bioconductor: phyloseq | Projects

10.3390/genes11080878

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community
Cited by: 29
Author(s): Maria A. Sierra, Qianhao Li, Smruti Pushalkar, Benjamin C. Paul, Tito A. Sandoval, Angela R. Kamer, Patricia Corby, Yuqi Guo, Ryan Richard Ruff, Alexander V. Alekseyenko, Xin Li, Deepak Saxena
Software Mentions: 2
Published: over 4 years ago

10.3390/md18050262

The Effects of the Marine-Derived Polysaccharides Laminarin and Chitosan on Aspects of Colonic Health in Pigs Challenged with Dextran Sodium Sulphate
Cited by: 14
Author(s): Ruth Rattigan, John V. O’Doherty, Stafford Vigors, M. F. Ryan, Rocco S. Sebastiano, John J. Callanan, Kevin Thornton, Gaurav Rajauria, Lekha Menon Margassery, Alan D. W. Dobson, Niall O’Leary, T. Sweeney
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.03629-20

Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells
Cited by: 7
Author(s): Keren Yanuka‐Golub, Vadim Dubinsky, Elisa Korenblum, Lea Reshef, Maya Ofek‐Lalzar, Judith Rishpon, Uri Gophna
Software Mentions: 2
Published: over 3 years ago

10.3390/molecules25030661

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment
Cited by: 35
Author(s): Joanna Brzeszcz, Piotr Kapusta, Teresa Steliga, A. Turkiewicz
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2020.01776

Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome
Cited by: 11
Author(s): Virginie Lemieux-Labonté, Nicole Dorville, Craig K. R. Willis, François‐Joseph Lapointe
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms9071358

Correction: Szopinska-Tokov et al. Investigating the Gut Microbiota Composition of Individuals with Attention-Deficit/Hyperactivity Disorder and Association with Symptoms. Microorganisms 2020, 8, 406
Cited by: 6
Author(s): Joanna Szopinska-Tokov, Sarita Dam, Jilly Naaijen, Prokopis Konstanti, Nanda Rommelse, Clara Belzer, Jan K. Buitelaar, Barbara Franke, Mirjam Bloemendaal, Esther Aarts, Alejandro Arias Vásquez
Software Mentions: 2
Published: over 3 years ago

10.1186/s13073-017-0409-1

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients
Cited by: 75
Author(s): Jessica Galloway-Peña, Daniel P. Smith, Pranoti Sahasrabhojane, W. Duncan Wadsworth, Bryan Fellman, Nadim J. Ajami, Elizabeth J. Shpall, Naval Daver, Michele Guindani, Joseph F. Petrosino, Dimitrios P. Kontoyiannis, Samuel A. Shelburne
Software Mentions: 2
Published: over 7 years ago

10.1186/s13073-017-0421-5

Ethnic and diet-related differences in the healthy infant microbiome
Cited by: 90
Author(s): Jennifer C. Stearns, Michael A. Zulyniak, Russell J. de Souza, Natalie Campbell, Michelle E. Fontes, Mateen Shaikh, Malcolm R. Sears, Allan B. Becker, Piushkumar J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, Milan Gupta, Joseph Beyene, Michael G. Surette, Sonia S. Anand
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.00530

Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate
Cited by: 6
Author(s): Alberto Scoma, Way Cern Khor, Marta Coma, Robert Heyer, Ruben Props, Jonas Schoelynck, Tim Bouts, Dirk Benndorf, Desheng Li, Hemin Zhang, Korneel Rabaey
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms9051051

Applications of Blocker Nucleic Acids and Non-Metazoan PCR Improves the Discovery of the Eukaryotic Microbiome in Ticks
Cited by: 2
Author(s): Yurie Taya, Gohta Kinoshita, Wessam Mohamed Ahmed Mohamed, Mohamed Abdallah Mohamed Moustafa, Shohei Ogata, Elisha Chatanga, Yuma Ohari, Kodai Kusakisako, Keita Matsuno, Nariaki Nonaka, Ryo Nakao
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9010012

Anaerobic Carbon Monoxide Uptake by Microbial Communities in Volcanic Deposits at Different Stages of Successional Development on O-yama Volcano, Miyake-jima, Japan
Cited by: 4
Author(s): Amber N. DePoy, Gary M. King, Hiroyuki Ohta
Software Mentions: 2
Published: almost 4 years ago

10.3390/microorganisms9061217

Effects of Magnesium Oxide and Magnesium Hydroxide Microparticle Foliar Treatment on Tomato PR Gene Expression and Leaf Microbiome
Cited by: 3
Author(s): Aggeliki Andreadelli, Spyros Petrakis, Antiopi Tsoureki, George Tsiolas, Sofia Michailidou, Penelope Baltzopoulou, Robert van Merkestein, P. K. G. Hodgson, Mark G. Sceats, George Karagiannakis, Antonios M. Makris
Software Mentions: 2
Published: over 3 years ago

10.1111/jre.12645

No differences in microbiome changes between anti‐adhesive and antibacterial ingredients in toothpastes during periodontal therapy
Cited by: 21
Author(s): Daniel Hagenfeld, Karola Prior, Inga Harks, Yvonne Jockel‐Schneider, Theodor W. May, Dag Harmsen, Ulrich Schlagenhauf, Benjamin Ehmke
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2020.596149

Metagenomic Analysis of the Gut Microbiota of Wild Mice, a Newly Identified Reservoir of Campylobacter
Cited by: 9
Author(s): Hyokeun Song, Junhyung Kim, Jae-Ho Guk, Woo-Hyun Kim, Hajin Nam, Jun-Gyo Suh, Je Kyung Seong, Seongbeom Cho
Software Mentions: 2
Published: almost 4 years ago

10.3390/brainsci10040242

Can Gut Microbiota Be a Good Predictor for Parkinson’s Disease? A Machine Learning Approach
Cited by: 20
Author(s): Daniele Pietrucci, Adelaide Teofani, Valeria Unida, Rocco Cerroni, Silvia Biocca, Alessandro Stefani, Alessandro Desideri
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms9061223

The Microbiota of Modified-Atmosphere-Packaged Cooked Charcuterie Products throughout Their Shelf-Life Period, as Revealed by a Complementary Combination of Culture-Dependent and Culture-Independent Analysis
Cited by: 12
Author(s): Evelyne Duthoo, Geertrui Rasschaert, Frédéric Leroy, Stefan Weckx, Marc Heyndrickx, Koen De Reu
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.02661

Tissue-Specific Microbiomes of the Red Sea Giant Clam Tridacna maxima Highlight Differential Abundance of Endozoicomonadaceae
Cited by: 14
Author(s): Susann Rossbach, Anny Cárdenas, Gabriela Perna, Carlos M. Duarte, Christian R. Voolstra
Software Mentions: 2
Published: almost 5 years ago

10.3390/microorganisms9020358

An Oral FMT Capsule as Efficient as an Enema for Microbiota Reconstruction Following Disruption by Antibiotics, as Assessed in an In Vitro Human Gut Model
Cited by: 11
Author(s): Cécile Verdier, Sylvain Denis, Cyrielle Gasc, Lilia Boucinha, Ophélie Uriot, Dominique Delmas, Joël Doré, Corentin Le Camus, Carole Schwintner, Stéphanie Blanquet‐Diot
Software Mentions: 2
Published: almost 4 years ago

10.3390/microorganisms8020265

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana
Cited by: 2
Author(s): Kiyonori Kawasaki, Kenji Ohya, Tsutomu Omatsu, Yukie Katayama, Yasuhiro Takashima, Tsuyoshi Kinoshita, Justice Opare Odoi, Kotaro Sawai, Hideto Fukushi, Hirohito Ogawa, Miho Inoue‐Murayama, Tetsuya Mizutani, Christopher Adenyo, Yoshiki Matsumoto, Boniface B. Kayang
Software Mentions: 2
Published: almost 5 years ago

10.3390/nu12040948

Bifidobacterium breve UCC2003 Exopolysaccharide Modulates the Early Life Microbiota by Acting as a Potential Dietary Substrate
Cited by: 19
Author(s): Deborah Püngel, Agatha Treveil, Matthew J. Dalby, Shabhonam Caim, Ian J. Colquhoun, Catherine Booth, Jennifer Ketskemety, Tamás Korcsmáros, Douwe van Sinderen, Melissa A. Lawson, Lindsay J. Hall
Software Mentions: 2
Published: over 4 years ago

10.1186/s12967-020-02231-0

Gut metabolomics profiling of non-small cell lung cancer (NSCLC) patients under immunotherapy treatment
Cited by: 106
Author(s): Andrea Botticelli, Pamela Vernocchi, Federico Marini, Andrea Quagliariello, Bruna Cerbelli, Sofia Reddel, Federica Del Chierico, Francesca Di Pietro, Raffaele Giusti, Alberta Tomassini, Ottavia Giampaoli, Alfredo Miccheli, Ilaria Grazia Zizzari, Marianna Nuti, Lorenza Putignani, Paolo Marchetti
Software Mentions: 2
Published: almost 5 years ago

10.1080/19490976.2021.1903826

Cohousing-mediated microbiota transfer from milk bioactive components-dosed mice ameliorate colitis by remodeling colonic mucus barrier and lamina propria macrophages
Cited by: 17
Author(s): Cong Liu, Shimeng Huang, Zhenhua Wu, Tiantian Li, Na Li, Bing Zhang, Dandan Han, Shilan Wang, Jiangchao Zhao, Junjun Wang
Software Mentions: 2
Published: almost 4 years ago

10.3390/microorganisms8050736

Metagenomic Analysis of Regularly Microwave-Treated and Untreated Domestic Kitchen Sponges
Cited by: 11
Author(s): Susanne Jacksch, Jyothi Thota, Sudarshan A. Shetty, Hauke Smidt, Sylvia Schnell, Markus Egert
Software Mentions: 2
Published: over 4 years ago

10.3390/bios11060170

Impact of Carbon Felt Electrode Pretreatment on Anodic Biofilm Composition in Microbial Electrolysis Cells
Cited by: 10
Author(s): Sabine Spiess, Jiří Kučera, Hathaichanok Seelajaroen, Amaia Sasiain, Sophie Thallner, Klemens Kremser, David P. Novak, Georg M. Guebitz, Marianne Haberbauer
Software Mentions: 2
Published: over 3 years ago

10.1080/19490976.2021.1926840

The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort
Cited by: 38
Author(s): Rachel C. Newsome, Josée Gauthier, María Celeste Hernández, George Abraham, Tanya O. Robinson, Hibbard E. Williams, Meredith Sloan, Anna H. Owings, Hannah Laird, Christian Taube, Yilianys Pride, Kenneth J. Wilson, Mohammad S Hasan, Adam Parker, Michal Senitko, Sarah C. Glover, Raad Z. Gharaibeh, Christian Jobin
Software Mentions: 2
Published: almost 4 years ago

10.1186/s42523-020-0024-0

Parrotfish predation drives distinct microbial communities in reef-building corals
Cited by: 22
Author(s): Leïla Ezzat, Thomas Lamy, Rebecca L. Maher, Katrina S. Munsterman, Kaitlyn Landfield, Emily R. Schmeltzer, Cody S. Clements, Rebecca L. Vega Thurber, Deron E. Burkepile
Software Mentions: 2
Published: almost 5 years ago

10.3390/microorganisms8010020

The Effect of Thermal Stress on the Bacterial Microbiome of Exaiptasia diaphana
Cited by: 15
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 2
Published: almost 5 years ago

10.3389/fcimb.2021.720674

The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment
Cited by: 29
Author(s): Veda D Khadka, Felix M. Key, Carolina Romo-González, Adrián Martínez-Gayosso, Blanca Lucina Campos-Cabrera, Armando Gerónimo-Gallegos, Tucker C Lynn, Carola Durán‐McKinster, Rafael Coria-Jiménez, Tami D. Lieberman, Maria Teresa García‐Romero
Software Mentions: 2
Published: about 3 years ago

10.1186/s13099-020-00386-1

The absence of murine cathelicidin-related antimicrobial peptide impacts host responses enhancing Salmonella enterica serovar Typhimurium infection
Cited by: 5
Author(s): Danisa M. Bescucci, Sandra Clarke, Catherine L. J. Brown, Valerie F. Boras, Tony Montina, Richard R. E. Uwiera, G. Douglas Inglis
Software Mentions: 2
Published: about 4 years ago

10.1128/mSphere.00048-20

Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia
Cited by: 17
Author(s): Sarah N. Robinson, Christine B. Peterson, Pranoti Sahasrabhojane, Nadim J. Ajami, Samuel A. Shelburne, Dimitrios P. Kontoyiannis, Jessica Galloway-Peña
Software Mentions: 2
Published: over 4 years ago

10.1186/s12866-018-1267-8

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance
Cited by: 4
Author(s): Filippo Pacchioni, Alfonso Esposito, Elisabetta Giacobazzi, Clotilde Bettua, Paolo Struffi, Olivier Jousson
Software Mentions: 2
Published: about 6 years ago

10.1128/mSystems.00517-20

Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy
Cited by: 12
Author(s): Nunzia Picone, Carmen Hogendoorn, Geert Cremers, Lianna Poghosyan, Arjan Pol, Theo A. van Alen, Antonina Lisa Gagliano, W. D’Alessandro, Paola Quatrini, Mike S. M. Jetten, Huub J. M. Op den Camp, Tom Berben
Software Mentions: 2
Published: almost 4 years ago

10.3389/fcimb.2021.639665

Vaginal Microbiota and Cytokine Levels Predict Preterm Delivery in Asian Women
Cited by: 30
Author(s): Manoj Kumar, Selvasankar Murugesan, Parul Singh, Marwa Saadaoui, Duaa Ahmed Elhag, Annalisa Terranegra, Basirudeen Syed Ahamed Kabeer, Alexandra K. Marr, Tomoshige Kino, Tobias Brummaier, Rose McGready, François Nosten, Souhaila Al Khodor
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8101486

Fecal Microbiota Transplant in Two Ulcerative Colitis Pediatric Cases: Gut Microbiota and Clinical Course Correlations
Cited by: 16
Author(s): Andrea Quagliariello, Federica Del Chierico, Sofia Reddel, Alessandra Russo, Andrea Onetti Muda, Patrizia D’Argenio, Giulia Angelino, Erminia Romeo, Luigi Dall’Oglio, Paola De Angelis, Lorenza Putignani
Software Mentions: 2
Published: about 4 years ago

10.3390/insects11060332

What Can the Bacterial Community of Atta sexdens (Linnaeus, 1758) Tell Us about the Habitats in Which This Ant Species Evolves?
Cited by: 4
Author(s): Manuela de Oliveira Ramalho, Carla Braga Martins, Maria Santina de Castro Morini, Odair Corrêa Bueno
Software Mentions: 2
Published: over 4 years ago

10.3390/insects12030204

Chance or Necessity—The Fungi Co−Occurring with Formica polyctena Ants
Cited by: 5
Author(s): Igor Siedlecki, Michał Gorczak, Alicja Okrasińska, Marta Wrzosek
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8091275

Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes
Cited by: 18
Author(s): Charlotte M. van der Graaf, Javier Sánchez España, Iñaki Yusta, Andrey Ilin, Sudarshan A. Shetty, Nicole J. Bale, Laura Villanueva, Alfons Johannes Maria Stams, Irene Sánchez‐Andrea
Software Mentions: 2
Published: over 4 years ago

10.1172/jci.insight.140940

Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma
Cited by: 71
Author(s): Angelo Limeta, Boyang Ji, Max Levin, Francesco Gatto, Jens Nielsen
Software Mentions: 2
Published: almost 4 years ago

10.3390/biology10090822

Profile of Bacterial Infections in COVID-19 Patients: Antimicrobial Resistance in the Time of SARS-CoV-2
Cited by: 9
Author(s): Irene Stefanini, Giuseppe De Renzi, Elisa Foddai, Elisa Cordani, Barbara Mognetti
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0219599

Phages in a thermoreversible sustained-release formulation targeting E. faecalis in vitro and in vivo
Cited by: 30
Author(s): Mor Shlezinger, Michael Friedman, Yael Houri‐Haddad, Ronen Hazan
Software Mentions: 2
Published: over 5 years ago

10.1093/jas/skaa338

Canola meal in nursery pig diets: growth performance and gut health
Cited by: 9
Author(s): Jinsu Hong, Saymore Petros Ndou, Sam Adams, Joy Scaria, T. A. Woyengo
Software Mentions: 2
Published: about 4 years ago

10.1186/s40104-019-0386-x

Dietary fibre enrichment of supplemental feed modulates the development of the intestinal tract in suckling piglets
Cited by: 21
Author(s): H.M.J. van Hees, Mark Davids, Dominiek Maes, Sam Millet, Sam Possemiers, L.A. den Hartog, Theo A. T. G. van Kempen, Geert Janssens
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms9061214

Gut Microbiota Dynamics in Natural Populations of Pintomyia evansi under Experimental Infection with Leishmania infantum
Cited by: 4
Author(s): Rafael José Vivero, Víctor Alfonso Castañeda-Monsalve, Lupe Romero, Gregory D. D. Hurst, Gloria Cadavid-Restrepo, Claudia Ximena Moreno Herrera
Software Mentions: 2
Published: over 3 years ago

10.1186/s40104-020-00531-5

Effects of brewers’ spent grain protein hydrolysates on gas production, ruminal fermentation characteristics, microbial protein synthesis and microbial community in an artificial rumen fed a high grain diet
Cited by: 23
Author(s): Ran Tao, Long Jin, Ranithri Abeynayake, A.M. Saleem, Xiumin Zhang, Dongyan Niu, Lingyun Chen, Wenzhu Yang
Software Mentions: 2
Published: almost 4 years ago

10.3390/biology10020148

Exploring the Gut Microbiome Alteration of the European Hare (Lepus europaeus) after Short-Term Diet Modifications
Cited by: 0
Author(s): Anna Padula, Marina Bambi, Chiara Mengoni, C. Greco, Nadia Mucci, Ilaria Greco, Alberto Masoni, Sara Del Duca, Giovanni Bacci, Giacomo Santini, Renato Fani, Marco Zaccaroni
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0137401

Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing
Cited by: 65
Author(s): Jakub Kreisinger, Dagmar Čížková, Lucie Kropáčková, Tomáš Albrecht
Software Mentions: 2
Published: about 9 years ago

10.3389/fendo.2020.602326

Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort
Cited by: 12
Author(s): Christian Diener, María de Lourdes Reyes-Escogido, Lilia M. Jiménez-Ceja, Mariana Matus, Claudia M. Gómez-Navarro, Nathaniel D. Chu, Vivian Zhong, M. Elizabeth Tejero, Eric J. Alm, Osbaldo Reséndis-Antonio, Rodolfo Guardado-Mendoza
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.ppat.1007083

A novel mouse model of Campylobacter jejuni enteropathy and diarrhea
Cited by: 45
Author(s): Natasa Giallourou, Gregory L. Medlock, David T. Bolick, Pedro Hqs Medeiros, Solanka Ellen Ledwaba, Glynis L. Kolling, Kenneth S. K. Tung, Patricia Guerry, Jonathan R. Swann
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008448

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production
Cited by: 58
Author(s): Lisa Osbelt, Sophie Thiemann, Nathiana Smit, Till Robin Lesker, Madita Schröter, Eric Galvez, Kerstin Schmidt‐Hohagen, Marina C. Pils, Sabrina Mühlen, Petra Dersch, Karsten Hiller, Dirk Schlüter, Meina Neumann‐Schaal, Till Strowig
Software Mentions: 2
Published: over 4 years ago

10.1186/s12917-020-02592-0

Antibiotic affects the gut microbiota composition and expression of genes related to lipid metabolism and myofiber types in skeletal muscle of piglets
Cited by: 11
Author(s): Honglin Yan, Bing Yu, Jeroen Degroote, Thomas Spranghers, Noémie Van Noten, Maryam Majdeddin, Mario Van Poucke, Luc Peelman, Jo De Vrieze, Nico Boon, Ingrid Gielen, Stefaan De Smet, Shuai Chen, Joris Michiels
Software Mentions: 2
Published: about 4 years ago

10.1530/ERC-17-0442

The microbiome in PTEN hamartoma tumor syndrome
Cited by: 5
Author(s): Victoria Byrd, Ted M. Getz, Roshan Padmanabhan, Hans Arora, Charis Eng
Software Mentions: 2
Published: over 6 years ago

10.1098/rspb.2019.2367

Intestinal microbes: an axis of functional diversity among large marine consumers
Cited by: 11
Author(s): Jarrod J. Scott, Thomas C. Adam, Alain Durán, Deron E. Burkepile, Douglas B. Rasher
Software Mentions: 2
Published: over 4 years ago

10.1186/s40168-020-00982-y

Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome
Cited by: 12
Author(s): Wisnu Adi Wicaksono, Peter Kusstatscher, Sabine Erschen, Tamara Reisenhofer-Graber, Martín Grube, Tomislav Cernava, Gabriele Berg
Software Mentions: 2
Published: almost 4 years ago

10.1002/ece3.6675

Scale‐dependent impact of land management on above‐ and belowground biodiversity
Cited by: 1
Author(s): Eleonore Louise Slabbert, Oliver Schweiger, Tesfaye Wubet, Antje Kautzner, Cornelia Baeßler, Harald Auge, Christiane Roscher, Tiffany M. Knight
Software Mentions: 2
Published: about 4 years ago

10.1111/1462-2920.14297

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment
Cited by: 39
Author(s): Albert Müller, Claus Pelikan, Júlia R. de Rezende, Kenneth Wasmund, Martina Putz, Clemens Glombitza, Kasper Urup Kjeldsen, Bo Barker Jørgensen, Alexander Loy
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2019.00069

Compartmentalization of Immune Response and Microbial Translocation in Decompensated Cirrhosis
Cited by: 32
Author(s): Camila Alvarez-Silva, Robert Schierwagen, Alessandra Pohlmann, Fernando Magdaleno, Frank Erhard Uschner, Patrick B. Ryan, Maria J. G. T. Vehreschild, Joan Clària, Eicke Latz, Benjamin Lelouvier, Manimozhiyan Arumugam, Jonel Trebicka
Software Mentions: 2
Published: almost 6 years ago

10.1002/ece3.4454

Fecal microbiota associated with phytohaemagglutinin‐induced immune response in nestlings of a passerine bird
Cited by: 11
Author(s): Jakub Kreisinger, Lucie Schmiedová, Adéla Petrželková, Oldřich Tomášek, Marie Kotasová Adámková, Romana Michálková, Jean Martin, Tomáš Albrecht
Software Mentions: 2
Published: about 6 years ago

10.1186/s40168-020-00904-y

Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis
Cited by: 22
Author(s): Wouter Sillen, Sofie Thijs, Gennaro Roberto Abbamondi, Roberto De La Torre Roche, Nele Weyens, Jason C. White, Jaco Vangronsveld
Software Mentions: 2
Published: about 4 years ago

10.1126/sciadv.abd7954

Prostaglandin E 2 promotes intestinal inflammation via inhibiting microbiota-dependent regulatory T cells
Cited by: 39
Author(s): Siobhan Crittenden, Marie Goepp, Jolinda Pollock, Calum T. Robb, Danielle J. Smyth, You Zhou, Robert Andrews, Victoria J. Tyrrell, Konstantinos Gkikas, Alexander Adima, Richard A. O’Connor, Luke C. Davies, Xuefeng Li, Hatti X. Yao, Gwo‐Tzer Ho, Xiaozhong Zheng, Amil Mair, Sonja Vermeren, Bin‐Zhi Qian, Damian J. Mole, Konstantinos Gerasimidis, Jürgen Schwarze, Richard M. Breyer, Mark J. Arends, Valerie Bridget O'Donnell, John P. Iredale, Stephen M. Anderton, Shuh Narumiya, Rick M. Maizels, Adriano G. Rossi, Sarah Howie, Chengcan Yao
Software Mentions: 2
Published: almost 4 years ago

10.1186/s40168-018-0498-0

Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC
Cited by: 26
Author(s): Lee Call, Barbara J. Stoll, Berthe C Oosterloo, Nadim J. Ajami, Fariha Sheikh, Anja Wittke, Rosaline Waworuntu, Brian M. Berg, Joseph F. Petrosino, Oluyinka O. Olutoye, Douglas G. Burrin
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0200095

Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano
Cited by: 15
Author(s): Marian León, Andrew D. Montecillo, Dale Pinili, Maria Auxilia T. Siringan, Doo-Sang Park
Software Mentions: 2
Published: over 6 years ago

10.1186/s12894-020-0576-z

Studying the urine microbiome in superficial bladder cancer: samples obtained by midstream voiding versus cystoscopy
Cited by: 24
Author(s): Suchitra K. Hourigan, Wei Zhu, Wendy S. W. Wong, Nicole C. Clemency, Marina Provenzano, Thierry Vilboux, John E. Niederhuber, John F. Deeken, Simon Chung, Kim McDaniel-Wiley, Donald L. Trump
Software Mentions: 2
Published: almost 5 years ago

10.1038/srep08695

Microbial communities on flower surfaces act as signatures of pollinator visitation
Cited by: 74
Author(s): Masayuki Ushio, Eri Yamasaki, Hiroyuki Takasu, Atsushi J. Nagano, Shohei Fujinaga, Mie N. Honjo, Mito Ikemoto, Shoko Sakai, Hiroshi Kudoh
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0169916

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin
Cited by: 18
Author(s): Luiz Fernando Würdig Roesch, Rita de Cássia dos Santos Silveira, Andrea Corso, Priscila Caroline Thiago Dobbler, Volker Mai, Bruna Schafer Rojas, Álvaro Macedo Laureano, Renato S. Procianoy
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms20092359

A Natural mtDNA Polymorphism in Complex III Is a Modifier of Healthspan in Mice
Cited by: 12
Author(s): Misa Hirose, Axel Künstner, Paul Schilf, Anna Katharina Tietjen, Olaf Jöhren, Patricia Huebbe, Gerald Rimbach, Jan Rupp, Markus Schwaninger, Hauke Busch, Saleh M. Ibrahim
Software Mentions: 2
Published: over 5 years ago

10.1002/ece3.5010

Bacterial communities within Phengaris (Maculinea) alcon caterpillars are shifted following transition from solitary living to social parasitism of Myrmica ant colonies
Cited by: 12
Author(s): Mark A. Szenteczki, Camille Pitteloud, Luca Pietro Casacci, Lucie Kešnerová, Melissa R. L. Whitaker, Philipp Engel, Roger Vila, Nadir Alvarez
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.01143-20

Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry
Cited by: 5
Author(s): Birge D. Özel Duygan, Sylvain Rey, Sabine Leocata, Lucie Baroux, Markus Seyfried, van der Peter Meer
Software Mentions: 2
Published: over 3 years ago

10.1186/s40793-020-00355-w

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America
Cited by: 7
Author(s): Renxing Liang, Maggie C. Y. Lau, Evan T. Saitta, Z. K. Garvin, Tullis C. Onstott
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.01591

Mobility of β-Lactam Resistance Under Bacterial Co-infection and Ampicillin Treatment in a Mouse Model
Cited by: 5
Author(s): Alexander Laskey, Marie Ottenbrite, John Devenish, Mingsong Kang, Mirjana Savic, Susan A. Nadin-Davis, John Chmara, Min Lin, James A. Robertson, Kyrylo Bessonov, Simone Gurnik, Kira Liu, John H. E. Nash, Andrew Scott, Edward Topp, Jiewen Guan
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.01222-20

A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community
Cited by: 13
Author(s): Susan Joseph, Joseph Aduse‐Opoku, Ahmed Hashim, Eveliina Hanski, Ricarda Streich, Sarah C. L. Knowles, Amy B. Pedersen, William Wade, Michael A. Curtis
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.02952

Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts
Cited by: 24
Author(s): Evan B Qu, Christopher R. Omelon, Aharon Oren, Victoria Meslier, Don A. Cowan, Gillian Maggs‐Kölling, Jocelyne DiRuggiero
Software Mentions: 2
Published: almost 5 years ago

10.1038/srep42634

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank
Cited by: 42
Author(s): Márcio Fernandes Alves Leite, Yao Pan, J. Bloem, Hein ten Berge, Eiko E. Kuramae
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2019.01018

Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods
Cited by: 43
Author(s): Adriana Rego, Francisco Raio, Teresa P. Martins, Hugo Leonardo Coelho Ribeiro, António G G Sousa, Joana Séneca, Mafalda S. Baptista, Charles K. Lee, S. Craig Cary, Vítor Ramos, Maria de Fátima Carvalho, Pedro N. Leão, Catarina Magalhães
Software Mentions: 2
Published: over 5 years ago

10.1038/srep45220

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot
Cited by: 23
Author(s): Grazieli Maboni, Adam Blanchard, Sara Frosth, Ceri E. Stewart, Richard D. Emes, Sabine Tötemeyer
Software Mentions: 2
Published: over 7 years ago

10.1186/s40168-016-0216-8

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease
Cited by: 121
Author(s): Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Andrew Nelson, Bashi̇r Abdulkadi̇r, Tom Skeath, Joseph F. Petrosino, John D. Perry, Janet Berrington, Stephen Cummings
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2019.02515

Chinese Black Truffle-Associated Bacterial Communities of Tuber indicum From Different Geographical Regions With Nitrogen Fixing Bioactivity
Cited by: 27
Author(s): Carlos Juan, Jiamei Li, Yang-Jing Tang, Yong-Mei Xing, Panzhe Qiao, Yang Li, Pei‐Gui Liu, Shun‐Xing Guo
Software Mentions: 2
Published: about 5 years ago

10.1002/ece3.4040

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus
Cited by: 3
Author(s): Amruta Varudkar, Uma Ramakrishnan
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0154642

Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows
Cited by: 44
Author(s): Jitka Kašparovská, Martina Pecinkova, Kateřina Dadáková, Ludmila Křížová, Sylvie Hadrová, Matej Lexa, Jan Lochman, Tomáš Kašparovský
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0090784

Meconium Microbiome Analysis Identifies Bacteria Correlated with Premature Birth
Cited by: 348
Author(s): Alexandria N. Ardissone, Diomel M. de la Cruz, Austin G. Davis-Richardson, Kevin Rechcigl, Nan Li, Jennifer C. Drew, Roberto Murgas-Torrazza, Rajesh Sharma, Mark L. Hudak, Eric W. Triplett, Josef Neu
Software Mentions: 2
Published: over 10 years ago

10.1007/s00394-019-02161-8

The impact of food additives, artificial sweeteners and domestic hygiene products on the human gut microbiome and its fibre fermentation capacity
Cited by: 67
Author(s): Konstantinos Gerasimidis, Katie Bryden, Xiufen Chen, Eleftheria Papachristou, Anais Verney, M.J. Roig, Richard Hansen, Ben Nichols, Rodanthi Papadopoulou, Alison Parrett
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0191499

Short term dynamics of the sputum microbiome among COPD patients
Cited by: 15
Author(s): Rohita Sinha, Lisa Weissenburger-Moser, Jennifer Clarke, Lynette M. Smith, Art J. Heires, Debra J. Romberger, Tricia D. LeVan
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.00273

Lactobacillus gasseri APC 678 Reduces Shedding of the Pathogen Clostridium difficile in a Murine Model
Cited by: 9
Author(s): Lisa Quigley, M. Coakley, Debebe Alemayehu, Mary C. Rea, Patrick G. Casey, Órla O’Sullivan, Eileen F. Murphy, Barry Kiely, Paul D. Cotter, Colin Hill, R. Paul Ross
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-07278-6

Bacteriophages as potential new mammalian pathogens
Cited by: 74
Author(s): George Tetz, Kelly V. Ruggles, Hua Zhou, Adriana Heguy, Aristotelis Tsirigos, Victor Tetz
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0226239

Microbiota composition of the dorsal patch of reproductive male Leptonycteris yerbabuenae
Cited by: 13
Author(s): Osiris Gaona, Daniel Cerqueda‐García, Luisa I. Falcón, Guillermo Vázquez-Domínguez, Patricia M. Valdespino-Castillo, Carla-Ximena Neri-Barrios
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-017-09842-6

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection
Cited by: 154
Author(s): Monica Di Paola, Cristina Sani, Ann Maria Clemente, Anna Iossa, Eloisa Perissi, Giuseppe Castronovo, Michele Tanturli, Damaríz Rivero, Federico Cozzolino, Duccio Cavalieri, Francesca Carozzi, Carlotta De Filippo, Maria Gabriella Torcia
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-018-0493-5

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms
Cited by: 60
Author(s): Brandon Brooks, Matthew R. Olm, Brian Firek, Robyn Baker, David Geller-McGrath, Sophia R. Reimer, Karina Ruth Soenjoyo, Jennifer S. Yip, Dylan Dahan, Brian C. Thomas, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.03092

Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern
Cited by: 20
Author(s): Camille Huot, Camille Clérissi, Benjamin Gourbal, Richard Galinier, David Timothy Duval, Ève Toulza
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0213975

Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection
Cited by: 34
Author(s): Smritee Dabee, Shaun Barnabas, Katie Lennard, Shameem Z. Jaumdally, Hoyam Gamieldien, Christina Balle, Anna‐Ursula Happel, Brandon D. Murugan, Anna‐Lise Williamson, Nonhlanhla N. Mkhize, Janan Dietrich, David A. Lewis, Francesca Chiodi, Thomas J. Hope, Robin J. Shattock, Glenda Gray, Linda‐Gail Bekker, Heather B. Jaspan, Jo‐Ann S. Passmore
Software Mentions: 2
Published: over 5 years ago

10.1093/database/baaa050

mAML: an automated machine learning pipeline with a microbiome repository for human disease classification
Cited by: 18
Author(s): Fenglong Yang, Quan Zou
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2021.730986

Temporal Changes in Vaginal Microbiota and Genital Tract Cytokines Among South African Women Treated for Bacterial Vaginosis
Cited by: 19
Author(s): Andile Mtshali, James Emmanuel San, Farzana Osman, Nigel Garrett, Christina Balle, Jennifer Giandhari, Harris Onywera, Khanyisile Mngomezulu, Gugulethu Mzobe, Túlio de Oliveira, Anne Rompalo, Adrian Mindel, Salim S. Abdool Karim, Jacques Ravel, Jo Ann S Passmore, Heather B. Jaspan, Lenine J. Liebenberg, Sinaye Ngcapu
Software Mentions: 2
Published: about 3 years ago

10.1038/s41396-019-0502-0

Metagenomic and chemical characterization of soil cobalamin production
Cited by: 42
Author(s): Xiaoliang Lü, Katherine R. Heal, Anitra E. Ingalls, Andrew C. Doxey, Josh D. Neufeld
Software Mentions: 2
Published: about 5 years ago

10.1186/s12866-020-01901-9

Examining the relationship between maternal body size, gestational glucose tolerance status, mode of delivery and ethnicity on human milk microbiota at three months post-partum
Cited by: 19
Author(s): Lauren LeMay-Nedjelski, James Butcher, Sylvia H. Ley, Michelle R. Asbury, Anthony J. Hanley, Alex Kiss, Sharon Unger, John W. Copeland, Pauline W. Wang, Bernard Zinman, Alain Stintzi, Deborah L. O’Connor
Software Mentions: 2
Published: over 4 years ago

10.1093/cdn/nzy070

Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity
Cited by: 11
Author(s): Antonio Vinicios Alves da Silva, Stephanie B Oliveira, Sara C. Di Rienzi, Kathleen Brown-Steinke, Lauren M Dehan, Jill K Rood, Vinicius Carreira, Hung Le, Elizabeth A. Maier, Kristina Betz, Eitaro Aihara, Ruth E. Ley, Geoffrey A. Preidis, Lanlan Shen, Sean R. Moore
Software Mentions: 2
Published: almost 6 years ago

10.3390/nu13030919

Enterolignan Production in a Flaxseed Intervention Study in Postmenopausal US Women of African Ancestry and European Ancestry
Cited by: 10
Author(s): Susan E. McCann, Meredith A.J. Hullar, David Tritchler, Eduardo Cortes-Gomez, Song Yao, Warren Davis, Tracey O’Connor, Deborah O. Erwin, Lilian U. Thompson, Yan Li, Johanna W. Lampe
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.01813

PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System
Cited by: 13
Author(s): Melanie Brede, Theresa Orton, Beate Pinior, Franz-Ferdinand Roch, Monika Dzieciol, Benjamin Zwirzitz, Martin Wagner, Gerhard Breves, Stefanie U. Wetzels
Software Mentions: 2
Published: over 4 years ago

10.1186/s42523-020-00067-z

The intestinal microbial composition in Greylag geese differs with steatosis induction mode: spontaneous or induced by overfeeding
Cited by: 1
Author(s): Christelle Knudsen, Julien Arroyo, Maxime Even, Laurent Cauquil, Géraldine Pascal, Xavier Fernández, Franck Lavigne, Stéphane Davail, Sylvie Combes, Karine Ricaud
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2017.01470

Personalization of the Microbiota of Donor Human Milk with Mother’s Own Milk
Cited by: 63
Author(s): Nicole Cacho, Natalie A. Harrison, Leslie A. Parker, Kaylie A. Padgett, Dominick J. Lemas, Guillermo Marcial, Nan Li, Laura E. Carr, Josef Neu, Graciela L. Lorca
Software Mentions: 2
Published: over 7 years ago

10.1186/s40168-020-00862-5

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste
Cited by: 97
Author(s): Stefan Dyksma, Lukas Jansen, Claudia Gallert
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-16287-4

Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression
Cited by: 16
Author(s): Irina Leonardi, Alexandra Gerstgrasser, Thomas Sebastian Benedikt Schmidt, Flora Nicholls, Bernhard Tewes, Roland Greinwald, Christian von Mering, Gerhard Rogler, Isabelle Frey-Wagner
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0167659

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf
Cited by: 12
Author(s): Jean‐David Grattepanche, George B. McManus, Laura A. Katz
Software Mentions: 2
Published: almost 8 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702