bioconductor: phyloseq | Projects

10.1371/journal.pone.0199664

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients
Cited by: 32
Author(s): Bahtiyar Yılmaz, Marianne R. Spalinger, Luc Biedermann, Yannick Franc, Nicolas Fournier, Jean‐Benoît Rossel, Pascal Juillerat, Gerhard Rogler, Andrew J. Macpherson, Michael Scharl
Software Mentions: 4
Published: over 6 years ago

10.1007/s00248-021-01700-3

Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity
Cited by: 9
Author(s): Florian Caillon, Katharina Besemer, Peter Peduzzi, Jakob Schelker
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-97337-w

DNA metabarcoding reveals the dietary composition in the endangered black-faced spoonbill
Cited by: 3
Author(s): Pei‐Yu Huang, Emily Shui Kei Poon, Anson Tsz Chun Wong, Ivy Wai Yan So, Yik-Hei Sung, Simon Yung Wa Sin
Software Mentions: 4
Published: about 3 years ago

10.1186/s12866-017-1092-5

Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone
Cited by: 43
Author(s): Stephanie L. Bond, Edouard Timsit, Matthew L. Workentine, Trevor W. Alexander, Renaud Léguillette
Software Mentions: 4
Published: over 7 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

10.1371/journal.pone.0250514

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea
Cited by: 8
Author(s): Grażyna Płaza, Łukasz Jałowiecki, Dominika Głowacka, Jakub Hubeny, Monika Harnisz, Ewa Korzeniewska
Software Mentions: 4
Published: over 3 years ago

10.1080/19490976.2021.1936378

Effect of COVID-19 precautions on the gut microbiota and nosocomial infections
Cited by: 9
Author(s): Armin Rashidi, Maryam Ebadi, Tauseef Ur Rehman, Heba Elhusseini, Harika Nalluri, Thomas Kaiser, Shernan G. Holtan, Alexander Khoruts, Daniel J. Weisdorf, Christopher Staley
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0159289

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris
Cited by: 352
Author(s): Sonja Oberbeckmann, A. Mark Osborn, Melissa B. Duhaime
Software Mentions: 4
Published: over 8 years ago

10.1128/MRA.00968-20

16S rRNA Gene Diversity of Bacterial Endophytes in Parasitic Cuscuta campestris and Its Helianthus annuus Host
Cited by: 0
Author(s): Adam T. Avila, Tricia A. Van Laar, John V. H. Constable, Katherine Waselkov
Software Mentions: 4
Published: about 4 years ago

10.1186/s13073-021-00856-4

Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India
Cited by: 29
Author(s): Camila Alvarez-Silva, Alireza Kashani, Torben Hansen, Nishal Kumar Pinna, Ranjit Mohan Anjana, Anirban Dutta, Shruti Saxena, Julie Støy, Ulla Kampmann, Trine Nielsen, Torben Jørgensen, Visvanathan Gnanaprakash, Rameshkumar Gnanavadivel, Sukumaran Aswath, Coimbatore Subramanian Shanthi Rani, Kristine Færch, Venkatesan Radha, Muthuswamy Balasubramanyam, G. Balakrish Nair, Bhabatosh Das, Henrik Vestergaard, Torben Hansen, Sharmila S. Mande, Viswanathan Mohan, Manimozhiyan Arumugam, Oluf Pedersen
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0252086

Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation
Cited by: 9
Author(s): Kerry McNally, Charles J. Innis, Adam Kennedy, Jennifer L. Bowen
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0231238

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources
Cited by: 5
Author(s): Sergi Compte-Port, Mireia Fillol, Frédéric Gich, Carles M. Borrego
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0219633

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve
Cited by: 72
Author(s): Kattayoun Kordy, Thaidra Gaufin, Martin Mwangi, Ли Фан, Chiara Cerini, Dong Hoon Lee, Helty Adisetiyo, Cora L. Woodward, Pia S. Pannaraj, Nicole H. Tobin, Grace M. Aldrovandi
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0168573

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil
Cited by: 33
Author(s): Seung‐Yoon Oh, Jonathan J. Fong, Myung Soo Park, Young Woon Lim
Software Mentions: 4
Published: almost 8 years ago

10.3390/toxins13010025

Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?
Cited by: 16
Author(s): Farhad Jalili, Hana Trigui, Juan Maldonado, Sarah Dorner, Arash Zamyadi, Ben Shapiro, Yves Terrat, Nathalie Fortin, Sébastien Sauvé, Michèle Prévost
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0212949

The nasal and oropharyngeal microbiomes of healthy livestock workers
Cited by: 15
Author(s): Ashley E. Kates, Mark Dalman, James C. Torner, Tara C. Smith
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0009597

Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections
Cited by: 8
Author(s): Katharina Stracke, Poom Adisakwattana, Suparat Phuanukoonnon, Tippayarat Yoonuan, Akkarin Poodeepiyasawat, Paron Dekumyoy, Kittipong Chaisiri, Alexandra Roth Schulze, Stephen Wilcox, Harin Karunajeewa, Rebecca J. Traub, Aaron R. Jex
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-90863-7

Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea
Cited by: 12
Author(s): Danijela Šantić, Kasia Piwosz, Frano Matić, Ana Vrdoljak Tomaš, Jasna Arapov, Jason Dean, Mladen Šolić, Michal Koblížek, Grozdan Kušpilić, Stefanija Šestanović
Software Mentions: 4
Published: over 3 years ago

10.1007/s12975-020-00863-4

Disruptions of Anaerobic Gut Bacteria Are Associated with Stroke and Post-stroke Infection: a Prospective Case–Control Study
Cited by: 60
Author(s): Bastiaan W. Haak, Willeke F. Westendorp, Tjitske S. R. van Engelen, Xanthe Brands, Matthijs C. Brouwer, Jan-Dirk Vermeij, Floor Hugenholtz, Aswin Verhoeven, Rico Derks, Martin Giera, Paul J. Nederkoorn, Willem M. de Vos, Diederik van de Beek, W. Joost Wiersinga
Software Mentions: 4
Published: about 4 years ago

10.14814/phy2.14199

Oral vancomycin treatment does not alter markers of postprandial inflammation in lean and obese subjects
Cited by: 10
Author(s): Guido J. Bakker, Johan G. Schnitzler, Siroon Bekkering, Nicolien C. de Clercq, Annefleur M. Koopen, Annick V. Hartstra, Emma C. E. Meessen, Torsten P. M. Scheithauer, Maaike Winkelmeijer, Geesje M. Dallinga‐Thie, Patrice D. Cani, E. Marleen Kemper, Maarten R. Soeters, Jeffrey Kroon, Albert K. Groen, Daniël H. van Raalte, Hilde Herrema, Max Nieuwdorp
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9326

Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea
Cited by: 2
Author(s): Yukino Mizutani, Tetsushi Mori, Taeko Miyazaki, Satoshi Fukuzaki, Reiji Tanaka
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-90198-3

Association of Candida albicans and Cbp+ Streptococcus mutans with early childhood caries recurrence
Cited by: 25
Author(s): Bruna Albuquerque Garcia, Natalia Acosta, Scott L. Tomar, Luiz Fernando Würdig Roesch, José A. Lemos, Leda Mugayar, Jacqueline Abranches
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.7552

Oceanographic habitat and the coral microbiomes of urban-impacted reefs
Cited by: 4
Author(s): Stephanie M. Rosales, Christopher D. Sinigalliano, Maribeth L. Gidley, Paul R. Jones, Lewis J. Gramer
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0176669

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study
Cited by: 33
Author(s): Mohan Pammi, Jacqueline O’Brien, Nadim J. Ajami, Matthew C. Wong, James Versalovic, Joseph F. Petrosino
Software Mentions: 4
Published: over 7 years ago

10.3390/jof5040095

9th Trends in Medical Mycology Held on 11–14 October 2019, Nice, France, Organized under the Auspices of EORTC-IDG and ECMM
Cited by: 14
Author(s): Jean Pierre Gangneux, Olivier Lortholary, Oliver A. Cornely, Livio Pagano
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.540404

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

10.1371/journal.pone.0245314

Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment
Cited by: 16
Author(s): Taylor Ely, Paul H. Barber, Lauren Man, Zachary Gold
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.4017

5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro.
Cited by: 7
Author(s): Eline Vanlancker, Barbara Vanhoecke, Andrea M. Stringer, Tom Van de Wiele
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.10231

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture
Cited by: 22
Author(s): John K. Pearman, Nigel Keeley, Susanna A. Wood, Olivier Laroche, Anastasija Zaiko, Georgia Thomson‐Laing, Laura Biessy, Javier Atalah, Xavier Pochon
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.6377

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis
Cited by: 50
Author(s): Bettina Glasl, Caitlin E. Smith, David G. Bourne, Nicole S. Webster
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.9307

Succession of bacterial communities on carrion is independent of vertebrate scavengers
Cited by: 8
Author(s): Cody R. Dangerfield, Ethan Frehner, Evan R. Buechley, Çağan H. Şekercioğlu, William J. Brazelton
Software Mentions: 4
Published: over 4 years ago

10.1186/s12866-020-01979-1

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog
Cited by: 14
Author(s): Randall R. Jiménez, Gilbert Alvarado, José Luís Sandoval, Simone Sommer
Software Mentions: 4
Published: about 4 years ago

10.1128/mBio.00824-21

Drosophila Antimicrobial Peptides and Lysozymes Regulate Gut Microbiota Composition and Abundance
Cited by: 52
Author(s): Alice Marra, Mark A. Hanson, Shu Kondo, Berra Erkoşar, Bruno Lemaître
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj.8492

Influence of host phylogeny, geographical location and seed harvesting diet on the bacterial community of globally distributed Pheidole ants
Cited by: 9
Author(s): Carla Braga Martins, Corrie S. Moreau
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.9367

Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis
Cited by: 7
Author(s): Paula Lado, Bo Liu, Michelle E. J. Allerdice, Christopher D. Paddock, Sandor E. Karpathy, Hans Klompen
Software Mentions: 4
Published: over 4 years ago

10.1128/mSphere.00226-16

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City
Cited by: 22
Author(s): Holly M. Bik, Julia M. Maritz, Albert Luong, Hakdong Shin, Maria Gloria Domínguez-Bello, Jane M. Carlton
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41390-021-01419-4

Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids
Cited by: 12
Author(s): Erin Felton, A. Millie Burrell, Hollis Chaney, Iman Sami, Anastassios C. Koumbourlis, Robert J. Freishtat, Keith A. Crandall, Andrea Hahn
Software Mentions: 4
Published: over 3 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

10.1128/mSphere.00382-18

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status
Cited by: 22
Author(s): Sarah M. Hird, Holly H. Ganz, Jonathan A. Eisen, Walter M. Boyce
Software Mentions: 4
Published: about 6 years ago

10.1128/mSphere.00626-18

Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity
Cited by: 15
Author(s): Sarahi L. Garcia, Anna J. Székely, Christoffer Bergvall, Martha Schattenhofer, Sari Peura
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0226128

Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats
Cited by: 70
Author(s): Emma K.A. Schmidt, Abel Torres-Espín, Pamela Raposo, Karen Madsen, Kristina A. Kigerl, Phillip G. Popovich, Keith K. Fenrich, Karim Fouad
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSphere.00730-19

Gut Microbiomes of the Eastern Oyster ( Crassostrea virginica ) and the Blue Mussel ( Mytilus edulis ): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities
Cited by: 43
Author(s): Melissa L. Pierce, J. Evan Ward
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13071-021-04859-3

Blastocystis in the faeces of children from six distant countries: prevalence, quantity, subtypes and the relation to the gut bacteriome
Cited by: 11
Author(s): Ondřej Cinek, Katerina Polackova, Rasha Odeh, Abeer Alassaf, Lenka Kramná, Mary Ann Ugochi Ibekwe, Edna Majaliwa, Gunduz Ahmadov, Bashir Mukhtar Elwasila Elmahi, Hanan Mekki, Sami Oikarinen, Jan Lebl, Mohammed A. Abdullah
Software Mentions: 4
Published: over 3 years ago

10.1016/j.wroa.2020.100056

Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households
Cited by: 5
Author(s): Erica R. Fuhrmeister, Ayşe Ercümen, Jessica A. Grembi, Mahfuza Islam, Amy J. Pickering, Kara L. Nelson
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-018-36355-7

An adaptive microbiome α-diversity-based association analysis method
Cited by: 27
Author(s): Hyunwook Koh
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2018.01647

Tucumã Oil Shifted Ruminal Fermentation, Reducing Methane Production and Altering the Microbiome but Decreased Substrate Digestibility Within a RUSITEC Fed a Mixed Hay – Concentrate Diet
Cited by: 29
Author(s): Aline Maria Pereira Cruz Ramos, Stephanie A. Terry, Devin B. Holman, Gerhard Breves, L. G. R. Pereira, André G. M. Silva, A. V. Chaves
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.01756

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage
Cited by: 78
Author(s): Victoria Mesa, José Luis Gallego, Ricardo González-Gil, Béatrice Lauga, Jesús Sánchez, Celia Méndez–García
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2020.580397

Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability
Cited by: 10
Author(s): Shuting Liu, Nicholas Baetge, Jacqueline Comstock, Keri Opalk, Rachel Parsons, Elisa R. Halewood, Chance English, Stephen J. Giovannoni, Luis M. Bolaños, Craig E. Nelson, Kevin L. Vergin, Craig A. Carlson
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2020.602404

Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking
Cited by: 7
Author(s): Lucie Rault, Pierre-Alexandre Lévêque, Sarah Barbey, Frédéric Launay, Hélène Larroque, Yves Le Loir, Pierre Germon, Jocelyne Guinard-Flament, Sergine Even
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2019.00346

Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera
Cited by: 56
Author(s): Brooke L. Weigel, Catherine A. Pfister
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00129

Broad and Fine Scale Variability in Bacterial Diversity and Cyanotoxin Quotas in Benthic Cyanobacterial Mats
Cited by: 8
Author(s): Georgia Thomson‐Laing, Jonathan Puddick, Olivier Laroche, Samantha Fulton, Konstanze Steiner, Mark W. Heath, Susanna A. Wood
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.01305

Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic Interactions
Cited by: 21
Author(s): Stefanos Banos, Deisy Morselli Gysi, Tim Richter-Heitmann, Frank Oliver Glöckner, Maarten Boersma, Karen Helen Wiltshire, Gunnar Gerdts, Antje Wichels, M. Reich
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2018.00297

Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks
Cited by: 10
Author(s): Tatiana V. Karpinets, Vancheswaran Gopalakrishnan, Jennifer A. Wargo, Andrew Futreal, Christopher W. Schadt, Jianhua Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.01245

Outbreaks of an Emerging Viral Disease Covary With Differences in the Composition of the Skin Microbiome of a Wild United Kingdom Amphibian
Cited by: 23
Author(s): Lewis J. Campbell, Trenton W. J. Garner, Kevin Hopkins, Amber Gieselle Firefly Griffiths, Xavier A. Harrison
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2017.00050

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird
Cited by: 52
Author(s): Jakub Kreisinger, Lucie Kropáčková, Adéla Petrželková, Marie Kotasová Adámková, Oldřich Tomášek, Jean‐François Martin, Romana Michálková, Tomáš Albrecht
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2019.00599

Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs
Cited by: 11
Author(s): Benjamin Zwirzitz, Beate Pinior, Barbara U. Metzler‐Zebeli, Monika Handler, Kristina Gense, Christian Knecht, Andrea Ladinig, Monika Dzieciol, Stefanie U. Wetzels, Martin Wagner, Stephan Schmitz‐Esser, Evelyne Mann
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.01249

Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration
Cited by: 12
Author(s): Laura Zinke, Brandi Kiel Reese, James McManus, C. G. Wheat, Beth N. Orcutt, Jan P. Amend
Software Mentions: 4
Published: over 6 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.2018.03344

Long Term Diversity and Distribution of Non-photosynthetic Cyanobacteria in Peri-Alpine Lakes
Cited by: 36
Author(s): Marie‐Ève Monchamp, Piet Spaak, Francesco Pomati
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2018.02878

Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea
Cited by: 51
Author(s): Kosuke Yamamoto, Yuh Shiwa, Taichiro Ishige, Hikaru Sakamoto, Keisuke Tanaka, Makoto Uchino, Naoto Tanaka, Suguru Oguri, Hiromasa Saitoh, Seiya Tsushima
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2021.703014

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds
Cited by: 14
Author(s): Flavia Tarquinio, Océane Attlan, Mathew A. Vanderklift, Oliver Berry, Andrew Bissett
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2020.00867

Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility
Cited by: 10
Author(s): Benjamin Schwan, Christian Abendroth, Adriel Latorre‐Pérez, Manuel Porcar, Cristina Vilanova, Christina Dornack
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2019.01850

Disease Specific Bacterial Communities in a Coralline Algae of the Northwestern Mediterranean Sea: A Combined Culture Dependent and -Independent Approach
Cited by: 13
Author(s): Gaëlle Quéré, Laurent Intertaglia, Claude Payri, Pierre E. Galand
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00380

Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities
Cited by: 32
Author(s): Emilie Macke, Martijn Callens, François Massol, Isabel Vanoverberghe, Luc De Meester, Ellen Decaestecker
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2021.718727

Soil Fungal Community in Grazed Inner Mongolian Grassland Adjacent to Coal-Mining Activity
Cited by: 2
Author(s): Liji Xie, Yinli Bi, Xianglei Li, Kun Wang, Peter Christie
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2021.627539

Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies
Cited by: 10
Author(s): Gertrude Wegl, Nikolaus Grabner, Andreas Köstelbauer, Viviana Klose, Mahdi Ghanbari
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2018.01534

Jellyfish Life Stages Shape Associated Microbial Communities, While a Core Microbiome Is Maintained Across All
Cited by: 24
Author(s): Michael D. Lee, Joshua D. Kling, Rubén Araya, Janja Ceh
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.01069

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity
Cited by: 6
Author(s): Andrea Hahn, Matthew L. Bendall, Keylie M. Gibson, Hollis Chaney, Iman Sami, Geovanny F. Pérez, Anastassios C. Koumbourlis, Timothy A. McCaffrey, Robert J. Freishtat, Keith A. Crandall
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.02558

Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments
Cited by: 14
Author(s): Claus Pelikan, Marion Jaussi, Kenneth Wasmund, Marit‐Solveig Seidenkrantz, Christof Pearce, Zou Zou A. Kuzyk, Craig W. Herbold, Hans Røy, Kasper Urup Kjeldsen, Alexander Loy
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2018.02094

Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique
Cited by: 27
Author(s): Melanie Eger, Michael Graz, Susanne Riede, Gerhard Breves
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2018.01363

Persistence of Cellulolytic Bacteria Fibrobacter and Treponema After Short-Term Corn Stover-Based Dietary Intervention Reveals the Potential to Improve Rumen Fibrolytic Function
Cited by: 66
Author(s): Xiao Xie, Chunlei Yang, Le Luo Guan, Jiakun Wang, Mingyuan Xue, Jian X. Liu
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.00322

Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut Microbiota
Cited by: 11
Author(s): Benjamin J. Korry, Damien J. Cabral, Peter Belenky
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2015.00891

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland
Cited by: 85
Author(s): Rebecca C. Mueller, Jayne Belnap, Cheryl R. Kuske
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2018.02926

Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios
Cited by: 25
Author(s): Juanjo Rodríguez, Christine Gallampois, Sari Timonen, Agneta Andersson, Hanna Sinkko, Peter Haglund, Åsa M. M. Berglund, Mátyás Ripszám, Daniela Figueroa, Mats Tysklind, Owen Rowe
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.584699

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom
Cited by: 8
Author(s): Keith Mitchell, Jiem R. Ronas, Christopher Dao, Amanda C. Freise, Serghei Mangul, Casey Shapiro, Jordan Moberg Parker
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2021.720513

DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data
Cited by: 8
Author(s): Daniel Loos, Lu Zhang, Christine Beemelmanns, Oliver Kurzai, Gianni Panagiotou
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.01636

Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications
Cited by: 12
Author(s): Magdalena N. Georgieva, Sergi Taboada, Ana Riesgo, Cristina Díez‐Vives, Fabio C. De Leo, Rachel M. Jeffreys, Jonathan T. Copley, Crispin T. S. Little, Pilar Ríos, Javier Cristobo, Jon Thomassen Hestetun, Adrian G. Glover
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2020.01686

Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts
Cited by: 11
Author(s): Noemi Procopio, Stefano Ghignone, Samuele Voyron, Marco Chiapello, Anna Williams, Andrew Chamberlain, Antonietta Mello, Michael Buckley
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2020.01981

Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency
Cited by: 62
Author(s): Steven McLoughlin, Charles Spillane, Noel A. Claffey, Pamela M. Smith, Tommy O’Rourke, M.G. Diskin, Sinéad M. Waters
Software Mentions: 4
Published: over 4 years ago

10.1186/s40104-020-00498-3

Dietary Bacillus spp. enhanced growth and disease resistance of weaned pigs by modulating intestinal microbiota and systemic immunity
Cited by: 34
Author(s): Yijie He, Cynthia Jinno, Kwang‐Wook Kim, Zhaohai Wu, Bin Tan, Xunde Li, Rose Whelan, Yanhong Liu
Software Mentions: 4
Published: about 4 years ago

10.3390/jcm8091424

Nutritional Therapy Modulates Intestinal Microbiota and Reduces Serum Levels of Total and Free Indoxyl Sulfate and P-Cresyl Sulfate in Chronic Kidney Disease (Medika Study)
Cited by: 73
Author(s): Biagio Raffaele Di Iorio, Maria Teresa Rocchetti, Maria De Angelis, Carmela Cosola, Stefania Marzocco, Lucia Di Micco, Ighli di Bari, Matteo Accetturo, Mirco Vacca, Marco Gobbetti, Mattia Di Iorio, Antonio Bellasi, Loreto Gesualdo
Software Mentions: 4
Published: about 5 years ago

10.3390/jcm10040840

Ketoanalogs’ Effects on Intestinal Microbiota Modulation and Uremic Toxins Serum Levels in Chronic Kidney Disease (Medika2 Study)
Cited by: 17
Author(s): Maria Teresa Rocchetti, Biagio Di Iorio, Mirco Vacca, Carmela Cosola, Stefania Marzocco, Ighli di Bari, Francesco Maria Calabrese, Roberto Ciarcia, Maria De Angelis, Loreto Gesualdo
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.ppat.1008236

The cervicovaginal mucus barrier to HIV-1 is diminished in bacterial vaginosis
Cited by: 45
Author(s): Thuy Hoang, Emily Toler, Kevin DeLong, Nomfuneko A. Mafunda, Seth M. Bloom, Hannah C. Zierden, Thomas R. Moench, Jenell S. Coleman, Justin Hanes, Douglas S. Kwon, Samuel K. Lai, Richard A. Cone, Laura M. Ensign
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12931-018-0950-5

Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study
Cited by: 56
Author(s): Daphnée Lamarche, Jennie Johnstone, Nicole Zytaruk, France Clarke, Lori Hand, Dessi Loukov, Jake C. Szamosi, Laura Rossi, L. Patrick Schenck, Chris P. Verschoor, Ellen McDonald, Maureen O. Meade, John C. Marshall, Dawn M. E. Bowdish, Tim Karachi, Diane Heels‐Ansdell, Deborah J. Cook, Michael G. Surette
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41597-019-0141-3

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot
Cited by: 8
Author(s): Antônio Pedro Camargo, Rafael Soares Correa de Souza, Patrícia de Britto Costa, Isabel Rodrigues Gerhardt, Ricardo A. Dante, Grazielle Sales Teodoro, Anna Abrahão, Hans Lambers, Marcelo Falsarella Carazzolle, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishna Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I. Min A. Chen, Natalia Ivanova, Nikos C. Kyrpides, Christa Pennacchio, Emiley A. Eloe‐Fadrosh, Paulo Arruda, Rafael S. Oliveira
Software Mentions: 4
Published: over 5 years ago

10.1038/srep18837

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems
Cited by: 49
Author(s): Oliver Grunert, Emma Hernandez-Sanabria, Ramiro Vílchez-Vargas, Ruy Jáuregui, Dietmar H. Pieper, Maaike Perneel, Marie-Christine Van Labeke, Dirk Reheul, Nico Boon
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-017-15955-9

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome
Cited by: 64
Author(s): María‐Soledad Benítez, Shannon L. Osborne, R. Michael Lehman
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-29971-w

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs
Cited by: 28
Author(s): Marion Lemaire, Samir Dou, Armelle Cahu, Michèle Formal, Laurence Le Normand, Véronique Rome, Isabelle Nogret, Stéphanie Ferret‐Bernard, Moez Rhimi, Isabelle Cuinet, Cécile Canlet, Marie Tremblay-Franco, Pascale Le Ruyet, Charlotte Baudry, Philippe Gérard, Isabelle Le Huërou‐Luron, Sophie Blat
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-31168-0

Marchantia liverworts as a proxy to plants’ basal microbiomes
Cited by: 41
Author(s): Luis David Alcaraz, Mariana Peimbert, Hugo R. Barajas, Ana Elena Dorantes-Acosta, John L. Bowman, Mario Arteaga-Vázquez
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-32361-x

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situ biofilm model
Cited by: 12
Author(s): Stefan Rupf, Cédric Christian Laczny, Valentina Galata, Christina Backes, Andreas Keller, Natalia Umanskaya, Arzu Erol, Sascha Tierling, Christina Lo Porto, Jörn Walter, Jasmin Kirsch, Matthias Hannig, Christian Hannig
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-34640-z

Reduced diversity of gut microbiota in two Aedes mosquitoes species in areas of recent invasion
Cited by: 30
Author(s): Fausta Rosso, Valentina Tagliapietra, Davide Albanese, Massimo Pindo, Frédéric Baldacchino, Daniele Arnoldi, Claudio Donati, Annapaola Rizzoli
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-34453-0

Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice
Cited by: 64
Author(s): Umesh D. Wankhade, Ying Zhang, Ping Kang, Maria P. Alfaro, Sree V. Chintapalli, Brian D. Piccolo, Kelly E. Mercer, Aline Andres, Keshari Thakali, Kartik Shankar
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-35230-9

Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women
Cited by: 35
Author(s): Lara R. Dugas, Beatriz Peñalver Bernabé, Medha Priyadarshini, Na Fei, Seo Jin Park, Laquita Brown, Jacob Plange‐Rhule, David E. Nelson, Evelyn Toh, Xiang Gao, Qunfeng Dong, Jun Sun, Stephanie Kliethermes, Neil Gottel, Amy Luke, Jack A. Gilbert, Brian T. Layden
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-37033-4

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow
Cited by: 14
Author(s): Wenli Li, Andrea Edwards, Christina Riehle, Madison S. Cox, Sarah M Raabis, Joseph H. Skarlupka, Andrew J. Steinberger, Jason G. Walling, Derek M. Bickhart, Garret Suen
Software Mentions: 4
Published: almost 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

10.1038/s41598-018-38049-6

Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota
Cited by: 30
Author(s): Jennifer Rosenbaum, Mykhaylo Usyk, Zigui Chen, Christine P. Zolnik, Heidi E. Jones, Levi Waldron, Jennifer Beam Dowd, Lorna E. Thorpe, Robert D. Burk
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-43522-x

Community profiling of the intestinal microbial community of juvenile Hammerhead Sharks (Sphyrna lewini) from the Rewa Delta, Fiji
Cited by: 9
Author(s): Natacha M. S. Juste-Poinapen, Yang Lü, Marta Ferreira, J Poinapen, Ciro Rico
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-44547-y

Disrupted Maturation of the Microbiota and Metabolome among Extremely Preterm Infants with Postnatal Growth Failure
Cited by: 57
Author(s): Noelle Younge, Christopher B. Newgard, C. Michael Cotten, Ronald N. Goldberg, Michael J. Muehlbauer, James R. Bain, Robert Stevens, Thomas M. O’Connell, John F. Rawls, Patrick C. Seed, Patricia L. Ashley
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-46018-w

Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost
Cited by: 66
Author(s): Jorge Domínguez, Manuel Aira, Allison R. Kolbe, María Gómez-Brandòn, Marcos Pérez‐Losada
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-48166-5

Enrichment of intracellular sulphur cycle –associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis
Cited by: 12
Author(s): I. Salonen, Panagiota-Myrsini Chronopoulou, Clare Bird, Gert‐Jan Reichart, Karoliina A. Koho
Software Mentions: 4
Published: over 5 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702