bioconductor: phyloseq | Projects

10.3389/fmicb.2021.662783

Metagenomic Investigation Uncovers Presence of Probiotic-Type Microbiome in Kalparasa® (Fresh Unfermented Coconut Inflorescence Sap)
Cited by: 5
Author(s): Madhuban Gopal, Sandeep Shil, Alka Gupta, K. B. Hebbar, M. Arivalagan
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.00973

Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits
Cited by: 15
Author(s): Tehya Read, Laurence Fortun-Lamothe, Géraldine Pascal, Malo Le Boulch, Laurent Cauquil, Béatrice Gabinaud, Carole Bannelier, Elodie Balmisse, Nicolas Destombes, Olivier Bouchez, Thierry Gidenne, Sylvie Combes
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.18820

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China
Cited by: 134
Author(s): Zhigang Ren, Jianwen Jiang, Haiyang Xie, Ang Li, Haifeng Lü, Shaoyan Xu, Lin Zhou, Hua Zhang, Guangying Cui, Xinhua Chen, Yuanxing Liu, Liming Wu, Nan Qin, Ranran Sun, Wei Wang, Weilin Wang, Shusen Zheng
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-51293-8

Beneficial effects of Lactobacillus reuteri 6475 on bone density in male mice is dependent on lymphocytes
Cited by: 23
Author(s): Fraser L. Collins, Naiomy Deliz Rios‐Arce, Jonathan D. Schepper, A. Daniel Jones, Laura Schaefer, Robert A. Britton, Laura R. McCabe, Narayanan Parameswaran
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2019.00585

A New Method to Correct for Habitat Filtering in Microbial Correlation Networks
Cited by: 17
Author(s): Vanessa Brisson, Jennifer E. Schmidt, Trent Northen, John P. Vogel, Amélie C. M. Gaudin
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2021.705436

A Central Role for Atg5 in Microbiota-Dependent Foxp3+ RORγt+ Treg Cell Preservation to Maintain Intestinal Immune Homeostasis
Cited by: 4
Author(s): Carlos Plaza-Sirvent, Bei Zhao, Alisha W. Bronietzki, Marina C. Pils, Neda Tafrishi, Marc Schuster, Till Strowig, Ingo Schmitz
Software Mentions: 1
Published: about 3 years ago

10.1186/s12877-020-1472-9

Effect of a polyphenol-rich dietary pattern on intestinal permeability and gut and blood microbiomics in older subjects: study protocol of the MaPLE randomised controlled trial
Cited by: 35
Author(s): Simone Guglielmetti, Stefano Bernardi, Cristian Del Bò, Antonio Cherubini, Marisa Porrini, Giorgio Gargari, Nicole Hidalgo‐Liberona, Raúl González‐Domínguez, Gregorio Peron, Raúl Zamora-Ros, Mark S. Winterbone, Benjamin Kirkup, Paul A. Kroon, Cristina Andrés‐Lacueva, Patrizia Riso
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2020.01421

The Impact of Oral Sodium Chloride Supplementation on Thrive and the Intestinal Microbiome in Neonates With Small Bowel Ostomies: A Prospective Cohort Study
Cited by: 12
Author(s): T. Trautmann, Corinna Bang, André Franke, Deirdre Vincent, Konrad Reinshagen, Michael Boettcher
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2020.01330

Intestinal Inflammation Induced by Soybean Meal Ingestion Increases Intestinal Permeability and Neutrophil Turnover Independently of Microbiota in Zebrafish
Cited by: 14
Author(s): Camila J. Solís, M. Kristina Hamilton, Mario Caruffo, Juan P. García-López, Paola Navarrete, Karen Guillemin, Carmen G. Feijóo
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-95842-6

Characterization of the virome associated with Haemagogus mosquitoes in Trinidad, West Indies
Cited by: 7
Author(s): Renee Ali, J. Jayaraj, Azad Mohammed, C. Chinnaraja, Christine V. F. Carrington, David W. Severson, Adesh Ramsubhag
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.543260

Microbial Signatures in Deep CO2-Saturated Miocene Sediments of the Active Hartoušov Mofette System (NW Czech Republic)
Cited by: 5
Author(s): Qi Liu, Karsten Adler, Daniel Lipus, Horst Kämpf, Robert Bussert, Birgit Plessen, Hans-Martin Schulz, Patryk Krauze, Fabian Horn, Dirk Wagner, Kai Mangelsdorf, Mashal Alawi
Software Mentions: 1
Published: almost 4 years ago

10.3390/ani10111955

Compositional and Functional Comparisons of the Microbiota in the Colostrum and Mature Milk of Dairy Goats
Cited by: 9
Author(s): Zhannur Niyazbekova, Xiaoting Yao, Mingjie Liu, Nomin Bold, Juan-Zhen Tong, Jianjun Chang, Yiping Wen, Li Li, Yong Wang, Dekun Chen, Wentao Ma
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0114804

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries
Cited by: 85
Author(s): Patricio Jeraldo, Krishna R. Kalari, Xianfeng Chen, Jaysheel Bhavsar, Ashutosh K. Mangalam, Bryan A. White, Heidi Nelson, Jean Pierre A. Kocher, Nicholas Chia
Software Mentions: 1
Published: almost 10 years ago

10.1042/BSR20210362

Gut microbial alterations in neonatal jaundice pre- and post-treatment
Cited by: 3
Author(s): Juan Ding, Xiao Ma, Liping Han, Xixi Zhao, Ang Li, Xin Qi, Weining Lian, Zhen Li, Hongyan Ren, Zhigang Ren
Software Mentions: 1
Published: over 3 years ago

10.1080/19490976.2021.1893113

SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota
Cited by: 68
Author(s): Harry Sokol, Vanessa Contreras, Pauline Maisonnasse, Aurore Desmons, Benoît Delache, Valentin Sencio, Arnaud Machelart, Angela Brisebarre, Lydie Humbert, Lucie Deryuter, Emilie Gauliard, Séverine Heumel, Dominique Rainteau, Nathalie Dereuddre‐Bosquet, Elisabeth Menu, Raphaël Ho Tsong Fang, Antonin Lamazière, Loïc Brot, Céline Wahl, Cyriane Oeuvray, Nathalie Rolhion, Sylvie van der Werf, Stéphanie Ferreira, Roger Le Grand, François Trottein
Software Mentions: 1
Published: almost 4 years ago

10.1093/gerona/glx197

Impact of Age-Related Mitochondrial Dysfunction and Exercise on Intestinal Microbiota Composition
Cited by: 27
Author(s): David Houghton, Christopher J. Stewart, Craig Stamp, Andrew Nelson, Nadim J. Ajami, Joseph F. Petrosino, Anil Wipat, Michael I. Trenell, Doug M. Turnbull, Laura C. Greaves
Software Mentions: 1
Published: about 7 years ago

10.3390/biomedicines9010066

Concurrent Prebiotic Intake Reverses Insulin Resistance Induced by Early-Life Pulsed Antibiotic in Rats
Cited by: 5
Author(s): Teja Klančič, Isabelle Laforest‐Lapointe, Jennifer Wong, Ashley C. Choo, Jodi E. Nettleton, Faye Chleilat, Marie‐Claire Arrieta, Raylene A. Reimer
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00851-19

Microbial Diversity of the Red Sea Urchin Loxechinus albus during Controlled Farming in Puerto Montt, Chile, Using 16S rRNA Gene Amplicon Sequencing
Cited by: 2
Author(s): Daniel A. Medina, Rudy Suárez, Marcos Godoy
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms19020565

Sjögren-Like Lacrimal Keratoconjunctivitis in Germ-Free Mice
Cited by: 54
Author(s): Changjun Wang, Mahira Zaheer, Fang Bian, Darin Quach, Alton G. Swennes, Robert A. Britton, Stephen C. Pflugfelder, Cintia S. de Paiva
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms7060169

The Influence of Microfungi on the Mycelial Growth of Ectomycorrhizal Fungus Tricholoma matsutake
Cited by: 6
Author(s): Seung‐Yoon Oh, Myung Soo Park, Young Woon Lim
Software Mentions: 1
Published: over 5 years ago

10.1155/2019/3827360

Characterization of Microbial Communities in a Dairy Farm Matrix in Ningxia, China, by 16S rDNA Analysis
Cited by: 3
Author(s): Wen Zhang, Li Wu, Ma Chenjie, Xiaoling Wu, Xunde Li, Jin Zeng, Guangcun Deng, Yujiong Wang
Software Mentions: 1
Published: about 5 years ago

10.1128/MRA.00178-21

16S rRNA Gene Amplicon Sequencing Data from Flooded Rice Paddy Mesocosms Treated with Different Silicon-Rich Soil Amendments
Cited by: 2
Author(s): Gretchen E. Dykes, Clara S. Chan, Angelia L. Seyfferth
Software Mentions: 1
Published: over 3 years ago

10.3389/fcimb.2021.720790

Oral Phenotype and Salivary Microbiome of Individuals With Papillon–Lefèvre Syndrome
Cited by: 1
Author(s): Giulia Melo Lettieri, Luander Medrado Santiago, Giancarlo Crosara Lettieri, Luiz Gustavo dos Anjos Borges, Letícia Marconatto, Laudimar Alves de Oliveira, Nailê Damé‐Teixeira, Loise Pedrosa Salles
Software Mentions: 1
Published: about 3 years ago

10.3389/fcimb.2019.00197

Evaluation of Methods for the Extraction of Microbial DNA From Vaginal Swabs Used for Microbiome Studies
Cited by: 26
Author(s): Valentina Di Mattei, Selvasankar Murugesan, Muna Al Hashmi, Rebecca Mathew, Nicola C. James, Parul Singh, Manoj Kumar, Arun Prasath Lakshmanan, Annalisa Terranegra, Souhaila Al Khodor, Sara Tomei
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0124726

Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation
Cited by: 53
Author(s): David R. Elliott, S. J. M. Caporn, Felix Nwaishi, R. Henrik Nilsson, Robin Sen
Software Mentions: 1
Published: over 9 years ago

10.1093/bioinformatics/btu693

Seed: a user-friendly tool for exploring and visualizing microbial community data
Cited by: 7
Author(s): Daniel Beck, Christopher Dennis, James A. Foster
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2018.00048

Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract
Cited by: 129
Author(s): Li Zhang, Weida Wu, Yuan‐Kun Lee, Jingjing Xie, Hongfu Zhang
Software Mentions: 1
Published: almost 7 years ago

10.7150/thno.43716

Parthenolide ameliorates colon inflammation through regulating Treg/Th17 balance in a gut microbiota-dependent manner
Cited by: 123
Author(s): Yaojiang Liu, Bo Tang, Fengchao Wang, Li Tang, Yuanyuan Lei, Ya Luo, Shengjie Huang, Min Ye, Ling-Yi Wu, Wei Wang, Shuang Liu, Shiming Yang, Xiao‐Fan Zhao
Software Mentions: 1
Published: almost 5 years ago

10.3389/fbioe.2015.00027

The Microbial Community of a Passive Biochemical Reactor Treating Arsenic, Zinc, and Sulfate-Rich Seepage
Cited by: 80
Author(s): Susan A. Baldwin, Maryam Khoshnoodi, Maryam Rezadehbashi, Marcus Taupp, Steven J. Hallam, Al Mattes, Hamed Sanei
Software Mentions: 1
Published: over 9 years ago

10.3389/fbioe.2020.565311

Anaerobic Conversion of Saline Phenol-Containing Wastewater Under Thermophilic Conditions in a Membrane Bioreactor
Cited by: 9
Author(s): Julian Muñoz Sierra, Victor S. Garcia Rea, Daniel Cerqueda‐García, Henri Spanjers, Jules B. van Lier
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-63688-z

Rebaudioside affords hepatoprotection ameliorating sugar sweetened beverage- induced nonalcoholic steatohepatitis
Cited by: 12
Author(s): Dong Xi, Jashdeep Bhattacharjee, Rosa Marı́a Salazar-González, Soyoung Park, Alice Jang, Mikako Warren, Russell Merritt, Sonia Michail, Sébastien G. Bouret, Rohit Kohli
Software Mentions: 1
Published: over 4 years ago

10.1007/s10532-021-09940-3

2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples
Cited by: 13
Author(s): Gunther Brucha, Andrea Aldas-Vargas, Zacchariah Ross, Peng Peng, Siavash Atashgahi, Hauke Smidt, Alette Langenhoff, Nora B. Sutton
Software Mentions: 1
Published: over 3 years ago

10.3390/foods10030635

Characterization of Artisanal Spontaneous Sourdough Wheat Bread from Central Greece: Evaluation of Physico-Chemical, Microbiological, and Sensory Properties in Relation to Conventional Yeast Leavened Wheat Bread
Cited by: 18
Author(s): Pavlina Katsi, Ioanna S. Kosma, Sofia Michailidou, Anagnostis Argiriou, Anastasia V. Badeka, Michael G. Kontominas
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-64788-6

The role of the adaptor molecule STING during Schistosoma mansoni infection
Cited by: 6
Author(s): Cristina de Fátima de Oliveira Brum Augusto de Souza, Rodrigo C. O. Sanches, Natan R. G. Assis, Fábio V. Marinho, Fábio S. Mambelli, Suellen B. Morais, Enrico G. T. Gimenez, Erika S. Guimarães, Thaís Castro, Sérgio C. Oliveira
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-65321-5

No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus)
Cited by: 5
Author(s): T. Franciscus Scheelings, Robert J. Moore, Thi Thu Hao Van, Marcel Klaassen, Richard D. Reina
Software Mentions: 1
Published: over 4 years ago

10.1007/s12223-021-00866-0

Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil
Cited by: 12
Author(s): Paul Iturbe-Espinoza, Bernd W. Brandt, Martin Braster, Matthijs Bonte, David M. Brown, Rob J.M. van Spanning
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0227707

Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer
Cited by: 20
Author(s): Ruizhong Miao, Taylor C. Badger, Kathleen Groesch, Paula L. Diaz-Sylvester, Teresa Wilson, Allen Ghareeb, Jongjin Anne Martin, Melissa Cregger, Michael Welge, Colleen Bushell, Loretta Auvil, Ruoqing Zhu, Laurent Brard, Andrea Braundmeier-Fleming
Software Mentions: 1
Published: almost 5 years ago

10.1128/mSystems.00232-21

Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System
Cited by: 5
Author(s): Thiyagarajan Gnanasekaran, Juliana Assis Geraldo, David Wilczek Ahrenkiel, Camila Alvarez-Silva, Carmen Saenz, Anzar Khan, Obaida Hanteer, Vithiagaran Gunalan, Kajetan Trošt, Thomas Moritz, Manimozhiyan Arumugam
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-020-66452-5

Effect of life stage and pesticide exposure on the gut microbiota of Aedes albopictus and Culex pipiens L
Cited by: 12
Author(s): Elijah O. Juma, Brian F. Allan, Chang‐Hyun Kim, Chris Stone, Christopher A. Dunlap, Ephantus J. Muturi
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.01869

Autoprobiotics as an Approach for Restoration of Personalised Microbiota
Cited by: 23
Author(s): Alexander Suvorov, Alena Karaseva, М. П. Котылева, Yulia Kondratenko, N. S. Lavrenova, Anton Korobeynikov, Petr Kozyrev, Tatiana Kramskaya, Galina Leontieva, I. V. Kudryavtsev, Deyin Guo, Alla Lapidus, Е. И. Ермоленко
Software Mentions: 1
Published: about 6 years ago

10.1111/eva.13158

Invasive freshwater snails form novel microbial relationships
Cited by: 7
Author(s): Laura Bankers, Dylan Dahan, Maurine Neiman, Claire Adrian‐Tucci, Crystal L. Frost, Gregory D. D. Hurst, Kayla C. King
Software Mentions: 1
Published: about 4 years ago

10.3390/toxins10110443

Impact of Dinophysis acuminata Feeding Mesodinium rubrum on Nutrient Dynamics and Bacterial Composition in a Microcosm
Cited by: 9
Author(s): Gao Rong Han, Chenlei Hua, Mengmeng Tong
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms8091394

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne
Cited by: 9
Author(s): Tong Liu, Anna Schnürer, Johanna Björkmalm, Karin Willquist, Emma Kreuger
Software Mentions: 1
Published: about 4 years ago

10.1186/s40793-020-00369-4

Falling bacterial communities from the atmosphere
Cited by: 24
Author(s): Cheolwoon Woo, Naomichi Yamamoto
Software Mentions: 1
Published: almost 4 years ago

10.1002/mbo3.672

Succession of embryonic and the intestinal bacterial communities of Atlantic salmon (Salmo salar) reveals stage‐specific microbial signatures
Cited by: 59
Author(s): Jep Lokesh, Viswanath Kiron, Detmer Sipkema, Jorge M.O. Fernandes, Truls Moum
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pntd.0006730

Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata
Cited by: 35
Author(s): Lucia C. Orantes, Carlota Monroy, Patricia L. Dorn, Lori Stevens, Donna M. Rizzo, L. A. Morrissey, John Hanley, Antonieta Rodas, Bethany Richards, Kimberly F. Wallin, Sara Helms Cahan
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pbio.3001070

Gut bacteria-derived 5-hydroxyindole is a potent stimulant of intestinal motility via its action on L-type calcium channels
Cited by: 17
Author(s): Barbora Waclawiková, Amber Bullock, Markus Schwalbe, Carmen Aranzamendi, Sieger Adriaan Nelemans, Gertjan van Dijk, Sahar El Aidy
Software Mentions: 1
Published: almost 4 years ago

10.14814/phy2.14159

Phenotypic effects of dietary stress in combination with a respiratory chain bypass in mice
Cited by: 7
Author(s): Praveen K. Dhandapani, Ari Löytynoja, Lars Paulín, Nahid Akhtar Khan, Anu Suomalainen, Petri Auvinen, Éric Dufour, Marten Szibor, Howard T. Jacobs
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-73156-3

Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
Cited by: 20
Author(s): Karol Perlejewski, Iwona Bukowska-Ośko, Małgorzata Rydzanicz, Agnieszka Pawełczyk, Kamila Caraballo Cortѐs, Sylwia Osuch, Marcin Paciorek, Tomasz Dzieciątkowski, Marek Radkowski, Tomasz Laskus
Software Mentions: 1
Published: about 4 years ago

10.1128/AEM.00318-21

Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community
Cited by: 17
Author(s): Beatriz Andreo-Jiménez, M.T. Schilder, E.H. Nijhuis, Dennis E. te Beest, J. Bloem, J.H.M. Visser, Gera van Os, Karst M. Brolsma, Wietse de Boer, J. Postma
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.00824-17

First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin
Cited by: 149
Author(s): Kaisa Koskinen, Manuela R. Păuşan, A. Perras, Michael W. Beck, Corinna Bang, Maximilian Mora, Anke Schilhabel, Ruth A. Schmitz, Christine Moissl-Eichinger
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms9040727

Changes in Gut Microbiota after a Four-Week Intervention with Vegan vs. Meat-Rich Diets in Healthy Participants: A Randomized Controlled Trial
Cited by: 15
Author(s): Eva Kohnert, Clemens Kreutz, Nadine Binder, Luciana Hannibal, Gregor Gorkiewicz, Alexander Müller, Maximilian Andreas Storz, Roman Huber, Ann-Kathrin Lederer
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-74137-2

Optimized DNA extraction and purification method for characterization of bacterial and fungal communities in lung tissue samples
Cited by: 14
Author(s): Vicente Pérez‐Brocal, Fabien Magne, Susana Ruiz-Ruiz, Carolina A. Ponce, R. Bustamante, Viviana San Martin, Mireya Gutierrez, Gianna Gatti, Sergio L. Vargas, Andrés Moya
Software Mentions: 1
Published: about 4 years ago

10.1128/AEM.02883-19

An In Vitro Pipeline for Screening and Selection of Citrus-Associated Microbiota with Potential Anti-“ Candidatus Liberibacter asiaticus” Properties
Cited by: 25
Author(s): Alex A. Blacutt, Nichole Ginnan, Tyler Dang, Sohrab Bodaghi, Georgios Vidalakis, Paul Ruegger, Beth B. Peacock, Polrit Viravathana, Flávia Campos Freitas Vieira, Christopher Drozd, Barbara Jablonska, James Borneman, Greg McCollum, Jennifer Cordoza, Jeremiah Meloch, Victoria Berry, Lia Lozano Salazar, Katherine N. Maloney, Philippe E. Rolshausen, M. Caroline Roper
Software Mentions: 1
Published: over 4 years ago

10.1186/s12979-019-0145-z

Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1−/Δ7 mice
Cited by: 117
Author(s): Benthe van der Lugt, Adriaan A. van Beek, Steven Aalvink, Ben Meijer, Bruno Sovran, Wilbert P. Vermeij, Renata M. C. Brandt, Willem M. de Vos, H.F.J. Savelkoul, Wilma T. Steegenga, Clara Belzer
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.6657

Robust and automatic definition of microbiome states
Cited by: 12
Author(s): Beatriz García-Jiménez, Mark D. Wilkinson
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms7080217

Investigation of the Potential Effects of Host Genetics and Probiotic Treatment on the Gut Bacterial Community Composition of Aquaculture-raised Pacific Whiteleg Shrimp, Litopenaeus vannamei
Cited by: 13
Author(s): Angela Landsman, Benoit St‐Pierre, Misael Rosales-Leija, Michael L. Brown, William R. Gibbons
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2021.674214

A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border
Cited by: 15
Author(s): Amity G. Zimmer‐Faust, Joshua A. Steele, Xianyi Xiong, Christopher Staley, Madison Griffith, Michael J. Sadowsky, Margarita Díaz, John F. Griffith
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.635781

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions
Cited by: 46
Author(s): Isabel Moreno-Indias, Leo Lahti, Miroslava Nedyalkova, Ilze Elbere, Gennady V. Roshchupkin, Muhamed Adilović, Önder Aydemir, Burcu Bakır-Güngör, Enrique Carrillo de Santa Pau, Domenica D’Elia, Mahesh S. Desai, Laurent Falquet, Aycan Gündoğdu, Karel Hron, Thomas Klammsteiner, Marta B. Lopes, Laura Judith Marcos-Zambrano, Cláudia Marques, Mike J. Mason, Patrick May, Lejla Pašić, Gianvito Pio, Sándor Pongor, Vasilis J. Promponas, Piotr Przymus, Julio Sáez-Rodríguez, Alexia Sampri, Rajesh Shigdel, Blaž Stres, Ramona Suharoschi, Jaak Truu, Ciprian-Octavian Truică, Baiba Vilne, Dimitriοs Vlachakis, Ercüment Yılmaz, Georg Zeller, Aldert Zomer, David Green, Marcus J. Claesson
Software Mentions: 1
Published: almost 4 years ago

10.3390/genes10120971

Human Endometrial Microbiota at Term of Normal Pregnancies
Cited by: 31
Author(s): Claudia Leoni, O Ceci, Caterina Manzari, Bruno Fosso, Mariateresa Volpicella, Alessandra Ferrari, Fiorella Paola, Graziano Pesole, Ettore Cicinelli, Luigi Ceci
Software Mentions: 1
Published: almost 5 years ago

10.3390/md17120680

The Effect of Increasing Inclusion Levels of a Fucoidan-Rich Extract Derived from Ascophyllum nodosum on Growth Performance and Aspects of Intestinal Health of Pigs Post-Weaning
Cited by: 9
Author(s): Ruth Rattigan, T. Sweeney, Stafford Vigors, Kevin Thornton, Gaurav Rajauria, O'Doherty Ajv
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.dib.2020.106171

16S rRNA gene amplicon dataset of prokaryotic communities from a subantarctic marine ecosystem: Ushuaia Bay and surrounding waters
Cited by: 0
Author(s): Clara Natalia Rodríguez-Flórez, Andrea Malits, Mariana Lozada
Software Mentions: 1
Published: about 4 years ago

10.1177/1753425919826367

The NLRP3 inflammasome mediates DSS-induced intestinal inflammation in Nod2 knockout mice
Cited by: 23
Author(s): Ben Umiker, Hyun‐Hee Lee, Julia Cope, Nadim J. Ajami, Jean Lainé, Christine Fregeau, Heidi Ferguson, Stephen E. Alves, Nunzio Sciammetta, Melanie A. Kleinschek, M Salmon
Software Mentions: 1
Published: almost 6 years ago

10.3389/fvets.2021.668120

A Multiomic Approach to Investigate the Effects of a Weight Loss Program on the Intestinal Health of Overweight Horses
Cited by: 6
Author(s): Nicola Walshe, Raúl Cabrera‐Rubio, Roisin Collins, Antonella Puggioni, V. Gath, Fiona Crispie, Paul D. Cotter, Lorraine Brennan, Grace Mulcahy, Vivienne Duggan
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.02720-20

Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats
Cited by: 5
Author(s): Chequita N. Brooks, Erin K. Field
Software Mentions: 1
Published: almost 4 years ago

10.1002/clt2.12041

Allergy‐related diseases and early gut fungal and bacterial microbiota abundances in children
Cited by: 2
Author(s): Kasper Schei, Melanie Rae Simpson, Torbjørn Øien, Saideh Salamati, Knut Rudi, Rønnaug Ødegård
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.604395

Microbial Diversity and Activity During the Biodegradation in Seawater of Various Substitutes to Conventional Plastic Cotton Swab Sticks
Cited by: 23
Author(s): Justine Jacquin, Nolwenn Callac, Jingguang Cheng, Carolane Giraud, Yonko Gorand, Clément Denoual, Mireille Pujo‐Pay, Pascal Conan, Anne-Leïla Meistertzheim, Valérie Barbe, Stéphane Bruzaud, Jean-François Ghiglione
Software Mentions: 1
Published: over 3 years ago

10.3389/fvets.2019.00029

Performance, Fermentation Characteristics and Composition of the Microbiome in the Digest of Piglets Kept on a Feed With Humic Acid-Rich Peat
Cited by: 12
Author(s): Christian Visscher, Julia Hankel, Andrea Nies, Birgit Keller, Eric Galvez, Till Strowig, Christoph A. Keller, Gerhard Breves
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13099-020-00352-x

Association of antimicrobial resistance and gut microbiota composition in human and non-human primates at an urban ecotourism site
Cited by: 8
Author(s): Chun Wie Chong, A. H. S. Alkatheeri, Niaz Ali, Z. H. Tay, Y. L. Lee, Sharmini Julita Paramasivam, Kamalan Jeevaratnam, Wai Yee Low, Swee Hua Erin Lim
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms20184415

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community
Cited by: 6
Author(s): Anna Szafranek-Nakonieczna, Anna Pytlak, Jarosław Grządziel, Adam Kubaczyński, Artur Banach, Andrzej Górski, Weronika Goraj, Agnieszka Kuźniar, Anna Gałązka, Zofia Stępniewska
Software Mentions: 1
Published: about 5 years ago

10.7554/eLife.64237

The gut microbiota is a transmissible determinant of skeletal maturation
Cited by: 22
Author(s): Abdul Malik Tyagi, Trevor Darby, Emory Hsu, Mingcan Yu, Subhashis Pal, Hamid Y. Dar, Jau‐Yi Li, Jonathan Adams, Rheinallt Jones, Roberto Pacifici
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.7661

Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs
Cited by: 25
Author(s): Jessica K. Jarett, Anne Carlson, Mariana Rossoni Serao, Jessica Strickland, Laurie Serfilippi, Holly H. Ganz
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2018.00567

Inhibitory Effects of Sulfate and Nitrate Reduction on Reductive Dechlorination of PCP in a Flooded Paddy Soil
Cited by: 22
Author(s): Yan Xu, Lili Xue, Qi Ye, Ashley E. Franks, Min Zhu, Xi Feng, Jianming Xu, Yan He
Software Mentions: 1
Published: over 6 years ago

10.1038/s41396-020-0734-z

Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat
Cited by: 13
Author(s): Judith M. Klatt, Gonzalo V. Gomez‐Saez, Steffi Meyer, Petra Pop Ristova, Pelin Yilmaz, Michael S. Granitsiotis, Jennifer L. Macalady, Gaute Lavik, Lùbos Polerecký, Solveig I Bühring
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.5961

Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA
Cited by: 15
Author(s): Alexander S. Honeyman, Maria L. Day, John R. Spear
Software Mentions: 1
Published: about 6 years ago

10.1186/s40168-020-00987-7

Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium
Cited by: 21
Author(s): Nsa Dada, Natapong Jupatanakul, Guillaume Minard, Sarah M. Short, Jewelna Akorli, Luis Martínez Villegas
Software Mentions: 1
Published: almost 4 years ago

10.3390/jof6040273

Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts
Cited by: 19
Author(s): Stephen A. James, Sarah Phillips, Andrea Telatin, David Baker, Rebecca Ansorge, Paul Clarke, Lindsay J. Hall, Simon R. Carding
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-86177-3

Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu “Sajino” Madre de Dios, Peru
Cited by: 8
Author(s): Jesús Rojas‐Jaimes, David Lindo-Seminario, Germán Correa-Núñez, Benoit Diringer
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0162803

Taxa of the Nasal Microbiome Are Associated with Influenza-Specific IgA Response to Live Attenuated Influenza Vaccine
Cited by: 60
Author(s): Hannah M. Salk, Whitney L. Simon, Nathaniel D. Lambert, Richard B. Kennedy, Diane E. Grill, Brian Kabat, Gregory A. Poland
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2021.637282

Coffee Consumption Modulates Amoxicillin-Induced Dysbiosis in the Murine Gut Microbiome
Cited by: 5
Author(s): Emma Diamond, Katharine Hewlett, Swathi Penumutchu, Alexei Belenky, Peter Belenky
Software Mentions: 1
Published: over 3 years ago

10.1080/20002297.2020.1830623

Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children
Cited by: 8
Author(s): Emily Skelly, Newell W. Johnson, Kostas Kapellas, Jeroen Kroon, Ratilal Lalloo, Laura S. Weyrich
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12866-020-01836-1

Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration
Cited by: 8
Author(s): Jing Li, Xiaoyue Zhang, Lin Xiao, Ke Liu, Yue Li, Ziwei Zhang, Qiang Chen, Xiaolin Ao, Decong Liao, Yunfu Gu, Menggen Ma, Xiumei Yu, Quanju Xiang, Ji Chen, Xiaoping Zhang, Tao Yang, Petri Penttinen, Ke Zhao
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0202636

Ammonia oxidizers in the sea-surface microlayer of a coastal marine inlet
Cited by: 5
Author(s): Shu-Kuan Wong, Minoru Ijichi, Ryo Kaneko, Kazuhiro Kogure, Koji Hamasaki
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0158622

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients
Cited by: 23
Author(s): Christian Munck, Jens Helby, Christian Grabow Westergaard, Celeste Porsbjerg, Vibeke Backer, Lars H. Hansen
Software Mentions: 1
Published: over 8 years ago

10.1128/mSphereDirect.00545-17

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice
Cited by: 36
Author(s): Darin Quach, Fraser L. Collins, Narayanan Parameswaran, Laura R. McCabe, Robert A. Britton
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-90251-1

Differential microbial assemblages associated with shikonin-producing Borage species in two distinct soil types
Cited by: 8
Author(s): Aliya Fazal, Minkai Yang, Zhongling Wen, Farman Ali, Ran Ren, Chenyu Hao, Xingyu Chen, Jiangyan Fu, Xuan Wang, Wencai Jie, Tongming Yin, Guihua Lü, Jinliang Qi, Yonghua Yang
Software Mentions: 1
Published: over 3 years ago

10.1128/mSphere.00092-18

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi
Cited by: 156
Author(s): Thomas A. Auchtung, Tatiana Fofanova, Christopher J. Stewart, Andrea K. Nash, Matthew C. Wong, Jonathan R. Gesell, Jennifer M. Auchtung, Nadim J. Ajami, Joseph F. Petrosino
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-020-04392-9

Microbiota characterization in Blastocystis-colonized and Blastocystis-free school-age children from Colombia
Cited by: 11
Author(s): Sergio Castañeda, Marina Muñoz, Ximena Villamizar, Paula C. Hernández, Luis Reinel Vásquez, Raúl Y. Tito, Juan David Ramírez
Software Mentions: 1
Published: about 4 years ago

10.3390/ani10122254

The Dynamic Changes of Gut Microbiota during the Perinatal Period in Sows
Cited by: 6
Author(s): Sun Lan, Yu Zhang, Wei Chen, Tian Lan, Yan Wang, Yinbao Wu, Xindi Liao, Jiandui Mi
Software Mentions: 1
Published: almost 4 years ago

10.1186/s42523-020-00059-z

Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota
Cited by: 13
Author(s): María Velasco-Galilea, Miriam Guivernau, M. Piles, Marc Viñas, O. Rafel, Armand Sánchez, Yuliaxis Ramayo-Caldas, Olga González‐Rodríguez, Juan Pablo Sánchez
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0173848

Alterations in airway microbiota in patients with PaO2/FiO2 ratio ≤ 300 after burn and inhalation injury
Cited by: 9
Author(s): Dana M. Walsh, Shaun D. McCullough, Scott Yourstone, Samuel Jones, Bruce A. Cairns, Corbin D. Jones, Ilona Jaspers, David Díaz-Sánchez
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0143603

Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China
Cited by: 132
Author(s): Xingdong Chen, Björn Winckler, Ming Lü, Hongwei Cheng, Ziyu Yuan, Yajun Yang, Li Jin, Ye W
Software Mentions: 1
Published: almost 9 years ago

10.3389/fmicb.2018.03010

Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences
Cited by: 62
Author(s): Adrián López-García, C. Pineda-Quiroga, Raquel Atxaerandio, Adrian Pérez, Itziar Hernández, A. García-Rodríguez, Óscar González-Recio
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2018.02435

Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility
Cited by: 38
Author(s): Blake W. Stamps, Menu B. Leddy, Megan H. Plumlee, Nur A. Hasan, Rita R. Colwell, John R. Spear
Software Mentions: 1
Published: about 6 years ago

10.3390/md18030157

Effect of a Laminarin Rich Macroalgal Extract on the Caecal and Colonic Microbiota in the Post-Weaned Pig
Cited by: 25
Author(s): Stafford Vigors, John V. O’Doherty, Ruth Rattigan, Mary J. McDonnell, Gaurav Rajauria, T. Sweeney
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.01131-20

Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration
Cited by: 32
Author(s): Karen Jordaan, Rachael Lappan, Xiyang Dong, Ian J. Aitkenhead, Sean K. Bay, Eleonora Chiri, Nimrod Wieler, Laura Meredith, Don A. Cowan, Steven L. Chown, Chris Greening
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2020.572314

Fungal Community, Metabolic Diversity, and Glomalin-Related Soil Proteins (GRSP) Content in Soil Contaminated With Crude Oil After Long-Term Natural Bioremediation
Cited by: 19
Author(s): Anna Gałązka, Jarosław Grządziel, Rafał Gałązka, Karolina Gawryjołek, Aleksandra Ukalska‐Jaruga, Bożena Smreczak
Software Mentions: 1
Published: about 4 years ago

10.1016/j.molmet.2018.07.002

Chronic d-serine supplementation impairs insulin secretion
Cited by: 24
Author(s): Lisa Suwandhi, Simone Hausmann, Alexander Braun, Tim Gruber, Silke S. Heinzmann, Eric Galvez, Achim Buck, Beata Legutko, Andreas Israel, Annette Feuchtinger, Elizabeth Haythorne, Harald Staiger, Martin Heni, Hans‐Ulrich Häring, Philippe Schmitt‐Kopplin, Axel Walch, Cristina García Cáceres, Matthias H. Tschöp, Guy A. Rutter, Till Strowig, Martin Elsner, Siegfried Ussar
Software Mentions: 1
Published: about 6 years ago

10.3390/ani11041184

Seasonal Influence on Rumen Microbiota, Rumen Fermentation, and Enteric Methane Emissions of Holstein and Jersey Steers under the Same Total Mixed Ration
Cited by: 9
Author(s): Mahfuzul Islam, Seon‐Ho Kim, A-Rang Son, S. Ramos, Chang Dae Jeong, Zhongtang Yu, Seungha Kang, Yong-Il Cho, Sung Sill Lee, Kwang-Keun Cho, Sang-Suk Lee
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.604173

Enhancing Phenol Conversion Rates in Saline Anaerobic Membrane Bioreactor Using Acetate and Butyrate as Additional Carbon and Energy Sources
Cited by: 7
Author(s): Victor S. Garcia Rea, Julian Muñoz Sierra, Laura M Fonseca Aponte, Daniel Cerqueda‐García, Kiyan M Quchani, Henri Spanjers, Jules B. van Lier
Software Mentions: 1
Published: almost 4 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702