bioconductor: phyloseq | Projects

10.1186/s13071-020-04565-6

Morphological identification of ticks and molecular detection of tick-borne pathogens from bare-nosed wombats (Vombatus ursinus)
Cited by: 6
Author(s): Danielle Beard, Hayley J. Stannard, Julie M. Old
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13071-020-04491-7

Relative contributions of various endogenous and exogenous factors to the mosquito microbiota
Cited by: 7
Author(s): Haikel N. Bogale, Matthew Cannon, Kalil Keita, Denka Camara, Yaya Barry, Moussa Keïta, Drissa Coulibaly, Abdoulaye K. Koné, Ogobara K. Doumbo, Mahamadou A. Théra, Christopher V. Plowe, Mark A. Travassos, Seth R. Irish, David Serre
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2018.03190

Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria
Cited by: 13
Author(s): Federico Baltar, Andres Gutiérrez‐Rodríguez, Moana Meyer, Isadora Skudelny, Sylvia G. Sander, Blair Thomson, Scott D. Nodder, Rob Middag, Sergio E. Morales
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40413-015-0074-z

The microbiome of the human lower airways: a next generation sequencing perspective
Cited by: 34
Author(s): Velma Aho, Pedro Pereira, Tari Haahtela, Ruby Pawankar, Petri Auvinen, Kaisa Koskinen
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmicb.2019.00870

Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States)
Cited by: 39
Author(s): Max Kolton, Ansley Marks, Rachel M. Wilson, Jeffrey P. Chanton, Joel E. Kostka
Software Mentions: 2
Published: over 5 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

10.1186/s12879-019-3674-3

Viral species richness and composition in young children with loose or watery stool in Ethiopia
Cited by: 17
Author(s): Kristen Aiemjoy, Eda Altan, Solomon Aragie, Dionna M. Fry, Tung Gia Phan, Xutao Deng, Melsew Chanyalew, Zerihun Tadesse, E. Kelly Callahan, Eric Delwart, Jeremy D. Keenan
Software Mentions: 2
Published: almost 6 years ago

10.1111/1751-7915.13837

Effect of concentration and hydraulic reaction time on the removal of pharmaceutical compounds in a membrane bioreactor inoculated with activated sludge
Cited by: 12
Author(s): Ana B. Rios‐Miguel, Mike S. M. Jetten, Cornelia U. Welte
Software Mentions: 2
Published: over 3 years ago

10.1128/AEM.01171-18

Metabolic Capability and Phylogenetic Diversity of Mono Lake during a Bloom of the Eukaryotic Phototroph Picocystis sp. Strain ML
Cited by: 7
Author(s): Blake W. Stamps, Heather S. Nunn, Victoria A. Petryshyn, Ronald S. Oremland, Laurence G. Miller, Michael R. Rosen, Kohen W. Bauer, Katherine Jenny Thompson, Elise M. Tookmanian, Anna R. Waldeck, S. J. Loyd, Hope A. Johnson, Bradley S. Stevenson, William M. Berelson, Frank A. Corsetti, John R. Spear
Software Mentions: 2
Published: about 6 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

10.1111/1751-7915.13482

Air‐side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome
Cited by: 19
Author(s): Nuria Fernandez‐Gonzalez, Chiara Pedizzi, Juan M. Lema, Marta Carballa
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.01366-16

Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity
Cited by: 22
Author(s): Ulaş Karaöz, Estelle Couradeau, Ulisses Nunes da Rocha, Hsiao Chien Lim, Trent Northen, Ferrán García-Pichel, Eoin L. Brodie
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-019-3021-0

VOLARE: visual analysis of disease-associated microbiome-immune system interplay
Cited by: 5
Author(s): Janet Siebert, C. Preston Neff, Jennifer M. Schneider, Emilie Regner, Neha Ohri, Kristine A. Kuhn, Brent E. Palmer, Catherine Lozupone, Carsten Görg
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-41195-0

Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria
Cited by: 37
Author(s): Ida Nordang Kieler, Melania Osto, Leoni Hugentobler, Lara Puetz, M. Thomas P. Gilbert, Torben Hansen, Oluf Pedersen, Claudia E Reusch, Eric Zini, Thomas Lutz, Charlotte Reinhard Bjørnvad
Software Mentions: 2
Published: over 5 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/s40168-016-0216-8

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

10.3390/md19040183

Effect of Supplementing Seaweed Extracts to Pigs until d35 Post-Weaning on Performance and Aspects of Intestinal Health
Cited by: 12
Author(s): Stafford Vigors, John V. O’Doherty, Ruth Rattigan, T. Sweeney
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.6414

Evaluation of DESS as a storage medium for microbial community analysis
Cited by: 17
Author(s): Kevin M Lee, Madison Adams, Jonathan L. Klassen
Software Mentions: 2
Published: almost 6 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

10.1038/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

10.3389/fmicb.2020.01469

Assessment of Gram- and Viability-Staining Methods for Quantifying Bacterial Community Dynamics Using Flow Cytometry
Cited by: 14
Author(s): Aurore Duquenoy, Samuel Bellais, Cyrielle Gasc, Carole Schwintner, Joël Doré, Vincent Thomas
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.4989

Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater
Cited by: 10
Author(s): Christophe Paul, Zhanna Bayrychenko, Thomas Junier, Sevasti Filippidou, Karin Beck, Matthieu Bueche, Gilbert Greub, Helmut Bürgmann, Pilar Junier
Software Mentions: 2
Published: over 6 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

10.1038/s41598-020-73614-y

Manipulation of the gut microbiota by the use of prebiotic fibre does not override a genetic predisposition to heart failure
Cited by: 7
Author(s): Hamdi Jama, April Fiedler, Kirill Tsyganov, Erin M. Nelson, Duncan Horlock, Michael Nakai, Helen Kiriazis, Chad Johnson, Xiao Jun Du, Charles R. Mackay, Francine Z. Marques, David M. Kaye
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-019-5607-3

Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
Cited by: 15
Author(s): Annageldi Tayyrov, Claire E. Stanley, Sophie Azevedo, Markus Künzler
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-93859-5

Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities
Cited by: 18
Author(s): Thomas Lamy, Kathleen J. Pitz, Francisco P. Chávez, Christie E. Yorke, Robert J. Miller
Software Mentions: 2
Published: over 3 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/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/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/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.2020.00983

Shifts in the Fecal Microbial Community of Cystoisospora suis Infected Piglets in Response to Toltrazuril
Cited by: 10
Author(s): Aruna Shrestha, Barbara U. Metzler‐Zebeli, Hamadi Karembé, Daniel Šperling, Simone Koger, Anja Joachim
Software Mentions: 2
Published: over 4 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

10.3390/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

10.1038/s41598-021-89606-5

Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor
Cited by: 2
Author(s): Minji Kim, Setu Bazie Tagele, HyungWoo Jo, Min‐Chul Kim, Young Hun Jung, Yeong-Jun Park, Jai-Hyun So, Hae Jin Kim, Ho Jin Kim, Dong-Geol Lee, Seunghyun Kang, Jae‐Ho Shin
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

10.1038/s41598-019-43814-2

High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly in peri-Alpine lakes
Cited by: 17
Author(s): Marie‐Ève Monchamp, Piet Spaak, Francesco Pomati
Software Mentions: 2
Published: over 5 years ago

10.1186/1472-6831-14-157

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant and periodontal sites
Cited by: 43
Author(s): Simone Schaumann, Ingmar Staufenbiel, Ralph Scherer, Markus B. Schilhabel, Andreas Winkel, Sascha Nico Stumpp, Jörg Eberhard, Meike Stiesch
Software Mentions: 2
Published: almost 10 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

10.3389/fmicb.2017.00801

Spatial Structure of the Mormon Cricket Gut Microbiome and its Predicted Contribution to Nutrition and Immune Function
Cited by: 25
Author(s): Chad C. Smith, Robert B. Srygley, Frank Healy, Karthikeyan Swaminath, Ulrich G. Mueller
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.6316

Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms
Cited by: 12
Author(s): Mikko Pyysalo, Pashupati P. Mishra, Kati Sundström, Terho Lehtimäki, Pekka J. Karhunen, Tanja Pessi
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

10.1186/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

10.3390/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

10.1038/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

10.3390/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

10.1038/s41598-019-45066-6

Association between the pig genome and its gut microbiota composition
Cited by: 54
Author(s): Daniel Crespo-Piazuelo, Lourdes Migura-García, Jordi Estellé, Lourdes Criado-Mesas, Manuel Revilla, Anna Castelló, María Muñoz, Juan García‐Casco, Ana Fernández, María Ballester, Josep María Folch
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.02246

A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship
Cited by: 16
Author(s): Laure Bellec, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Lucile Durand, Nicolas Gayet, Daniela Zeppilli
Software Mentions: 2
Published: about 6 years ago

10.14814/phy2.13649

Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans
Cited by: 24
Author(s): Christian Fischer Pedersen, Umer Zeeshan Ijaz, Edith Gallagher, Felicity Horton, Richard J. Ellis, Etana Joy Jaiyeola, Thibaut Duparc, David Russell‐Jones, Paul Hinton, Patrice D. Cani, Roberto M. La Ragione, M. Denise Robertson
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-98248-6

Ruminant fat intake improves gut microbiota, serum inflammatory parameter and fatty acid profile in tissues of Wistar rats
Cited by: 2
Author(s): Larissa de Brito Medeiros, Susana P. Alves, Rui J.B. Bessa, Juliana Késsia Barbosa Soares, Camila Neves Meireles Costa, Jailane de Souza Aquino, Gerlane Coelho Bernardo Guerra, Daline Fernandes de Souza Araújo, Lydiane Tavares Toscano, Alexandre Silva, Adriano Francisco Alves, Mateus Lacerda Pereira Lemos, Wydemberg J. Araújo, Ariosvaldo Nunes de Medeiros, Celso José Bruno de Oliveira, Rita de Cássia Ramos do Egypto Queiroga
Software Mentions: 2
Published: about 3 years ago

10.1186/s40168-017-0242-1

New evidences on the altered gut microbiota in autism spectrum disorders
Cited by: 599
Author(s): Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Daniela Renzi, Antonino Calabrò, Carlotta De Filippo
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-020-70443-x

Effect of cereal fermentation and carbohydrase supplementation on growth, nutrient digestibility and intestinal microbiota in liquid-fed grow-finishing pigs
Cited by: 14
Author(s): A. Torres-Pitarch, Gillian E. Gardiner, Paul Cormican, Mary C. Rea, Fiona Crispie, John V. O’Doherty, Pierre Cozannet, Tomás Ryan, James T. Cullen, Peadar G. Lawlor
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.00315

The Microbial Diversity of Cabbage Pest Delia radicum Across Multiple Life Stages
Cited by: 6
Author(s): Tijs J. M. van den Bosch, Cornelia U. Welte
Software Mentions: 2
Published: over 4 years ago

10.3390/antibiotics9090631

Antimicrobial Resistance, an Update from the Ward: Increased Incidence of New Potential Pathogens and Site of Infection-Specific Antibacterial Resistances
Cited by: 4
Author(s): Irene Stefanini, Martina Boni, Paola Silvaplana, Paola Lovera, Stefania Pelassa, Giuseppe De Renzi, Barbara Mognetti
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2021.669937

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes
Cited by: 9
Author(s): Gaëtan Martin, Antti J. Rissanen, Sarahi L. Garcia, Maliheh Mehrshad, Moritz Buck, Sari Peura
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.4197

A historical legacy of antibiotic utilization on bacterial seed banks in sediments
Cited by: 8
Author(s): Laura Madueño, Christophe Paul, Thomas Junier, Zhanna Bayrychenko, Sevasti Filippidou, Karin Beck, Gilbert Greub, Helmut Bürgmann, Pilar Junier
Software Mentions: 2
Published: almost 7 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

10.3390/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: about 3 years ago

10.3389/fmicb.2016.01040

Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica
Cited by: 43
Author(s): Heather N. Buelow, Ara S. Winter, David Van Horn, John E. Barrett, M. N. Gooseff, Egbert Schwartz, Cristina Takacs-Vesbach
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-020-70683-x

Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype
Cited by: 9
Author(s): Sahar Abdelrazek, Sulbha Choudhari, Jyothi Thimmapuram, Petr Šimon, Micaela Colley, Tesfaye Mengiste, Lori Hoagland
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-46904-3

Co-cultivation of the marine sponge Halichondria panicea and its associated microorganisms
Cited by: 16
Author(s): Stephen Knobloch, Ragnar Jóhannsson, V. Marteinsson
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-017-0229-y

Optimization of DNA extraction for advancing coral microbiota investigations
Cited by: 33
Author(s): Laura Weber, Emelia DeForce, Amy Apprill
Software Mentions: 2
Published: almost 8 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.0194272

Behaviour during transportation predicts stress response and lower airway contamination in horses
Cited by: 30
Author(s): Barbara Padalino, Sharanne Raidal, Peter Knight, Pietro Celi, L. B. Jeffcott, Gary Muscatello
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2021.619632

Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
Cited by: 12
Author(s): Washington Logroño, Denny Popp, Marcell Nikolausz, Paul Kluge, Hauke Harms, Sabine Kleinsteuber
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

10.1038/s41598-018-20967-0

Diversity and metabolic potential of the microbiota associated with a soil arthropod
Cited by: 29
Author(s): Simon Bahrndorff, Nadieh de Jonge, Jacob Kjerulf Hansen, Jannik Mørk Skovgaard Lauritzen, Lasse Holt Spanggaard, Mathias Hamann Sørensen, Morten Yde, Jeppe Lund Nielsen
Software Mentions: 2
Published: almost 7 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

10.1038/s41598-019-40911-0

Nutrient-based diet modifications impact on the gut microbiome of the Javan slow loris (Nycticebus javanicus)
Cited by: 18
Author(s): Francis Cabana, Jonathan B. Clayton, K. A. I. Nekaris, W. Wirdateti, Dan Knights, Henning Seedorf
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.543260

Microbial Signatures in Deep CO2-Saturated Miocene Sediments of the Active Hartoušov Mofette System (NW Czech Republic)
Cited by: 5
Author(s): Qi Liu, Karsten Adler, Daniel Lipus, Horst Kämpf, Robert Bussert, Birgit Plessen, Hans-Martin Schulz, Patryk Krauze, Fabian Horn, Dirk Wagner, Kai Mangelsdorf, Mashal Alawi
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-86177-3

Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu “Sajino” Madre de Dios, Peru
Cited by: 8
Author(s): Jesús Rojas‐Jaimes, David Lindo-Seminario, Germán Correa-Núñez, Benoit Diringer
Software Mentions: 1
Published: over 3 years ago

10.1186/s12866-020-01836-1

Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration
Cited by: 8
Author(s): Jing Li, Xiaoyue Zhang, Lin Xiao, Ke Liu, Yue Li, Ziwei Zhang, Qiang Chen, Xiaolin Ao, Decong Liao, Yunfu Gu, Menggen Ma, Xiumei Yu, Quanju Xiang, Ji Chen, Xiaoping Zhang, Tao Yang, Petri Penttinen, Ke Zhao
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.02435

Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility
Cited by: 38
Author(s): Blake W. Stamps, Menu B. Leddy, Megan H. Plumlee, Nur A. Hasan, Rita R. Colwell, John R. Spear
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pntd.0006730

Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata
Cited by: 35
Author(s): Lucia C. Orantes, Carlota Monroy, Patricia L. Dorn, Lori Stevens, Donna M. Rizzo, L. A. Morrissey, John Hanley, Antonieta Rodas, Bethany Richards, Kimberly F. Wallin, Sara Helms Cahan
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2018.03010

Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences
Cited by: 62
Author(s): Adrián López-García, C. Pineda-Quiroga, Raquel Atxaerandio, Adrian Pérez, Itziar Hernández, A. García-Rodríguez, Óscar González-Recio
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2021.637282

Coffee Consumption Modulates Amoxicillin-Induced Dysbiosis in the Murine Gut Microbiome
Cited by: 5
Author(s): Emma Diamond, Katharine Hewlett, Swathi Penumutchu, Alexei Belenky, Peter Belenky
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pbio.3001070

Gut bacteria-derived 5-hydroxyindole is a potent stimulant of intestinal motility via its action on L-type calcium channels
Cited by: 17
Author(s): Barbora Waclawiková, Amber Bullock, Markus Schwalbe, Carmen Aranzamendi, Sieger Adriaan Nelemans, Gertjan van Dijk, Sahar El Aidy
Software Mentions: 1
Published: almost 4 years ago

10.14814/phy2.14159

Phenotypic effects of dietary stress in combination with a respiratory chain bypass in mice
Cited by: 7
Author(s): Praveen K. Dhandapani, Ari Löytynoja, Lars Paulín, Nahid Akhtar Khan, Anu Suomalainen, Petri Auvinen, Éric Dufour, Marten Szibor, Howard T. Jacobs
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.6657

Robust and automatic definition of microbiome states
Cited by: 12
Author(s): Beatriz García-Jiménez, Mark D. Wilkinson
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-90251-1

Differential microbial assemblages associated with shikonin-producing Borage species in two distinct soil types
Cited by: 8
Author(s): Aliya Fazal, Minkai Yang, Zhongling Wen, Farman Ali, Ran Ren, Chenyu Hao, Xingyu Chen, Jiangyan Fu, Xuan Wang, Wencai Jie, Tongming Yin, Guihua Lü, Jinliang Qi, Yonghua Yang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12877-020-1472-9

Effect of a polyphenol-rich dietary pattern on intestinal permeability and gut and blood microbiomics in older subjects: study protocol of the MaPLE randomised controlled trial
Cited by: 35
Author(s): Simone Guglielmetti, Stefano Bernardi, Cristian Del Bò, Antonio Cherubini, Marisa Porrini, Giorgio Gargari, Nicole Hidalgo‐Liberona, Raúl González‐Domínguez, Gregorio Peron, Raúl Zamora-Ros, Mark S. Winterbone, Benjamin Kirkup, Paul A. Kroon, Cristina Andrés‐Lacueva, Patrizia Riso
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.01869

Autoprobiotics as an Approach for Restoration of Personalised Microbiota
Cited by: 23
Author(s): Alexander Suvorov, Alena Karaseva, М. П. Котылева, Yulia Kondratenko, N. S. Lavrenova, Anton Korobeynikov, Petr Kozyrev, Tatiana Kramskaya, Galina Leontieva, I. V. Kudryavtsev, Deyin Guo, Alla Lapidus, Е. И. Ермоленко
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.7661

Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs
Cited by: 25
Author(s): Jessica K. Jarett, Anne Carlson, Mariana Rossoni Serao, Jessica Strickland, Laurie Serfilippi, Holly H. Ganz
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2018.00048

Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract
Cited by: 129
Author(s): Li Zhang, Weida Wu, Yuan‐Kun Lee, Jingjing Xie, Hongfu Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1128/AEM.00318-21

Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community
Cited by: 17
Author(s): Beatriz Andreo-Jiménez, M.T. Schilder, E.H. Nijhuis, Dennis E. te Beest, J. Bloem, J.H.M. Visser, Gera van Os, Karst M. Brolsma, Wietse de Boer, J. Postma
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.5961

Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA
Cited by: 15
Author(s): Alexander S. Honeyman, Maria L. Day, John R. Spear
Software Mentions: 1
Published: about 6 years ago

10.1128/AEM.02883-19

An In Vitro Pipeline for Screening and Selection of Citrus-Associated Microbiota with Potential Anti-“ Candidatus Liberibacter asiaticus” Properties
Cited by: 25
Author(s): Alex A. Blacutt, Nichole Ginnan, Tyler Dang, Sohrab Bodaghi, Georgios Vidalakis, Paul Ruegger, Beth B. Peacock, Polrit Viravathana, Flávia Campos Freitas Vieira, Christopher Drozd, Barbara Jablonska, James Borneman, Greg McCollum, Jennifer Cordoza, Jeremiah Meloch, Victoria Berry, Lia Lozano Salazar, Katherine N. Maloney, Philippe E. Rolshausen, M. Caroline Roper
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2017.01495

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity
Cited by: 30
Author(s): Filipa Dias, Jorge T. Antunes, Tiago Ribeiro, Joana Azevedo, Vı́tor Vasconcelos, Pedro N. Leão
Software Mentions: 1
Published: over 7 years ago

10.1186/s13071-020-04392-9

Microbiota characterization in Blastocystis-colonized and Blastocystis-free school-age children from Colombia
Cited by: 11
Author(s): Sergio Castañeda, Marina Muñoz, Ximena Villamizar, Paula C. Hernández, Luis Reinel Vásquez, Raúl Y. Tito, Juan David Ramírez
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2014.00613

Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN
Cited by: 36
Author(s): Penny L. Morrill, William J. Brazelton, Leonie Kohl, Amanda Rietze, Sarah M. Miles, H. Kavanagh, M. O. Schrenk, Susan E. Ziegler, Susan Q. Lang
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2021.662783

Metagenomic Investigation Uncovers Presence of Probiotic-Type Microbiome in Kalparasa® (Fresh Unfermented Coconut Inflorescence Sap)
Cited by: 5
Author(s): Madhuban Gopal, Sandeep Shil, Alka Gupta, K. B. Hebbar, M. Arivalagan
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-95842-6

Characterization of the virome associated with Haemagogus mosquitoes in Trinidad, West Indies
Cited by: 7
Author(s): Renee Ali, J. Jayaraj, Azad Mohammed, C. Chinnaraja, Christine V. F. Carrington, David W. Severson, Adesh Ramsubhag
Software Mentions: 1
Published: over 3 years ago

10.1016/j.molmet.2018.07.002

Chronic d-serine supplementation impairs insulin secretion
Cited by: 24
Author(s): Lisa Suwandhi, Simone Hausmann, Alexander Braun, Tim Gruber, Silke S. Heinzmann, Eric Galvez, Achim Buck, Beata Legutko, Andreas Israel, Annette Feuchtinger, Elizabeth Haythorne, Harald Staiger, Martin Heni, Hans‐Ulrich Häring, Philippe Schmitt‐Kopplin, Axel Walch, Cristina García Cáceres, Matthias H. Tschöp, Guy A. Rutter, Till Strowig, Martin Elsner, Siegfried Ussar
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2021.644861

Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing
Cited by: 13
Author(s): Harinder Singh, Thomas H. Clarke, Lauren Brinkac, Chris Greco, Karen E. Nelson
Software Mentions: 1
Published: over 3 years ago

10.1111/mec.15620

Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers
Cited by: 26
Author(s): Filipa M. S. Martins, Miguel Porto, Maria João Feio, Bastian Egeter, Aurélie Bonin, Sónia R. Q. Serra, Pierre Taberlet, Pedro Beja
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.01538

Insights in the Global Genetics and Gut Microbiome of Black Soldier Fly, Hermetia illucens: Implications for Animal Feed Safety Control
Cited by: 31
Author(s): Fathiya M. Khamis, Fidelis L. O. Ombura, Komivi Senyo Akutse, Sevgan Subramanian, Samira A. Mohamed, Komi K. M. Fiaboe, Weerachai Saijuntha, Joop J. A. van Loon, Marcel Dicke, Thomas Dubois, Sunday Ekesi, Chrysantus M. Tanga
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2017.02527

Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog
Cited by: 7
Author(s): H. M. Sapers, Jennifer Ronholm, Isabelle Raymond-Bouchard, Raven Comrey, G. R. Osinski, Lyle G. Whyte
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms7060169

The Influence of Microfungi on the Mycelial Growth of Ectomycorrhizal Fungus Tricholoma matsutake
Cited by: 6
Author(s): Seung‐Yoon Oh, Myung Soo Park, Young Woon Lim
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: phyloseq

Papers Mentioning phyloseq 1,702