bioconductor: dada2 | Projects | Ecosyste.ms: Papers

10.1186/s40168-020-00841-w

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
Cited by: 49
Author(s): Isabel F. Escapa, Yanmei Huang, Tsute Chen, Maoxuan Lin, Alexis Kokaras, Floyd E. Dewhirst, Katherine P. Lemon
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.54318

Rapamycin rejuvenates oral health in aging mice
Cited by: 52
Author(s): Jonathan Y. An, Kristopher A. Kerns, Andrew Ouellette, Laura Robinson, H Douglas Morris, Catherine C. Kaczorowski, So-Il Park, Title Mekvanich, Alex Kang, Jeffrey S. McLean, Timothy C. Cox, Matt Kaeberlein
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-021-02372-y

Function-adaptive clustered nanoparticles reverse Streptococcus mutans dental biofilm and maintain microbiota balance
Cited by: 9
Author(s): Fatemeh Ostadhossein, Parikshit Moitra, Esra Altun, Debapriya Dutta, Dinabandhu Sar, Indu Tripathi, Shih Hsuan Hsiao, Valeriya Kravchuk, Shuming Nie, Dipanjan Pan
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-021-01058-1

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact
Cited by: 7
Author(s): Émie Audet‐Gilbert, François‐Étienne Sylvain, Sidki Bouslama, Nicolas Derôme
Software Mentions: 5
Published: over 3 years ago

10.1002/ece3.6196

Competition with insectivorous ants as a contributor to low songbird diversity at low elevations in the eastern Himalaya
Cited by: 12
Author(s): K. Supriya, Trevor D. Price, Corrie S. Moreau
Software Mentions: 5
Published: over 4 years ago

10.1111/ele.13082

Linking phytoplankton community metabolism to the individual size distribution
Cited by: 20
Author(s): Daniel Padfield, Angus Buckling, Ruth Warfield, Chris D. Lowe, Gabriel Yvon‐Durocher
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-77289-3

Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes
Cited by: 4
Author(s): Meghan H. Shilts, Christian Rosas‐Salazar, Christian Edward Cyril Lynch, Andrey Tovchigrechko, Helen H. Boone, Patty Russell, Alexandra Connolly, Kaitlin Costello, Megan D McCollum, Annie Mai, Derek Wiggins, Seesandra V. Rajagopala, Shibu Yooseph, R. Stokes Peebles, Tina V. Hartert, Suman Das
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12903-021-01439-w

Microbiological findings in early and late implant loss: an observational clinical case-controlled study
Cited by: 12
Author(s): Michael Korsch, Silke‐Mareike Marten, Dominic A. Stoll, Christopher Prechtl, Andreas Dötsch
Software Mentions: 5
Published: over 3 years ago

10.3390/foods9121851

Austrian Raw-Milk Hard-Cheese Ripening Involves Successional Dynamics of Non-Inoculated Bacteria and Fungi
Cited by: 12
Author(s): Narciso M. Quijada, Stephan Schmitz‐Esser, Benjamin Zwirzitz, C. Guse, Cameron Strachan, Martin Wagner, Stefanie U. Wetzels, Evelyne Selberherr, Monika Dzieciol
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-70249-x

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study
Cited by: 5
Author(s): Tereza Matějková, Petra Hájková, Romana Stopková, Michał Stanko, Jean‐François Martin, Jakub Kreisinger, Pavel Stopka
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-65329-x

Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase
Cited by: 9
Author(s): Max‐Bernhard Ballhausen, Rebecca E. Hewitt, Matthias C. Rillig
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-64393-7

Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study
Cited by: 13
Author(s): Manuela de Oliveira Ramalho, Christophe Duplais, Jérôme Orivel, Alain Déjean, Joshua C. Gibson, Andrew V. Suarez, Corrie S. Moreau
Software Mentions: 5
Published: over 4 years ago

10.3390/microorganisms9030641

A Mouse Model Suggests That Heart Failure and Its Common Comorbidity Sleep Fragmentation Have No Synergistic Impacts on the Gut Microbiome
Cited by: 4
Author(s): Olfat Khannous-Lleiffe, Jesse R. Willis, Ester Saus, Ignacio Cabrera-Aguilera, Isaac Almendros, Ramón Farré, David Gozal, Núria Farré, Toni Gabaldón
Software Mentions: 5
Published: over 3 years ago

10.3389/fcimb.2019.00339

Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses
Cited by: 17
Author(s): Allison R. Kolbe, Eduardo Castro-Nallar, Diego Preciado, Marcos Pérez‐Losada
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2020.595555

Antibiotic Treatment for Chronic Rhinosinusitis: Prescription Patterns and Associations With Patient Outcome and the Sinus Microbiota
Cited by: 16
Author(s): Christian A Lux, Brett Wagner Mackenzie, James Johnston, Melissa Zoing, Kristi Biswas, Michael W. Taylor, Richard Douglas
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-019-43907-y

Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño
Cited by: 31
Author(s): Allison R. Kolbe, Manuel Aira, María Gómez-Brandòn, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-24126-3

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species
Cited by: 31
Author(s): Barbora Pafčo, Dagmar Čížková, Jakub Kreisinger, Hideo Hasegawa, Peter Vallo, Kathryn Shutt, Angelique Todd, Klára J. Petrželková, David Modrý
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.01846

The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer
Cited by: 14
Author(s): James P. J. Hall, Ellie Harrison, Katariina Pärnänen, Marko Virta, Michael A. Brockhurst
Software Mentions: 5
Published: over 4 years ago

10.1111/jvim.15671

Effects of nebulized dexamethasone on the respiratory microbiota and mycobiota and relative equine herpesvirus‐1, 2, 4, 5 in an equine model of asthma
Cited by: 8
Author(s): Stephanie L. Bond, Matthew L. Workentine, Jana Hundt, James R. Gilkerson, Renaud Léguillette
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.ppat.1009487

Lipocalin 2 modulates dendritic cell activity and shapes immunity to influenza in a microbiome dependent manner
Cited by: 6
Author(s): Martin L. Watzenboeck, Barbara Drobits, Sophie Zahalka, Anna-Dorothea Gorki, Asma Farhat, Federica Quattrone, Anastasiya Hladik, Karin Lakovits, Gabriel Richard, Therese Lederer, Birgit Strobl, Gijs A. Versteeg, Louis Boon, Philipp Starkl, Sylvia Knapp
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.675798

Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts
Cited by: 4
Author(s): Emily N. Junkins, Bradley S. Stevenson
Software Mentions: 4
Published: over 3 years ago

10.1111/jbg.12539

Genetic relationships between feed efficiency and gut microbiome in pig lines selected for residual feed intake
Cited by: 15
Author(s): Amir Aliakbari, Olivier Zemb, Yvon Billon, Céline Barilly, Ingrid Ahn, Juliette Riquet, Hélène Gilbert
Software Mentions: 4
Published: over 3 years ago

10.3389/fvets.2020.00126

Non-invasive Assessment of Fecal Stress Biomarkers in Hunting Dogs During Exercise and at Rest
Cited by: 12
Author(s): Augusta Zannoni, Marco Pietra, Alba Gaspardo, Pier Attilio Accorsi, Monica Barone, Silvia Turroni, Luca Laghi, Chenglin Zhu, Patrizia Brigidi, Monica Forni
Software Mentions: 4
Published: over 4 years ago

10.1002/ece3.5992

Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers
Cited by: 13
Author(s): Víctor Hugo Jarquín‐Díaz, Alice Balard, Anna Mácová, Jenny Jost, Tabea Roth von Szepesbéla, Karin Berktold, Steffen Tank, Jana Kvičerová, Emanuel Heitlinger
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.590212

Gut Microbiomes Differ Among Dietary Types and Stool Consistency in the Captive Red Wolf (Canis rufus)
Cited by: 19
Author(s): Morgan Bragg, Elizabeth W. Freeman, Haw Chuan Lim, Nucharin Songsasen, Carly R. Muletz‐Wolz
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.5364

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
Cited by: 218
Author(s): Jacob T. Nearing, Gavin M. Douglas, A. Comeau, Morgan G. I. Langille
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.8417

16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates
Cited by: 17
Author(s): Qiang Chen, William A. Meyer, Qiuwei Zhang, James F. White
Software Mentions: 4
Published: almost 5 years ago

10.1093/jas/skaa181

The effect of maternal antibiotic use in sows on intestinal development in offspring
Cited by: 10
Author(s): Astrid de Greeff, Dirkjan Schokker, Petra Roubos-van den Hil, P. Ramaekers, S.A. Vastenhouw, Frank Harders, Alex Bossers, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.8042

Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA
Cited by: 44
Author(s): Ângelo F. Bernardino, Fabiano Sviatopolk-Mirsky Pais, Louisi Souza de Oliveira, Fabrício Ângelo Gabriel, Tiago Osório Ferreira, Hermano Melo Queiroz, Ana Carolina de Azevedo Mazzuco
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.ppat.1008236

The cervicovaginal mucus barrier to HIV-1 is diminished in bacterial vaginosis
Cited by: 45
Author(s): Thuy Hoang, Emily Toler, Kevin DeLong, Nomfuneko A. Mafunda, Seth M. Bloom, Hannah C. Zierden, Thomas R. Moench, Jenell S. Coleman, Justin Hanes, Douglas S. Kwon, Samuel K. Lai, Richard A. Cone, Laura M. Ensign
Software Mentions: 4
Published: almost 5 years ago

10.1111/1462-2920.14929

Methane oxidation and methylotroph population dynamics in groundwater mesocosms
Cited by: 17
Author(s): Olukayode Kuloyo, S. Emil Ruff, Aaron G. Cahill, Liam Connors, Jackie Zorz, Isabella Hrabě de Angelis, Michael Nightingale, Bernhard Mayer, Marc Strous
Software Mentions: 4
Published: almost 5 years ago

10.1111/1758-2229.12728

Gut microbial compositions mirror caste‐specific diets in a major lineage of social insects
Cited by: 30
Author(s): Saria Otani, Mariya Zhukova, N’golo Abdoulaye Koné, Rafael R. da Costa, Aram Mikaelyan, Panagiotis Sapountzis, Michael Poulsen
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-020-00835-8

Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima
Cited by: 21
Author(s): Isis Guibert, Gaël Lecellier, Gergely Torda, Xavier Pochon, Véronique Berteaux‐Lecellier
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-42911-6

Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman
Cited by: 30
Author(s): Raeid M. M. Abed, Alexandra Tamm, Christiane Hassenrück, Ahmed Al‐Rawahi, Emilio Rodríguez‐Caballero, Sabine Fiedler, Stefanie Maier, Bettina Weber
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.01363

Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System
Cited by: 47
Author(s): Ali Srour, Hala A. Ammar, Arjun Subedi, Mirian F. Pimentel, Rachel L. Cook, Jason P. Bond, Ahmad M. Fakhoury
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.27629

Bacteriome and mycobiome and bacteriome-mycobiome interactions in head and neck squamous cell carcinoma
Cited by: 22
Author(s): Elizabeth Shay, Naseer Sangwan, Roshan Padmanabhan, Scott Lundy, Brian B. Burkey, Charis Eng
Software Mentions: 4
Published: over 4 years ago

10.3390/ani11051372

Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs
Cited by: 0
Author(s): Emily Van Syoc, Natália Carrillo Gaeta, Erika Ganda
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2021.667257

Microbiome Structure of the Aphid Myzus persicae (Sulzer) Is Shaped by Different Solanaceae Plant Diets
Cited by: 12
Author(s): Bin He, Xiaoyulong Chen, Hong Yang, Tomislav Cernava
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00163-18

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
Cited by: 90
Author(s): Vincent Caruso, Xubo Song, Mark Asquith, Lisa Karstens
Software Mentions: 4
Published: over 5 years ago

10.3389/fcimb.2019.00271

Successional Dynamics in the Gut Microbiome Determine the Success of Clostridium difficile Infection in Adult Pig Models
Cited by: 4
Author(s): Stephanie D. Jurburg, Jan J. B. W. J. Cornelissen, Paulo de Boer, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.01721

Alpine Snow Algae Microbiome Diversity in the Coast Range of British Columbia
Cited by: 19
Author(s): Kurt M. Yakimovich, Casey B. Engstrom, Lynne M. Quarmby
Software Mentions: 4
Published: over 4 years ago

10.1186/s40104-020-00459-w

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens
Cited by: 33
Author(s): Joel J. Maki, Elizabeth Bobeck, Matthew J. Sylte, Torey Looft
Software Mentions: 4
Published: over 4 years ago

10.1128/mSystems.00471-20

Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors
Cited by: 14
Author(s): Ezequiel Santillan, Florentin Constancias, Stefan Wuertz
Software Mentions: 4
Published: about 4 years ago

10.3390/microorganisms7030072

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

10.1371/journal.pone.0236944

Impact of time and temperature on gut microbiota and SCFA composition in stool samples
Cited by: 9
Author(s): Janet L. Cunningham, Ludvig Bramstång, Abhijeet Singh, Shishanthi Jayarathna, Annica J. Rasmusson, Ali A. Moazzami, Bettina Müller
Software Mentions: 4
Published: over 4 years ago

10.3390/jcm9072036

Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods
Cited by: 2
Author(s): Jarosław Biliński, Mikołaj Dziurzyński, Paweł Grzesiowski, Edyta Podsiadły, Anna Stelmaszczyk-Emmel, Tomasz Dzieciątkowski, Łukasz Dziewit, Grzegorz W. Basak
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pntd.0007921

Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection
Cited by: 18
Author(s): Amin Addetia, Lauren C. Tantalo, Michelle J. Lin, Hong Xie, Meei‐Li Huang, Christina M. Marra, Alexander L. Greninger
Software Mentions: 4
Published: over 4 years ago

10.1128/mSphere.00354-20

Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment
Cited by: 14
Author(s): Kasia Piwosz, Ana Vrdoljak, Thijs Frenken, Juan Manuel González‐Olalla, Danijela Šantić, R. Michael L. McKay, Kristian Spilling, Louis Guttman, Petr Znachor, Izabela Mujakić, Lívia Kolesár Fecskeová, Luca Zoccarato, Martina Hanusová, Andrea Pessina, Tom Reich, Hans‐Peter Grossart, Michal Koblížek
Software Mentions: 4
Published: about 4 years ago

10.1038/s41396-019-0568-8

Gut microbiota structure differs between honeybees in winter and summer
Cited by: 157
Author(s): Lucie Kešnerová, Olivier Emery, Michaël Troilo, Joanito Liberti, Berra Erkoşar, Philipp Engel
Software Mentions: 4
Published: almost 5 years ago

10.1128/mBio.00824-21

Drosophila Antimicrobial Peptides and Lysozymes Regulate Gut Microbiota Composition and Abundance
Cited by: 52
Author(s): Alice Marra, Mark A. Hanson, Shu Kondo, Berra Erkoşar, Bruno Lemaître
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj.11956

Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity
Cited by: 1
Author(s): Patricia Vélez, Yunuen Tapia-Torres, Felipe Garcı́a-Oliva, Jaime Gasca-Pineda
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1008073

Genetic determinants of gut microbiota composition and bile acid profiles in mice
Cited by: 67
Author(s): Julia H. Kemis, Vanessa Linke, Kelsey L Barrett, Frederick J. Boehm, Lindsay L. Traeger, Mark P. Keller, Mary E. Rabaglia, Kathryn L. Schueler, Donald S. Stapleton, Daniel M. Gatti, Gary A. Churchill, Daniel Amador‐Noguez, John N. Russell, Brian S. Yandell, Karl W. Broman, Joshua J. Coon, Alan D. Attie, Federico E. Rey
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-63401-0

Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation
Cited by: 22
Author(s): Claire E. Couch, Holly K. Arnold, Rachel S. Crowhurst, Anna E. Jolles, Thomas J. Sharpton, Marci F. Witczak, Clinton W. Epps, Brianna R. Beechler
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-020-03591-6

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
Cited by: 1
Author(s): Yulia Kondratenko, Anton Korobeynikov, Alla Lapidus
Software Mentions: 4
Published: over 4 years ago

10.14814/phy2.14199

Oral vancomycin treatment does not alter markers of postprandial inflammation in lean and obese subjects
Cited by: 10
Author(s): Guido J. Bakker, Johan G. Schnitzler, Siroon Bekkering, Nicolien C. de Clercq, Annefleur M. Koopen, Annick V. Hartstra, Emma C. E. Meessen, Torsten P. M. Scheithauer, Maaike Winkelmeijer, Geesje M. Dallinga‐Thie, Patrice D. Cani, E. Marleen Kemper, Maarten R. Soeters, Jeffrey Kroon, Albert K. Groen, Daniël H. van Raalte, Hilde Herrema, Max Nieuwdorp
Software Mentions: 4
Published: over 5 years ago

10.1186/s40104-021-00545-7

Evaluation of curcumin and copper acetate against Salmonella Typhimurium infection, intestinal permeability, and cecal microbiota composition in broiler chickens
Cited by: 20
Author(s): Anaisa A. Leyva-Diaz, Daniel Hernández-Patlán, Bruno Solís-Cruz, Bishnu Adhikari, Young Min Kwon, Juan D. Latorre, Xóchitl Hernández-Velasco, Benjamín Fuente-Martínez, Billy M. Hargis, Raquel López‐Arellano, Guillermo Téllez–Isaías
Software Mentions: 4
Published: almost 4 years ago

10.3390/cancers12113425

The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma
Cited by: 29
Author(s): Zigui Chen, Pak-Kin Wong, Cherrie W K Ng, Linda Lan, S. Fung, Jing W Li, Liuyang Cai, Pu Liao, Qianqian Mou, Sunny H. Wong, William Ka Kei Wu, Ryan J. Li, Katie Meehan, Vivian Wai Yan Lui, Chit Chow, Kwok Wai Lo, Amy B.W. Chan, Siaw Shi Boon, Eric S. H. Lau, Zenon W C Yeung, K.C. Allen Chan, Eddy W.Y. Wong, Alfred Sze‐Lok Cheng, Jun Yu, Paul Kay Sheung Chan, Jason Ying Kuen Chan
Software Mentions: 4
Published: about 4 years ago

10.1186/s42523-021-00120-5

Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta)
Cited by: 7
Author(s): Klara Filek, Adriana Trotta, Romana Gračan, Antonio Di Bello, Marialaura Corrente, Sunčica Bosak
Software Mentions: 4
Published: about 3 years ago

10.1128/mSystems.00633-21

Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape
Cited by: 13
Author(s): Zhanshan Sam
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-020-60304-y

Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling
Cited by: 15
Author(s): Gábor Fidler, Emese Tolnai, Anikó Stágel, Judit Remenyik, László Stündl, Ferenc Gál, Sándor Bíró, Melinda Paholcsek
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-90863-7

Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea
Cited by: 12
Author(s): Danijela Šantić, Kasia Piwosz, Frano Matić, Ana Vrdoljak Tomaš, Jasna Arapov, Jason Dean, Mladen Šolić, Michal Koblížek, Grozdan Kušpilić, Stefanija Šestanović
Software Mentions: 4
Published: over 3 years ago

10.1016/j.csbj.2020.12.011

Active phase prebiotic feeding alters gut microbiota, induces weight-independent alleviation of hepatic steatosis and serum cholesterol in high-fat diet-fed mice
Cited by: 11
Author(s): Shreya Ghosh, Yifan Yang, Linghua Wang, Chenhong Zhang, Liping Zhao
Software Mentions: 4
Published: almost 4 years ago

10.1002/cam4.1965

Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development
Cited by: 62
Author(s): Talima Pearson, J. Gregory Caporaso, Monica Yellowhair, Nicholas A. Bokulich, Megha Padi, Denise J. Roe, Betsy C. Wertheim, Mark Linhart, Jessica A. Martinez, Cherae Bilagody, Heidie Hornstra, David S. Alberts, Peter Lance, Patricia A. Thompson
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-83851-4

Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice
Cited by: 30
Author(s): Payel Kundu, Eileen Ruth S. Torres, Keaton Stagaman, Kristin B. Kasschau, Mariam Okhovat, Sarah Holden, Samantha Ward, Kimberly A. Nevonen, Brett A. Davis, Takashi Saito, Takaomi C. Saido, Lucia Carbone, Thomas J. Sharpton, Jacob Raber
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-018-0584-3

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
Cited by: 59
Author(s): Justin D. Silverman, Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee, Lawrence A. David
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms8030438

The Interplay between Mucosal Microbiota Composition and Host Gene-Expression is Linked with Infliximab Response in Inflammatory Bowel Diseases
Cited by: 41
Author(s): Nikolas Dovrolis, George Michalopoulos, George Theodoropoulos, Konstantinos Arvanitidis, George Kolios, Leonardo Antonio Sechi, Aristidis G. Eliopoulos, Maria Gazouli
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms9061330

Dental Biofilm and Saliva Microbiome and Its Interplay with Pediatric Allergies
Cited by: 6
Author(s): Nicole Birgit Arweiler, Vivien Rahmel, Bilal Alashkar Alhamwe, Fahd Alhamdan, Michael Zemlin, Sébastien Boutin, Alexander H. Dalpke, Harald Renz
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9081739

Minimal Associations between Short-Term Dietary Intake and Salivary Microbiome Composition
Cited by: 2
Author(s): Judith Kim, Minyi Lee, Brittany L. Baldwin-Hunter, Quinn S. Solfisburg, Charles J. Lightdale, Tal Korem, Chin Hur, Julian A. Abrams
Software Mentions: 3
Published: over 3 years ago

10.1038/s41396-020-00883-w

Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter
Cited by: 5
Author(s): Darshan Neubauer, О. В. Колмакова, Jason N. Woodhouse, Robert Taube, Kai Mangelsdorf, Michail I. Gladyshev, Katrin Premke, Hans‐Peter Grossart
Software Mentions: 3
Published: almost 4 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 3 years ago

10.3390/nu13030820

Microbiota Changes in Fathers Consuming a High Prebiotic Fiber Diet Have Minimal Effects on Male and Female Offspring in Rats
Cited by: 3
Author(s): Faye Chleilat, Alana Schick, Raylene A. Reimer
Software Mentions: 3
Published: over 3 years ago

10.3390/ph14090931

Pilot Sub-Study of the Effect of Hepatitis C Cure by Glecaprevir/Pibrentasvir on the Gut Microbiome of Patients with Chronic Hepatitis C Genotypes 1 to 6 in the Mythen Study
Cited by: 4
Author(s): Bahtiyar Yılmaz, Lisa Ruckstuhl, Beat Müllhaupt, Lorenzo Magenta, Melanie Harrer Kuster, Olivier Clerc, Ralph Torgler, Nasser Semmo
Software Mentions: 3
Published: about 3 years ago

10.1007/s00248-019-01477-6

Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation
Cited by: 13
Author(s): Amisha T. Poret-Peterson, Nada Sayed, Nathaniel Glyzewski, Holly Forbes, Enid T. González-Orta, Daniel A. Kluepfel
Software Mentions: 3
Published: almost 5 years ago

10.1111/1751-7915.13702

Network analysis and functional estimation of the microbiome reveal the effects of cashew nut shell liquid feeding on methanogen behaviour in the rumen
Cited by: 9
Author(s): Koki Maeda, Van Thu Nguyen, Tomoyuki Suzuki, Keita Yamada, Kushi Kudo, Chie Hikita, Van Phong Le, Minh Chon Nguyen, Naohiro Yoshida
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0240336

Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene
Cited by: 10
Author(s): Harutaro Kenmotsu, Kiichi Uchida, Yuu Hirose, Toshihiko Eki
Software Mentions: 3
Published: about 4 years ago

10.3390/jof7040244

Microbiome Status of Cider-Apples, from Orchard to Processing, with a Special Focus on Penicillium expansum Occurrence and Patulin Contamination
Cited by: 10
Author(s): Reem Al Riachy, Caroline Strub, Noël Durand, Benjamin Guibert, Hugues Guichard, Florentin Constancias, Vincent Chochois, Félicie Lopez-Lauri, Angélique Fontana, Sabine Schorr‐Galindo
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0215918

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

10.3390/biom11070999

Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization
Cited by: 3
Author(s): Helena Torrell, Adrià Ceretó-Massagué, Polina Kazakova, Lorena García, Hector H. Palacios, Núria Canela
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.7767

Social environment and genetics underlie body site‐specific microbiomes of Yellowstone National Park gray wolves (Canis lupus)
Cited by: 6
Author(s): Alexandra L. DeCandia, Kira A. Cassidy, Daniel R. Stahler, Erin A. Stahler, Bridgett M. vonHoldt
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.6104

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities
Cited by: 22
Author(s): Janina Schenk, Nils Kleinbölting, Walter Traunspurger
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.isci.2021.102659

The impact of propagule pressure on whole community invasions in biomethane-producing communities
Cited by: 5
Author(s): Pawel Sierocinski, Jesica Soria Pascual, Daniel Padfield, Mike Salter, Angus Buckling
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.564408

Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life
Cited by: 10
Author(s): Stephanie D. Jurburg, Alex Bossers
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.653314

Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities
Cited by: 5
Author(s): Stanislav N. Iablokov, Pavel S. Novichkov, Andrei L. Osterman, Dmitry A. Rodionov
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2018.03331

Fecal Microbiota of Toxigenic Clostridioides difficile-Associated Diarrhea
Cited by: 28
Author(s): Marta Hernández, Mónica de Frutos, David Rodrı́guez-Làzaro, Luis López-Urrutia, Narciso M. Quijada, José María Eiros
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2020.00285

The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient
Cited by: 27
Author(s): Dayu Zou, Jie Pan, Zongbao Liu, Chuanlun Zhang, Hongbin Liu, Meng Li
Software Mentions: 3
Published: over 4 years ago

10.1128/AEM.02200-17

Promising Prebiotic Candidate Established by Evaluation of Lactitol, Lactulose, Raffinose, and Oligofructose for Maintenance of a Lactobacillus-Dominated Vaginal Microbiota
Cited by: 48
Author(s): Stephanie L. Collins, Amy McMillan, Shannon Seney, Charlotte van der Veer, Remco Kort, Mark W. Sumarah, Gregor Reid
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.645070

Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes
Cited by: 4
Author(s): Yue Dong, Yixuan Li, Pinjing He, Zongling Wang, Shiliang Fan, Zhixin Zhang, Xuelei Zhang, Qinzeng Xu
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2020.586148

Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM
Cited by: 8
Author(s): Marta M. Varela, Tamara Rodríguez‐Ramos, Elisa Guerrero-Feijóo, Mar Nieto‐Cid
Software Mentions: 3
Published: about 4 years ago

10.3389/fvets.2019.00308

A Pine Enhanced Biochar Does Not Decrease Enteric CH4 Emissions, but Alters the Rumen Microbiota
Cited by: 24
Author(s): Stephanie A. Terry, Gabriel de Oliveira Ribeiro, Robert J. Gruninger, A. V. Chaves, K. A. Beauchemin, E. K. Okine, Tim A. McAllister
Software Mentions: 3
Published: about 5 years ago

10.1080/19490976.2021.1966261

Impact of healthy aging on active bacterial assemblages throughout the gastrointestinal tract
Cited by: 5
Author(s): Kerstin Schütte, Christian Schulz, Ramiro Vílchez-Vargas, Riccardo Vasapolli, Frederike Palm, Bianca Simon, Dirk Schomburg, Anke Lux, Robert Geffers, Dietmar H. Pieper, Alexander Link, Peter Malfertheiner
Software Mentions: 3
Published: almost 4 years ago

10.1210/clinem/dgaa382

Effect of Gut Microbiota and PNPLA3 rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth
Cited by: 39
Author(s): Ayesha Monga Kravetz, Todd Testerman, Brittany Galuppo, Joerg Graf, Bridget Pierpont, Stephan Siebel, Richard Feinn, Nicola Santoro
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-25081-9

Diversity, structure and sources of bacterial communities in earthworm cocoons
Cited by: 19
Author(s): Manuel Aira, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-26313-8

Impact of the griffithsin anti-HIV microbicide and placebo gels on the rectal mucosal proteome and microbiome in non-human primates
Cited by: 26
Author(s): Lauren Girard, Kenzie Birse, Johanna B. Holm, Pawel Gajer, Mike Humphrys, David Garber, Patricia C. Guenthner, Laura Noël‐Romas, Max Abou, Stuart McCorrister, Garrett Westmacott, Lin Wang, Lisa C. Rohan, Nobuyuki Matoba, Janet M. McNicholl, Kenneth E. Palmer, Jacques Ravel, Adam Burgener
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-43280-w

Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota
Cited by: 78
Author(s): Sang‐Won Lee, Tae-Min La, Hong-Jae Lee, In‐Soo Choi, Chang‐Seon Song, Seung‐Yong Park
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-46070-6

Contrasting microbial community responses to salinization and straw amendment in a semiarid bare soil and its wheat rhizosphere
Cited by: 18
Author(s): Márton Szoboszlay, Astrid Näther, Bei Liu, Angel Carrillo, Thelma Castellanos, Kornelia Smalla, Zhongjun Jia, Christoph C. Tebbe
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-57367-x

Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics
Cited by: 28
Author(s): Reilly O. Cooper, Clayton E. Cressler
Software Mentions: 3
Published: almost 5 years ago

10.3390/nu12051532

Human Milk Oligosaccharide Supplementation Affects Intestinal Barrier Function and Microbial Composition in the Gastrointestinal Tract of Young Sprague Dawley Rats
Cited by: 19
Author(s): Faye Chleilat, Teja Klančič, Kyle Ma, Alana Schick, Jodi E. Nettleton, Raylene A. Reimer
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-88823-2

Evaluation of changes in intestinal microbiota in Crohn’s disease patients after anti-TNF alpha treatment
Cited by: 17
Author(s): Laura Sanchis-Artero, Juan F. Martínez-Blanch, Sergio Manresa-Vera, Ernesto Cortés‐Castell, Marina Valls-Gandia, Marisa Iborra, Jose Maria Paredes-Arquiola, Maia Boscá-Watts, José María Huguet, Rafael Gil-Borrás, Josefa Rodríguez-Morales, Xavier Cortés-Rizo
Software Mentions: 3
Published: over 3 years ago

10.1186/s42523-020-00062-4

Changes in the faecal microbiome of pied tamarins (Saguinus bicolor) associated with chronic, recurrent diarrhoea and weight loss
Cited by: 4
Author(s): Peter Richards‐Rios, Paul Wigley, Javier López, Dominic Wormell, Alberto Rodríguez Barbón
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-94468-y

Comparative analysis of the bronchoalveolar microbiome in Portuguese patients with different chronic lung disorders
Cited by: 5
Author(s): Susana Seixas, Allison R. Kolbe, Sílvia Cristina Vieira Gomes, Maria Sucena, Catarina Sousa, Luís Rodrigues, Gilberto Teixeira, Paula Pinto, Tiago Abreu, Cristina Bárbara, Júlio Semedo, Leonor Mota, Ana Sofía Carvalho, Rune Matthiesen, Patrícia Marques, Marcos Pérez‐Losada
Software Mentions: 3
Published: over 3 years ago

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