuel Tejada, Juan Parrado
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2017.01263

Application of Mycorrhiza and Soil from a Permaculture System Improved Phosphorus Acquisition in Naranjilla
Cited by: 13
Author(s): Sarah Symanczik, Michelle Gisler, Cécile Thonar, Klaus Schlaeppi, Marcel van der Heijden, Ansgar Kahmen, Thomas Boller, Paul Mäder
Software Mentions: 3
Published: about 9 years ago

10.3389/fpubh.2020.584953

Alterations in the Gut Microbiota of Zebrafish (Danio rerio) in Response to Water-Soluble Crude Oil Components and Its Mixture With a Chemical Dispersant
Cited by: 9
Author(s): Carlos Eduardo González-Penagos, Jesús Alejandro Zamora‐Briseño, Daniel Cerqueda‐García, Mónica Améndola-Pimenta, Juan Antonio Pérez-Vega, Emanuel Hernández-Nuñéz, Rossanna Rodríguez-Canul
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.4991

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands
Cited by: 24
Author(s): Anthony Barboza, Victor Satler Pylro, Rodrigo Josemar Seminot Jacques, Paulo Ivonir Gubiani, Fernando Luíz Ferreira de Quadros, Júlio Kuhn da Trindade, Eric W. Triplett, Luiz Fernando Würdig Roesch
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.11406

Shiftwork, functional bowel symptoms, and the microbiome
Cited by: 4
Author(s): Ann E. Rogers, Yi‐Juan Hu, Ye Yue, Emily F. Wissel, Robert A. Petit, Simone A. Jarrett, Jennifer Christie, Timothy D. Read
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.659

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types
Cited by: 83
Author(s): Jenna M. Lang, Jonathan A. Eisen, Angela M. Zivkovic
Software Mentions: 3
Published: almost 12 years ago

10.3389/fvets.2021.692521

Oral Vaccination Reduces the Effects of Lawsonia intracellularis Challenge on the Swine Small and Large Intestine Microbiome
Cited by: 2
Author(s): Fernando Leite, Brittanie Winfield, Elizabeth A. Miller, Bonnie Weber, Timothy J. Johnson, Fred Sylvia, Erika Vasquez, Fábio A. Vannucci, Dana Beckler, Richard E. Isaacson
Software Mentions: 3
Published: about 5 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: over 7 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 5 years ago

10.1371/journal.pone.0244489

Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta)
Cited by: 3
Author(s): Matthew Parks, Cameron Kedy, Casey Skalla
Software Mentions: 2
Published: almost 6 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 7 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 6 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 8 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 7 years ago

10.1371/journal.pone.0219599

Phages in a thermoreversible sustained-release formulation targeting E. faecalis in vitro and in vivo
Cited by: 30
Author(s): Mor Shlezinger, Michael Friedman, Yael Houri‐Haddad, Ronen Hazan
Software Mentions: 2
Published: about 7 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: over 5 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: about 9 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 5 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: about 5 years ago

10.1371/journal.pone.0179443

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments
Cited by: 61
Author(s): Anders Lanzén, Katrine Lekang, Inge Jonassen, Eric M. Thompson, Christofer Troedsson
Software Mentions: 2
Published: over 9 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 5 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: about 5 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: about 8 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: almost 6 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: over 5 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 6 years ago

10.1038/s41598-021-89606-5

Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor
Cited by: 2
Author(s): Minji Kim, Setu Bazie Tagele, HyungWoo Jo, Min‐Chul Kim, Young Hun Jung, Yeong-Jun Park, Jai-Hyun So, Hae Jin Kim, Ho Jin Kim, Dong-Geol Lee, Seunghyun Kang, Jae‐Ho Shin
Software Mentions: 2
Published: over 5 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 12 years ago

10.1038/s42003-020-0838-z

Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn
Cited by: 36
Author(s): Magdalena Mayr, M. Zimmermann, Jason Dey, Andreas Brand, Bernhard Wehrli, Helmut Bürgmann
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-020-1106-y

Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data
Cited by: 21
Author(s): Birge D. Özel Duygan, Noushin Hadadi, Ambrin Farizah Babu, Markus Seyfried, van der Peter Meer
Software Mentions: 2
Published: about 6 years ago

10.1093/cdn/nzy070

Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity
Cited by: 11
Author(s): Antonio Vinicios Alves da Silva, Stephanie B Oliveira, Sara C. Di Rienzi, Kathleen Brown-Steinke, Lauren M Dehan, Jill K Rood, Vinicius Carreira, Hung Le, Elizabeth A. Maier, Kristina Betz, Eitaro Aihara, Ruth E. Ley, Geoffrey A. Preidis, Lanlan Shen, Sean R. Moore
Software Mentions: 2
Published: almost 8 years ago

10.1093/database/baaa050

mAML: an automated machine learning pipeline with a microbiome repository for human disease classification
Cited by: 18
Author(s): Fenglong Yang, Quan Zou
Software Mentions: 2
Published: almost 7 years ago

10.1002/ece3.4040

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus
Cited by: 3
Author(s): Amruta Varudkar, Uma Ramakrishnan
Software Mentions: 2
Published: over 8 years ago

10.1002/ece3.5010

Bacterial communities within Phengaris (Maculinea) alcon caterpillars are shifted following transition from solitary living to social parasitism of Myrmica ant colonies
Cited by: 12
Author(s): Mark A. Szenteczki, Camille Pitteloud, Luca Pietro Casacci, Lucie Kešnerová, Melissa R. L. Whitaker, Philipp Engel, Roger Vila, Nadir Alvarez
Software Mentions: 2
Published: over 7 years ago

10.1002/ece3.4454

Fecal microbiota associated with phytohaemagglutinin‐induced immune response in nestlings of a passerine bird
Cited by: 11
Author(s): Jakub Kreisinger, Lucie Schmiedová, Adéla Petrželková, Oldřich Tomášek, Marie Kotasová Adámková, Romana Michálková, Jean Martin, Tomáš Albrecht
Software Mentions: 2
Published: about 8 years ago

10.1002/ece3.6675

Scale‐dependent impact of land management on above‐ and belowground biodiversity
Cited by: 1
Author(s): Eleonore Louise Slabbert, Oliver Schweiger, Tesfaye Wubet, Antje Kautzner, Cornelia Baeßler, Harald Auge, Christiane Roscher, Tiffany M. Knight
Software Mentions: 2
Published: about 6 years ago

10.3390/molecules25030661

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment
Cited by: 35
Author(s): Joanna Brzeszcz, Piotr Kapusta, Teresa Steliga, A. Turkiewicz
Software Mentions: 2
Published: over 6 years ago

10.1530/ERC-17-0442

The microbiome in PTEN hamartoma tumor syndrome
Cited by: 5
Author(s): Victoria Byrd, Ted M. Getz, Roshan Padmanabhan, Hans Arora, Charis Eng
Software Mentions: 2
Published: over 8 years ago

10.3390/microorganisms9071358

Correction: Szopinska-Tokov et al. Investigating the Gut Microbiota Composition of Individuals with Attention-Deficit/Hyperactivity Disorder and Association with Symptoms. Microorganisms 2020, 8, 406
Cited by: 6
Author(s): Joanna Szopinska-Tokov, Sarita Dam, Jilly Naaijen, Prokopis Konstanti, Nanda Rommelse, Clara Belzer, Jan K. Buitelaar, Barbara Franke, Mirjam Bloemendaal, Esther Aarts, Alejandro Arias Vásquez
Software Mentions: 2
Published: over 5 years ago

10.1111/1462-2920.14297

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment
Cited by: 39
Author(s): Albert Müller, Claus Pelikan, Júlia R. de Rezende, Kenneth Wasmund, Martina Putz, Clemens Glombitza, Kasper Urup Kjeldsen, Bo Barker Jørgensen, Alexander Loy
Software Mentions: 2
Published: about 8 years ago

10.3390/microorganisms9051051

Applications of Blocker Nucleic Acids and Non-Metazoan PCR Improves the Discovery of the Eukaryotic Microbiome in Ticks
Cited by: 2
Author(s): Yurie Taya, Gohta Kinoshita, Wessam Mohamed Ahmed Mohamed, Mohamed Abdallah Mohamed Moustafa, Shohei Ogata, Elisha Chatanga, Yuma Ohari, Kodai Kusakisako, Keita Matsuno, Nariaki Nonaka, Ryo Nakao
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9010012

Anaerobic Carbon Monoxide Uptake by Microbial Communities in Volcanic Deposits at Different Stages of Successional Development on O-yama Volcano, Miyake-jima, Japan
Cited by: 4
Author(s): Amber N. DePoy, Gary M. King, Hiroyuki Ohta
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40793-020-00355-w

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America
Cited by: 7
Author(s): Renxing Liang, Maggie C. Y. Lau, Evan T. Saitta, Z. K. Garvin, Tullis C. Onstott
Software Mentions: 2
Published: over 6 years ago

10.1007/s00394-019-02161-8

The impact of food additives, artificial sweeteners and domestic hygiene products on the human gut microbiome and its fibre fermentation capacity
Cited by: 67
Author(s): Konstantinos Gerasimidis, Katie Bryden, Xiufen Chen, Eleftheria Papachristou, Anais Verney, M.J. Roig, Richard Hansen, Ben Nichols, Rodanthi Papadopoulou, Alison Parrett
Software Mentions: 2
Published: almost 7 years ago

10.3390/microorganisms9061217

Effects of Magnesium Oxide and Magnesium Hydroxide Microparticle Foliar Treatment on Tomato PR Gene Expression and Leaf Microbiome
Cited by: 3
Author(s): Aggeliki Andreadelli, Spyros Petrakis, Antiopi Tsoureki, George Tsiolas, Sofia Michailidou, Penelope Baltzopoulou, Robert van Merkestein, P. K. G. Hodgson, Mark G. Sceats, George Karagiannakis, Antonios M. Makris
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-93859-5

Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities
Cited by: 18
Author(s): Thomas Lamy, Kathleen J. Pitz, Francisco P. Chávez, Christie E. Yorke, Robert J. Miller
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms9061223

The Microbiota of Modified-Atmosphere-Packaged Cooked Charcuterie Products throughout Their Shelf-Life Period, as Revealed by a Complementary Combination of Culture-Dependent and Culture-Independent Analysis
Cited by: 12
Author(s): Evelyne Duthoo, Geertrui Rasschaert, Frédéric Leroy, Stefan Weckx, Marc Heyndrickx, Koen De Reu
Software Mentions: 2
Published: over 5 years ago

10.1093/femsec/fiy127

Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates
Cited by: 25
Author(s): Lloyd D. Potts, Luis J Perez Calderon, Evangelia Gontikaki, Lehanne Keith, Cécile Gubry‐Rangin, James A. Anderson, Ursula Witte
Software Mentions: 2
Published: over 8 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 6 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 9 years ago

10.3390/microorganisms9020358

An Oral FMT Capsule as Efficient as an Enema for Microbiota Reconstruction Following Disruption by Antibiotics, as Assessed in an In Vitro Human Gut Model
Cited by: 11
Author(s): Cécile Verdier, Sylvain Denis, Cyrielle Gasc, Lilia Boucinha, Ophélie Uriot, Dominique Delmas, Joël Doré, Corentin Le Camus, Carole Schwintner, Stéphanie Blanquet‐Diot
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2020.596149

Metagenomic Analysis of the Gut Microbiota of Wild Mice, a Newly Identified Reservoir of Campylobacter
Cited by: 9
Author(s): Hyokeun Song, Junhyung Kim, Jae-Ho Guk, Woo-Hyun Kim, Hajin Nam, Jun-Gyo Suh, Je Kyung Seong, Seongbeom Cho
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms8020265

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana
Cited by: 2
Author(s): Kiyonori Kawasaki, Kenji Ohya, Tsutomu Omatsu, Yukie Katayama, Yasuhiro Takashima, Tsuyoshi Kinoshita, Justice Opare Odoi, Kotaro Sawai, Hideto Fukushi, Hirohito Ogawa, Miho Inoue‐Murayama, Tetsuya Mizutani, Christopher Adenyo, Yoshiki Matsumoto, Boniface B. Kayang
Software Mentions: 2
Published: over 6 years ago

10.3389/fcimb.2021.720674

The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment
Cited by: 29
Author(s): Veda D Khadka, Felix M. Key, Carolina Romo-González, Adrián Martínez-Gayosso, Blanca Lucina Campos-Cabrera, Armando Gerónimo-Gallegos, Tucker C Lynn, Carola Durán‐McKinster, Rafael Coria-Jiménez, Tami D. Lieberman, Maria Teresa García‐Romero
Software Mentions: 2
Published: about 5 years ago

10.3389/fcimb.2021.639665

Vaginal Microbiota and Cytokine Levels Predict Preterm Delivery in Asian Women
Cited by: 30
Author(s): Manoj Kumar, Selvasankar Murugesan, Parul Singh, Marwa Saadaoui, Duaa Ahmed Elhag, Annalisa Terranegra, Basirudeen Syed Ahamed Kabeer, Alexandra K. Marr, Tomoshige Kino, Tobias Brummaier, Rose McGready, François Nosten, Souhaila Al Khodor
Software Mentions: 2
Published: over 5 years ago

10.3389/fendo.2020.602326

Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort
Cited by: 12
Author(s): Christian Diener, María de Lourdes Reyes-Escogido, Lilia M. Jiménez-Ceja, Mariana Matus, Claudia M. Gómez-Navarro, Nathaniel D. Chu, Vivian Zhong, M. Elizabeth Tejero, Eric J. Alm, Osbaldo Reséndis-Antonio, Rodolfo Guardado-Mendoza
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: almost 7 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 5 years ago

10.3389/fimmu.2019.00069

Compartmentalization of Immune Response and Microbial Translocation in Decompensated Cirrhosis
Cited by: 32
Author(s): Camila Alvarez-Silva, Robert Schierwagen, Alessandra Pohlmann, Fernando Magdaleno, Frank Erhard Uschner, Patrick B. Ryan, Maria J. G. T. Vehreschild, Joan Clària, Eicke Latz, Benjamin Lelouvier, Manimozhiyan Arumugam, Jonel Trebicka
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2021.730986

Temporal Changes in Vaginal Microbiota and Genital Tract Cytokines Among South African Women Treated for Bacterial Vaginosis
Cited by: 19
Author(s): Andile Mtshali, James Emmanuel San, Farzana Osman, Nigel Garrett, Christina Balle, Jennifer Giandhari, Harris Onywera, Khanyisile Mngomezulu, Gugulethu Mzobe, Túlio de Oliveira, Anne Rompalo, Adrian Mindel, Salim S. Abdool Karim, Jacques Ravel, Jo Ann S Passmore, Heather B. Jaspan, Lenine J. Liebenberg, Sinaye Ngcapu
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2019.03107

Using Precisely Defined in vivo Microbiotas to Understand Microbial Regulation of IgE
Cited by: 21
Author(s): Madeleine Wyss, Kirsty Brown, Christine E. Thomson, Mia Elizabeth Koegler, Fernanda Fernandes Terra, Vina Fan, Francesca Ronchi, Dominique Bihan, Ian A. Lewis, Markus B. Geuking, Kathy D. McCoy
Software Mentions: 2
Published: over 6 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 6 years ago

10.1038/s41598-021-94498-6

Variations in the oral microbiome are associated with depression in young adults
Cited by: 33
Author(s): Benjamin Wingfield, Coral Lapsley, Andrew McDowell, Georgios Miliotis, Margaret McLafferty, Siobhan O’Neill, Sonya Coleman, TM McGinnity, Anthony J. Bjourson, Elaine Murray
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2020.01776

Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome
Cited by: 11
Author(s): Virginie Lemieux-Labonté, Nicole Dorville, Craig K. R. Willis, François‐Joseph Lapointe
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2020.00530

Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate
Cited by: 6
Author(s): Alberto Scoma, Way Cern Khor, Marta Coma, Robert Heyer, Ruben Props, Jonas Schoelynck, Tim Bouts, Dirk Benndorf, Desheng Li, Hemin Zhang, Korneel Rabaey
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8050736

Metagenomic Analysis of Regularly Microwave-Treated and Untreated Domestic Kitchen Sponges
Cited by: 11
Author(s): Susanne Jacksch, Jyothi Thota, Sudarshan A. Shetty, Hauke Smidt, Sylvia Schnell, Markus Egert
Software Mentions: 2
Published: over 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 6 years ago

10.3390/microorganisms8010020

The Effect of Thermal Stress on the Bacterial Microbiome of Exaiptasia diaphana
Cited by: 15
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 2
Published: almost 7 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 7 years ago

10.3389/fmicb.2017.01470

Personalization of the Microbiota of Donor Human Milk with Mother’s Own Milk
Cited by: 63
Author(s): Nicole Cacho, Natalie A. Harrison, Leslie A. Parker, Kaylie A. Padgett, Dominick J. Lemas, Guillermo Marcial, Nan Li, Laura E. Carr, Josef Neu, Graciela L. Lorca
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2019.02661

Tissue-Specific Microbiomes of the Red Sea Giant Clam Tridacna maxima Highlight Differential Abundance of Endozoicomonadaceae
Cited by: 14
Author(s): Susann Rossbach, Anny Cárdenas, Gabriela Perna, Carlos M. Duarte, Christian R. Voolstra
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-021-98248-6

Ruminant fat intake improves gut microbiota, serum inflammatory parameter and fatty acid profile in tissues of Wistar rats
Cited by: 2
Author(s): Larissa de Brito Medeiros, Susana P. Alves, Rui J.B. Bessa, Juliana Késsia Barbosa Soares, Camila Neves Meireles Costa, Jailane de Souza Aquino, Gerlane Coelho Bernardo Guerra, Daline Fernandes de Souza Araújo, Lydiane Tavares Toscano, Alexandre Silva, Adriano Francisco Alves, Mateus Lacerda Pereira Lemos, Wydemberg J. Araújo, Ariosvaldo Nunes de Medeiros, Celso José Bruno de Oliveira, Rita de Cássia Ramos do Egypto Queiroga
Software Mentions: 2
Published: about 5 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702