bioconductor: phyloseq | Projects

10.3390/microorganisms9030557

The Composition and Diversity of the Gut Microbiota in Children Is Modifiable by the Household Dogs: Impact of a Canine-Specific Probiotic
Cited by: 10
Author(s): Carlos Gómez-Gallego, Mira Forsgren, Marta Selma‐Royo, Merja Nermes, María Carmen Collado, Seppo Salminen, Shea Beasley, Erika Isolauri
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-43274-8

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome
Cited by: 55
Author(s): Rebecca L. Maher, Mallory M. Rice, Ryan McMinds, Deron E. Burkepile, Rebecca Vega Thurber
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-019-43875-3

Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health
Cited by: 77
Author(s): Keylie M. Gibson, Bryan Nguyen, Laura Neumann, Michele A. Miller, Peter Buss, Savel R. Daniels, Michelle Ahn, Keith A. Crandall, Budhan S. Pukazhenthi
Software Mentions: 7
Published: over 7 years ago

10.7717/peerj.8056

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

10.1186/s42523-021-00092-6

Metatranscriptomic analyses reveal ruminal pH regulates fiber degradation and fermentation by shifting the microbial community and gene expression of carbohydrate-active enzymes
Cited by: 15
Author(s): Meng M. Li, Robin R. White, Le Luo Guan, Laura Harthan, M.D. Hanigan
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-018-26930-3

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period
Cited by: 64
Author(s): Shebl E. Salem, Thomas W. Maddox, Adam Berg, Philipp Antczak, Julian M. Ketley, Nicola Williams, Debra Archer
Software Mentions: 7
Published: over 8 years ago

10.1007/s11274-019-2737-3

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization
Cited by: 15
Author(s): Priscila Caroline Thiago Dobbler, Volker Mai, Renato S. Procianoy, Rita de Cássia dos Santos Silveira, Andrea Corso, Luiz Fernando Würdig Roesch
Software Mentions: 7
Published: about 7 years ago

10.3389/fcimb.2021.733619

Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures
Cited by: 8
Author(s): Elizabeth H. Byrne, M Fărcăşanu, Seth M. Bloom, Nondumiso Xulu, Jiawu Xu, Barry L. Hykes, Nomfuneko A. Mafunda, Matthew R. Hayward, Mary Dong, Krista Dong, Thandeka Gumbi, Fransisca Xolisile Ceasar, Nasreen Ismail, Thumbi Ndung’u, Christina Gosmann, Musie Ghebremichael, Scott A. Handley, Caroline Mitchell, Alexandra Chloé Villani, Douglas S. Kwon
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2021.719486

Compositional Shift of Bacterial, Archaeal, and Fungal Communities Is Dependent on Trophic Lifestyles in Rice Paddy Soil
Cited by: 5
Author(s): Hyun Kim, Jongbum Jeon, Kiseok Keith Lee, Yong-Hwan Lee
Software Mentions: 7
Published: about 5 years ago

10.1186/s40168-019-0684-8

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Cited by: 38
Author(s): Luís Pedro Coelho, Renato Alves, Paulo P. Monteiro, Jaime Huerta-Cepas, Ana T. Freitas, Peer Bork
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0250344

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome
Cited by: 13
Author(s): Arnon Gal, Patrick C. Barko, Patrick J. Biggs, Kristene Gedye, Anne C. Midwinter, David A. Williams, Richard K. Burchell, P. Pazzi
Software Mentions: 7
Published: over 5 years ago

10.1093/gigascience/giaa135

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology
Cited by: 33
Author(s): Christina Weißbecker, Beatrix Schnabel, Anna Heintz‐Buschart
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmolb.2021.656204

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse
Cited by: 12
Author(s): Núria Mach, Marco Moroldo, Andrea Rau, Jérôme Lecardonnel, Laurence Le Moyec, Céline Robert, Éric Barrey
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2018.01073

Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function
Cited by: 28
Author(s): Jacob W. Bledsoe, Geoffrey C. Waldbieser, Kelly S. Swanson, Brian Peterson, Brian C. Small
Software Mentions: 7
Published: over 8 years ago

10.1053/j.gastro.2017.10.007

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
Cited by: 199
Author(s): Kate J. Howell, Judith Kraiczy, Komal Nayak, Marco Gasparetto, Alex Ross, Claire Lee, Tim N. Mak, Bon–Kyoung Koo, Nitin Kumar, Trevor D. Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Software Mentions: 7
Published: over 8 years ago

10.7189/jogh.11.04047

Topical emollient therapy with sunflower seed oil alters the skin microbiota of young children with severe acute malnutrition in Bangladesh: A randomised, controlled study
Cited by: 3
Author(s): Natalie Fischer, Gary L. Darmstadt, K. M. Shahunja, Jonathan Crowther, Lindsay Kendall, Rachel A. Gibson, Tahmeed Ahmed, David A. Relman
Software Mentions: 7
Published: about 5 years ago

10.5808/GI.2019.17.1.e6

Statistical Analysis of Metagenomics Data
Cited by: 147
Author(s): M. Luz Calle
Software Mentions: 7
Published: over 7 years ago

10.3389/fmicb.2020.00669

Patterns in Microbial Assemblages Exported From the Meltwater of Arctic and Sub-Arctic Glaciers
Cited by: 20
Author(s): Tyler J. Kohler, Petra Vinšová, Lukáš Falteisek, Jakub D. Žárský, Jacob C. Yde, Jade E. Hatton, Jon R. Hawkings, Guillaume Lamarche-Gagnon, Eran Hood, Karen A. Cameron, Marek Stibal
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2017.00358

Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions
Cited by: 38
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pone.0218636

Characterizing the postmortem human bone microbiome from surface-decomposed remains
Cited by: 23
Author(s): Alexandra L. Emmons, Amy Z. Mundorff, Sarah W. Keenan, Jonathan Davoren, Janna M. Andronowski, David Carter, Jennifer M. DeBruyn
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2019.02037

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

10.1080/19490976.2020.1840764

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

10.1371/journal.pone.0250783

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores
Cited by: 12
Author(s): John K. Pearman, Georgia Thomson‐Laing, Jamie Howarth, Marcus J. Vandergoes, L. M. Thompson, Andrew Rees, Susanna A. Wood
Software Mentions: 7
Published: over 5 years ago

10.3390/genes10070484

Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback
Cited by: 25
Author(s): Robert A Steury, Mark Currey, William A. Cresko, Brendan J. M. Bohannan
Software Mentions: 7
Published: over 7 years ago

10.3389/fmicb.2020.00789

Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach
Cited by: 18
Author(s): Nico Salmaso, Bruno Adriano, Massimo Pindo
Software Mentions: 7
Published: over 6 years ago

10.1111/gcb.15302

Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewater
Cited by: 44
Author(s): Francis J. Burdon, Yaohui Bai, Marta Reyes, Manu Tamminen, Philipp Staudacher, Simon Mangold, Heinz Singer, Katja Räsänen, Adriano Joss, Scott D. Tiegs, Jukka Jokela, Rik I.L. Eggen, Christian Stamm
Software Mentions: 7
Published: about 6 years ago

10.3389/fmicb.2021.658116

Endophytic Fungal Community of Tobacco Leaves and Their Potential Role in the Formation of “Cherry-Red” Tobacco
Cited by: 4
Author(s): Yonglei Jiang, Xing Chen, Gaokun Zhao, Jiahong Liu, Yan Xie, Yong Li, Huaguo Gu, Congming Zou
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0227434

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
Cited by: 237
Author(s): Andrei Prodan, Valentina Tremaroli, Harald Brolin, Aeilko H. Zwinderman, Max Nieuwdorp, Evgeni Levin
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-020-02144-7

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding
Cited by: 32
Author(s): Toby Wilkinson, Daniel Korir, Moses Ogugo, Robert D. Stewart, Mick Watson, Edith Paxton, John P. Goopy, Christelle Robert
Software Mentions: 7
Published: about 6 years ago

10.3389/fmicb.2021.685937

Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota
Cited by: 10
Author(s): Martı́n Aluja, Jesús Alejandro Zamora‐Briseño, Vicente Pérez‐Brocal, Alma Altúzar-Molina, Larissa Guillén, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Enrique Ibarra-Laclette, Alexandro Alonso-Sánchez, Andrés Moya
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2021.645784

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure
Cited by: 1
Author(s): Scott Klasek, Marcus T. Brock, Hilary G. Morrison, Cynthia Weinig, Loïs Maignien
Software Mentions: 7
Published: over 5 years ago

10.1038/s41396-020-0654-y

Dark septate endophyte improves salt tolerance of native and invasive lineages of Phragmites australis
Cited by: 41
Author(s): Martina Gonzalez Mateu, Andrew H. Baldwin, Jude E. Maul, Stephanie A. Yarwood
Software Mentions: 7
Published: over 6 years ago

10.1128/mSphere.00169-17

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
Cited by: 52
Author(s): Alexandra M. Linz, Benjamin C. Crary, Ashley Shade, Sarah M. Owens, Jack A. Gilbert, Rob Knight, Katherine D. McMahon
Software Mentions: 7
Published: over 9 years ago

10.3390/insects11060373

Susceptibility of Red Mason Bee Larvae to Bacterial Threats Due to Microbiome Exchange with Imported Pollen Provisions
Cited by: 22
Author(s): Anna Voulgari‐Kokota, Ingolf Steffan‐Dewenter, Alexander Keller
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2020.585943

Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring
Cited by: 5
Author(s): Avishek Dutta, Ben Smith, Thomas Goldman, Leanne Walker, Matthew Streets, Bob Eden, Reinhard Dirmeier, Jeff S. Bowman
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmicb.2020.566619

Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers
Cited by: 13
Author(s): Anita Dame-Korevaar, Jannigje G. Kers, Jeanet van der Goot, Francisca C. Velkers, Daniela Ceccarelli, Dik Mevius, Arjan Stegeman, E.A.J. Fischer
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0233943

Effects of parity, blood progesterone, and non-steroidal anti-inflammatory treatment on the dynamics of the uterine microbiota of healthy postpartum dairy cows
Cited by: 17
Author(s): Osvaldo Bogado Pascottini, J. F. W. Sprícigo, Sabrina J. Van Schyndel, B. Mion, Joyce D. Rousseau, J. Scott Weese, S.J. LeBlanc
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2021.662159

Effect of Fecal Microbiota Transplantation Combined With Mediterranean Diet on Insulin Sensitivity in Subjects With Metabolic Syndrome
Cited by: 20
Author(s): Annefleur M. Koopen, Eduardo L. Almeida, Ilias Attaye, Julia J. Witjes, Elena Rampanelli, Soumia Majait, E. Marleen Kemper, Johannes H.M. Levels, Alinda W.M. Schimmel, Hilde Herrema, Torsten P. M. Scheithauer, Werner Frei, Lars Ove Dragsted, Bolette Hartmann, Jens J. Holst, Paul W. O’Toole, Albert K. Groen, Max Nieuwdorp
Software Mentions: 7
Published: over 5 years ago

10.1128/mBio.03396-20

Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes
Cited by: 21
Author(s): Rozlyn C.T. Boutin, Hind Sbihi, Ryan J. McLaughlin, Aria S. Hahn, Kishori M. Konwar, Rachelle Loo, Darlene Dai, Charisse Petersen, Fiona S. L. Brinkman, Geoffrey L. Winsor, Malcolm R. Sears, Theo J. Moraes, Allan B. Becker, Meghan B. Azad, Piush J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 7
Published: over 5 years ago

10.1128/IAI.00147-20

Niche- and Gender-Dependent Immune Reactions in Relation to the Microbiota Profile in Pediatric Patients with Otitis Media with Effusion
Cited by: 10
Author(s): Frida Enoksson, Alicia Ruiz Rodriguez, Chikondi Peno, Carlos Balcazar Lopez, Fredrik Tjernström, Debby Bogaert, Anders P. Håkansson, Caroline Bergenfelz
Software Mentions: 7
Published: about 6 years ago

10.3389/fmicb.2021.640253

In vitro Fermentation Reveals Changes in Butyrate Production Dependent on Resistant Starch Source and Microbiome Composition
Cited by: 22
Author(s): June Teichmann, Darrell Cockburn
Software Mentions: 7
Published: over 5 years ago

10.1093/gigascience/giaa022

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
Cited by: 28
Author(s): Haris Zafeiropoulos, Ha Quoc Viet, Katerina Vasileiadou, Antonis Potirakis, Christos Arvanitidis, Pantelis Topalis, Christina Pavloudi, Evangelos Pafilis
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0219235

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data
Cited by: 17
Author(s): Stephen Woloszynek, Joshua Chang Mell, Zhengqiao Zhao, Gideon Simpson, Michael O’Connor, Gail Rosen
Software Mentions: 7
Published: almost 7 years ago

10.1038/s42003-021-02315-7

Human encroachment into wildlife gut microbiomes
Cited by: 29
Author(s): Gloria Fackelmann, Mark A. F. Gillingham, Julian Schmid, Alexander Christoph Heni, Kerstin Wilhelm, Nina Schwensow, Simone Sommer
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2021.569791

Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem
Cited by: 15
Author(s): Yaqi You, Ken Aho, Kathleen A. Lohse, Stacy G. Schwabedissen, Rhesa N. Ledbetter, Timothy S. Magnuson
Software Mentions: 7
Published: over 5 years ago

10.1128/mBio.03701-20

Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders
Cited by: 8
Author(s): Angelina Angelova, Barbara Berx, Eileen Bresnan, Samantha B. Joye, Andrew Free, Tony Gutiérrez
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0230945

Timescales of variation in diversity and production of bacterioplankton assemblages in the Lower Mississippi River
Cited by: 3
Author(s): Jason T. Payne, Colin R. Jackson, Justin Millar, Clifford A. Ochs
Software Mentions: 7
Published: over 6 years ago

10.1128/mBio.02723-20

Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development
Cited by: 17
Author(s): Kathleen Beilsmith, Matthew Perisin, Joy Bergelson
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2018.02404

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia
Cited by: 11
Author(s): Martina Prazeres
Software Mentions: 7
Published: about 8 years ago

10.3389/fpls.2019.01246

Temporal Dynamics of the Sap Microbiome of Grapevine Under High Pierce’s Disease Pressure
Cited by: 43
Author(s): Elizabeth Deyett, Philippe E. Rolshausen
Software Mentions: 7
Published: about 7 years ago

10.1080/19490976.2021.1921927

Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells <i>in vitro</i>
Cited by: 7
Author(s): Dušan Radojević, Sergej Tomić, Dušan Mihajlović, Maja Tolinački, Bojan Pavlović, Dragana Vučević, Svetlana Bojić, Nataša Golić, Miodrag Čolić, Jelena Đokić
Software Mentions: 7
Published: almost 6 years ago

10.3389/fpls.2020.602645

Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products
Cited by: 11
Author(s): Vinício Oliosi Favero, Rita Hilário de Carvalho, Victória Monteiro da Motta, Ana Beatriz Carneiro Leite, Márcia Reed Rodrigues Coelho, Gustavo Ribeiro Xavier, Norma Gouvêa Rumjanek, Segundo Urquiaga
Software Mentions: 7
Published: almost 6 years ago

10.3389/fpls.2019.01405

Fungicides and the Grapevine Wood Mycobiome: A Case Study on Tracheomycotic Ascomycete Phaeomoniella chlamydospora Reveals Potential for Two Novel Control Strategies
Cited by: 16
Author(s): Giovanni Del Frari, Alex Gobbi, Marie Rønne Aggerbeck, Helena Oliveira, Lars Hestbjerg Hansen, Ricardo B. Ferreira
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0237079

A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand
Cited by: 17
Author(s): Anya Sophia Noble, Stevie Noe, Michael J. Clearwater, Charles K. Lee
Software Mentions: 7
Published: about 6 years ago

10.1080/19490976.2021.1927634

Influence of pig farming on human Gut Microbiota: role of airborne microbial communities
Cited by: 5
Author(s): Julia Moor, Tsering Wüthrich, Suzanne Aebi, Nadezda Mostacci, Gudrun Overesch, Anne Oppliger, Markus Hilty
Software Mentions: 7
Published: almost 6 years ago

10.3389/fpls.2019.01313

A Bioinformatics Guide to Plant Microbiome Analysis
Cited by: 45
Author(s): Rares Calin Lucaciu, Claus Pelikan, Samuel M. Gerner, Christos Zioutis, Stephan Köstlbacher, Harald Marx, Craig W. Herbold, Hannes Schmidt, Thomas Rattei
Software Mentions: 7
Published: almost 7 years ago

10.3389/fmicb.2020.586437

Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen
Cited by: 13
Author(s): Mohamed Kamal Abdelhamid, Narciso M. Quijada, Monika Dzieciol, Tamas Hatfaludi, Ivana Bilić, Evelyne Selberherr, Dieter Liebhart, Claudia Heß, Michael Heß, Surya Paudel
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13073-018-0586-6

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
Cited by: 96
Author(s): Vanessa L. Hale, Patricio Jeraldo, Jun Chen, Michael B. Mundy, Jingwen Yao, Sambhawa Priya, Gary Keeney, Kelly Lyke, Jason M. Ridlon, Bryan A. White, Amy J. French, Stephen N. Thibodeau, Christian Diener, Osbaldo Reséndis-Antonio, Jaime Gransee, Tumpa Dutta, Xuan Mai Petterson, Jaeyun Sung, Ran Blekhman, Lisa A. Boardman, David W. Larson, Heidi Nelson, Nicholas Chia
Software Mentions: 6
Published: almost 8 years ago

10.3389/fmicb.2020.610009

Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease
Cited by: 28
Author(s): Citlalli A Aquino, Ryan M Besemer, Christopher M. DeRito, Jan Kocian, Ian Porter, Peter T. Raimondi, Jordan E Rede, Lauren M. Schiebelhut, Jed P. Sparks, John P. Wares, Ian Hewson
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-021-02400-4

mbImpute: an accurate and robust imputation method for microbiome data
Cited by: 23
Author(s): Ruochen Jiang, Wei Vivian Li, Jingyi Jessica Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-021-02306-1

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox
Cited by: 101
Author(s): Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa, Georg Zeller
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2020.01860

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

10.7554/eLife.21887

A phylogenetic transform enhances analysis of compositional microbiota data
Cited by: 239
Author(s): Justin D. Silverman, Alex D. Washburne, Sayan Mukherjee, Lawrence A. David
Software Mentions: 6
Published: over 9 years ago

10.3389/fmicb.2018.02868

Comparison of Bacterial Diversity in Air and Water of a Major Urban Center
Cited by: 24
Author(s): M. Elias Dueker, Shaya Regina French, Gregory D. O’Mullan
Software Mentions: 6
Published: almost 8 years ago

10.1186/s13059-019-1908-8

Host-associated microbiomes are predicted by immune system complexity and climate
Cited by: 45
Author(s): Douglas C. Woodhams, Molly C. Bletz, C. Guilherme Becker, Hayden A. Bender, Daniel Buitrago-Rosas, Hannah Diebboll, Roger Huynh, Patrick J. Kearns, Jordan G. Kueneman, Emmi Kurosawa, Brandon LaBumbard, Casandra Lyons, Kerry McNally, Klaus Schliep, Nachiket Shankar, Amanda G. Tokash-Peters, Miguel Vences, Ross Whetstone
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2021.623799

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management
Cited by: 11
Author(s): Ahmad Nuruddin Khoiri, Supapon Cheevadhanarak, Jiraporn Jirakkakul, Sudarat Dulsawat, Peerada Prommeenate, Anuwat Tachaleat, Kanthida Kusonmano, Songsak Wattanachaisaereekul, Sawannee Sutheeworapong
Software Mentions: 6
Published: over 5 years ago

10.3390/genes11111291

The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1
Cited by: 13
Author(s): Bradley L. Bearson, Julian Trachsel, Daniel C. Shippy, Sathesh K Sivasankaran, B. J. Kerr, Crystal L. Loving, Brian W. Brunelle, Shelby M Curry, Nicholas K. Gabler, Shawn M. D. Bearson
Software Mentions: 6
Published: almost 6 years ago

10.3390/genes10070524

MODIMA, a Method for Multivariate Omnibus Distance Mediation Analysis, Allows for Integration of Multivariate Exposure–Mediator–Response Relationships
Cited by: 13
Author(s): Bashir Hamidi, Kristin Wallace, Alexander V. Alekseyenko
Software Mentions: 6
Published: over 7 years ago

10.3389/fnmol.2021.723317

Dynamic Changes in the Levels of Amyloid-β42 Species in the Brain and Periphery of APP/PS1 Mice and Their Significance for Alzheimer’s Disease
Cited by: 13
Author(s): Liding Zhang, Changwen Yang, Yanqing Li, Shiqi Niu, Xiaohan Liang, Zhihong Zhang, Qi Luo, Haiming Luo
Software Mentions: 6
Published: about 5 years ago

10.1038/s41396-021-00895-0

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets
Cited by: 22
Author(s): Danièle De Luca, Roberta Piredda, Diana Sarno, Wiebe H. C. F. Kooistra
Software Mentions: 6
Published: over 5 years ago

10.3389/fnut.2019.00045

What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study
Cited by: 135
Author(s): Kimberly A. Lackey, Janet E. Williams, Courtney L. Meehan, Jessica A. Zachek, Elizabeth D. Benda, William J. Price, James A. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Linda J. Kvist, Gloria E. Otoo, Cristina García-Carral, Esther Jiménez, Lorena Ruíz, Juan M. Rodríguez, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Michelle K. McGuire
Software Mentions: 6
Published: over 7 years ago

10.1128/mSystems.00540-20

Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution
Cited by: 29
Author(s): Sean K. Bay, Melodie A. McGeoch, Osnat Gillor, Nimrod Wieler, David J. Palmer, D. James Baker, Steven L. Chown, Chris Greening
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0242675

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata
Cited by: 20
Author(s): Maureen W. Ihua, Jamie A. FitzGerald, Freddy Guihéneuf, Stephen A. Jackson, Marcus J. Claesson, Dagmar B. Stengel, Alan D. W. Dobson
Software Mentions: 6
Published: almost 6 years ago

10.1128/mSystems.00003-19

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil
Cited by: 39
Author(s): Alan W. Bowsher, Patrick J. Kearns, Ashley Shade
Software Mentions: 6
Published: over 7 years ago

10.1128/mSystems.00232-18

Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems
Cited by: 31
Author(s): Sara F. Paver, Daniel Muratore, Ryan J. Newton, Maureen L. Coleman
Software Mentions: 6
Published: almost 8 years ago

10.3390/jof7080607

The Diplodia Tip Blight Pathogen Sphaeropsis sapinea Is the Most Common Fungus in Scots Pines’ Mycobiome, Irrespective of Health Status—A Case Study from Germany
Cited by: 12
Author(s): Kathrin Blumenstein, Johanna Bußkamp, Gitta Jutta Langer, Ewald Langer, Eeva Terhonen
Software Mentions: 6
Published: about 5 years ago

10.1038/s41423-021-00647-2

The microbiota is dispensable for the early stages of peripheral regulatory T cell induction within mesenteric lymph nodes
Cited by: 16
Author(s): Carolin Wiechers, Mangge Zou, Eric Galvez, Michael Beckstette, Maria F. Ebel, Till Strowig, Jochen Huehn, Joern Pezoldt
Software Mentions: 6
Published: over 5 years ago

10.1016/j.xcrm.2020.100077

Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study
Cited by: 108
Author(s): Cristina Alcon-Giner, Matthew J. Dalby, Shabhonam Caim, Jennifer Ketskemety, Alexander Shaw, Kathleen Sim, Melissa A. Lawson, Raymond Kiu, Charlotte Leclaire, Lisa Chalklen, Magdalena Kujawska, Suparna Mitra, Fahmina Fardus‐Reid, Gusztav Belteki, Katherine McColl, Jonathan R. Swann, J. Simon Kroll, Paul Clarke, Lindsay J. Hall
Software Mentions: 6
Published: about 6 years ago

10.3390/cells8060517

Fecal Microbiota Transplantation Controls Murine Chronic Intestinal Inflammation by Modulating Immune Cell Functions and Gut Microbiota Composition
Cited by: 46
Author(s): Claudia Burrello, Maria Rita Giuffrè, Angeli Dominique Macandog, Angélica Díaz‐Basabe, Fulvia Milena Cribiù, Gianluca Lopez, Francesca Borgo, Luigi Nezi, Flavio Caprioli, Maurizio Vecchi, Federica Facciotti
Software Mentions: 6
Published: over 7 years ago

10.1007/s00784-020-03613-w

Limited antimicrobial efficacy of oral care antiseptics in microcosm biofilms and phenotypic adaptation of bacteria upon repeated exposure
Cited by: 22
Author(s): Sophia R. Schwarz, Stefanie Hirsch, Andreas Hiergeist, Christian Kirschneck, Denise Muehler, Karl‐Anton Hiller, Tim Maisch, Ali Al‐Ahmad, André Gessner, Wolfgang Buchalla, Fabian Cieplik
Software Mentions: 6
Published: about 6 years ago

10.1038/s42003-019-0610-4

Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure
Cited by: 4
Author(s): Francisco J. A. Nascimento, Martin Dahl, Diana Deyanova, Liberatus D. Lyimo, Holly M. Bik, Taruna Schuelke, Tiago José Pereira, Mats Björk, Simon Creer, Martin Gullström
Software Mentions: 6
Published: about 7 years ago

10.1038/s42003-021-01712-2

Feedback mechanisms stabilise degraded turf algal systems at a CO2 seep site
Cited by: 10
Author(s): Ben P. Harvey, Ro Allen, Sylvain Agostini, Linn Hoffmann, Koetsu Kon, Tina C. Summerfield, Shigeki Wada, Jason M. Hall-Spencer
Software Mentions: 6
Published: over 5 years ago

10.1128/mSystems.00043-17

The Skin Microbiome of Cohabiting Couples
Cited by: 86
Author(s): Ashley A. Ross, Andrew C. Doxey, Josh D. Neufeld
Software Mentions: 6
Published: about 9 years ago

10.1128/mSphere.00455-21

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition
Cited by: 9
Author(s): Heather L. Deel, Alexandra L. Emmons, Jennifer Kiely, Franklin E. Damann, David Carter, Aaron M. Lynne, Rob Knight, Zhenjiang Xu, Sibyl R. Bucheli, Jessica L. Metcalf
Software Mentions: 6
Published: about 5 years ago

10.1242/dmm.041947

Temporal evolution of the microbiome, immune system, and epigenome with disease progression in ALS mice
Cited by: 44
Author(s): Claudia Figueroa‐Romero, Kai Guo, Benjamin J. Murdock, Ximena Paez-Colasante, Christine M. Bassis, Kristen A. Mikhail, Kristen D. Raue, Matthew C. Evans, Ghislaine F. Taubman, Andrew J. McDermott, Phillipe D. O’Brien, Masha G. Savelieff, Junguk Hur, Eva L. Feldman
Software Mentions: 6
Published: almost 8 years ago

10.1002/ece3.5361

Drivers and patterns of microbial community assembly in a Lyme disease vector
Cited by: 30
Author(s): Lisa I. Couper, Jessica Y. Kwan, Joyce Ma, Andrea Swei
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0258069

Does algae β-glucan affect the fecal bacteriome in dairy calves?
Cited by: 6
Author(s): G.F. Virgínio, Maria Eduarda Reis, Ana Paula da Silva, Ariany Faria de Toledo, Amanda Moelemberg Cezar, Lucas William Mendes, L.F. Greco, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 6
Published: about 5 years ago

10.1128/mSphere.00798-19

Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy
Cited by: 37
Author(s): Medini K. Annavajhala, Sobia Khan, Sean B. Sullivan, Jainil P. Shah, Lauren Pass, Karolina Kister, Heather Kunen, Victor Chiang, Gwennaëlle Monnot, Christopher L. Ricupero, Rebecca A. Mazur, Peter Gordon, Annemieke de Jong, Sunil Wadhwa, Michael T. Yin, Ryan T. Demmer, Anne‐Catrin Uhlemann
Software Mentions: 6
Published: over 6 years ago

10.1002/ece3.7171

Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats
Cited by: 3
Author(s): Carly R. Muletz‐Wolz, Erin E. Wilson Rankin, Sarah McGrath‐Blaser, Madhvi X. Venkatraman, Jesús E. Maldonado, Daniel S. Gruner, Robert C. Fleischer
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0251136

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study
Cited by: 7
Author(s): Martijn G H Sanders, Tamar Nijsten, Joost Verlouw, Robert Kraaij, Luba M. Pardo
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0204317

Association of metformin administration with gut microbiome dysbiosis in healthy volunteers
Cited by: 85
Author(s): Ilze Elbere, Ineta Kalniņa, Ivars Silamiķelis, Ilze Konrāde, Linda Zaharenko, Kristine Sekace, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Dita Gudrā, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 6
Published: about 8 years ago

10.1128/mBio.03162-20

Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island
Cited by: 5
Author(s): Brad Griesenauer, Camila González-Beiras, Katherine R. Fortney, Huaiying Lin, Xiang Gao, Charmie Godornes, David E. Nelson, Barry P. Katz, Sheila A. Lukehart, Oriol Mitjà, Qunfeng Dong, Stanley M. Spinola
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0169339

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA
Cited by: 51
Author(s): Kathleen H. Lavoie, Ara S. Winter, Kaitlyn J. H. Read, Evan M. Hughes, M. Spilde, Diana E. Northup
Software Mentions: 6
Published: over 9 years ago

10.3390/insects11040217

Host Plants Influence the Symbiont Diversity of Eriosomatinae (Hemiptera: Aphididae)
Cited by: 14
Author(s): Tingting Xu, Li‐Yun Jiang, Jing Chen, Ge‐Xia Qiao
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2020.01528

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation
Cited by: 7
Author(s): Nicholas C. Dove, Timothy J. Rogers, Christy Leppanen, Daniel Simberloff, James A. Fordyce, Veronica A. Brown, Anthony V. LeBude, Thomas G. Ranney, Melissa Cregger
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2021.659918

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species
Cited by: 12
Author(s): Alice Risely, Mark A. F. Gillingham, Arnaud Béchet, Stefan Dominik Brändel, Alexander Christoph Heni, Marco Heurich, Sebastian Menke, Marta B. Manser, Marco Tschapka, . Wasimuddin, Simone Sommer
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22115981

Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract
Cited by: 8
Author(s): Adrian Low, Melissa Soh, Sou Miyake, Vanessa Zhi Jie Aw, Jian Feng, Adeline Wong, Henning Seedorf
Software Mentions: 6
Published: over 5 years ago

10.1080/19490976.2021.1874815

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer
Cited by: 33
Author(s): Kellyanne Duncan, Kelly Carey-Ewend, Shipra Vaishnava
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0250401

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru
Cited by: 5
Author(s): Pedro E. Romero, Erika Calla-Quispe, Camila Castillo-Vilcahuaman, Mateo Yokoo, Hammerly Lino Fuentes-Rivera, Jorge L. Ramírez, André Ampuero, Alfredo J. Ibáñez, Paolo Wong
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0235159

Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding
Cited by: 13
Author(s): Kathleen J. Pitz, Jinchen Guo, Shannon B. Johnson, Tracy L. Campbell, Haibin Zhang, Robert C. Vrijenhoek, Francisco P. Chávez, Jonathan B. Geller
Software Mentions: 6
Published: over 6 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702