bioconductor: phyloseq | Projects

10.1093/cid/ciz906

Gut Microbiota Features Associated With Campylobacter Burden and Postnatal Linear Growth Deficits in a Peruvian Birth Cohort
Cited by: 19
Author(s): Saba Rouhani, Nicholas W. Griffin, Pablo Peñataro Yori, Maribel Paredes Olórtegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H. Moulton, Eric R. Houpt, Michael J. Barratt, Margaret Kosek, Jeffrey I. Gordon
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms9040718

Effects of Clinical Wastewater on the Bacterial Community Structure from Sewage to the Environment
Cited by: 5
Author(s): Ilse Verburg, H. Pieter J. van Veelen, Karola Waar, John W. A. Rossen, Alex Friedrich, Lucía Hernández Leal, Silvia García-Cobos, Heike Schmitt
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.540404

The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra
Cited by: 10
Author(s): Ingeborg J. Klarenberg, Christoph Keuschnig, Denis Warshan, Ingibjörg S. Jónsdóttir, Oddur Vilhelmsson
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0226835

Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation
Cited by: 21
Author(s): Josefine Hantschel, Severin Weis, Karl‐Herbert Schäfer, Michael D. Menger, Matthias Kohl, Markus Egert, Matthias W. Laschke
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-82362-6

Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet
Cited by: 11
Author(s): Kelsey E. Witt, Karthik Yarlagadda, Julie M. Allen, Alyssa C. Bader, Mary Simon, Seppe Kuehn, Kelly S. Swanson, Tzu Wen L. Cross, Kristin M. Hedman, Stanley H. Ambrose, Ripan S. Malhi
Software Mentions: 4
Published: almost 4 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

10.3389/fmicb.2021.684233

Maternal Antibiotic Treatment Disrupts the Intestinal Microbiota and Intestinal Development in Neonatal Mice
Cited by: 8
Author(s): Chung-Ming Chen, Hsiu Chu Chou, Yu Yang
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2019.02874

Lifestyle-Induced Microbial Gradients: An Indian Perspective
Cited by: 6
Author(s): Rashmi Singh, Mohammed Monzoorul Haque, Sharmila S. Mande
Software Mentions: 4
Published: almost 5 years ago

10.1128/AEM.01336-19

Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction
Cited by: 11
Author(s): Maria Fernanda Campa, Stephen M. Techtmann, Mallory P. Ladd, Jun Yan, Megan Patterson, Amanda Garcia de Matos Amaral, Kimberly E. Carter, Nikea Ulrich, Christopher J. Grant, Robert L. Hettich, Regina Lamendella, Terry C. Hazen
Software Mentions: 4
Published: about 5 years ago

10.1186/s10020-021-00311-5

Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism
Cited by: 27
Author(s): Eder Orlando Méndez-Salazar, Janitzia Vázquez‐Mellado, Carlos S. Casimiro-Soriguer, Joaquín Dopazo, Cankut Çubuk, Yessica Zamudio-Cuevas, Adriana Francisco-Balderas, Karina Martínez-Flores, Javier Fernández‐Torres, Carlos Lozada, Carlos Pineda, Austreberto Sánchez-González, Luis H. Silveira, Ana I. Burguete-García, Citlalli Orbe-Orihuela, Alfredo Lagunas‐Martínez, Alonso Vazquez-Gomez, Alberto López‐Reyes, Berenice Palacios‐González, Gabriela Angélica Martínez‐Nava
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms9020221

The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time
Cited by: 9
Author(s): Ilaria Patuzzi, Massimiliano Orsini, Veronica Cibin, Sara Petrin, Eleonora Mastrorilli, Alessia Tiengo, Federica Gobbo, Salvatore Catania, Lisa Barco, Antonia Ricci, Carmen Losasso
Software Mentions: 4
Published: almost 4 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

10.3390/ani11010084

A Single Dose of Synbiotics and Vitamins at Birth Affects Piglet Microbiota before Weaning and Modifies Post-Weaning Performance
Cited by: 5
Author(s): Marion Girard, M. Tretola, Giuseppe Bee
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.6090

Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from theFirmicutesphylum
Cited by: 34
Author(s): Craig Anderson, Michelle E. Peterson, Rebekah A. Frampton, Simon Bulman, Sandi Keenan, D. Curtin
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.3536

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment
Cited by: 21
Author(s): Ellen M. Black, Michael S. Chimenti, Craig L. Just
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0181964

Regulation of type 1 diabetes development and B-cell activation in nonobese diabetic mice by early life exposure to a diabetogenic environment
Cited by: 15
Author(s): Alessandra Riva, Maja Wållberg, Francesca Ronchi, Richard M. R. Coulson, Andrew P. Sage, Lucy Thorne, Ian Goodfellow, Kathleen McCoy, Miyuki Azuma, Anne Cooke, Robert Busch
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0183716

Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen
Cited by: 93
Author(s): Nadja Danner, Alexander Keller, Stephan Härtel, Ingolf Steffan‐Dewenter
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.9424

An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications
Cited by: 5
Author(s): Deborah D. Iwanowicz, Judy Wu‐Smart, Tuğçe Olgun, Matthew Smart, Clint R. V. Otto, Dawn Lopez, Jay D. Evans, Robert S. Cornman
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.9015

Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems
Cited by: 51
Author(s): Sreejata Bandopadhyay, Henry Y. Sintim, Jennifer M. DeBruyn
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0231942

Putting the microbiota to work: Epigenetic effects of early life antibiotic treatment are associated with immune-related pathways and reduced epithelial necrosis following Salmonella Typhimurium challenge in vitro
Cited by: 4
Author(s): Matheus O. Costa, Janelle M Fouhse, Ana Paula P. Silva, Benjamin P. Willing, John C. S. Harding
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.2837

Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet
Cited by: 19
Author(s): Luis David Alcaraz, Apolinar M. Hernández, Mariana Peimbert
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0112763

Bacterial Endophytic Communities in the Grapevine Depend on Pest Management
Cited by: 101
Author(s): A. Campisano, Livio Antonielli, Michael Pancher, Sohail Yousaf, Massimo Pindo, I. Pertot
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0204629

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing
Cited by: 64
Author(s): Simon Poirier, Olivier Rué, R. Peguilhan, Gwendoline Coeuret, Monique Zagorec, Marie‐Christine Champomier‐Vergès, Valentin Loux, Stéphane Chaillou
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0215872

Incubation and grazing effects on spirotrich ciliate diversity inferred from molecular analyses of microcosm experiments
Cited by: 6
Author(s): Jean‐David Grattepanche, Doris L. Juarez, Cameah Corin Wood, George B. McManus, Laura A. Katz
Software Mentions: 3
Published: over 5 years ago

10.20411/pai.v4i1.269

Microbiomes of Inflammatory Thoracic Aortic Aneurysms Due to Giant Cell Arteritis and Clinically Isolated Aortitis Differ From Those of Non-Inflammatory Aneurysms
Cited by: 18
Author(s): Ted M. Getz, Gary S. Hoffman, Roshan Padmanabhan, Alexandra Villa‐Forte, Eric E. Roselli, Eugene H. Blackstone, Douglas R. Johnston, Gösta Pettersson, Edward G. Soltesz, Lars Svensson, Leonard H. Calabrese, Alison Clifford, Charis Eng
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0174890

Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers
Cited by: 33
Author(s): Jason T. Payne, Justin Millar, Colin R. Jackson, Clifford A. Ochs
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0217296

Influence of own mother's milk and different proportions of formula on intestinal microbiota of very preterm newborns
Cited by: 17
Author(s): Adriana Zanella, Rita de Cássia dos Santos Silveira, Luiz Fernando Würdig Roesch, Andrea Corso, Priscila Caroline Thiago Dobbler, Volker Mai, Renato S. Procianoy
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-87017-0

The larval environment strongly influences the bacterial communities of Aedes triseriatus and Aedes japonicus (Diptera: Culicidae)
Cited by: 6
Author(s): Elijah O. Juma, Brian F. Allan, Chang‐Hyun Kim, Chris Stone, Christopher A. Dunlap, Ephantus J. Muturi
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0178755

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries
Cited by: 29
Author(s): Mikel Aguirre, David Abad, Aitor Albaina, Lauren Cralle, María Soledad Goñi-Urriza, Andone Estonba, Iratxe Zarraonaindia
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0242108

Broiler chickens and early life programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects
Cited by: 16
Author(s): Gustavo A. Ramírez, Ella Richardson, Jory Clark, Jitendra Keshri, Yvonne Drechsler, M. E. Berrang, Richard J. Meinersmann, N. A. Cox, Brian B. Oakley
Software Mentions: 3
Published: about 4 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

10.1371/journal.pone.0232699

Azolla filiculoides L. as a source of metal-tolerant microorganisms
Cited by: 22
Author(s): Artur Banach, Agnieszka Kuźniar, Jarosław Grządziel, Agnieszka Woliñska
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0237262

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet
Cited by: 11
Author(s): F. Albonico, Claudia Barelli, Davide Albanese, Mattia Manica, Erika Partel, Fausta Rosso, Silvia Ripellino, Massimo Pindo, Claudio Donati, A. Zecconi, Michele Mortarino, Heidi C. Hauffe
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0219982

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae
Cited by: 12
Author(s): Osiris Gaona, Selene Gómez-Acata, Daniel Cerqueda‐García, Carla Ximena Neri-Barrios, Luisa I. Falcón
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0151594

Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions
Cited by: 49
Author(s): Hennersdorf Philipp, Sonja Kleinertz, Stefan Theisen, Muslihudeen A. Abdul-Aziz, Grit Mrotzek, Harry W. Palm, Hans Peter Saluz
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0223128

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia
Cited by: 22
Author(s): Joan T. Price, Bellington Vwalika, Marcia M. Hobbs, Julie A. Nelson, Elizabeth M. Stringer, Fei Zou, Katelyn J. Rittenhouse, Andrea Azcárate-Peril, Margaret P. Kasaro, Jeffrey S. A. Stringer
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0219070

Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology
Cited by: 14
Author(s): Melissa R. L. Whitaker, Christopher C. M. Baker, Shayla Salzman, Dino J. Martins, Naomi E. Pierce
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers12123702

Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank
Cited by: 15
Author(s): Ulrike Wirth, Debora Garzetti, Lara Jochum, Stefanie Spriewald, Florian Kühn, Matthias Ilmer, Serene M. L. Lee, Hanno Nieß, Alexandr V. Bazhin, Joachim Andrassy, Jens Werner, Bärbel Stecher, Tobias S. Schiergens
Software Mentions: 3
Published: almost 4 years ago

10.3390/v11040347

Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application
Cited by: 15
Author(s): Yuting Li, Hao Sun, Wei Yang, Guanxiong Chen, Xu Hui
Software Mentions: 3
Published: over 5 years ago

10.1186/s13567-019-0633-3

In-feed resin acids reduce matrix metalloproteinase activity in the ileal mucosa of healthy broilers without inducing major effects on the gut microbiota
Cited by: 22
Author(s): Manuel A. Aguirre, Juhani Vuorenmaa, Eija Valkonen, Hannele Kettunen, Chana Callens, Freddy Haesebrouck, Richard Ducatelle, Filip Van Immerseel, Evy Goossens
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13024-021-00427-6

Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson’s disease
Cited by: 170
Author(s): Velma Aho, Madelyn C. Houser, Pedro Pereira, Jianjun Chang, Knut Rudi, Lars Paulín, Vicki Hertzberg, Petri Auvinen, Malú G. Tansey, Filip Scheperjans
Software Mentions: 3
Published: almost 4 years ago

10.1093/cid/ciz905

Diarrhea as a Potential Cause and Consequence of Reduced Gut Microbial Diversity Among Undernourished Children in Peru
Cited by: 32
Author(s): Saba Rouhani, Nicholas W. Griffin, Pablo Peñataro Yori, Jeanette L. Gehrig, Maribel Paredes Olórtegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H. Moulton, Eric R. Houpt, Michael J. Barratt, Margaret Kosek, Jeffrey I. Gordon
Software Mentions: 3
Published: about 5 years ago

10.3390/molecules25235638

Activity and Diversity of Microorganisms in Root Zone of Plant Species Spontaneously Inhabiting Smelter Waste Piles
Cited by: 15
Author(s): Sylwia Siebielec, Grzegorz Siebielec, Piotr Sugier, Małgorzata Woźniak, Jarosław Grządziel, Anna Gałązka, Tomasz Stuczyński
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-020-01582-0

Curbing gastrointestinal infections by defensin fragment modifications without harming commensal microbiota
Cited by: 4
Author(s): Louis Koeninger, Lisa Osbelt, Anne Berscheid, Judith Wendler, Jürgen Berger, Katharina Hipp, Till Robin Lesker, Marina C. Pils, Nisar P. Malek, Benjamin Anderschou Holbech Jensen, Heike Brötz‐Oesterhelt, Till Strowig, Jan Wehkamp
Software Mentions: 3
Published: almost 4 years ago

10.1111/mec.14895

Biodiversity–function relationships in methanogenic communities
Cited by: 25
Author(s): Pawel Sierocinski, Florian Bayer, Gabriel Yvon‐Durocher, Melia Burdon, Tobias Großkopf, Mark Alston, David Swarbreck, P. J. Hobbs, Orkun S. Soyer, Angus Buckling
Software Mentions: 3
Published: about 6 years ago

10.1016/j.dib.2020.106143

An intensive multilocation temporal dataset of fungal and bacterial communities in the root and rhizosphere of Brassica napus
Cited by: 4
Author(s): Navid Bazghaleh, Jennifer K. Bell, Steven D. Mamet, Zayda Piedad Morales Moreira, Zelalem M. Taye, Shanay Williams, Charlotte E. Norris, Tanner Dowhy, Melissa M. Arcand, Eric G. Lamb, Matthew G. Links, Steven J. Shirtliffe, Sally Vail, Steven D. Siciliano, Bobbi L. Helgason
Software Mentions: 3
Published: over 4 years ago

10.1016/j.dib.2020.105467

An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus
Cited by: 3
Author(s): Navid Bazghaleh, Steven D. Mamet, Jennifer K. Bell, Zayda Piedad Morales Moreira, Zelalem M. Taye, Shanay Williams, Melissa M. Arcand, Eric G. Lamb, Steven J. Shirtliffe, Sally Vail, Steven D. Siciliano, Bobbi L. Helgason
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms8050642

Temporal Dynamics of Bacterial Communities in a Pilot-Scale Vermireactor Fed with Distilled Grape Marc
Cited by: 14
Author(s): María Gómez-Brandòn, Manuel Aira, Natielo Almeida Santana, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 3
Published: over 4 years ago

10.3390/ani11071975

A Standard Scale to Measure Equine Keeper Status and the Effect of Metabolic Tendency on Gut Microbiome Structure
Cited by: 0
Author(s): A. Johnson, Amy S. Biddle
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.6814

Jumping the green wall: The use of PNA‐DNA clamps to enhance microbiome sampling depth in wildlife microbiome research
Cited by: 3
Author(s): Luis Víquez-R, Ramona Fleischer, Kerstin Wilhelm, Marco Tschapka, Simone Sommer
Software Mentions: 3
Published: about 4 years ago

10.1002/ece3.7605

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

10.1002/ece3.5758

Elucidating cryptic dynamics of Theileria communities in African buffalo using a high‐throughput sequencing informatics approach
Cited by: 18
Author(s): Caroline K. Glidden, Anson V. Koehler, Ross S. Hall, Muhammad Saeed, Mauricio J. C. Coppo, Brianna R. Beechler, Bryan Charleston, Robin B. Gasser, Anna E. Jolles, Abdul Jabbar
Software Mentions: 3
Published: almost 5 years ago

10.3390/microorganisms9091843

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome
Cited by: 9
Author(s): Kishan Mahmud, Kendall Lee, Nicholas S. Hill, Anaas Mergoum, Ali Missaoui
Software Mentions: 3
Published: about 3 years ago

10.3390/ani9030098

Evaluation of Black Soldier Fly (Hermetia illucens) Larvae and Pre-Pupae Raised on Household Organic Waste, as Potential Ingredients for Poultry Feed
Cited by: 73
Author(s): Kiyonori Kawasaki, Yuka Hashimoto, A. Nosrati Hori, T. Kawasaki, Hirofumi Hirayasu, Shun–ichiro Iwase, Akira Hashizume, Atsushi Ido, Chiemi Miura, Takeshi Miura, Satoshi Nakamura, Tomohiro Seyama, Yoshiki Matsumoto, Koji Kasai, Yuji Fujitani
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms9020370

Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model
Cited by: 12
Author(s): Hyunjoon Park, Soyoung Yeo, Seok‐Won Kang, Chul Sung Huh
Software Mentions: 3
Published: almost 4 years ago

10.3390/ani11051433

Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution
Cited by: 11
Author(s): Michele Berlanda, Giada Innocente, Barbara Simionati, Barbara Di Camillo, Sonia Facchin, Maria Cecilia Giron, Edoardo Savarino, Federico Sebastiani, Francesca Fiorio, Ilaria Patuzzi
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-92966-7

Fenofibrate promotes PPARα-targeted recovery of the intestinal epithelial barrier at the host-microbe interface in dogs with diabetes mellitus
Cited by: 8
Author(s): Katti R. Crakes, Jully Pires, Nina Quach, Riley E Ellis-Reis, Rachel L. Greathouse, Kathyrnne A Chittum, Jörg M. Steiner, Patricia A. Pesavento, Stanley L. Marks, Satya Dandekar, Chen Gilor
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9071359

Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria
Cited by: 17
Author(s): Elisa Bona, Nadia Massa, Omrane Toumatia, Giorgia Novello, Patrizia Cesaro, Valeria Todeschini, Lara Boatti, Flavio Mignone, Houda Titouah, Abdelghani Zitouni, Graziano Lingua, Francesco Vuolo, Elisa Gamalero
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9081734

Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata)
Cited by: 1
Author(s): Carolina Osuna‐Mascaró, Jorge Doña, Kevin P. Johnson, Manuel de Rojas
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

10.12688/f1000research.22035.2

Staphylococcus aureus nasal carriage and microbiome composition among medical students from Colombia: a cross-sectional study
Cited by: 8
Author(s): Niradiz Reyes, Oscar Montes, Stephanie Figueroa, Raj K. Tiwari, Christopher C. Sollecito, Rebecca Emmerich, Mykhaylo Usyk, Jan Geliebter, Robert D. Burk
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms8050638

Intestinal Microbiota of Fattening Pigs Offered Non-Fermented and Fermented Liquid Feed with and without the Supplementation of Non-Fermented Coarse Cereals
Cited by: 14
Author(s): Sebastian Bunte, Richard Grone, Birgit Keller, Christoph A. Keller, Eric Galvez, Till Strowig, Josef Kamphues, Julia Hankel
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms8121861

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community
Cited by: 3
Author(s): Claudia Sala, Hanne Mordhorst, Josephine Grützke, Annika Brinkmann, Thomas Nordahl Petersen, Casper Sahl Poulsen, Paul D. Cotter, Fiona Crispie, Richard J. Ellis, Gastone Castellani, Clara Amid, Mikhayil Hakhverdyan, Soizick Le Guyader, Gerardo Manfreda, Joël Mossong, Andreas Nitsche, Catherine Ragimbeau, Julien Schaeffer, Jørgen Schlundt, Moon Y. F. Tay, Frank Møller Aarestrup, René S. Hendriksen, Sünje Johanna Pamp, Alessandra De Cesare
Software Mentions: 3
Published: about 4 years ago

10.1093/femsec/fiz033

Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes
Cited by: 44
Author(s): Dean J. Horton, Kevin R. Theis, Donald G Uzarski, Deric R. Learman
Software Mentions: 3
Published: over 5 years ago

10.1016/j.foodhyd.2019.06.006

Changes in stool frequency following chicory inulin consumption, and effects on stool consistency, quality of life and composition of gut microbiota
Cited by: 31
Author(s): Anthony Watson, David Houghton, Peter Avery, Christopher J. Stewart, Elaine E. Vaughan, P Meyer, Minse J.J. de Bos Kuil, P.J.M. Weijs, Kirsten Brandt
Software Mentions: 3
Published: about 5 years ago

10.3389/fbioe.2020.00192

Microbial Community Redundancy and Resilience Underpins High-Rate Anaerobic Treatment of Dairy-Processing Wastewater at Ambient Temperatures
Cited by: 20
Author(s): Lara M. Paulo, Juan Castilla-Archilla, Javier Ramiro-García, José Antonio Escamez-Picón, Dermot Hughes, Thérèse Mahony, Michael J. Murray, Paul Wilmes, Vincent O’Flaherty
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.648639

Fiber Derived Microbial Metabolites Prevent Acute Kidney Injury Through G-Protein Coupled Receptors and HDAC Inhibition
Cited by: 23
Author(s): Yunzi Liu, Yan J. Li, Yik Wen Loh, Julian Singer, Weiping Zhu, Laurence Macia, Charles R. Mackay, Weiming Wang, Steven J. Chadban, Huiling Wu
Software Mentions: 3
Published: over 3 years ago

10.3390/ani11051335

Bacillus Subtilis 29784 as a Feed Additive for Broilers Shifts the Intestinal Microbial Composition and Supports the Production of Hypoxanthine and Nicotinic Acid
Cited by: 11
Author(s): Pearl Choi, Lamya Rhayat, Eric Pinloche, Estelle Devillard, Ellen De Paepe, Lynn Vanhaecke, Freddy Haesebrouck, Richard Ducatelle, Filip Van Immerseel, Evy Goossens
Software Mentions: 3
Published: over 3 years ago

10.3389/fcimb.2021.656674

Oral Microbiome Characteristics in Patients With Autoimmune Hepatitis
Cited by: 11
Author(s): Benchen Rao, Jiamin Lou, Haifeng Lü, Hongxia Liang, Juan Li, Hao Zhou, Yijun Fan, Hua Zhang, Ying Sun, Yawen Zou, Zhongwen Wang, Yan Jiang, Zhigang Ren, Zujiang Yu
Software Mentions: 3
Published: over 3 years ago

10.3389/fcimb.2020.00398

A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis
Cited by: 6
Author(s): Brett Wagner Mackenzie, Annie G. West, David W. Waite, Christian A Lux, Richard Douglas, Michael W. Taylor, Kristi Biswas
Software Mentions: 3
Published: over 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

10.3389/fcimb.2020.00342

Fecal Microbiomes Distinguish Patients With Autoimmune Hepatitis From Healthy Individuals
Cited by: 31
Author(s): Jiamin Lou, Yan Jiang, Benchen Rao, Ang Li, Shuzhe Ding, Hang Yan, Hao Zhou, Zhenguo Liu, Qingmiao Shi, Guangying Cui, Zujiang Yu, Zhigang Ren
Software Mentions: 3
Published: over 4 years ago

10.3389/fcimb.2016.00078

Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity?
Cited by: 169
Author(s): Lisa Karstens, Mark Asquith, Sean Davin, Patrick Stauffer, Damien A. Fair, W. Thomas Gregory, James T. Rosenbaum, Shannon K. McWeeney, Rahel Nardos
Software Mentions: 3
Published: over 8 years ago

10.3389/fcimb.2020.00167

Significant Short-Term Shifts in the Microbiomes of Smokers With Periodontitis After Periodontal Therapy With Amoxicillin & Metronidazole as Revealed by 16S rDNA Amplicon Next Generation Sequencing
Cited by: 5
Author(s): Daniel Hagenfeld, Johannes Matern, Karola Prior, Inga Harks, Peter Eickholz, K. Lorenz, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Dag Harmsen, Benjamin Ehmke
Software Mentions: 3
Published: over 4 years ago

10.3389/fcimb.2021.595554

Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort
Cited by: 4
Author(s): Milkessa HaileMariam, Yu Yoshida, Harinder Singh, Takele Teklu, Biniam Wondale, Adane Worku, Aboma Zewude, Stephanie Mounaud, Tamara Tsitrin, Mengistu Legesse, Gobena Ameni, Rembert Pieper
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2015.00348

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
Cited by: 223
Author(s): Alejandra Escobar‐Zepeda, Arturo Vera‐Ponce de León, Alejandro Sánchez-Flores
Software Mentions: 3
Published: almost 9 years ago

10.3390/nu10122009

Gut Microbiota and Endothelial Dysfunction Markers in Obese Mexican Children and Adolescents
Cited by: 80
Author(s): Khemlal Nirmalkar, Selvasankar Murugesan, María Luisa Pizano-Zárate, Loan Edel Villalobos-Flores, Cristina García-González, Rosa María Morales-Hernández, Jorge A. Núñez-Hernández, Fernando Hernández-Quiroz, María del Socorro Romero Figueroa, César Hernández‐Guerrero, Carlos Hoyo‐Vadillo, Jaime García‐Mena
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2020.00838

IL-22 Paucity in APECED Is Associated With Mucosal and Microbial Alterations in Oral Cavity
Cited by: 13
Author(s): Epp Kaleviste, Malte Rühlemann, Jaanika Kärner, Liis Haljasmägi, Liina Tserel, Elin Org, Katarina Trebušak Podkrajšek, Tadej Battelino, Corinna Bang, André Franke, Pärt Peterson, Kai Kisand
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2017.01914

Feeding Immunity: Physiological and Behavioral Responses to Infection and Resource Limitation
Cited by: 27
Author(s): Sarah A. Budischak, Christina Hansen, Quentin Caudron, Romain Garnier, Tyler R. Kartzinel, István Pelczer, Clayton E. Cressler, Anieke van Leeuwen, Andrea L. Graham
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmed.2021.586875

Impact on the Gut Microbiota of Intensive and Prolonged Antimicrobial Therapy in Patients With Bone and Joint Infection
Cited by: 7
Author(s): Benoît Levast, Nicolas Benech, Cyrielle Gasc, Cécile Batailler, Éric Senneville, Sébastien Lustig, Cécile Pouderoux, David Boutoille, Lilia Boucinha, Frédéric‐Antoine Dauchy, Valérie Zeller, Marianne Maynard, Charles Cazanave, Thanh-Thuy Thi, Jérôme Josse, Joël Doré, Frédéric Laurent, Tristan Ferry
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-95099-z

Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge
Cited by: 27
Author(s): Jorge Domínguez, Manuel Aira, Keith A. Crandall, Marcos Pérez‐Losada
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8101482

Seasonal Variations in Soil Microbiota Profile of Termite (Syntermes wheeleri) Mounds in the Brazilian Tropical Savanna
Cited by: 9
Author(s): Helena Ipe Pinheiro Guimaraes, Renata Henrique Santana, Rafaella Silveira Sousa, Otávio Henrique Bezerra Pinto, Betânia Ferraz Quirino, Cristine Chaves Barreto, Mercedes Maria da Cunha Bustamante
Software Mentions: 3
Published: about 4 years ago

10.3390/microorganisms9010113

Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA
Cited by: 7
Author(s): Tanvi Govil, Manasi Paste, Dipayan Samanta, Aditi David, Kian Mau Goh, Xiangkai Li, David R. Salem, Rajesh K. Sani
Software Mentions: 3
Published: almost 4 years ago

10.3390/microorganisms9081752

Modulation of the Mucosa-Associated Microbiome Linked to the PTPN2 Risk Gene in Patients with Primary Sclerosing Cholangitis and Ulcerative Colitis
Cited by: 6
Author(s): Luisa Denoth, Pascal Juillerat, Andreas E. Kremer, Gerhard Rogler, Michael Scharl, Bahtiyar Yılmaz, Sena Bluemel
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.676880

Outbreaks of Root Rot Disease in Different Aged American Ginseng Plants Are Associated With Field Microbial Dynamics
Cited by: 16
Author(s): Ji Li, Fahad Nasir, Lei Tian, Jingjing Chang, Yu Sun, Jianfeng Zhang, Xiujun Li, Chunjie Tian
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8122022

Comparative Microbiome and Metabolome Analyses of the Marine Tunicate Ciona intestinalis from Native and Invaded Habitats
Cited by: 15
Author(s): Caroline Utermann, Martina Blümel, Kathrin Busch, Larissa Buedenbender, Ya‐Ping Lin, Brad Haltli, Russell G. Kerr, Elizabeta Briski, Ute Hentschel, Deniz Taşdemir
Software Mentions: 3
Published: almost 4 years ago

10.3390/nu12020290

Long-Term Blackcurrant Supplementation Modified Gut Microbiome Profiles in Mice in an Age-Dependent Manner: An Exploratory Study
Cited by: 13
Author(s): Lei Cao, Sang Gil Lee, Melissa M. Melough, Junichi Sakaki, Kendra Maas, Sung I. Koo
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2021.694406

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera
Cited by: 2
Author(s): I. Salonen, Panagiota-Myrsini Chronopoulou, Hidetaka Nomaki, Dewi Langlet, Masashi Tsuchiya, Karoliina A. Koho
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8121941

Impacts of Wet Market Modernization Levels and Hygiene Practices on the Microbiome and Microbial Safety of Wooden Cutting Boards in Hong Kong
Cited by: 11
Author(s): Wing Yui Ngan, Subramanya Rao, Long Chung Chan, Patrick T. Sekoai, Yunfeng Pu, Yuan Yao, Aster Hei Yiu Fung, Olivier Habimana
Software Mentions: 3
Published: almost 4 years ago

10.3390/microorganisms9010021

Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions
Cited by: 8
Author(s): Abdul Ghafar, Anson V. Koehler, Ross S. Hall, Charles G. Gauci, Robin B. Gasser, Abdul Jabbar
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2020.596156

Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms
Cited by: 1
Author(s): Wen Qin, Frederik Hammes
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2017.00431

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment
Cited by: 22
Author(s): Pauliina Rajala, Malin Bomberg
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2019.02368

Microbial Communities in Bioswale Soils and Their Relationships to Soil Properties, Plant Species, and Plant Physiology
Cited by: 8
Author(s): Olivia L Brodsky, Katherine L. Shek, Devin Dinwiddie, Sarah G. Bruner, Amanjit Gill, Jessica M. K. Hoch, Matthew I. Palmer, Krista L. McGuire
Software Mentions: 3
Published: about 5 years ago

10.3390/microorganisms8060872

Arbuscular Mycorrhizal Fungal Communities of Native Plant Species under High Petroleum Hydrocarbon Contamination Highlights Rhizophagus as a Key Tolerant Genus
Cited by: 10
Author(s): Soon‐Jae Lee, Mengxuan Kong, Marc St‐Arnaud, Mohamed Hijri
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-98119-0

The importance of environmental microbes for Drosophila melanogaster during seasonal macronutrient variability
Cited by: 4
Author(s): Lucy Rebecca Davies, Volker Loeschcke, Mads Fristrup Schou, Andreas Schramm, Torsten Nygård Kristensen
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-021-98519-2

Changes in microbial community phylogeny and metabolic activity along the water column uncouple at near sediment aphotic layers in fjords
Cited by: 2
Author(s): Sven P. Tobias-Hünefeldt, Stephen R. Wing, Federico Baltar, Sergio E. Morales
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2018.01410

Humic Substances Alter Ammonia Production and the Microbial Populations Within a RUSITEC Fed a Mixed Hay – Concentrate Diet
Cited by: 18
Author(s): Stephanie A. Terry, Aline Maria Pereira Cruz Ramos, Devin B. Holman, Tim A. McAllister, Gerhard Breves, A. V. Chaves
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms7090282

Differential Impact of Subtherapeutic Antibiotics and Ionophores on Intestinal Microbiota of Broilers
Cited by: 31
Author(s): Kelsy Robinson, Sage Becker, Yingping Xiao, Wentao Lyu, Qing Yang, Huiling Zhu, Hua Yang, Jiangchao Zhao, Guolong Zhang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-99028-y

The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes
Cited by: 10
Author(s): María Velasco-Galilea, M. Piles, Yuliaxis Ramayo-Caldas, Juan Pablo Sánchez
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2019.00461

Spatial Variability of Antarctic Surface Snow Bacterial Communities
Cited by: 19
Author(s): Lucie Malard, Marie Šabacká, Iordanis Magiopoulos, Matthew C. Mowlem, Andy Hodson, Martyn Tranter, Martín J. Siegert, David A. Pearce
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702