bioconductor: phyloseq | Projects

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

10.3389/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

10.3389/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

10.7717/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: over 7 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 8 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 5 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 8 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: over 7 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

10.7717/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: over 8 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

10.3389/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.2021.676610

Native AMF Communities in an Italian Vineyard at Two Different Phenological Stages of Vitis vinifera
Cited by: 2
Author(s): Patrizia Cesaro, Nadia Massa, Elisa Bona, Giorgia Novello, Valeria Todeschini, Lara Boatti, Flavio Mignone, Elisa Gamalero, Graziella Berta, Graziano Lingua
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2021.621069

Zooming Into the Microbiota of Home-Made and Industrial Kefir Produced in Greece Using Classical Microbiological and Amplicon-Based Metagenomics Analyses
Cited by: 29
Author(s): Μαρία Κάζου, Andriana Grafakou, Effie Tsakalidou, Marina Georgalaki
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

10.1038/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

10.3390/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

10.3389/fmicb.2021.700256

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community
Cited by: 6
Author(s): Abhijeet Singh, Jan Moestedt, A.J. van den Berg, Anna Schnürer
Software Mentions: 2
Published: about 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

10.3389/fmicb.2017.02321

Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities
Cited by: 23
Author(s): Theodore M. Flynn, Jason C. Koval, Stephanie M. Greenwald, Sarah M. Owens, Kenneth M. Kemner, Dionysios A. Antonopoulos
Software Mentions: 2
Published: almost 9 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

10.3389/fmicb.2021.675763

Directional Selection of Microbial Community Reduces Propionate Accumulation in Glycerol and Glucose Anaerobic Bioconversion Under Elevated pCO2
Cited by: 11
Author(s): Pamela Ceron-Chafla, Yu Ting Chang, Korneel Rabaey, Jules B. van Lier, Ralph E.F. Lindeboom
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.01671

Metagenomic Characterization of Indoor Dust Bacterial and Fungal Microbiota in Homes of Asthma and Non-asthma Patients Using Next Generation Sequencing
Cited by: 18
Author(s): Jean‐Pierre Gangneux, Mohamed Sassi, Pierre Lemire, Pierre Le Cann
Software Mentions: 2
Published: about 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: 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

10.3389/fmicb.2018.03190

Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria
Cited by: 13
Author(s): Federico Baltar, Andres Gutiérrez‐Rodríguez, Moana Meyer, Isadora Skudelny, Sylvia G. Sander, Blair Thomson, Scott D. Nodder, Rob Middag, Sergio E. Morales
Software Mentions: 2
Published: almost 8 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

10.3389/fmicb.2019.00870

Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States)
Cited by: 39
Author(s): Max Kolton, Ansley Marks, Rachel M. Wilson, Jeffrey P. Chanton, Joel E. Kostka
Software Mentions: 2
Published: over 7 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: almost 8 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

10.3389/fmicb.2020.01469

Assessment of Gram- and Viability-Staining Methods for Quantifying Bacterial Community Dynamics Using Flow Cytometry
Cited by: 14
Author(s): Aurore Duquenoy, Samuel Bellais, Cyrielle Gasc, Carole Schwintner, Joël Doré, Vincent Thomas
Software Mentions: 2
Published: over 6 years ago

10.1186/s42523-020-0024-0

Parrotfish predation drives distinct microbial communities in reef-building corals
Cited by: 22
Author(s): Leïla Ezzat, Thomas Lamy, Rebecca L. Maher, Katrina S. Munsterman, Kaitlyn Landfield, Emily R. Schmeltzer, Cody S. Clements, Rebecca L. Vega Thurber, Deron E. Burkepile
Software Mentions: 2
Published: over 6 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

10.3390/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

10.3390/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

10.3390/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

10.3390/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

10.3390/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/fmicb.2018.02246

A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship
Cited by: 16
Author(s): Laure Bellec, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Lucile Durand, Nicolas Gayet, Daniela Zeppilli
Software Mentions: 2
Published: about 8 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

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

10.3389/fmicb.2016.01040

Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica
Cited by: 43
Author(s): Heather N. Buelow, Ara S. Winter, David Van Horn, John E. Barrett, M. N. Gooseff, Egbert Schwartz, Cristina Takacs-Vesbach
Software Mentions: 2
Published: about 10 years ago

10.3389/fmicb.2021.619632

Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
Cited by: 12
Author(s): Washington Logroño, Denny Popp, Marcell Nikolausz, Paul Kluge, Hauke Harms, Sabine Kleinsteuber
Software Mentions: 2
Published: over 5 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

10.3390/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

10.3389/fmicb.2020.01938

Distinct Temporal Succession of Bacterial Communities in Early Marine Biofilms in a Portuguese Atlantic Port
Cited by: 26
Author(s): Jorge T. Antunes, António G G Sousa, Joana Azevedo, Adriana Rego, Pedro N. Leão, Vítor Vasconcelos
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2016.01227

Age and Gender Affect the Composition of Fungal Population of the Human Gastrointestinal Tract
Cited by: 146
Author(s): Francesco Strati, Monica Di Paola, Irene Stefanini, Davide Albanese, Lisa Rizzetto, Paolo Lionetti, Antonino Calabrò, Olivier Jousson, Claudio Donati, Duccio Cavalieri, Carlotta De Filippo
Software Mentions: 2
Published: about 10 years ago

10.3389/fmicb.2015.01342

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions
Cited by: 81
Author(s): Cristina Riquelme, Jennifer J.M. Hathaway, Maria de Lurdes Enes Dapkevicius, Ana Z. Miller, Ara Kooser, Diana E. Northup, Valme Jurado, Octavio Fernández, Cesáreo Sáiz‐Jiménez, Naowarat Cheeptham
Software Mentions: 2
Published: almost 11 years ago

10.3390/toxics9080192

Cutaneous Effects of In Utero and Lactational Exposure of C57BL/6J Mice to 2,3,7,8-Tetrachlorodibenzo-p-dioxin
Cited by: 3
Author(s): Jyoti Bhuju, Kristin M. Olesen, Clarisse S. Muenyi, Tejesh Patel, Robert W. Read, Lauren Thompson, Omar Skalli, Qi Zheng, Elizabeth A. Grice, Carrie Hayes Sutter, Thomas R. Sutter
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms8101486

Fecal Microbiota Transplant in Two Ulcerative Colitis Pediatric Cases: Gut Microbiota and Clinical Course Correlations
Cited by: 16
Author(s): Andrea Quagliariello, Federica Del Chierico, Sofia Reddel, Alessandra Russo, Andrea Onetti Muda, Patrizia D’Argenio, Giulia Angelino, Erminia Romeo, Luigi Dall’Oglio, Paola De Angelis, Lorenza Putignani
Software Mentions: 2
Published: about 6 years ago

10.3390/microorganisms8091275

Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes
Cited by: 18
Author(s): Charlotte M. van der Graaf, Javier Sánchez España, Iñaki Yusta, Andrey Ilin, Sudarshan A. Shetty, Nicole J. Bale, Laura Villanueva, Alfons Johannes Maria Stams, Irene Sánchez‐Andrea
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2017.01078

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms
Cited by: 15
Author(s): Adam Šťovíček, Ani Azatyan, M. I. M. Soares, Osnat Gillor
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2015.01454

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps
Cited by: 66
Author(s): Marco Meola, Anna Lazzaro, Josef Zeyer
Software Mentions: 2
Published: almost 11 years ago

10.3390/microorganisms9061214

Gut Microbiota Dynamics in Natural Populations of Pintomyia evansi under Experimental Infection with Leishmania infantum
Cited by: 4
Author(s): Rafael José Vivero, Víctor Alfonso Castañeda-Monsalve, Lupe Romero, Gregory D. D. Hurst, Gloria Cadavid-Restrepo, Claudia Ximena Moreno Herrera
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2017.01464

Intestinal Bacterial Communities of Trypanosome-Infected and Uninfected Glossina palpalis palpalis from Three Human African Trypanomiasis Foci in Cameroon
Cited by: 12
Author(s): F. Jacob, Tresor Tito Tanekou Melachio, Guy R. Njitchouang, Geoffrey Gimonneau, Flobert Njiokou, Luc Abate, Richard Christen, Julie Réveillaud, Anne Geiger
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2020.606825

Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis
Cited by: 11
Author(s): Pamela M. Smith, Sinéad M. Waters, Ruth Gómez Expósito, Hauke Smidt, Crea Carberry, Matthew S. McCabe
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.587979

Effects of Bacterial Supplementation on Black Soldier Fly Growth and Development at Benchtop and Industrial Scale
Cited by: 16
Author(s): Emilia Kooienga, Courtney N. Baugher, Morgan Currin, Jeffery K. Tomberlin, Heather R. Jordan
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.00311

Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome
Cited by: 42
Author(s): Camille Clérissi, Julien de Lorgeril, Bruno Petton, Aude Lucasson, Jean-Michel Escoubas, Yannick Gueguen, Lionel Dégremont, Guillaume Mitta, Ève Toulza
Software Mentions: 2
Published: over 6 years ago

10.1093/jas/skaa338

Canola meal in nursery pig diets: growth performance and gut health
Cited by: 9
Author(s): Jinsu Hong, Saymore Petros Ndou, Sam Adams, Joy Scaria, T. A. Woyengo
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40104-019-0386-x

Dietary fibre enrichment of supplemental feed modulates the development of the intestinal tract in suckling piglets
Cited by: 21
Author(s): H.M.J. van Hees, Mark Davids, Dominiek Maes, Sam Millet, Sam Possemiers, L.A. den Hartog, Theo A. T. G. van Kempen, Geert Janssens
Software Mentions: 2
Published: almost 7 years ago

10.1186/s40104-020-00531-5

Effects of brewers’ spent grain protein hydrolysates on gas production, ruminal fermentation characteristics, microbial protein synthesis and microbial community in an artificial rumen fed a high grain diet
Cited by: 23
Author(s): Ran Tao, Long Jin, Ranithri Abeynayake, A.M. Saleem, Xiumin Zhang, Dongyan Niu, Lingyun Chen, Wenzhu Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-020-00982-y

Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome
Cited by: 12
Author(s): Wisnu Adi Wicaksono, Peter Kusstatscher, Sabine Erschen, Tamara Reisenhofer-Graber, Martín Grube, Tomislav Cernava, Gabriele Berg
Software Mentions: 2
Published: over 5 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 8 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: over 7 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 7 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: almost 6 years ago

10.1371/journal.ppat.1007083

A novel mouse model of Campylobacter jejuni enteropathy and diarrhea
Cited by: 45
Author(s): Natasa Giallourou, Gregory L. Medlock, David T. Bolick, Pedro Hqs Medeiros, Solanka Ellen Ledwaba, Glynis L. Kolling, Kenneth S. K. Tung, Patricia Guerry, Jonathan R. Swann
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1008448

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production
Cited by: 58
Author(s): Lisa Osbelt, Sophie Thiemann, Nathiana Smit, Till Robin Lesker, Madita Schröter, Eric Galvez, Kerstin Schmidt‐Hohagen, Marina C. Pils, Sabrina Mühlen, Petra Dersch, Karsten Hiller, Dirk Schlüter, Meina Neumann‐Schaal, Till Strowig
Software Mentions: 2
Published: over 6 years ago

10.1098/rspb.2019.2367

Intestinal microbes: an axis of functional diversity among large marine consumers
Cited by: 11
Author(s): Jarrod J. Scott, Thomas C. Adam, Alain Durán, Deron E. Burkepile, Douglas B. Rasher
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-020-00904-y

Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis
Cited by: 22
Author(s): Wouter Sillen, Sofie Thijs, Gennaro Roberto Abbamondi, Roberto De La Torre Roche, Nele Weyens, Jason C. White, Jaco Vangronsveld
Software Mentions: 2
Published: about 6 years ago

10.1186/s40168-018-0498-0

Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC
Cited by: 26
Author(s): Lee Call, Barbara J. Stoll, Berthe C Oosterloo, Nadim J. Ajami, Fariha Sheikh, Anja Wittke, Rosaline Waworuntu, Brian M. Berg, Joseph F. Petrosino, Oluyinka O. Olutoye, Douglas G. Burrin
Software Mentions: 2
Published: over 8 years ago

10.1128/mBio.01366-16

Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity
Cited by: 22
Author(s): Ulaş Karaöz, Estelle Couradeau, Ulisses Nunes da Rocha, Hsiao Chien Lim, Trent Northen, Ferrán García-Pichel, Eoin L. Brodie
Software Mentions: 2
Published: over 8 years ago

10.1126/sciadv.abd7954

Prostaglandin E 2 promotes intestinal inflammation via inhibiting microbiota-dependent regulatory T cells
Cited by: 39
Author(s): Siobhan Crittenden, Marie Goepp, Jolinda Pollock, Calum T. Robb, Danielle J. Smyth, You Zhou, Robert Andrews, Victoria J. Tyrrell, Konstantinos Gkikas, Alexander Adima, Richard A. O’Connor, Luke C. Davies, Xuefeng Li, Hatti X. Yao, Gwo‐Tzer Ho, Xiaozhong Zheng, Amil Mair, Sonja Vermeren, Bin‐Zhi Qian, Damian J. Mole, Konstantinos Gerasimidis, Jürgen Schwarze, Richard M. Breyer, Mark J. Arends, Valerie Bridget O'Donnell, John P. Iredale, Stephen M. Anderton, Shuh Narumiya, Rick M. Maizels, Adriano G. Rossi, Sarah Howie, Chengcan Yao
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-016-0216-8

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease
Cited by: 121
Author(s): Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Andrew Nelson, Bashi̇r Abdulkadi̇r, Tom Skeath, Joseph F. Petrosino, John D. Perry, Janet Berrington, Stephen Cummings
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep08695

Microbial communities on flower surfaces act as signatures of pollinator visitation
Cited by: 74
Author(s): Masayuki Ushio, Eri Yamasaki, Hiroyuki Takasu, Atsushi J. Nagano, Shohei Fujinaga, Mie N. Honjo, Mito Ikemoto, Shoko Sakai, Hiroshi Kudoh
Software Mentions: 2
Published: over 11 years ago

10.1186/s40168-018-0493-5

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms
Cited by: 60
Author(s): Brandon Brooks, Matthew R. Olm, Brian Firek, Robyn Baker, David Geller-McGrath, Sophia R. Reimer, Karina Ruth Soenjoyo, Jennifer S. Yip, Dylan Dahan, Brian C. Thomas, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 2
Published: over 8 years ago

10.1038/srep42634

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank
Cited by: 42
Author(s): Márcio Fernandes Alves Leite, Yao Pan, J. Bloem, Hein ten Berge, Eiko E. Kuramae
Software Mentions: 2
Published: over 9 years ago

10.1038/srep45220

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot
Cited by: 23
Author(s): Grazieli Maboni, Adam Blanchard, Sara Frosth, Ceri E. Stewart, Richard D. Emes, Sabine Tötemeyer
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-07278-6

Bacteriophages as potential new mammalian pathogens
Cited by: 74
Author(s): George Tetz, Kelly V. Ruggles, Hua Zhou, Adriana Heguy, Aristotelis Tsirigos, Victor Tetz
Software Mentions: 2
Published: about 9 years ago

10.1186/s40168-020-00862-5

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste
Cited by: 97
Author(s): Stefan Dyksma, Lukas Jansen, Claudia Gallert
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-09842-6

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection
Cited by: 154
Author(s): Monica Di Paola, Cristina Sani, Ann Maria Clemente, Anna Iossa, Eloisa Perissi, Giuseppe Castronovo, Michele Tanturli, Damaríz Rivero, Federico Cozzolino, Duccio Cavalieri, Francesca Carozzi, Carlotta De Filippo, Maria Gabriella Torcia
Software Mentions: 2
Published: about 9 years ago

10.1186/s40168-017-0242-1

New evidences on the altered gut microbiota in autism spectrum disorders
Cited by: 599
Author(s): Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Daniela Renzi, Antonino Calabrò, Carlotta De Filippo
Software Mentions: 2
Published: over 9 years ago

10.1186/s40168-017-0229-y

Optimization of DNA extraction for advancing coral microbiota investigations
Cited by: 33
Author(s): Laura Weber, Emelia DeForce, Amy Apprill
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-16287-4

Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression
Cited by: 16
Author(s): Irina Leonardi, Alexandra Gerstgrasser, Thomas Sebastian Benedikt Schmidt, Flora Nicholls, Bernhard Tewes, Roland Greinwald, Christian von Mering, Gerhard Rogler, Isabelle Frey-Wagner
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-018-20967-0

Diversity and metabolic potential of the microbiota associated with a soil arthropod
Cited by: 29
Author(s): Simon Bahrndorff, Nadieh de Jonge, Jacob Kjerulf Hansen, Jannik Mørk Skovgaard Lauritzen, Lasse Holt Spanggaard, Mathias Hamann Sørensen, Morten Yde, Jeppe Lund Nielsen
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-21255-7

Vaccination Against Lawsonia intracellularis Decreases Shedding of Salmonella enterica serovar Typhimurium in Co-Infected Pigs and Alters the Gut Microbiome
Cited by: 20
Author(s): Fernando Leite, Randall S. Singer, Tonya Ward, Connie J. Gebhart, Richard E. Isaacson
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-23679-7

Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study
Cited by: 21
Author(s): Nikea Ulrich, Veronica Kirchner, Rebecca Drucker, Justin Wright, Christopher J. McLimans, Terry C. Hazen, Maria Fernanda Campa, Christopher J. Grant, Regina Lamendella
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-017-0352-9

Laboratory colonization stabilizes the naturally dynamic microbiome composition of field collected Dermacentor andersoni ticks
Cited by: 28
Author(s): Cory A. Gall, Glen A. Scoles, Krisztián Mágori, Kathleen L. Mason, Kelly A. Brayton
Software Mentions: 2
Published: almost 9 years ago

10.1186/s40168-018-0467-7

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species
Cited by: 27
Author(s): Katharina Fietz, Christian Olaf Rye Hintze, Mikkel Skovrind, Tue Kjærgaard Nielsen, Morten T. Limborg, Marcus Anders Krag, Per J. Palsbøll, Lars Hestbjerg Hansen, Peter Rask Møller, M. Thomas P. Gilbert
Software Mentions: 2
Published: over 8 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 9 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

10.1038/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 8 years ago

10.1128/mBio.02820-19

Long-Term Effects of Early-Life Antibiotic Exposure on Resistance to Subsequent Bacterial Infection
Cited by: 42
Author(s): C. Roubaud-Baudron, Victoria Ruiz, Alexander M. Swan, Bruce A. Vallance, Ceren Özkul, Zhiheng Pei, Jackie Li, Thomas Battaglia, Guillermo I. Perez-Perez, Martin J. Blaser
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.01917-20

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome
Cited by: 25
Author(s): Bridget L. Hansen, Rita de Cássia Pessotti, Monika Fischer, Alyssa Collins, Laila El-Hifnawi, Mira D. Liu, Matthew F. Traxler
Software Mentions: 2
Published: about 6 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: over 7 years ago

10.1111/jre.12645

No differences in microbiome changes between anti‐adhesive and antibacterial ingredients in toothpastes during periodontal therapy
Cited by: 21
Author(s): Daniel Hagenfeld, Karola Prior, Inga Harks, Yvonne Jockel‐Schneider, Theodor W. May, Dag Harmsen, Ulrich Schlagenhauf, Benjamin Ehmke
Software Mentions: 2
Published: over 7 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

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702