bioconductor: ALDEx2 | Projects | Ecosyste.ms: Papers

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago

10.3390/biomedicines9020144

Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation
Cited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago

10.3390/cells10061292

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background
Cited by: 1
Author(s): Axel Künstner, Rédouane Aherrahrou, Misa Hirose, Petra Bruse, Saleh M. Ibrahim, Hauke Busch, Jeanette Erdmann, Zouhair Aherrahrou
Software Mentions: 15
Published: over 3 years ago

10.1038/s41598-020-59849-9

Response of the human gut and saliva microbiome to urbanization in Cameroon
Cited by: 25
Author(s): Ana Lokmer, Sophie Aflalo, Norbert Amougou, Sophie Lafosse, Alain Froment, Francis Ekwin Tabe, Mathilde Poyet, Mathieu Groussin, Rihlat Saïd-Mohamed, Laure Ségurel
Software Mentions: 14
Published: almost 5 years ago

10.1080/19490976.2021.1888673

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

10.3390/cancers12051142

Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer
Cited by: 55
Author(s): Marc Clos-García, Koldo Garcia, Cristina Alonso, Marta Iruarrizaga‐Lejarreta, Mauro D’Amato, Anais Crespo, Águeda Iglesias, Joaquín Cubiella, Luís Bujanda, Juan Manuel Falcón‐Pérez
Software Mentions: 14
Published: over 4 years ago

10.1186/s40168-020-00914-w

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
Cited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: about 4 years ago

10.1186/s12859-021-04193-6

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Cited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago

10.1128/mSystems.00404-19

Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria <i>In Vitro</i>
Cited by: 13
Author(s): Kaitlyn Oliphant, Kyla Cochrane, Kathleen Schroeter, Michelle Daigneault, Sandi Yen, Elena F. Verdú, Emma Allen‐Vercoe
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: over 3 years ago

10.1007/s13238-020-00724-8

A practical guide to amplicon and metagenomic analysis of microbiome data
Cited by: 311
Author(s): Yong‐Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai
Software Mentions: 9
Published: over 4 years ago

10.1186/s12864-018-4870-z

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
Cited by: 11
Author(s): Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Software Mentions: 9
Published: over 6 years ago

10.3389/fmicb.2021.654135

Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica
Cited by: 3
Author(s): Adam J. Solon, Claire F. Mastrangelo, Lara Vimercati, Pacifica Sommers, John L. Darcy, Eli M. S. Gendron, Dorota L. Porazinska, Steven K. Schmidt
Software Mentions: 9
Published: over 3 years ago

10.7717/peerj.4555

Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities
Cited by: 10
Author(s): Hauke Kegler, Christiane Hassenrück, Pia Kegler, Tim C Jennerjahn, Muhammad Lukman, Jamaluddin Jompa, Astrid Gärdes
Software Mentions: 9
Published: over 6 years ago

10.7717/peerj.9017

Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon
Cited by: 10
Author(s): Jake Ivan P. Baquiran, Michael Angelou L. Nada, Niño Posadas, Dana P. Manogan, Patrick C. Cabaitan, Cecilia Conaco
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0257471

Deciphering the low abundance microbiota of presumed aseptic hip and knee implants
Cited by: 2
Author(s): Charles Carr, Hannah Wilcox, Jeremy P. Burton, Sharanya Menon, Kait F. Al, David B. O’Gorman, Brent A. Lanting, Edward M. Vasarhelyi, Michael E. Neufeld, Matthew G. Teeter
Software Mentions: 8
Published: over 3 years ago

10.1186/s40168-016-0208-8

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
Cited by: 124
Author(s): Jonathan Thorsen, Asker Brejnrod, Martin Steen Mortensen, Morten Arendt Rasmussen, Jakob Stokholm, Waleed Abu Al‐Soud, Søren J. Sørensen, Hans Bisgaard, Johannes Waage
Software Mentions: 8
Published: about 8 years ago

10.1186/s12864-020-6703-0

Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction
Cited by: 26
Author(s): Xubo Qian, Yong‐Xin Liu, Xiaohong Ye, Wen Jie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wen-Qin Wang, Weihan Wang, Xianning Zhang, Meiping Lu
Software Mentions: 8
Published: over 4 years ago

10.1002/ece3.5249

Immune and environment‐driven gene expression during invasion: An eco‐immunological application of RNA‐Seq
Cited by: 15
Author(s): D. Selechnik, Mark F. Richardson, Richard Shine, Gregory P. Brown, Lee A. Rollins
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-021-99046-w

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

10.3390/nu12113524

Metabolic Responses to Butyrate Supplementation in LF- and HF-Fed Mice Are Cohort-Dependent and Associated with Changes in Composition and Function of the Gut Microbiota
Cited by: 8
Author(s): Sun Hye Lee, Trina A. Knotts, Michael L. Goodson, Mariana Barboza, Elyse V. Wudeck, Grace England, Helen E. Raybould
Software Mentions: 7
Published: about 4 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 5 years ago

10.1186/s12920-020-00808-8

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
Cited by: 11
Author(s): Timothy A. McCaffrey, Georges St. Laurent, Dmitry Shtokalo, Денис Антонец, Yuri Vyatkin, Dan Jones, Eleanor Battison, Joel T. Nigg
Software Mentions: 7
Published: about 4 years ago

10.1038/s42003-021-02581-5

Selective feeding in Southern Ocean key grazers—diet composition of krill and salps
Cited by: 17
Author(s): Nora‐Charlotte Pauli, Katja Metfies, Evgeny A. Pakhomov, Stefan Neuhaus, Martín Graeve, Philipp Wenta, Clara M. Flintrop, Thomas H. Badewien, Morten Hvitfeldt Iversen, Bettina Meyer
Software Mentions: 7
Published: over 3 years ago

10.3390/nu13061905

Microbiota and Metabolite Modifications after Dietary Exclusion of Dairy Products and Reduced Consumption of Fermented Food in Young and Older Men
Cited by: 4
Author(s): Jinyoung Kim, Kathryn J. Burton-Pimentel, Charlotte Fleuti, Carola Blaser, Valentin Scherz, René Badertscher, Corinne Marmonier, Noëlle Lyon-Belgy, A. Caillé, Véronique Pidou, Adeline Blot, Claire Bertelli, Jérémie David, Ueli Bütikofer, Gilbert Greub, Dominique Dardevet, Sergio Polakof, Guy Vergères
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0251136

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

10.3389/fmicb.2021.640386

The Molecular Information About Deadwood Bacteriomes Partly Depends on the Targeted Environmental DNA
Cited by: 9
Author(s): Maraike Probst, Judith Ascher‐Jenull, Heribert Insam, María Gómez-Brandòn
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2021.717990

Resistance and Vulnerability of Honeybee (Apis mellifera) Gut Bacteria to Commonly Used Pesticides
Cited by: 15
Author(s): Ana Cuesta-Maté, Justinn Renelies‐Hamilton, Per Kryger, Annette Bruun Jensen, Veronica M. Sinotte, Michael Poulsen
Software Mentions: 6
Published: over 3 years ago

10.12688/f1000research.15858.1

Visualizing balances of compositional data: A new alternative to balance dendrograms
Cited by: 13
Author(s): Thomas P. Quinn
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-021-98089-3

Biopsy bacterial signature can predict patient tissue malignancy
Cited by: 10
Author(s): Glenn Hogan, Julia Eckenberger, Neegam Narayanen, Sidney P. Walker, Marcus J. Claesson, Mark Corrigan, Deirdre O’Hanlon, Mark Tangney
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-87384-8

Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere
Cited by: 11
Author(s): Shinichi Yamazaki, Hossein Mardani-Korrani, Rumi Kaida, Kumiko Ochiai, Masaru Kobayashi, Atsushi J. Nagano, Yoshiharu Fujii, Akifumi Sugiyama, Yosuke Aoki
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-70535-8

Bacterial microbiota diversity and composition in red and white wines correlate with plant-derived DNA contributions and botrytis infection
Cited by: 16
Author(s): Alena M. Bubeck, Lena C. Preiss, Anna Jung, Elisabeth Dörner, Daniel Podlesny, Marija Kulis, Cynthia Maddox, Cesar Arze, Christian Zörb, Nikolaus Merkt, W. Florian Fricke
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-020-00830-z

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation
Cited by: 27
Author(s): Camilla Urbaniak, Hernan Lorenzi, James B. Thissen, Crystal Jaing, Brian Crucian, Clarence F. Sams, Duane L. Pierson, Kasthuri Venkateswaran, Satish K. Mehta
Software Mentions: 6
Published: over 4 years ago

10.1186/s42523-020-00054-4

Microbial co-occurrence networks of gut microbiota reveal community conservation and diet-associated shifts in cichlid fishes
Cited by: 18
Author(s): Joan Lluís Riera, Laura Baldo
Software Mentions: 6
Published: about 4 years ago

10.1186/s40168-020-00962-2

Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions
Cited by: 8
Author(s): Joshua M. Lyte, James Keane, Julia Eckenberger, Nicholas B. Anthony, Sandip Shrestha, Daya Marasini, Karrie M. Daniels, Valentina Caputi, Annie Donoghue, Mark Lyte
Software Mentions: 6
Published: almost 4 years ago

10.1093/gigascience/giz107

A field guide for the compositional analysis of any-omics data
Cited by: 162
Author(s): Thomas P. Quinn, Ionas Erb, Gregory B. Gloor, Cédric Notredame, Mark F. Richardson, Tamsyn M. Crowley
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms8101566

The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light Pollution
Cited by: 6
Author(s): Jake Ivan P. Baquiran, Michael Angelou L. Nada, Celine Luisa D. Campos, Sherry Lyn G. Sayco, Patrick C. Cabaitan, Yaeli Rosenberg, Inbal Ayalon, Oren Levy, Cecilia Conaco
Software Mentions: 6
Published: about 4 years ago

10.3390/ph14070635

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

10.3389/fmicb.2021.701796

L-Canavanine, a Root Exudate From Hairy Vetch (Vicia villosa) Drastically Affecting the Soil Microbial Community and Metabolite Pathways
Cited by: 7
Author(s): Hossein Mardani-Korrani, Masaru Nakayasu, Shinichi Yamazaki, Yosuke Aoki, Rumi Kaida, Takashi Motobayashi, Masaru Kobayashi, Naoko Ohkama‐Ohtsu, Yosei Oikawa, Akifumi Sugiyama, Yoshiharu Fujii
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0221543

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
Cited by: 18
Author(s): Paltu Kumar Dhal, Gérmán A. Kopprio, Astrid Gärdes
Software Mentions: 6
Published: almost 5 years ago

10.1128/mBio.01500-19

Dissecting the Gene Expression, Localization, Membrane Topology, and Function of the Plasmodium falciparum STEVOR Protein Family
Cited by: 38
Author(s): Jan Stephan Wichers, Jochen Scholz, Jan Strauss, Susanne Witt, Andrés Lill, Laura-Isabell Ehnold, Niklas Neupert, Benjamin Liffner, Renke Lühken, Michaela Petter, Stephan Lorenzen, Danny W. Wilson, Christian Löw, Catherine Lavazec, Iris Bruchhaus, Egbert Tannich, Tim‐Wolf Gilberger, Anna Bachmann
Software Mentions: 5
Published: over 5 years ago

10.3389/fpls.2020.575861

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization
Cited by: 29
Author(s): María Illescas, M. Belén Rubio, Víctor Hernández-Ruiz, María E. Morán-Diez, Ángel Emilio Martínez de Alba, Carlos Nicolás, Enrique Monte, Rosa Hermosa
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2021.659179

Investigation of Spaceflight Induced Changes to Astronaut Microbiomes
Cited by: 25
Author(s): Michael D. Morrison, James B. Thissen, Fathi Karouia, Satish K. Mehta, Camilla Urbaniak, Kasthuri Venkateswaran, David J. Smith, Crystal Jaing
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2018.02457

Bacterial Abundance and Community Composition in Pond Water From Shrimp Aquaculture Systems With Different Stocking Densities
Cited by: 61
Author(s): Yustian Rovi Alfiansah, Christiane Hassenrück, Andreas Kunzmann, Arief Taslihan, Jens Harder, Astrid Gärdes
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0248967

The pulmonary mycobiome—A study of subjects with and without chronic obstructive pulmonary disease
Cited by: 13
Author(s): Einar Marius Hjellestad Martinsen, Tomas Mikal Eagan, Elise Orvedal Leiten, Ingvild Haaland, Gunnar Reksten Husebø, Kristel Svalland Knudsen, Christine Drengenes, Walter Sanseverino, Andreu Paytuví-Gallart, Rune Nielsen
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0222737

Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions
Cited by: 6
Author(s): Márton Szoboszlay, Astrid Näther, Ewen Mullins, Christoph C. Tebbe
Software Mentions: 5
Published: about 5 years ago

10.1186/s40168-015-0146-x

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Cited by: 91
Author(s): Yue Jiang, Xuejian Xiong, Jayne S. Danska, John Parkinson
Software Mentions: 5
Published: almost 9 years ago

10.1128/mSystems.00053-18

Balances: a New Perspective for Microbiome Analysis
Cited by: 173
Author(s): Javier Rivera Pinto, J. J. Egozcue, Vera Pawlowsky‐Glahn, Roger Paredes, Marc Noguera‐Julian, M. Luz Calle
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-018-0534-0

Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies
Cited by: 55
Author(s): Connor R. Fitzpatrick, Patricia Lu‐Irving, John W. Copeland, David S. Guttman, Pauline W. Wang, David A. Baltrus, Katrina M. Dlugosch, Marc T. J. Johnson
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-018-0612-3

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota
Cited by: 16
Author(s): Ana Popović, Céline Bourdon, Pauline W. Wang, David S. Guttman, Wieger Voskuijl, Michael E. Grigg, Robert Bandsma, John Parkinson
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-018-37505-7

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats
Cited by: 27
Author(s): Suzana Stanisavljević, Aleksa Čepić, Svetlana Bojić, Katarina Veljović, Sanja Mihajlović, Neda Djedović, Bojan Jevtić, Miljana Momčilović, Milica Lazarević, Marija Mostarica Stojković, Djordje Miljković, Nataša Golić
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-021-04061-3

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries
Cited by: 2
Author(s): Liangliang Zhang, Yushu Shi, Kim Anh, Christine B. Peterson, Robert R. Jenq
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: over 6 years ago

10.1186/s12866-020-02002-3

Lifestyle modifications result in alterations in the gut microbiota in obese children
Cited by: 21
Author(s): Ky Young Cho
Software Mentions: 4
Published: almost 4 years ago

10.1186/2049-2618-2-15

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
Cited by: 707
Author(s): Andrew D. Fernandes, Jennifer Reid, Jean M. Macklaim, T.A. McMurrough, David R. Edgell, Gregory B. Gloor
Software Mentions: 4
Published: over 10 years ago

10.1186/s40168-019-0724-4

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight
Cited by: 65
Author(s): Peng Jiang, Stefan J. Green, George E. Chlipala, Fred W. Turek, Martha Hotz Vitaterna
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms9071495

Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
Cited by: 15
Author(s): Tim Piel, Giovanni Sandrini, Gerard Muyzer, Corina P. D. Brussaard, Pieter C. Slot, Maria J. van Herk, Jef Huisman, P. Visser
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms9061297

Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction
Cited by: 1
Author(s): Valentín Pérez-Hernández, Mario Hernández-Guzmán, Marco Luna‐Guido, Yendi E. Navarro‐Noya, Elda M. Romero-Tepal, Luc Dendooven
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms8101550

Seasonal and Nutrient Supplement Responses in Rumen Microbiota Structure and Metabolites of Tropical Rangeland Cattle
Cited by: 19
Author(s): Gonzalo Martínez Fernández, Jinzhen Jiao, Jagadish Padmanabha, Stuart E. Denman, Christopher S. McSweeney
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.5984

Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions
Cited by: 5
Author(s): Nataly Guevara, Christiane Hassenrück, Pier Luigi Buttigieg, Astrid Gärdes
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0232453

Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques
Cited by: 13
Author(s): Charlotte H. Wang, Linda Wu, Zengyan Wang, Magdy S. Alabady, Daniel Parson, Zainab Molumo, Sarah C. Fankhauser
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0187044

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples
Cited by: 19
Author(s): Kalie F. Beckers, Christopher Schulz, Gary W. Childers
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0231838

Crewmember microbiome may influence microbial composition of ISS habitable surfaces
Cited by: 47
Author(s): Aram Avila-Herrera, James B. Thissen, Camilla Urbaniak, Nicholas A. Be, David J. Smith, Fathi Karouia, Satish K. Mehta, Kasthuri Venkateswaran, Crystal Jaing
Software Mentions: 4
Published: over 4 years ago

10.3389/fendo.2020.606530

Gastrointestinal Helminth Infection Improves Insulin Sensitivity, Decreases Systemic Inflammation, and Alters the Composition of Gut Microbiota in Distinct Mouse Models of Type 2 Diabetes
Cited by: 15
Author(s): Zainab Khudhair, Rafid Alhallaf, Ramon M. Eichenberger, Jen Whan, Andreas Kupz, Matthew A. Field, Lutz Krause, David T. Wilson, Norelle L. Daly, Paul Giacomin, Javier Sotillo, Alex Loukas
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2018.03203

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity
Cited by: 61
Author(s): Nicola Vitulo, Wilson José Fernandes Lemos, Matteo Calgaro, Marco Confalone, Giovanna E. Felis, Giacomo Zapparoli, Tiziana Nardi
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2017.00266

Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments
Cited by: 34
Author(s): Katy Hoffmann, Christiane Hassenrück, Verena Salman-Carvalho, Moritz Holtappels, Christina Bienhold
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2018.00809

Conditionally Rare Taxa Contribute but Do Not Account for Changes in Soil Prokaryotic Community Structure
Cited by: 12
Author(s): Rachel Kaminsky, Sergio E. Morales
Software Mentions: 4
Published: over 6 years ago

10.1080/19490976.2020.1814107

Young versus aged microbiota transplants to germ-free mice: increased short-chain fatty acids and improved cognitive performance
Cited by: 58
Author(s): Jun-Young Lee, Venugopal Reddy Venna, David J. Durgan, Huanan Shi, Jacob Hudobenko, Nagireddy Putluri, Joseph F. Petrosino, Louise D. McCullough, Robert M. Bryan
Software Mentions: 4
Published: over 4 years ago

10.1038/srep14174

A multi-platform metabolomics approach identifies highly specific biomarkers of bacterial diversity in the vagina of pregnant and non-pregnant women
Cited by: 97
Author(s): Amy McMillan, Stephen Rulisa, Mark W. Sumarah, Jean M. Macklaim, Justin B. Renaud, Jordan E. Bisanz, Gregory B. Gloor, Gregor Reid
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-16520-0

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Cited by: 130
Author(s): Thomas P. Quinn, Mark F. Richardson, David Lovell, Tamsyn M. Crowley
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-021-81551-7

The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content
Cited by: 8
Author(s): Stephanie Hereira-Pacheco, Yendi E. Navarro‐Noya, Luc Dendooven
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-82311-3

Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country
Cited by: 61
Author(s): Jacky Dwiyanto, Md Hamed Hussain, Daniel D. Reidpath, Kuan Shion Ong, Aisha A Qasim, S. W. H. Lee, S. M. Lee, Su Chern Foo, Chun Wie Chong, Sadequr Rahman
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-92517-0

Impact of a bacterial consortium on the soil bacterial community structure and maize (Zea mays L.) cultivation
Cited by: 13
Author(s): Laura Natali Afanador-Barajas, Yendi E. Navarro‐Noya, Marco Luna‐Guido, Luc Dendooven
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-99127-w

Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
Cited by: 10
Author(s): Tanweer Goolam Mahomed, Rph Peters, Mushal Allam, Arshad Ismail, Senzo Mtshali, Akhter Goolam Mahomed, Veronica Ueckermann, Marleen M. Kock, M.M. Ehlers
Software Mentions: 4
Published: about 3 years ago

10.1038/s41398-020-01073-0

Enduring neurobehavioral effects induced by microbiota depletion during the adolescent period
Cited by: 35
Author(s): Gilliard Lach, Christine Fülling, Thomaz F.S. Bastiaanssen, Fiona Fouhy, Aoife Donovan, Ana Paula Ventura-Silva, Catherine Stanton, Timothy G. Dinan, John F. Cryan
Software Mentions: 4
Published: about 4 years ago

10.1080/20002297.2020.1746494

Co-occurrence of yeast, streptococci, dental decay, and gingivitis in the post-partum period: results of a longitudinal study
Cited by: 6
Author(s): Kirtana Ramadugu, Freida Blostein, Deesha Bhaumik, Wenwen Jiang, Elyse Davis, Elizabeth Salzman, Usha Srinivasan, Carl F. Marrs, Katherine Neiswanger, Daniel W. McNeil, Mary L. Marazita, Betsy Foxman
Software Mentions: 4
Published: almost 5 years ago

10.3390/nu13010201

Genistein Reduces the Risk of Local Mammary Cancer Recurrence and Ameliorates Alterations in the Gut Microbiota in the Offspring of Obese Dams
Cited by: 15
Author(s): Fábia de Oliveira Andrade, Fang Liu, Xiyuan Zhang, Mariana Rosim, Caroline Dani, Idalia M. Cruz, Thomas T.Y. Wang, William G. Helferich, Robert W. Li, Leena Hilakivi‐Clarke
Software Mentions: 4
Published: almost 4 years ago

10.3390/nu12113422

PROVIT: Supplementary Probiotic Treatment and Vitamin B7 in Depression—A Randomized Controlled Trial
Cited by: 59
Author(s): Eva Reininghaus, Martina Platzer, Alexandra Kohlhammer-Dohr, Carlo Hamm, Sabrina Mörkl, Susanne Bengesser, Frederike T. Fellendorf, Theressa Lahousen-Luxenberger, Birgitta Leitner-Afschar, Helmut Schöggl, Daniela Amberger-Otti, Walter Wurm, Robert Queissner, Armin Birner, Valerie S Falzberger, Annamaria Painold, Werner Fitz, Jolana Wagner-Skacel, Martina Brunnmayr, Alexandra Rieger, Alexander Maget, Renate Unterweger, Karin Schwalsberger, Bernd Reininghaus, Melanie Lenger, Thomaz F.S. Bastiaanssen, Nina Dalkner
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-019-46070-6

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

10.3389/fmicb.2018.00870

Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes
Cited by: 30
Author(s): Ditte V. Vestergaard, Gitte Juel Holst, Ioannis Basinas, Grethe Elholm, Vivi Schlünssen, Allan Linneberg, Tina Šantl-Temkiv, Kai Finster, Torben Sigsgaard, Ian P. G. Marshall
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-66361-7

Persistence of plastic debris and its colonization by bacterial communities after two decades on the abyssal seafloor
Cited by: 52
Author(s): Stefan Krause, Massimiliano Molari, Elena V. Gorb, Elke Kossel, Matthias Haeckel
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.631882

Crop Rotation With Cress Increases Cucumber Yields by Regulating the Composition of the Rhizosphere Soil Microbial Community
Cited by: 18
Author(s): Xiaoya Gong, Jie Shi, Xingang Zhou, Tao Yuan, Danmei Gao, Fengzhi Wu
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2021.648455

Resistance, Resilience, and Recovery of Dryland Soil Bacterial Communities Across Multiple Disturbances
Cited by: 12
Author(s): Blaire Steven, Michala L. Phillips, Jayne Belnap, La Verne Gallegos‐Graves, Cheryl R. Kuske, Sasha C. Reed
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0235682

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
Cited by: 16
Author(s): Sarah J Vancuren, Scott J Dos Santos, Janet E. Hill
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-71495-9

Low levels of salivary metals, oral microbiome composition and dental decay
Cited by: 12
Author(s): Elyse Davis, Kelly M. Bakulski, Jaclyn M. Goodrich, Karen E. Peterson, Mary L. Marazita, Betsy Foxman
Software Mentions: 3
Published: over 4 years ago

10.1016/j.ebiom.2020.103176

Bifidobacterium longum counters the effects of obesity: Partial successful translation from rodent to human
Cited by: 48
Author(s): Harriët Schellekens, Cristina Torres‐Fuentes, Marcel van de Wouw, Caitríona M. Long-Smith, Avery Mitchell, Conall Strain, Kirsten Berding, Thomaz F.S. Bastiaanssen, Kieran Rea, Anna V. Golubeva, Silvia Arboleya, Mathieu Verpaalen, Matteo M. Pusceddu, Amy Murphy, Fiona Fouhy, Kiera Murphy, R. Paul Ross, Lal Bahadur Roy, Catherine Stanton, Timothy G. Dinan, John F. Cryan
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2019.02410

Skin Exposure to Narrow Band Ultraviolet (UVB) Light Modulates the Human Intestinal Microbiome
Cited by: 72
Author(s): Else S. Bosman, Arianne Albert, Harvey Lui, Jan P. Dutz, Bruce A. Vallance
Software Mentions: 3
Published: about 5 years ago

10.3390/nu12051468

Recipe for a Healthy Gut: Intake of Unpasteurised Milk Is Associated with Increased Lactobacillus Abundance in the Human Gut Microbiome
Cited by: 27
Author(s): Mary I. Butler, Thomaz F.S. Bastiaanssen, Caitríona M. Long-Smith, Kirsten Berding, Sabrina Mörkl, Anne-Marie Cusack, Conall Strain, Kizkitza Busca, Penny Porteous-Allen, Marcus J. Claesson, Catherine Stanton, John F. Cryan, Darina Allen, Timothy G. Dinan
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-019-0666-x

Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces
Cited by: 139
Author(s): Aleksandra Checinska Sielaff, Camilla Urbaniak, Ganesh Babu Malli Mohan, В. П. Степанов, Quyen Tran, Jason M. Wood, Jeremiah J. Minich, Daniel McDonald, Teresa Mayer, Rob Knight, Fathi Karouia, George E. Fox, Kasthuri Venkateswaran
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-019-0548-x

Placental microRNAs in pregnancies with early onset intrauterine growth restriction and preeclampsia: potential impact on gene expression and pathophysiology
Cited by: 72
Author(s): Zain Awamleh, Gregory B. Gloor, V. K. M. Han
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-97007-x

Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome
Cited by: 7
Author(s): Petri Vänni, Mysore V. Tejesvi, Sofia Ainonen, Marjo Renko, Katja Korpela, Jarmo A. Salo, Niko Paalanne, Terhi Tapiainen
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-94205-5

On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples
Cited by: 13
Author(s): Shan Sun, Xiangzhu Zhu, Xiang Huang, Harvey J. Murff, Reid M. Ness, Douglas L. Seidner, Alicia Sorgen, Ivory C. Blakley, Chang Yu, Qi Dai, M. Andrea Azcárate-Peril, Martha J. Shrubsole, Anthony A. Fodor
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9071366

Effect of Fungicide Application on Lowbush Blueberries Soil Microbiome
Cited by: 6
Author(s): Austin W. Lloyd, David Percival, Svetlana N. Yurgel
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2017.02224

Microbiome Datasets Are Compositional: And This Is Not Optional
Cited by: 1,478
Author(s): Gregory B. Gloor, Jean M. Macklaim, Vera Pawlowsky‐Glahn, J. J. Egozcue
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0135620

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types
Cited by: 90
Author(s): Arianne Albert, Bonnie Chaban, Emily Wagner, John Schellenberg, Matthew G. Links, Julie van Schalkwyk, Gregor Reid, Sean M. Hemmingsen, Janet E. Hill, Deborah Money
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0224909

Sequence count data are poorly fit by the negative binomial distribution
Cited by: 28
Author(s): Stijn Hawinkel, J. C. W. Rayner, Luc Bijnens, Olivier Thas
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-021-01125-7

Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice
Cited by: 40
Author(s): Ryo Aoki, Masayoshi Onuki, Katsumi Hattori, Masato Ito, Takahiro Yamada, Kohei Kamikado, Yun Gi Kim, Nobuhiro Nakamoto, Ikuo Kimura, Julie Clarke, Takanori Kanai, Koji Hase
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0235225

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses
Cited by: 3
Author(s): Mary M. Donato, Olivia Johnson, Blaire Steven, Beth A. Lawrence
Software Mentions: 3
Published: over 4 years ago

10.3389/fbioe.2020.603145

No Tangible Effects of Field-Grown Cisgenic Potatoes on Soil Microbial Communities
Cited by: 9
Author(s): Sascha Krause, Astrid Näther, Vilma Ortiz Cortes, Ewen Mullins, G.J.T. Kessel, L.A.P. Lotz, Christoph C. Tebbe
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-18506-4

Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces
Cited by: 69
Author(s): Camilla Urbaniak, Aleksandra Checinska Sielaff, K. G. Frey, Jonathan Allen, Nitin Kumar Singh, Crystal Jaing, Kevin Wheeler, Kasthuri Venkateswaran
Software Mentions: 3
Published: almost 7 years ago

Projects: bioconductor: ALDEx2

Papers Mentioning ALDEx2 136