bioconductor: phyloseq | Projects

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: 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: almost 5 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

10.1186/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

10.3390/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

10.1038/s41598-021-92405-7

Microplastics accumulate fungal pathogens in terrestrial ecosystems
Cited by: 73
Author(s): Gerasimos Gkoutselis, Stephan Rohrbach, Janno Harjes, Martin Obst, Andreas Brachmann, Marcus A. Horn, Gerhard Rambold
Software Mentions: 6
Published: about 5 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: about 7 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

10.3389/fmicb.2018.00387

The Intestinal Mycobiota in Wild Zebrafish Comprises Mainly Dothideomycetes While Saccharomycetes Predominate in Their Laboratory-Reared Counterparts
Cited by: 23
Author(s): Prabhugouda Siriyappagouder, Viswanath Kiron, Jep Lokesh, Moger Rajeish, Martina Kopp, Jorge M. O. Fernandes
Software Mentions: 6
Published: over 8 years ago

10.3389/fmicb.2020.526545

Nutrients and Pharmaceuticals Structure Bacterial Core Communities in Urban and Montane Stream Biofilms
Cited by: 4
Author(s): Elizabeth M. Ogata, Michelle A. Baker, Emma J. Rosi, Trevor B. Smart, Donald Long, Zachary T. Aanderud
Software Mentions: 6
Published: almost 6 years ago

10.1128/mBio.02495-18

The Transcriptional Cycle Is Suited to Daytime N 2 Fixation in the Unicellular Cyanobacterium “ Candidatus Atelocyanobacterium thalassa” (UCYN-A)
Cited by: 28
Author(s): María del Carmen Muñoz-Marín, Irina N. Shilova, Tianshu Shi, Hanna Farnelid, Ana María Cabello, Jonathan P. Zehr
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2020.574110

Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens
Cited by: 28
Author(s): Itzel A. Solís-García, Oscar Ceballos-Luna, Elvis Marian Cortazar-Murillo, Damaris Desgarennes, Edith Garay‐Serrano, Violeta Patiño-Conde, Edgar Guevara-Avendaño, Alfonso Méndez-Bravo, Frédérique Reverchon
Software Mentions: 6
Published: over 5 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

10.3389/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

10.3389/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

10.1128/AEM.02555-20

Microbial Community Shifts Reflect Losses of Native Soil Carbon with Pyrogenic and Fresh Organic Matter Additions and Are Greatest in Low-Carbon Soils
Cited by: 6
Author(s): Thea Whitman, Silene DeCiucies, Kelly Hanley, Akio Enders, Jamie Woolet, Johannes Lehmann
Software Mentions: 6
Published: over 5 years ago

10.1093/femsec/fiaa205

Effects of simulated drought on biological soil quality, microbial diversity and yields under long-term conventional and organic agriculture
Cited by: 23
Author(s): Dominika Kundel, Natacha Bodenhausen, Helene Bracht Jørgensen, Jaak Truu, Klaus Birkhofer, Katarina Hedlund, Paul Mäder, Andreas Fließbach
Software Mentions: 6
Published: almost 6 years ago

10.3390/plants9121801

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil
Cited by: 10
Author(s): Andrey A. Belimov, А. И. Шапошников, D. S. Syrova, Arina Kichko, Polina Guro, O. S. Yuzikhin, T. S. Azarova, Anna L Sazanova, E. A. Sekste, Vladimir A Litvinskiy, Vladimir V. Nosikov, А. А. Завалин, E. E. Andronov, Vera I. Safronova
Software Mentions: 6
Published: almost 6 years ago

10.1186/s40168-021-01053-6

Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues
Cited by: 60
Author(s): Talisa Doering, Marlene Wall, Lalita Putchim, Tipwimon Rattanawongwan, Roman Schroeder, Ute Hentschel, Anna Krystyna Roik
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-017-0314-2

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis
Cited by: 61
Author(s): Fiona Whelan, Michael G. Surette
Software Mentions: 6
Published: about 9 years ago

10.1098/rstb.2019.0242

Phylogenetic conservation of soil bacterial responses to simulated global changes
Cited by: 41
Author(s): Kazuo Isobe, Nicholas J. Bouskill, Eoin L. Brodie, Erika A. Sudderth, Jennifer B. H. Martiny
Software Mentions: 6
Published: over 6 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: about 5 years ago

10.1186/s12917-019-2205-1

Acute changes in the colonic microbiota are associated with large intestinal forms of surgical colic
Cited by: 8
Author(s): Shebl E. Salem, Thomas W. Maddox, Philipp Antczak, Julian M. Ketley, Nicola Williams, Debra Archer
Software Mentions: 6
Published: almost 7 years ago

10.7717/peerj.10237

Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species
Cited by: 4
Author(s): Benjamin D. Gallo, John M. Farrell, Brian F. Leydet
Software Mentions: 6
Published: almost 6 years ago

10.1093/femsec/fiz108

Diversity of tryptophan halogenases in sponges of the genus Aplysina
Cited by: 9
Author(s): Johanna Gutleben, Jasper J. Koehorst, Kyle McPherson, Shirley A. Pomponi, René H. Wijffels, Hauke Smidt, Detmer Sipkema
Software Mentions: 6
Published: about 7 years ago

10.3389/fmicb.2016.00399

Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities
Cited by: 21
Author(s): Megan A. Rúa, Emily Wilson, S. D. Steele, Arielle R. Munters, Jason D. Hoeksema, A. Carolin Frank
Software Mentions: 6
Published: over 10 years ago

10.1186/s12887-020-02067-z

Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment
Cited by: 15
Author(s): Romy D. Zwittink, Diny van Zoeren‐Grobben, Ingrid B. Renes, Richard A. van Lingen, Obbe F. Norbruis, Rocı́o Martı́n, Liesbeth J. Groot Jebbink, Jan Knol, Clara Belzer
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.12135

Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics
Cited by: 9
Author(s): Ashley K. Coons, Kathrin Busch, Mark Lenz, Ute Hentschel, Erik Borchert
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2021.592725

Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome
Cited by: 13
Author(s): Henry Joseph Oduor Ogola, Ramganesh Selvarajan, Memory Tekere
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.3674

Microbiome succession during ammonification in eelgrass bed sediments
Cited by: 21
Author(s): Cassandra L. Ettinger, Susan L. Williams, Jessica M. Abbott, John J. Stachowicz, Jonathan A. Eisen
Software Mentions: 6
Published: about 9 years ago

10.1186/s12882-020-01773-1

The urinary microbiome shows different bacterial genera in renal transplant recipients and non-transplant patients at time of acute kidney injury – a pilot study
Cited by: 10
Author(s): Daniela Gerges, Peter Pichler, Alexander Zimprich, Christoph Hotzy, Wolfgang Barousch, Rita Lang, Elisabeth Lobmeyr, Sabina Baumgartner‐Parzer, Ludwig Wagner, Wolfgang Winnicki
Software Mentions: 6
Published: over 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

10.3390/ijms21176283

Differential Profiles of Gut Microbiota and Metabolites Associated with Host Shift of Plutella xylostella
Cited by: 22
Author(s): Fei‐Ying Yang, Hafiz Sohaib Ahmed Saqib, Junhui Chen, Qian‐Qian Ruan, Liette Vasseur, Weiyi He, Minsheng You
Software Mentions: 6
Published: about 6 years ago

10.7717/peerj.12035

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere
Cited by: 4
Author(s): Ankit T. Hinsu, Ashvin Dumadiya, Anjali Joshi, Rohitkumar Kotadiya, Kavan N. Andharia, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.5715

Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests
Cited by: 24
Author(s): Luis E. Castañeda, Tohru Miura, Roland Sánchez, Olga Barbosa
Software Mentions: 6
Published: almost 8 years ago

10.3390/pathogens10040396

Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?
Cited by: 4
Author(s): Ewa Sajnaga, Marcin Skowronek, Agnieszka Kalwasińska, Waldemar Kazimierczak, Karolina Ferenc, Magdalena Lis, Adrian Wiater
Software Mentions: 6
Published: over 5 years ago

10.3390/pathogens10081063

Gut Microbiota in Military International Travelers with Doxycycline Malaria Prophylaxis: Towards the Risk of a Simpson Paradox in the Human Microbiome Field
Cited by: 1
Author(s): Émilie Javelle, Aurélie Mayet, Matthieu Million, Anthony Levasseur, Rodrigue S. Allodji, Catherine Marimoutou, Chrystel Lavagna, Jérôme Desplans, Pierre-Édouard Fournier, Didier Raoult, Gaëtan Texier
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2017.01379

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis)
Cited by: 25
Author(s): Obed Hernández‐Gómez, Jason T. Hoverman, Rod N. Williams
Software Mentions: 6
Published: about 9 years ago

10.1002/ece3.3597

Gut microbiota composition is associated with environmental landscape in honey bees
Cited by: 94
Author(s): Julia C. Jones, Carmelo Fruciano, Falk Hildebrand, Hasan Al Toufalilia, Nicholas J. Balfour, Peer Bork, Philipp Engel, Francis L. W. Ratnieks, William O. Hughes
Software Mentions: 6
Published: almost 9 years ago

10.1186/s40168-020-00943-5

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species
Cited by: 26
Author(s): Antonio Suppa, Jouni Kvist, Xiaojing Li, Vignesh Dhandapani, Hanan Almulla, Antoine Y. Tian, Stephen Kissane, Jian Zhou, Alessio Perotti, Hayley Mangelson, Kyle W. Langford, Valeria Rossi, James B. Brown, Luisa Orsini
Software Mentions: 6
Published: almost 6 years ago

10.1186/s40168-019-0686-6

Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets
Cited by: 32
Author(s): Anukriti Sharma, Miles Richardson, Lauren Cralle, Christopher E. Stamper, Juan P. Maestre, Kelly A. Stearns‐Yoder, Teodor T. Postolache, Katherine L Bates, Kerry A. Kinney, Lisa A. Brenner, Christopher A. Lowry, Jack A. Gilbert, Andrew J. Hoisington
Software Mentions: 6
Published: over 7 years ago

10.1186/s40168-019-0705-7

Microbial indicators of environmental perturbations in coral reef ecosystems
Cited by: 109
Author(s): Bettina Glasl, David G. Bourne, Pedro R. Frade, Torsten Thomas, Britta Schaffelke, Nicole S. Webster
Software Mentions: 6
Published: over 7 years ago

10.1038/s41396-021-00987-x

Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria
Cited by: 14
Author(s): François Thomas, Nolwen Le Duff, Ting-Di Wu, Aurélie Cébron, Stéphane Uroz, Pascal Riera, Cédric Leroux, Gwenn Tanguy, Erwan Legeay, Jean‐Luc Guerquin‐Kern
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

10.1128/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

10.1038/s41396-020-00844-3

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles
Cited by: 45
Author(s): Annelein Meisner, L. Basten Snoek, Joseph Nesme, Elizabeth Dent, Samuel Jacquiod, Aimée T. Classen, Anders Priemé
Software Mentions: 6
Published: over 5 years ago

10.1002/ece3.3638

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)
Cited by: 54
Author(s): Michael S. Robeson, Kamil Khanipov, George Golovko, Samantha M. Wisely, Michael D. White, Michael J. Bodenchuck, Timothy J. Smyser, Yuriy Fofanov, Noah Fierer, Antoinette J. Piaggio
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0248030

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome
Cited by: 22
Author(s): Heidi M.-L. Wipf, Devin Coleman‐Derr
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-018-0449-9

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool
Cited by: 113
Author(s): Jo De Vrieze, Ameet J. Pinto, William T. Sloan, Umer Zeeshan Ijaz
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0236574

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya
Cited by: 11
Author(s): Edward Nderitu Karanja, Andreas Fließbach, Noah Adamtey, Anne Kelly Kambura, Martha W. Musyoka, Komi K. M. Fiaboe, Romano Mwirichia
Software Mentions: 6
Published: about 6 years ago

10.3389/fmicb.2016.02064

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
Cited by: 177
Author(s): Manoeli Lupatini, G.W. Korthals, Mattias de Hollander, Thierry Janssens, Eiko E. Kuramae
Software Mentions: 6
Published: over 9 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/ani11092597

Effect of a Low-Methane Diet on Performance and Microbiome in Lactating Dairy Cows Accounting for Individual Pre-Trial Methane Emissions
Cited by: 3
Author(s): Juana Catarina Cariri Chagas, Mohammad Ramin, Ruth Gómez Expósito, Hauke Smidt, S.J. Krizsan
Software Mentions: 6
Published: about 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: almost 6 years ago

10.1186/s13071-019-3761-8

Regional biogeography of microbiota composition in the Chagas disease vector Rhodnius pallescens
Cited by: 15
Author(s): Troy J. Kieran, Kaylee M. H. Arnold, Jesse C. Thomas, Christina P. Varian, Azäel Saldaña, José E. Calzada, Nicole L. Gottdenker
Software Mentions: 6
Published: almost 7 years ago

10.3390/microorganisms6030068

Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll
Cited by: 2
Author(s): Catherine Burke, Delaney Burnard, Adam Polkinghorne, Jonathan K. Webb, Wilhelmina M. Huston
Software Mentions: 6
Published: about 8 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

10.1038/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

10.1128/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

10.3390/microorganisms9030492

The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
Cited by: 11
Author(s): Barry Linnane, Aaron M. Walsh, Calum J. Walsh, Fiona Crispie, Órla O’Sullivan, Paul D. Cotter, Michael McDermott, J. A. A. Renwick, Paul McNally
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-021-01031-y

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals
Cited by: 25
Author(s): Tina Keller‐Costa, Asunción Lago‐Lestón, J. Saraiva, Rodolfo Brizola Toscan, Sandra Godinho Silva, Jorge M. S. Gonçalves, Cymon J. Cox, Nikos C. Kyrpides, Ulisses Nunes da Rocha, Rodrigo Costa
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0187612

Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus
Cited by: 39
Author(s): Jocelyn M. Wessels, Julie Lajoie, Danielle Vitali, Kenneth Omollo, Joshua Kimani, Julius Oyugi, Juliana Cheruiyot, Murungaru Kimani, Joseph Maina Mungai, Maureen Akolo, Jennifer C. Stearns, Michael G. Surette, Keith R. Fowke, Charu Kaushic
Software Mentions: 6
Published: almost 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

10.3390/microorganisms8030368

Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk Microbiota
Cited by: 8
Author(s): Alexandre J.K. Ouamba, Gisèle LaPointe, Simon Dufour, Denis Roy
Software Mentions: 6
Published: over 6 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

10.3389/fmicb.2021.642197

Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life
Cited by: 25
Author(s): Modupe Coker, Hannah E. Laue, Anne G. Hoen, Margaret Hilliard, Erika Dade, Zhigang Li, Thomas J. Palys, Hilary G. Morrison, Emily Baker, Margaret R. Karagas, Juliette C. Madan
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms8121978

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea
Cited by: 8
Author(s): Bruno Francesco Rodrigues de Oliveira, Isabelle Rodrigues Lopes, Anna Luiza Bauer Canellas, Guilherme Muricy, Alan D. W. Dobson, Marinella Silva Laport
Software Mentions: 6
Published: almost 6 years ago

10.3390/microorganisms8071004

Relationship between the Oral and Vaginal Microbiota of South African Adolescents with High Prevalence of Bacterial Vaginosis
Cited by: 11
Author(s): Christina Balle, Rachel Esra, Enock Havyarimana, Shameem Z. Jaumdally, Katie Lennard, Iyaloo N. Konstantinus, Shaun Barnabas, Anna‐Ursula Happel, Katherine Gill, Tanya Pidwell, Jairam R. Lingappa, Hoyam Gamieldien, Linda‐Gail Bekker, Jo‐Ann S. Passmore, Heather B. Jaspan
Software Mentions: 6
Published: about 6 years ago

10.1007/s00248-020-01656-w

Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations
Cited by: 2
Author(s): Edisa García Hernández, Matty P. Berg, A. Raoul Van Oosten, Christian Smit, Joana Falcão Salles
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2021.645362

Larval Diet Abundance Influences Size and Composition of the Midgut Microbiota of Aedes aegypti Mosquitoes
Cited by: 13
Author(s): Hannah J. MacLeod, George Dimopoulos, Sarah M. Short
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2021.675693

Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities
Cited by: 10
Author(s): Jialin Hu, Jonathan D. Richwine, Patrick D. Keyser, Lidong Li, Fei Yao, Sindhu Jagadamma, Jennifer M. DeBruyn
Software Mentions: 6
Published: about 5 years ago

10.1111/1751-7915.13323

Diet and diet‐associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi)
Cited by: 56
Author(s): Jackson Wilkes Walburn, Bernd Wemheuer, Torsten Thomas, Elizabeth Copeland, Wayne A. O’Connor, Mark A. Booth, D. Stewart Fielder, Suhelen Egan
Software Mentions: 6
Published: almost 8 years ago

10.18632/aging.103168

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis
Cited by: 103
Author(s): Jianquan He, Shuaimei Xu, Bangzhou Zhang, Chuanxing Xiao, Zhangran Chen, Fuyou Si, Jifan Fu, Xiaobo Lin, Guohua Zheng, Guangchuang Yu, Jian Chen
Software Mentions: 6
Published: over 6 years ago

10.1002/ece3.6934

Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirds
Cited by: 7
Author(s): Ramona Fleischer, Alice Risely, Paquita E. A. Hoeck, Lukas F. Keller, Simone Sommer
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12862-021-01773-1

Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distance
Cited by: 5
Author(s): Jiří Reif, Lucie Schmiedová, Jakub Kreisinger, Tomáš Albrecht, Jiří Reif, Tomasz S. Osiejuk, Radka Reifová
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms8020279

Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica
Cited by: 9
Author(s): Adriana Rego, António G G Sousa, João P. Santos, Francisco Pascoal, João Canário, Pedro N. Leão, Catarina Magalhães
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-015-0069-6

Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure
Cited by: 108
Author(s): Adrienne B. Narrowe, Munira Albuthi-Lantz, Erin P. Smith, Kimberly J Bower, Timberley M. Roane, Alan M. Vajda, Christopher S. Miller
Software Mentions: 6
Published: over 11 years ago

10.3390/microorganisms8070982

Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural Starter
Cited by: 10
Author(s): Lucas von Gastrow, Marie‐Noëlle Madec, Victoria Chuat, S. Lubac, Clémence Morinière, Sébastien Lê, Sylvain Santoni, Delphine Sicard, Florence Valence
Software Mentions: 6
Published: about 6 years ago

10.3389/fmicb.2020.574137

Persistence of Suspected Probiotic Organisms in Preterm Infant Gut Microbiota Weeks After Probiotic Supplementation in the NICU
Cited by: 17
Author(s): Efrah I. Yousuf, Marília Sá Carvalho, Sara Dizzell, Stephanie Kim, Elizabeth Gunn, Jennifer Twiss, Lucy Giglia, Connie Stuart, Eileen K. Hutton, Katherine M. Morrison, Jennifer C. Stearns
Software Mentions: 6
Published: about 6 years ago

10.3389/fmicb.2018.00792

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations
Cited by: 25
Author(s): Jessica Chopyk, Sarah Allard, Daniel J. Nasko, Anthony Bui, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 6
Published: over 8 years ago

10.3390/microorganisms9010076

Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics
Cited by: 44
Author(s): Katharina Kesy, Matthias Labrenz, Brittan S. Scales, Bernd Kreikemeyer, Sonja Oberbeckmann
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms7100473

Rapid Bacterial Community Changes during Vermicomposting of Grape Marc Derived from Red Winemaking
Cited by: 18
Author(s): María Gómez-Brandòn, Manuel Aira, Allison R. Kolbe, Nariane de Andrade, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0239681

The Znt7-null mutation has sex dependent effects on the gut microbiota and goblet cell population in the mouse colon
Cited by: 3
Author(s): Mary E. Kable, Niknaz Riazati, Catherine P. Kirschke, Junli Zhao, Surapun Tepaamorndech, Liping Huang
Software Mentions: 6
Published: almost 6 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

10.3389/fmicb.2020.00954

Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite
Cited by: 22
Author(s): Fátima Jorge, Nolwenn M. Dheilly, Robert Poulin
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-019-0734-2

Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics
Cited by: 94
Author(s): Chengying Shi, Leen Beller, Ward Deboutte, Kwe Claude Yinda, Leen Delang, Anubis Vega-Rúa, Anna‐Bella Failloux, Jelle Matthijnssens
Software Mentions: 6
Published: about 7 years ago

10.3389/fmicb.2018.00674

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop
Cited by: 38
Author(s): Késia Silva Lourenço, Noriko A. Cassman, Agata Pijl, Johannes A. van Veen, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-017-15554-8

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women
Cited by: 7
Author(s): Supriya D. Mehta, Ashish Pradhan, Stefan J. Green, Ankur Naqib, Elijah Odoyo-June, Charlotte A. Gaydos, Sheila M. Barry, Alan Landay, Robert C. Bailey
Software Mentions: 6
Published: almost 9 years ago

10.12688/f1000research.16680.1

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
Cited by: 105
Author(s): Gaurav S. Kandlikar, Zachary Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan J. B. Kraft, Jordan Moberg Parker, Joshua Sprague, David J. Kushner, Emily Curd
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41598-018-25927-2

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses
Cited by: 24
Author(s): Zhongming Ge, Alexander Sheh, Yan Feng, Sureshkumar Muthupalani, Lili Ge, Chuanwu Wang, Susanna Kurnick, Anthony Mannion, Mark T. Whary, James G. Fox
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-018-29277-x

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model
Cited by: 50
Author(s): Jonathan B. Clayton, Gabriel A. Al‐Ghalith, Ha Thang Long, Bui Van Tuan, Francis Cabana, Hu Huang, Pajau Vangay, Tonya Ward, Vo Van Minh, Nguyen Ai Tam, Nguyen Tat Dat, Dominic A. Travis, Michael P. Murtaugh, Herbert H. Covert, Kenneth E. Glander, Tilo Nadler, Barbara Toddes, John Chih Mun Sha, Randy Singer, Dan Knights, Timothy J. Johnson
Software Mentions: 6
Published: about 8 years ago

10.3390/microorganisms8071015

Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino Children
Cited by: 16
Author(s): Maria Julia Golloso-Gubat, Quinten R Ducarmon, Robby Carlo A. Tan, Romy D. Zwittink, Ed J. Kuijper, Jacus S. Nacis, Noelle Lyn C Santos
Software Mentions: 6
Published: about 6 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: about 5 years ago

10.1002/brb3.2259

Changes in the gut microbiome associated with infliximab in patients with bipolar disorder
Cited by: 3
Author(s): Aadil Bharwani, Jake C. Szamosi, Valerie H. Taylor, Yena Lee, Asem Bala, Rodrigo B. Mansur, Mehala Subramaniapillai, Michael G. Surette, Roger S. McIntyre
Software Mentions: 6
Published: over 5 years ago

10.3389/fcimb.2017.00262

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition
Cited by: 32
Author(s): Emanuel Heitlinger, Susana Carolina Martins Ferreira, Dagmar Thierer, Heribert Hofer, Marion L. East
Software Mentions: 6
Published: over 9 years ago

10.1186/s42523-020-00057-1

Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics
Cited by: 12
Author(s): Amy M. Van Cise, Paul R. Wade, Caroline E. C. Goertz, Kathleen A. Burek‐Huntington, Kim M. Parsons, Tonya M. Clauss, Roderick C. Hobbs, Amy Apprill
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13068-020-01855-0

Lignin intermediates lead to phenyl acid formation and microbial community shifts in meso- and thermophilic batch reactors
Cited by: 7
Author(s): Eva Maria Prem, Mira Mutschlechner, Blaž Stres, Paul Illmer, Andreas Otto Wagner
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms9051060

Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America
Cited by: 42
Author(s): Keisha Harrison, Chris Curtin
Software Mentions: 6
Published: over 5 years ago

10.1111/1751-7915.13450

Environmental filtering increases with elevation for the assembly of gut microbiota in wild pikas
Cited by: 47
Author(s): Huan Li, Rui Zhou, Jun Zhu, Xiaodan Huang, Jiapeng Qu
Software Mentions: 6
Published: over 7 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702