bioconductor: phyloseq | Projects

10.3389/fmicb.2020.00993

The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets
Cited by: 71
Author(s): Thomas Klammsteiner, Andreas Walter, Tajda Bogataj, Carina Desirée Heussler, Blaž Stres, Florian M. Steiner, Birgit C. Schlick‐Steiner, Wolfgang Arthofer, Heribert Insam
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2021.684233

Maternal Antibiotic Treatment Disrupts the Intestinal Microbiota and Intestinal Development in Neonatal Mice
Cited by: 8
Author(s): Chung-Ming Chen, Hsiu Chu Chou, Yu Yang
Software Mentions: 4
Published: over 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 6 years ago

10.3389/fmicb.2020.00133

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun
Cited by: 15
Author(s): Vandana R. Prabhu, . Wasimuddin, Ranganathan Kamalakkannan, Moolamkudy Suresh Arjun, Muniyandi Nagarajan
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2021.656889

Frozen Mother’s Own Milk Can Be Used Effectively to Personalize Donor Human Milk
Cited by: 3
Author(s): Monica Lamberti, Natalie A. Harrison, Marion M Bendixen, Evon M. DeBose-Scarlett, Sharon Thompson, Josef Neu, Leslie A. Parker, Graciela L. Lorca
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00980

Comparison of Bacterial and Fungal Composition and Their Chemical Interaction in Free Tropospheric Air and Snow Over an Entire Winter Season at Mount Sonnblick, Austria
Cited by: 11
Author(s): Nora Els, Marion Greilinger, Michael Reisecker, Romie Tignat-Perrier, Kathrin Baumann‐Stanzer, Anne Kasper-Giebl, Birgit Sattler, Catherine Larose
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2020.00581

The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato
Cited by: 16
Author(s): Johannes B Herpell, Florian Schindler, Mersad Bejtović, Lena Fragner, Bocar Diallo, Anke Bellaire, Susanne Kublik, Bärbel U. Foesel, Silvia Gschwendtner, Melina Kerou, Michael Schloter, Wolfram Weckwerth
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2021.675798

Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts
Cited by: 4
Author(s): Emily N. Junkins, Bradley S. Stevenson
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2019.00069

Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment
Cited by: 37
Author(s): Kimberley Warren‐Rhodes, Kevin C. Lee, Stephen Archer, Nathalie A. Cabrol, Linda Ng-Boyle, David Wettergreen, K. Zacny, Stephen B. Pointing
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.584222

Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea
Cited by: 8
Author(s): Paul A. Steiner, Javier Geijo, Eduard Fadeev, Aleix Obiol, Eva Sintes, Thomas Rattei, Gerhard J. Herndl
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.01287

Quorum Sensing Signals Alter in vitro Soil Virus Abundance and Bacterial Community Composition
Cited by: 12
Author(s): Xiaolong Liang, Regan E. Wagner, Bingxue Li, Ning Zhang, Mark Radosevich
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.02043

Protists Within Corals: The Hidden Diversity
Cited by: 23
Author(s): Camille Clérissi, Sébastien Brunet, Jérémie Vidal-Dupiol, Mehdi Adjeroud, Pierre Lepage, Laure Guillou, Jean-Michel Escoubas, Ève Toulza
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2020.491425

Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems
Cited by: 5
Author(s): Erin Jones, Natasha A. Griffin, Julia E. Kelso, Gregory T. Carling, Michelle A. Baker, Zachary T. Aanderud
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2017.00457

Core Microbiota and Metabolome of Vitis vinifera L. cv. Corvina Grapes and Musts
Cited by: 19
Author(s): Irene Stefanini, Silvia Carlin, Noemi Tocci, Davide Albanese, Claudio Donati, Pietro Franceschi, Michele Paris, Alberto Zenato, Silvano Tempesta, Alberto Bronzato, Urška Vrhovšek, Fulvio Mattivi, Duccio Cavalieri
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2013.00279

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter
Cited by: 59
Author(s): C. Ryan Penton, Timothy A. Johnson, John F. Quensen, Shoko Iwai, James R. Cole, James M. Tiedje
Software Mentions: 4
Published: almost 14 years ago

10.3389/fmicb.2019.01206

Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem
Cited by: 70
Author(s): Racha El Hage, Emma Hernandez-Sanabria, Marta Calatayud, Ruben Props, Tom Van de Wiele
Software Mentions: 4
Published: over 7 years ago

10.3389/fnut.2020.00083

Vitamin B12 Deficiency Alters the Gut Microbiota in a Murine Model of Colitis
Cited by: 37
Author(s): Eberhard Lurz, Rachael Horne, Pekka Määttänen, Richard Wu, Steven R. Botts, Bo Li, Laura Rossi, Kathene C. Johnson‐Henry, Agostino Pierro, Michael G. Surette, Philip M. Sherman
Software Mentions: 4
Published: over 6 years ago

10.3389/fphys.2016.00606

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Cited by: 30
Author(s): Alejandra Contreras, Benjamin Cocom-Chan, Georgina Hernández-Montes, Tobías Portillo-Bobadilla, Osbaldo Resendis‐Antonio
Software Mentions: 4
Published: almost 10 years ago

10.3389/fphys.2021.668645

A Holistic Assessment of Polyethylene Fiber Ingestion in Larval and Juvenile Japanese Medaka Fish
Cited by: 4
Author(s): Elizabeth DiBona, Lee J. Pinnell, Annika Heising-Huang, Simon Joscha Geist, John Turner, Frauke Seemann
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2019.01697

Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management
Cited by: 19
Author(s): Paula Harkes, Joris J.M. van Steenbrugge, S.J.J. van den Elsen, Afnan Khalil Ahmad Suleiman, J.J. de Haan, M.H.M. Holterman, J. Helder
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2020.00993

Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition?
Cited by: 14
Author(s): Zhiguang Qiu, Juntao Wang, Manuel Delgado‐Baquerizo, Pankaj Trivedi, Eleonora Egidi, Yi-Min Chen, Haiyang Zhang, Brajesh K. Singh
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2020.572741

Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine (Lupinus angustifolius)
Cited by: 15
Author(s): Ana A. Robles-Aguilar, Oliver Grunert, Emma Hernandez-Sanabria, Mohamed Mysara, Erik Meers, Nico Boon, Nicolai David Jablonowski
Software Mentions: 4
Published: almost 6 years ago

10.3389/fvets.2020.00616

An Assessment of the Stability of the Canine Oral Microbiota After Probiotic Administration in Healthy Dogs Over Time
Cited by: 10
Author(s): Sara E. Bell, Andrea K. Nash, Brian M. Zanghi, Cynthia M. Otto, Erin Perry
Software Mentions: 4
Published: about 6 years ago

10.3389/fvets.2020.00438

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats
Cited by: 2
Author(s): Andrea Balboni, Giovanni Franzo, Luca Bano, Stefano Arcangeli, Alessia Rizzardi, Lorenza Urbani, Sofia Segatore, Federica Serafini, Francesco Dondi, Mara Battilani
Software Mentions: 4
Published: about 6 years ago

10.1186/s13073-021-00843-9

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
Cited by: 42
Author(s): Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 4
Published: over 5 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 5 years ago

10.1080/19490976.2021.1875797

Early life environmental exposures have a minor impact on the gut ecosystem following a natural birth
Cited by: 6
Author(s): Nishat Tasnim, Candice Quin, S K Gill, Chunping Dai, Miranda M. Hart, Deanna L. Gibson
Software Mentions: 4
Published: almost 6 years ago

10.1080/19490976.2021.1897209

The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome
Cited by: 6
Author(s): John P. Haran, Doyle V. Ward, Shakti Bhattarai, Ethan Loew, Protiva Dutta, Amanda Higgins, Beth A. McCormick, Vanni Bucci
Software Mentions: 4
Published: almost 6 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 6 years ago

10.1016/j.jaci.2017.08.041

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting
Cited by: 159
Author(s): Marie‐Claire Arrieta, Andrea Arévalo, Leah T. Stiemsma, Pedro A. Dimitriu, Martha Chico, Sofia Loor, Maritza Vaca, Rozlyn C.T. Boutin, Evan Morien, Mingliang Jin, Stuart E. Turvey, Jens Walter, Laura Wegener Parfrey, Philip J. Cooper, B. Brett Finlay
Software Mentions: 4
Published: about 8 years ago

10.1093/jas/skaa181

The effect of maternal antibiotic use in sows on intestinal development in offspring
Cited by: 10
Author(s): Astrid de Greeff, Dirkjan Schokker, Petra Roubos-van den Hil, P. Ramaekers, S.A. Vastenhouw, Frank Harders, Alex Bossers, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-54855-y

Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays
Cited by: 51
Author(s): Stephanie M. Rosales, Margaret W. Miller, Dana E. Williams, Nikki Traylor-Knowles, Benjamin Young, Xaymara M. Serrano
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-60562-w

Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression
Cited by: 19
Author(s): Elvia Ramírez-Carrillo, Osiris Gaona, Javier Nieto, Andrés Sánchez-Quinto, Daniel Cerqueda‐García, Luisa I. Falcón, Olga A. Rojas-Ramos, Isaac González‐Santoyo
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-61092-1

Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning
Cited by: 35
Author(s): Miguel de Celis, Ignacio Belda, Rüdiger Ortiz‐Álvarez, Lucía Arregui, Domingo Marquina, Susana Serrano, Andrés de la Oliva Santos
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-61817-2

Blood meal sources and bacterial microbiome diversity in wild-caught tsetse flies
Cited by: 21
Author(s): Alex Kiarie Gaithuma, Junya Yamagishi, Kyoko Hayashida, Nobuyoshi Kawai, Boniface Namangala, Chihiro Sugimoto
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-69602-x

Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast
Cited by: 6
Author(s): Catharina Vendl, Eve Slavich, Bernd Wemheuer, Tiffanie M. Nelson, Belinda C. Ferrari, Torsten Thomas, Tracey L. Rogers
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-73515-0

Preliminary insights into the impact of primary radiochemotherapy on the salivary microbiome in head and neck squamous cell carcinoma
Cited by: 15
Author(s): Christina Kumpitsch, Christine Moissl-Eichinger, Jakob Pock, Dietmar Thurnher, Axel Wolf
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-78525-6

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia
Cited by: 11
Author(s): Katrina West, Zoe T. Richards, Euan S. Harvey, Robert Susac, Alicia Grealy, Michael Bunce
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-79055-x

Simultaneous allergic traits in dogs and their owners are associated with living environment, lifestyle and microbial exposures
Cited by: 13
Author(s): Jenni Lehtimäki, Hanna Sinkko, Anna Hielm‐Björkman, Tiina Laatikainen, Lasse Ruokolainen, Hannes Lohi
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-80444-5

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt
Cited by: 23
Author(s): Adrienn Tóth, István Csabai, Gergely Maróti, Ákos Jerzsele, Attila Dubecz, Árpád V. Patai, Maura Fiona Judge, Sára Ágnes Nagy, László Makrai, Krisztián Bànyai, G. Szita, Norbert Solymosi
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-81507-x

Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus
Cited by: 6
Author(s): Hua Zha, Fengping Liu, Zongxin Ling, Kevin Chang, Jiezuan Yang, Lanjuan Li
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-80982-6

Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment in a randomized trial of preterm infants
Cited by: 34
Author(s): Jordan T. Russell, J. Lauren Ruoss, Diomel de la Cruz, Nan Li, Catalina Bazacliu, Laura Patton, Kelley Lobean McKinley, Timothy J. Garrett, Richard A. Polin, Eric W. Triplett, Josef Neu
Software Mentions: 4
Published: over 5 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: over 5 years ago

10.1038/s41598-021-82362-6

Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet
Cited by: 11
Author(s): Kelsey E. Witt, Karthik Yarlagadda, Julie M. Allen, Alyssa C. Bader, Mary Simon, Seppe Kuehn, Kelly S. Swanson, Tzu Wen L. Cross, Kristin M. Hedman, Stanley H. Ambrose, Ripan S. Malhi
Software Mentions: 4
Published: over 5 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 5 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 5 years ago

10.1038/s41598-021-97790-7

Glycosaminoglycan biosynthesis pathway in host genome is associated with Helicobacter pylori infection
Cited by: 0
Author(s): Dingxue Hu, Yueqi Lu, Daoming Wang, Chao Nie, Yan Li
Software Mentions: 4
Published: about 5 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 5 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 5 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 6 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: almost 6 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 5 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 10 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: almost 8 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 7 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 7 years ago

10.1128/mSphere.01237-20

Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity
Cited by: 16
Author(s): Jialin Hu, Virginia L. Jin, Julie Y. M. Konkel, Sean M. Schaeffer, Liesel G Schneider, Jennifer M. DeBruyn
Software Mentions: 4
Published: over 5 years ago

10.1128/mSphere.00936-20

Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients
Cited by: 18
Author(s): Skye Fishbein, Tiffany Hink, Kimberly A. Reske, Candice Cass, Emily Struttmann, Zainab Hassan Iqbal, Sondra Seiler, Jennie H. Kwon, Carey‐Ann D. Burnham, Gautam Dantas, Erik R. Dubberke
Software Mentions: 4
Published: over 5 years ago

10.1128/mSphere.00083-21

Exposure to Parasitic Protists and Helminths Changes the Intestinal Community Structure of Bacterial Communities in a Cohort of Mother-Child Binomials from a Semirural Setting in Mexico
Cited by: 8
Author(s): Oswaldo Partida-Rodríguez, Miriam Nieves-Ramı́rez, Isabelle Laforest‐Lapointe, Eric Brown, Laura Wegener Parfrey, A Valadez-Salazar, Lisa Thorson, Patricia Morán, Enrique González, E. Ortiz Rascón, Ulises Magaña, E. Hernández, Liliana Rojas-Velázquez, Javier Torres, Marie Claire Arrieta, Cecilia Ximénez, B. Brett Finlay
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00133-16

SSUnique: Detecting Sequence Novelty in Microbiome Surveys
Cited by: 4
Author(s): Michael D. J. Lynch, Josh D. Neufeld
Software Mentions: 4
Published: almost 10 years ago

10.1128/mSystems.00290-19

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments
Cited by: 149
Author(s): Lisa Karstens, Mark Asquith, Sean Davin, Damien A. Fair, W. Thomas Gregory, Alan J. Wolfe, Jonathan Braun, Shannon K. McWeeney
Software Mentions: 4
Published: about 7 years ago

10.1128/mSystems.00566-19

Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands
Cited by: 22
Author(s): Nana Liu, Huifeng Hu, Wenqi Ma, Ye Deng, Yuqing Liu, Baihui Hao, Xinying Zhang, Dimitar Dimitrov, Xiaojuan Feng, Zhiheng Wang
Software Mentions: 4
Published: almost 7 years ago

10.1128/mSystems.00547-19

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
Cited by: 31
Author(s): Quinten R Ducarmon, Bastian Hornung, A. R. Geelen, E. Kuijper, Romy D. Zwittink
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00334-20

Human Milk Oligosaccharides Modulate the Risk for Preterm Birth in a Microbiome-Dependent and -Independent Manner
Cited by: 9
Author(s): Manuela-Raluca Pausan, V Kolovetsiou-Kreiner, Gesa Richter, Tobias Madl, Elisabeth Giselbrecht, Barbara Obermayer‐Pietsch, Eva-Christine Weiss, Evelyn Jantscher-Krenn, Christine Moissl-Eichinger
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00640-20

Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes
Cited by: 34
Author(s): Chengying Shi, Lu Zhao, Evans Atoni, Weihua Zeng, Xiaomin Hu, Jelle Matthijnssens, Zhiming Yuan, Han Xia
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.01114-20

Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese
Cited by: 7
Author(s): Zhengyao Xue, Jason T. Brooks, Zachary Quart, Eric Stevens, Mary E. Kable, J. Heidenreich, J. W. McLeod, Maria L. Marco
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00319-21

Facial Skin Microbiota-Mediated Host Response to Pollution Stress Revealed by Microbiome Networks of Individual
Cited by: 7
Author(s): Lu Wang, Yining Xu, Chung-Ching Chu, Zehua Jing, Yabin Chen, Jingsong Zhang, Mingming Pu, Tingyan Mi, Yaping Du, Zong-Qi Liang, Chandraprabha Doraiswamy, Tao Zeng, Jiarui Wu, Luonan Chen
Software Mentions: 4
Published: about 5 years ago

10.1038/s41396-019-0568-8

Gut microbiota structure differs between honeybees in winter and summer
Cited by: 157
Author(s): Lucie Kešnerová, Olivier Emery, Michaël Troilo, Joanito Liberti, Berra Erkoşar, Philipp Engel
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41396-020-0686-3

Ecological succession in the vaginal microbiota during pregnancy and birth
Cited by: 39
Author(s): Morten Arendt Rasmussen, Jonathan Thorsen, Maria Gloria Domínguez-Bello, Martin J. Blaser, Martin Steen Mortensen, Asker Brejnrod, Samir A. Shah, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Urvish Trivedi, Hans Bisgaard, Søren J. Sørensen, Jakob Stokholm
Software Mentions: 4
Published: over 6 years ago

10.1038/s41396-021-00988-w

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem
Cited by: 68
Author(s): Ya Jou Chen, Pok Man Leung, Jennifer L. Wood, Sean K. Bay, Philip Hugenholtz, Adam J. Kessler, Guy Shelley, David W. Waite, Ashley E. Franks, Perran L. M. Cook, Chris Greening
Software Mentions: 4
Published: over 5 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 7 years ago

10.3390/ijerph18073742

Do Rural Second Homes Shape Commensal Microbiota of Urban Dwellers? A Pilot Study among Urban Elderly in Finland
Cited by: 4
Author(s): Mika Saarenpää, Marja I. Roslund, Riikka Puhakka, Mira Grönroos, Nan Hui, Noora Nurminen, Olli H. Laitinen, Heikki Hyöty, Ondřej Cinek, Aki Sinkkonen
Software Mentions: 4
Published: over 5 years ago

10.3390/ijerph18126348

Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test
Cited by: 4
Author(s): Francesco Spennati, Salvatore La China, G. Siracusa, Simona Di Gregorio, A. Bardi, Valeria Tigini, Greg Mori, David Gabriel, Giulio Munz
Software Mentions: 4
Published: over 5 years ago

10.7448/IAS.18.5.20479

8th IAS Conference on HIV Pathogenesis, Treatment & Prevention 19-22 July 2015, Vancouver, Canada
Cited by: 9
Author(s):
Software Mentions: 4
Published: over 11 years ago

10.7554/eLife.67740

Bacterial–fungal interactions in the neonatal gut influence asthma outcomes later in life
Cited by: 16
Author(s): Rozlyn C.T. Boutin, Charisse Petersen, Sarah E. Woodward, Antonio Serapio-Palacios, Tahereh Bozorgmehr, Rachelle Loo, Alina Chalanuchpong, Mihai Cirstea, Bernard C. Lo, Kelsey E. Huus, Weronika Barcik, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Kelly M. McNagny, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.54792

Gut Helicobacter presentation by multiple dendritic cell subsets enables context-specific regulatory T cell generation
Cited by: 18
Author(s): Emilie V. Russler-Germain, Jaeu Yi, Shannon Young, Katherine Nutsch, Ho-Lun Wong, Teresa L. Ai, Jiani N. Chai, Vivek Durai, Daniel H. Kaplan, Ronald N. Germain, Kenneth M. Murphy, Chyi-Song Hsieh
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.36741

Convergence between the microcosms of Southeast Asian and North American pitcher plants
Cited by: 26
Author(s): Leonora S. Bittleston, Charles J. Wolock, Bakhtiar Effendi Yahya, Xin Yue Chan, Kok Gan Chan, Naomi E. Pierce, Anne Pringle
Software Mentions: 4
Published: about 8 years ago

10.3390/ijms21093262

Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations
Cited by: 5
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe
Software Mentions: 4
Published: over 6 years ago

10.1186/s12986-020-00538-9

Combined Lycium barbarum polysaccharides and C-phycocyanin increase gastric Bifidobacterium relative abundance and protect against gastric ulcer caused by aspirin in rats
Cited by: 14
Author(s): Shu-Yu Hsieh, Yu Lian, I‐Hsuan Lin, Yuxing Yang, Alexey A. Tinkov, Anatoly V. Skalny, Jane C.-J. Chao
Software Mentions: 4
Published: almost 6 years ago

10.3390/nu13051559

Maternal Vegetable and Fruit Consumption during Pregnancy and Its Effects on Infant Gut Microbiome
Cited by: 13
Author(s): Hsien Yu Fan, Yu Tang Tung, Yu Yang, Justin Bo-Kai Hsu, Cheng Yang Lee, Tzu Hao Chang, Emily Chia Yu Su, Rong Hong Hsieh, Yang Ching Chen
Software Mentions: 4
Published: over 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 8 years ago

10.18632/oncotarget.27629

Bacteriome and mycobiome and bacteriome-mycobiome interactions in head and neck squamous cell carcinoma
Cited by: 22
Author(s): Elizabeth Shay, Naseer Sangwan, Roshan Padmanabhan, Scott Lundy, Brian B. Burkey, Charis Eng
Software Mentions: 4
Published: over 6 years ago

10.3390/nu13061937

Characterizing the Effects of Calcium and Prebiotic Fiber on Human Gut Microbiota Composition and Function Using a Randomized Crossover Design—A Feasibility Study
Cited by: 8
Author(s): Lara Yoon, Karin B. Michels
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-49829-z

Adenovirus infection is associated with altered gut microbial communities in a non-human primate
Cited by: 27
Author(s): . Wasimuddin, Victor M. Corman, Jörg U. Ganzhorn, Jacques Rakotondranary, Yedidya R. Ratovonamana, Christian Drosten, Simone Sommer
Software Mentions: 4
Published: about 7 years ago

10.3390/nu11061425

Mixed Spices at Culinary Doses Have Prebiotic Effects in Healthy Adults: A Pilot Study
Cited by: 24
Author(s): Qing-Yi Lu, Anna Rasmussen, Jieping Yang, Ru-Po Lee, Jianjun Huang, Paul Shao, Catherine L. Carpenter, Irene Gilbuena, Gail Thames, Susanne M. Henning, David Heber, Zhaoping Li
Software Mentions: 4
Published: over 7 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: over 7 years ago

10.3390/nu12051257

Prebiotic Effects of Partially Hydrolyzed Guar Gum on the Composition and Function of the Human Microbiota—Results from the PAGODA Trial
Cited by: 35
Author(s): Simon Reider, Simon Moosmang, J Tragust, Lovro Trgovec-Greif, Simon Tragust, Lorenz Perschy, Nicole Przysiecki, Sonja Sturm, Herbert Tilg, Hermann Stuppner, Thomas Rattei, Alexander R. Moschen
Software Mentions: 4
Published: over 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: over 7 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 7 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: over 7 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 8 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 7 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: almost 9 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: almost 8 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: about 7 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: 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 7 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: about 8 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 7 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 8 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702