bioconductor: microbiome | Projects

10.1080/19490976.2021.1888673

Links between gut microbiome composition and fatty liver disease in a large population sample
Cited by: 31
Author(s): Matti O. Ruuskanen, Fredrik Åberg, Ville Männistö, Aki S. Havulinna, Guillaume Méric, Yang Liu, Rohit Loomba, Yoshiki Vázquez-Baeza, Anupriya Tripathi, Liisa Valsta, Michael Inouye, Pekka Jousilahti, Veikko Salomaa, Mohit Jain, Rob Knight, Leo Lahti, Teemu J. Niiranen
Software Mentions: 14
Published: almost 4 years ago

10.3389/fmicb.2021.709611

Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System
Cited by: 2
Author(s): Yousri Abdelhafiz, Jorge M. O. Fernandes, Simone Larger, Davide Albanese, Claudio Donati, Omid Jafari, Artem Nedoluzhko, Viswanath Kiron
Software Mentions: 14
Published: about 3 years ago

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: over 4 years ago

10.3390/microorganisms9061167

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad
Cited by: 10
Author(s): Amanda C. Ramdass, Sephra N. Rampersad
Software Mentions: 14
Published: over 3 years ago

10.1098/rspb.2021.0552

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome
Cited by: 9
Author(s): Xavier A. Harrison, Allan D. McDevitt, Jenny C. Dunn, Sarah M. Griffiths, Chiara Benvenuto, Richard Birtles, Jean P. Boubli, Kevin Bown, Calum Bridson, Darren R. Brooks, Samuel S. Browett, Ruth F. Carden, Julian Chantrey, Friederike Clever, Ilaria Coscia, Katie L. Edwards, Nicolas Ferry, Ian Goodhead, Andrew Highlands, Jane Hopper, Joseph A. Jackson, Robert Jehle, Mariane da Cruz Kaizer, Tony King, Jessica M. D. Lea, Jessica L Lenka, Alexandra McCubbin, Jack McKenzie, Bárbara Lins Caldas de Moraes, Denise O'Meara, Poppy Pescod, Richard F. Preziosi, Jennifer K. Rowntree, Susanne Shultz, Matthew J. Silk, Jennifer E. Stockdale, William O. C. Symondson, Mariana Villalba de la Peña, Susan L. Walker, Michael D. Wood, Rachael E. Antwis
Software Mentions: 14
Published: over 3 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: over 3 years ago

10.1128/mSphere.00481-19

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities
Cited by: 15
Author(s): Ryan B. Ghannam, Laura G. Schaerer, Timothy Butler, Stephen M. Techtmann
Software Mentions: 11
Published: over 4 years ago

10.1186/s42523-020-00045-5

Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)
Cited by: 4
Author(s): Emily Dodd, Melissa L. Pierce, Jonathan S. F. Lee, Rachel Poretsky
Software Mentions: 11
Published: over 4 years ago

10.3389/fmicb.2020.619226

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island
Cited by: 4
Author(s): Ahmed Taïbi, Ronan Rivallan, Véronique Broussolle, Dominique Pallet, Sylvie Lortal, Jean-Christophe Meile, Florentin Constancias
Software Mentions: 11
Published: almost 4 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: over 4 years ago

10.3389/fmicb.2019.02291

Reduced Gut Microbiome Diversity and Metabolome Differences in Rhinoceros Species at Risk for Iron Overload Disorder
Cited by: 25
Author(s): Terri L. Roth, Alexandra D. Switzer, Miki Watanabe-Chailland, Elisabeth M. Bik, David A. Relman, Lindsey E. Romick-Rosendale, Nicholas J. Ollberding
Software Mentions: 11
Published: about 5 years ago

10.3390/microorganisms9081723

Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System
Cited by: 7
Author(s): Jacques Gonzalès, Justine Marchix, Laetitia Aymeric, Catherine Le Berre‐Scoul, Johanna Zoppi, Philippe Bordron, Marie Burel, Laetitia Davidovic, J. L. Richard, Alexandru Gaman, Florian Lejuste, Julie Z. Brouillet, Françoise Le Vacon, Samuel Chaffron, Marion Leboyer, Hélène Boudin, Michel Neunlist
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-71663-x

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: about 4 years ago

10.1038/s41598-020-79875-x

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models
Cited by: 23
Author(s): Marta Relvas, Alba Regueira-Iglesias, Carlos Balsa-Castro, Filomena Salazar, José Júlio Pacheco, Cristina Cabral, Corsina Velazco de Henriques, Inmaculada Tomás
Software Mentions: 10
Published: almost 4 years ago

10.3389/fmicb.2021.706214

Dietary Exposure of Pacific Oyster (Crassostrea gigas) Larvae to Compromised Microalgae Results in Impaired Fitness and Microbiome Shift
Cited by: 5
Author(s): Julien Vignier, Olivier Laroche, Anne Rolton, Pandora Wadsworth, K. Kumanan, Branwen Trochel, Xavier Pochon, Nathan King
Software Mentions: 10
Published: over 3 years ago

10.1080/19490976.2021.1957408

Imbalance of the intestinal virome and altered viral-bacterial interactions caused by a conditional deletion of the vitamin D receptor
Cited by: 14
Author(s): Jilei Zhang, Yongguo Zhang, Yinglin Xia, Jun Sun
Software Mentions: 9
Published: almost 4 years ago

10.3389/fmicb.2020.556793

Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt
Cited by: 3
Author(s): Antonios Michas, Mourad Harir, Marianna Lucio, Gisle Vestergaard, Anne M. Himmelberg, Philippe Schmitt‐Kopplin, Tillmann Lueders, Dimitris G. Hatzinikolaou, Anne Schöler, Ralf Rabus, Michael Schloter
Software Mentions: 9
Published: about 4 years ago

10.3389/fmicb.2019.02320

Saccharomyces cerevisiae Induces Immune Enhancing and Shapes Gut Microbiota in Social Wasps
Cited by: 18
Author(s): Niccolò Meriggi, Monica Di Paola, Francesco Vitali, Damaríz Rivero, Federico Cappa, Francesco Turillazzi, Agnese Gori, Leonardo Dapporto, L. Beani, Stefano Turillazzi, Duccio Cavalieri
Software Mentions: 9
Published: about 5 years ago

10.3390/microorganisms9061313

Influential Insider: Wolbachia, an Intracellular Symbiont, Manipulates Bacterial Diversity in Its Insect Host
Cited by: 5
Author(s): Morgane Ourry, Agathe Crosland, Valérie Lopez, Stéphane A. P. Derocles, Christophe Mougel, Anne‐Marie Cortesero, Denis Poinsot
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-021-88943-9

Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages
Cited by: 17
Author(s): Ankit T. Hinsu, Nilam J. Tulsani, Ketankumar Panchal, Ramesh Pandit, Basanti Jyotsana, Nishant A. Dafale, N. B. Patil, Hemant J. Purohit, Chaitanya Joshi, Subhash J. Jakhesara
Software Mentions: 9
Published: over 3 years ago

10.3389/fmicb.2020.00175

Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients
Cited by: 10
Author(s): Johanna Gutleben, Catarina Loureiro, Laura Adriana Ramírez Romero, Sudarshan A. Shetty, René H. Wijffels, Hauke Smidt, Detmer Sipkema
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0229887

Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets
Cited by: 4
Author(s): Jueeli D. Vaidya, S. van Gastelen, Hauke Smidt, Caroline M. Plugge, Joan E. Edwards
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-020-62186-6

Site-specific molecular analysis of the bacteriota on worn spectacles
Cited by: 4
Author(s): Birgit Fritz, Melanie März, Severin Weis, Siegfried Wahl, Focke Ziemssen, Markus Egert
Software Mentions: 9
Published: over 4 years ago

10.1186/s12866-021-02299-8

Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina
Cited by: 5
Author(s): Martina Prazeres, Thomas E. Roberts, Shadrina Fildzah Ramadhani, Steve S. Doo, Christiane Schmidt, Marleen Stuhr, Willem Renema
Software Mentions: 9
Published: about 3 years ago

10.1002/ece3.6221

Effects of captivity, diet, and relocation on the gut bacterial communities of white‐footed mice
Cited by: 18
Author(s): Pauline van Leeuwen, Nadia Mykytczuk, Gabriela F. Mastromonaco, Albrecht I. Schulte‐Hostedde
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2018.01868

Exposure to Yeast Shapes the Intestinal Bacterial Community Assembly in Zebrafish Larvae
Cited by: 29
Author(s): Prabhugouda Siriyappagouder, Jorge Galindo-Villegas, Jep Lokesh, Victoriano Mulero, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 8
Published: over 6 years ago

10.3389/fmicb.2018.03247

Lactobacillus Dominate in the Intestine of Atlantic Salmon Fed Dietary Probiotics
Cited by: 45
Author(s): S. R. Gupta, Adriána Fečkaninová, Jep Lokesh, Jana Koščová, Mette Sørensen, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 8
Published: almost 6 years ago

10.3390/microorganisms9091943

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network
Cited by: 6
Author(s): Milan Varsadiya, Tim Urich, Gustaf Hugelius, Jiří Bárta
Software Mentions: 8
Published: about 3 years ago

10.1038/s41598-021-99046-w

Using fecal immunochemical tubes for the analysis of the gut microbiome has the potential to improve colorectal cancer screening
Cited by: 7
Author(s): Kertu Liis Krigul, Oliver Aasmets, Kreete Lüll, Tõnis Org, Elin Org
Software Mentions: 8
Published: about 3 years ago

10.1002/ece3.7579

Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding
Cited by: 36
Author(s): Melissa R. Ingala, Nancy B. Simmons, Claudia Wultsch, Konstantinos Krampis, Kaiya L. Provost, Susan L. Perkins
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2021.644828

The Cheese Production Facility Microbiome Exhibits Temporal and Spatial Variability
Cited by: 12
Author(s): Jared Johnson, Chris Curtin, Joy Waite‐Cusic
Software Mentions: 8
Published: over 3 years ago

10.1128/Spectrum.00536-21

Mild and Severe SARS-CoV-2 Infection Induces Respiratory and Intestinal Microbiome Changes in the K18-hACE2 Transgenic Mouse Model
Cited by: 16
Author(s): Brittany Seibert, C. Joaquín Cáceres, Stivalis Cárdenas-García, Silvia Carnaccini, Ginger Geiger, Daniela S. Rajão, Elizabeth A. Ottesen, Daniel R. Pérez
Software Mentions: 8
Published: about 3 years ago

10.3390/nu13093295

Associations between Maternal Diet, Body Composition and Gut Microbial Ecology in Pregnancy
Cited by: 14
Author(s): Meghan L. Ruebel, Stephanie Gilley, Clark Sims, Ying Zhang, Donald Turner, Sree V. Chintapalli, Brian D. Piccolo, Aline Andres, Kartik Shankar
Software Mentions: 8
Published: about 3 years ago

10.1038/s41598-019-47953-4

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial
Cited by: 61
Author(s): Xuan He, Mariana Parenti, Tove Grip, Bo Lönnerdal, Niklas Timby, Magnus Domellöf, Olle Hernell, Carolyn M. Slupsky
Software Mentions: 8
Published: over 5 years ago

10.3390/microorganisms9071454

First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes
Cited by: 8
Author(s): Julia Moll, Friederike Roy, Claus Bässler, Jacob Heilmann‐Clausen, Martin Hofrichter, Harald Kellner, Doris Krabel, Jan Henrik Schmidt, François Buscot, Björn Hoppe
Software Mentions: 8
Published: over 3 years ago

10.3390/microorganisms9091873

Nutrient Enrichment Predominantly Affects Low Diversity Microbiomes in a Marine Trophic Symbiosis between Algal Farming Fish and Corals
Cited by: 5
Author(s): Adriana Messyasz, Rebecca L. Maher, Sonora S. Meiling, Rebecca Vega Thurber
Software Mentions: 8
Published: about 3 years ago

10.3389/fmicb.2021.654108

Gut Microbiota of Drosophila subobscura Contributes to Its Heat Tolerance and Is Sensitive to Transient Thermal Stress
Cited by: 22
Author(s): Angélica Jaramillo, Luis E. Castañeda
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2019.02761

Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition
Cited by: 6
Author(s): Thomas Hartinger, Joan E. Edwards, Ruth Gómez Expósito, Hauke Smidt, Cajo J. F. ter Braak, N. Gresner, K. H. Südekum
Software Mentions: 8
Published: almost 5 years ago

10.3389/fmicb.2021.632935

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events
Cited by: 19
Author(s): Benjamin Zwirzitz, Stefanie U. Wetzels, Emmanuel D. Dixon, Svenja Fleischmann, Evelyne Selberherr, Sarah Thalguter, Narciso M. Quijada, Monika Dzieciol, Martin Wagner, Beatrix Stessl
Software Mentions: 8
Published: almost 4 years ago

10.3390/microorganisms8060961

The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia
Cited by: 10
Author(s): Aldian Irma Amaruddin, Firdaus Hamid, J. Koopman, Munawir Muhammad, Eric A. T. Brienen, Lisette van Lieshout, A. R. Geelen, Sitti Wahyuni, Ed J. Kuijper, Erliyani Sartono, Maria Yazdanbakhsh, Romy D. Zwittink
Software Mentions: 7
Published: over 4 years ago

10.1186/s12931-020-01392-2

Characterisation of microbiota in saliva, bronchoalveolar lavage fluid, non-malignant, peritumoural and tumour tissue in non-small cell lung cancer patients: a cross-sectional clinical trial
Cited by: 27
Author(s): Rea Bingula, Edith Filaire, Ioana Molnar, Eve Delmas, Jean‐Yves Berthon, Marie‐Paule Vasson, Annick Bernalier-Donadille, Marc Filaire
Software Mentions: 7
Published: over 4 years ago

10.1128/IAI.00147-20

Niche- and Gender-Dependent Immune Reactions in Relation to the Microbiota Profile in Pediatric Patients with Otitis Media with Effusion
Cited by: 10
Author(s): Frida Enoksson, Alicia Ruiz Rodriguez, Chikondi Peno, Carlos Balcazar Lopez, Fredrik Tjernström, Debby Bogaert, Anders P. Håkansson, Caroline Bergenfelz
Software Mentions: 7
Published: about 4 years ago

10.1080/19490976.2020.1840764

Dynamics of the bacterial gut microbiota during controlled human infection with <i>Necator americanus</i> larvae
Cited by: 6
Author(s): Quinten R Ducarmon, Marie-Astrid Hoogerwerf, Jacqueline J. Janse, A. R. Geelen, J. Koopman, Romy D. Zwittink, Jelle J. Goeman, Ed J. Kuijper, Meta Roestenberg
Software Mentions: 7
Published: about 4 years ago

10.1186/s42523-021-00130-3

Differential effects of elevated nest temperature and parasitism on the gut microbiota of wild avian hosts
Cited by: 5
Author(s): Melissa R. Ingala, Lauren Albert, Alyssa Addesso, Mackenzie J. Watkins, Sarah A. Knutie
Software Mentions: 7
Published: about 3 years ago

10.3390/microorganisms8050677

The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile
Cited by: 21
Author(s): Monique J. T. Crobach, Quinten R Ducarmon, Elisabeth M. Terveer, Céline Harmanus, Ingrid M J G Sanders, Kees Verduin, Ed J. Kuijper, Romy D. Zwittink
Software Mentions: 7
Published: over 4 years ago

10.1080/19490976.2021.1921927

Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells <i>in vitro</i>
Cited by: 7
Author(s): Dušan Radojević, Sergej Tomić, Dušan Mihajlović, Maja Tolinački, Bojan Pavlović, Dragana Vučević, Svetlana Bojić, Nataša Golić, Miodrag Čolić, Jelena Đokić
Software Mentions: 7
Published: almost 4 years ago

10.3389/fmicb.2019.02037

Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon
Cited by: 41
Author(s): S. R. Gupta, Jep Lokesh, Yousri Abdelhafiz, Prabhugouda Siriyappagouder, Ronan Pierre, Mette Sørensen, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-021-92513-4

High-throughput 16S rRNA gene sequencing of the microbial community associated with palm oil mill effluents of two oil processing systems
Cited by: 2
Author(s): Benedicte Ella Zranseu Aka, Theodore N. Djéni, Simon Laurent Tiemele Amoikon, Jan Kannengießer, Naaila Ouazzani, Marcellin Koffi Djè
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-019-46118-7

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology
Cited by: 24
Author(s): Sandra Plancade, Allison Clark, Catherine Philippe, Jean‐Christophe Helbling, Marie‐Pierre Moisan, Diane Esquerré, Laurence Le Moyec, Céline Robert, Éric Barrey, Núria Mach
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2020.566619

Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers
Cited by: 13
Author(s): Anita Dame-Korevaar, Jannigje G. Kers, Jeanet van der Goot, Francisca C. Velkers, Daniela Ceccarelli, Dik Mevius, Arjan Stegeman, E.A.J. Fischer
Software Mentions: 7
Published: about 4 years ago

10.7717/peerj.8056

Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral
Cited by: 18
Author(s): Mallory M. Rice, Rebecca L. Maher, Rebecca Vega Thurber, Deron E. Burkepile
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2018.02404

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia
Cited by: 11
Author(s): Martina Prazeres
Software Mentions: 7
Published: about 6 years ago

10.3389/fmolb.2021.656204

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse
Cited by: 12
Author(s): Núria Mach, Marco Moroldo, Andrea Rau, Jérôme Lecardonnel, Laurence Le Moyec, Céline Robert, Éric Barrey
Software Mentions: 7
Published: over 3 years ago

10.3390/insects11060373

Susceptibility of Red Mason Bee Larvae to Bacterial Threats Due to Microbiome Exchange with Imported Pollen Provisions
Cited by: 22
Author(s): Anna Voulgari‐Kokota, Ingolf Steffan‐Dewenter, Alexander Keller
Software Mentions: 7
Published: over 4 years ago

10.3390/microorganisms8010061

Prenatal Transfer of Gut Bacteria in Rock Pigeon
Cited by: 14
Author(s): Maurine W. Dietz, Joana Falcão Salles, Bin‐Yan Hsu, Cor Dijkstra, Ton G. G. Groothuis, Marco van der Velde, Yvonne I. Verkuil, B. Irene Tieleman
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12887-020-02067-z

Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment
Cited by: 15
Author(s): Romy D. Zwittink, Diny van Zoeren‐Grobben, Ingrid B. Renes, Richard A. van Lingen, Obbe F. Norbruis, Rocı́o Martı́n, Liesbeth J. Groot Jebbink, Jan Knol, Clara Belzer
Software Mentions: 6
Published: over 4 years ago

10.3390/microorganisms7120596

Dietary Saccharomyces cerevisiae boulardii CNCM I-1079 Positively Affects Performance and Intestinal Ecosystem in Broilers during a Campylobacter jejuni Infection
Cited by: 22
Author(s): Francesca Romana Massacci, Carmela Lovito, Silvia Tofani, Michele Tentellini, Domenica Anna Genovese, Alessia Arcangela Pia De Leo, Paola Papa, Chiara Francesca Magistrali, Elisabetta Manuali, Massimo Trabalza‐Marinucci, Livia Moscati, Claudio Forte
Software Mentions: 6
Published: about 5 years ago

10.3390/microorganisms8071015

Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino Children
Cited by: 16
Author(s): Maria Julia Golloso-Gubat, Quinten R Ducarmon, Robby Carlo A. Tan, Romy D. Zwittink, Ed J. Kuijper, Jacus S. Nacis, Noelle Lyn C Santos
Software Mentions: 6
Published: over 4 years ago

10.3390/microorganisms8121978

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea
Cited by: 8
Author(s): Bruno Francesco Rodrigues de Oliveira, Isabelle Rodrigues Lopes, Anna Luiza Bauer Canellas, Guilherme Muricy, Alan D. W. Dobson, Marinella Silva Laport
Software Mentions: 6
Published: almost 4 years ago

10.3390/ani11092597

Effect of a Low-Methane Diet on Performance and Microbiome in Lactating Dairy Cows Accounting for Individual Pre-Trial Methane Emissions
Cited by: 3
Author(s): Juana Catarina Cariri Chagas, Mohammad Ramin, Ruth Gómez Expósito, Hauke Smidt, S.J. Krizsan
Software Mentions: 6
Published: about 3 years ago

10.3390/pathogens10081063

Gut Microbiota in Military International Travelers with Doxycycline Malaria Prophylaxis: Towards the Risk of a Simpson Paradox in the Human Microbiome Field
Cited by: 1
Author(s): Émilie Javelle, Aurélie Mayet, Matthieu Million, Anthony Levasseur, Rodrigue S. Allodji, Catherine Marimoutou, Chrystel Lavagna, Jérôme Desplans, Pierre-Édouard Fournier, Didier Raoult, Gaëtan Texier
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.12035

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere
Cited by: 4
Author(s): Ankit T. Hinsu, Ashvin Dumadiya, Anjali Joshi, Rohitkumar Kotadiya, Kavan N. Andharia, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 6
Published: about 3 years ago

10.3390/ph14070635

Probiotic Bacteria with High Alpha-Gal Content Protect Zebrafish against Mycobacteriosis
Cited by: 10
Author(s): Iván Pacheco, Sandra Díaz-Sánchez, Marinela Contreras, Margarita Villar, Alejandro Cabezas-Cruz, Christian Gortázar, José de la Fuente
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-85460-7

Early socialization and environmental enrichment of lactating piglets affects the caecal microbiota and metabolomic response after weaning
Cited by: 7
Author(s): Mireia Saladrigas-García, Matilde D’Angelo, Heng-Lun Ko, Sara Traserra, Pau Nolis, Yuliaxis Ramayo-Caldas, Josep María Folch, P. Vergara, Pol Llonch, José Francisco Pérez, S. M. Martín‐Orúe
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-82573-x

Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees
Cited by: 19
Author(s): Karen M. Kapheim, Makenna M. Johnson, Maggi Jolley
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0251231

Assessment of the gut bacterial microbiome and metabolome of girls and women with Rett Syndrome
Cited by: 6
Author(s): Santosh Thapa, Alamelu Venkatachalam, Nabeel Khan, Mohammed Naqvi, Miriam Balderas, Jessica K. Runge, Anthony M. Haag, Kathleen M. Hoch, Daniel G. Glaze, Ruth Ann Luna, Kathleen J. Motil
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0251136

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study
Cited by: 7
Author(s): Martijn G H Sanders, Tamar Nijsten, Joost Verlouw, Robert Kraaij, Luba M. Pardo
Software Mentions: 6
Published: over 3 years ago

10.1093/femsec/fiz108

Diversity of tryptophan halogenases in sponges of the genus Aplysina
Cited by: 9
Author(s): Johanna Gutleben, Jasper J. Koehorst, Kyle McPherson, Shirley A. Pomponi, René H. Wijffels, Hauke Smidt, Detmer Sipkema
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2020.00954

Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite
Cited by: 22
Author(s): Fátima Jorge, Nolwenn M. Dheilly, Robert Poulin
Software Mentions: 6
Published: over 4 years ago

10.1186/s12866-021-02245-8

Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944)
Cited by: 5
Author(s): Andrea Nuzzo, Stephanie Van Horn, Christopher Traini, Caroline M. Perry, Étienne Dumont, Nicole Scangarella-Oman, David F. Gardiner, James R. Brown
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2021.659918

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species
Cited by: 12
Author(s): Alice Risely, Mark A. F. Gillingham, Arnaud Béchet, Stefan Dominik Brändel, Alexander Christoph Heni, Marco Heurich, Sebastian Menke, Marta B. Manser, Marco Tschapka, . Wasimuddin, Simone Sommer
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2020.526545

Nutrients and Pharmaceuticals Structure Bacterial Core Communities in Urban and Montane Stream Biofilms
Cited by: 4
Author(s): Elizabeth M. Ogata, Michelle A. Baker, Emma J. Rosi, Trevor B. Smart, Donald Long, Zachary T. Aanderud
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2020.01860

Seasonal and Spatial Variations in Bacterial Communities From Tetrodotoxin-Bearing and Non-tetrodotoxin-Bearing Clams
Cited by: 7
Author(s): Laura Biessy, John K. Pearman, Kirsty F. Smith, Ian Hawes, Susanna A. Wood
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-66028-3

Sward type alters the relative abundance of members of the rumen microbial ecosystem in dairy cows
Cited by: 7
Author(s): Pamela M. Smith, Daniel Enríquez-Hidalgo, Deirdre Hennessy, Matthew S. McCabe, David A. Kenny, A. K. Kelly, Sinéad M. Waters
Software Mentions: 5
Published: over 4 years ago

10.1186/s42523-021-00084-6

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis
Cited by: 5
Author(s): Adrian Muwonge, Anbu K. Karuppannan, Tanja Opriessnig
Software Mentions: 5
Published: over 3 years ago

10.1186/s42523-021-00115-2

Environmentally enriched housing conditions affect pig welfare, immune system and gut microbiota in early life
Cited by: 21
Author(s): Caifang Wen, I.D.E. van Dixhoorn, Dirkjan Schokker, H. Woelders, Norbert Stockhofe-Zurwieden, Johanna M.J. Rebel, Hauke Smidt
Software Mentions: 5
Published: over 3 years ago

10.1186/s12866-021-02129-x

The infant gut resistome is associated with E. coli and early-life exposures
Cited by: 23
Author(s): Rebecca M. Lebeaux, Modupe Coker, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Benjamin D. Ross, Emily Baker, Margaret R. Karagas, Juliette C. Madan, Anne G. Hoen
Software Mentions: 5
Published: over 3 years ago

10.3390/life11030246

Postoperative Complications Are Associated with Long-Term Changes in the Gut Microbiota Following Colorectal Cancer Surgery
Cited by: 7
Author(s): Felix C. F. Schmitt, Martin Schneider, William Mathejczyk, Markus A. Weigand, Jane C. Figueiredo, Christopher I. Li, David Shibata, Erin M. Siegel, Adetunji T. Toriola, Cornelia M. Ulrich, Alexis Ulrich, Sébastien Boutin, Biljana Gigic
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms8020308

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems
Cited by: 206
Author(s): Jesse R. Willis, Toni Gabaldón
Software Mentions: 5
Published: almost 5 years ago

10.3390/microorganisms7080233

Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon
Cited by: 35
Author(s): S. R. Gupta, Jorge M.O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0037818

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
Cited by: 511
Author(s): Sujatha Srinivasan, Noah G. Hoffman, Martin Morgan, F. A. Matsen, Tina L. Fiedler, Richard Hall, Frederick J. Ross, Connor O. McCoy, Roger E. Bumgarner, Jeanne M. Marrazzo, David N. Fredricks
Software Mentions: 5
Published: over 12 years ago

10.3390/cancers12030628

tRNA Queuosine Modification Enzyme Modulates the Growth and Microbiome Recruitment to Breast Tumors
Cited by: 35
Author(s): Jilei Zhang, Rong Lü, Yongguo Zhang, Żaneta Matuszek, Wen Zhang, Yinglin Xia, Tao Pan, Jun Sun
Software Mentions: 5
Published: over 4 years ago

10.1007/s00125-021-05464-w

Markers of metabolic health and gut microbiome diversity: findings from two population-based cohort studies
Cited by: 25
Author(s): Semi Zouiouich, Erikka Loftfield, Inge Huybrechts, Vivian Viallon, Panayiotis Louca, Emily Vogtmann, Philippa M Wells, Claire J. Steves, Karl‐Heinz Herzig, Cristina Menni, Marjo‐Riitta Järvelin, Rashmi Sinha, Marc J. Gunter
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.711359

Circulating Levels of the Short-Chain Fatty Acid Acetate Mediate the Effect of the Gut Microbiome on Visceral Fat
Cited by: 67
Author(s): Ana Nogal, Panayiotis Louca, Mengjie Zhang, Philippa M Wells, Claire J. Steves, Tim D. Spector, Mario Falchi, Ana M. Valdes, Cristina Menni
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.616730

Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity
Cited by: 10
Author(s): Scott F. George, Noah Fierer, J. S. Levy, Byron J. Adams
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2020.01614

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)
Cited by: 7
Author(s): Pamela M. Smith, Sinéad M. Waters, David A. Kenny, T. M. Boland, J. S. Heffernan, A. K. Kelly
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.00681

Rhodobacterales and Rhizobiales Are Associated With Stony Coral Tissue Loss Disease and Its Suspected Sources of Transmission
Cited by: 82
Author(s): Stephanie M. Rosales, Abigail S. Clark, Lindsay K. Huebner, Rob Ruzicka, Erinn M. Muller
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2019.00717

Disentangling the Influence of Environment, Host Specificity and Thallus Differentiation on Bacterial Communities in Siphonous Green Seaweeds
Cited by: 23
Author(s): Kathryn Lee Morrissey, Levent Çavaş, Anne Willems, Olivier De Clerck
Software Mentions: 5
Published: over 5 years ago

10.3389/fvets.2019.00260

A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum
Cited by: 16
Author(s): Michael J. Rothrock, Aude Locatelli, Kristina M. Feye, Andrew J Caudill, Jean Guard, Kelli L. Hiett, Steven C. Ricke
Software Mentions: 5
Published: over 5 years ago

10.1186/s40635-021-00398-4

Pulmonary and intestinal microbiota dynamics during Gram-negative pneumonia-derived sepsis
Cited by: 8
Author(s): Nora S. Wolff, Max C. Jacobs, W. Joost Wiersinga, Floor Hugenholtz
Software Mentions: 5
Published: over 3 years ago

10.1093/ajcn/nqab077

Associations of healthy food choices with gut microbiota profiles
Cited by: 33
Author(s): Kari K. Koponen, Aaro Salosensaari, Matti O. Ruuskanen, Aki S. Havulinna, Satu Männistö, Pekka Jousilahti, Joonatan Palmu, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Jon G. Sanders, Guillaume Méric, Susan Cheng, Michael Inouye, Mohit Jain, Teemu J. Niiranen, Liisa Valsta, Rob Knight, Veikko Salomaa
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.00348

Mycobiome Diversity in Traditionally Prepared Starters for Alcoholic Beverages in India by High-Throughput Sequencing Method
Cited by: 21
Author(s): Shankar Prasad Sha, Mangesh V. Suryavanshi, Jyoti Prakash Tamang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-97790-7

Glycosaminoglycan biosynthesis pathway in host genome is associated with Helicobacter pylori infection
Cited by: 0
Author(s): Dingxue Hu, Yueqi Lu, Daoming Wang, Chao Nie, Yan Li
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-021-98979-6

Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac–Moruga mud volcano in South Trinidad
Cited by: 1
Author(s): Amanda C. Ramdass, Sephra N. Rampersad
Software Mentions: 4
Published: about 3 years ago

10.3390/md19080442

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India
Cited by: 4
Author(s): Jamseel Moopantakath, Madangchanok Imchen, Ranjith Kumavath, Rosa María Martínez‐Espinosa
Software Mentions: 4
Published: over 3 years ago

10.3390/biomedicines9030266

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

10.1128/mSystems.00547-19

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
Cited by: 31
Author(s): Quinten R Ducarmon, Bastian Hornung, A. R. Geelen, E. Kuijper, Romy D. Zwittink
Software Mentions: 4
Published: almost 5 years ago

10.1080/20002297.2019.1633194

Bacterial biofilm composition in healthy subjects with and without caries experience.
Cited by: 37
Author(s): Kyrill Schoilew, Helena Ueffing, Alexander H. Dalpke, Björn Wolff, Cornelia Frese, Diana Wolff, Sébastien Boutin
Software Mentions: 4
Published: almost 6 years ago

10.3389/fvets.2020.00438

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats
Cited by: 2
Author(s): Andrea Balboni, Giovanni Franzo, Luca Bano, Stefano Arcangeli, Alessia Rizzardi, Lorenza Urbani, Sofia Segatore, Federica Serafini, Francesco Dondi, Mara Battilani
Software Mentions: 4
Published: over 4 years ago

10.1007/s00204-021-03132-x

The diarrhetic shellfish-poisoning toxin, okadaic acid, provokes gastropathy, dysbiosis and susceptibility to bacterial infection in a non-rodent bioassay, Galleria mellonella
Cited by: 13
Author(s): Helena Emery, William Traves, Andrew F. Rowley, Christopher J. Coates
Software Mentions: 4
Published: over 3 years ago

Projects: bioconductor: microbiome

Papers Mentioning microbiome 114