Ecosyste.ms: Papers

10.7717/peerj.11915

Fungi in soil and understory have coupled distribution patterns
Cited by: 4
Author(s): André Boraks, Anthony S. Amend
Software Mentions: 2
Published: about 3 years ago

10.3390/ijms21010298

Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies
Cited by: 100
Author(s): Raf Winand, Bert Bogaerts, Stefan Hoffman, Loïc Lefevre, Maud Delvoye, Julien Van Braekel, Qiang Fu, Nancy Roosens, Sigrid C. J. De Keersmaecker, Kevin Vanneste
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-017-09906-7

Reference-based RADseq resolves robust relationships among closely related species of lichen-forming fungi using metagenomic DNA
Cited by: 29
Author(s): Felix Grewe, Jen-Pen Huang, Steven D. Leavitt, H. Thorsten Lumbsch
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-15345-1

Short-term effects of non-grazing on plants, soil biota and aboveground-belowground links in Atlantic mountain grasslands
Cited by: 15
Author(s): Lur Epelde, Anders Lanzén, Iker Mijangos, Estibaliz Sarrionandia, Mikel Anza, Carlos Garbisu
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.11285

Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples
Cited by: 4
Author(s): Robert S. Cornman, Jennifer A. Fike, Sara J. Oyler‐McCance, Paul M. Cryan
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.5871

An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA
Cited by: 19
Author(s): Robert S. Cornman, James E. McKenna, Jennifer A. Fike, Sara J. Oyler‐McCance, Robin Johnson
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-26947-8

Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens
Cited by: 37
Author(s): Fiona Paul, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-42183-0

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota
Cited by: 362
Author(s): Dae Wook Kang, James B. Adams, Devon M. Coleman, Elena L. Pollard, Juan Maldonado, Sharon McDonough-Means, J. Gregory Caporaso, Rosa Krajmalnik‐Brown
Software Mentions: 2
Published: over 5 years ago

10.1186/s12862-019-1355-x

Contrasting evolutionary origins of two mountain endemics: Saxifraga wahlenbergii (Western Carpathians) and S. styriaca (Eastern Alps)
Cited by: 14
Author(s): Natalia Tkach, Martin Röser, Tomasz Suchan, Elżbieta Cieślak, Peter Schönswetter, Michał Ronikier
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-54203-0

Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs
Cited by: 32
Author(s): Maria Gruenberg, Anita Lerch, Hans‐Peter Beck, Ingrid Felger
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-019-55290-9

Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn’s disease
Cited by: 84
Author(s): Kinga Kowalska-Duplaga, Tomasz Gosiewski, Przemysław Kapusta, Agnieszka Sroka-Oleksiak, Andrzej Wędrychowicz, Stanisław Pieczarkowski, Agnieszka H. Ludwig-Słomczyńska, Paweł Wołkow, Krzysztof Fyderek
Software Mentions: 2
Published: almost 5 years ago

10.3390/pathogens9080638

Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs
Cited by: 23
Author(s): Caitlin E. Older, Aline Rodrigues Hoffmann, Kathleen Hoover, Frane Banović
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-59771-0

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes
Cited by: 66
Author(s): Anders Benteson Nygaard, Hege Smith Tunsjø, Roger Meisal, Colin Charnock
Software Mentions: 2
Published: over 4 years ago

10.1111/1755-0998.13293

Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
Cited by: 23
Author(s): Mads Radmer Jensen, Eva Egelyng Sigsgaard, Shenglin Liu, Andrea Manica, Steffen Bach, Michael Møller Hansen, Peter Rask Möller, Philip Francis Thomsen
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

10.3390/microorganisms9020342

Unveiling the Bovine Epimural Microbiota Composition and Putative Function
Cited by: 22
Author(s): Cátia Pacífico, Renée M. Petri, Sara Ricci, Elsayed Mickdam, Stefanie U. Wetzels, Viktoria Neubauer, Qendrim Zebeli
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms22137173

Influence of a High-Impact Multidimensional Rehabilitation Program on the Gut Microbiota of Patients with Multiple Sclerosis
Cited by: 12
Author(s): Monica Barone, Laura Mendozzi, Federica D’Amico, Marina Saresella, Simone Rampelli, Federica Piancone, Francesca La Rosa, Ivana Marventano, Mario Clerici, Alessia d’Arma, Luigi Pugnetti, Valentina Rossi, Marco Candela, Patrizia Brigidi, Silvia Turroni
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9091796

Metagenomic Analysis of Bacterial Communities in Agricultural Soils from Vietnam with Special Attention to Phosphate Solubilizing Bacteria
Cited by: 16
Author(s): Anna Hegyi, Tran Bao Khuyen Nguyen, Katalin Posta
Software Mentions: 2
Published: about 3 years ago

10.3390/microorganisms8020173

Peritoneal Microbiome in End-Stage Renal Disease Patients and the Impact of Peritoneal Dialysis Therapy
Cited by: 14
Author(s): Liliana Simões-Silva, Ricardo Araújo, Manuel Pestana, Isabel Soares-Silva, Benedita Sampaio‐Maia
Software Mentions: 2
Published: almost 5 years ago

10.1128/mSphere.00292-18

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA
Cited by: 23
Author(s): Nora Grahl, Emily L. Dolben, Laura Filkins, Alex W. Crocker, Sven D. Willger, Hilary G. Morrison, Mitchell L. Sogin, Alix Ashare, Alex H. Gifford, Nicholas J. Jacobs, Joseph D. Schwartzman, Deborah A. Hogan
Software Mentions: 2
Published: about 6 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/s40168-020-00897-8

Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish
Cited by: 12
Author(s): Andreas Härer, Julián Torres‐Dowdall, Sina J. Rometsch, Elizabeth Yohannes, Gonzalo Machado‐Schiaffino, Axel Meyer
Software Mentions: 2
Published: about 4 years ago

10.1186/s40168-018-0490-8

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner
Cited by: 141
Author(s): Sara Lundgren, Juliette C. Madan, Jennifer A. Emond, Hilary G. Morrison, Brock C. Christensen, Margaret R. Karagas, Anne G. Hoen
Software Mentions: 2
Published: over 6 years ago

10.3390/nu13041092

A Polyphenol Enriched Variety of Apple Alters Circulating Immune Cell Gene Expression and Faecal Microbiota Composition in Healthy Adults: A Randomized Controlled Trial
Cited by: 18
Author(s): Matthew P. G. Barnett, Wayne Young, Kelly Armstrong, Diane Brewster, Janine M. Cooney, Stephanie Ellett, Richard V. Espley, William A. Laing, Paul Maclean, Tony K. McGhie, Greg Pringle, Nicole C. Roy, Lynnette R. Ferguson
Software Mentions: 2
Published: over 3 years ago

10.1002/mbo3.453

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
Cited by: 42
Author(s): Sylwia Zielińska, Piotr Radkowski, Aleksandra Blendowska, Agnieszka H. Ludwig-Gałęzowska, Jerzy Łoś, Marcin Łoś
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2021.639868

Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei
Cited by: 6
Author(s): Fernan Santiago Mejía-Alvarado, Thaura Ghneim-Herrera, Carmenza E. Góngora, Pablo Benavides, Lucio Navarro-Escalante
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.01861

Comparison of the Total, Diazotrophic and Ammonia-Oxidizing Bacterial Communities Between Under Organic and Conventional Greenhouse Farming
Cited by: 4
Author(s): Chen Chen, Hui Han, Ting Xu, Yuanda Lv, Kelin Hu, Xue Xian Li, Yuhui Qiao, Guo-Chun Ding, Ji Li
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.01354

Water Microbiota in Greenhouses With Soilless Cultures of Tomato by Metabarcoding and Culture-Dependent Approaches
Cited by: 4
Author(s): Adeline Picot, José F. Cobo‐Díaz, Audrey Pawtowski, Christelle Donot, Fabienne Legrand, Gaétan Le Floch, F. Déniel
Software Mentions: 2
Published: over 4 years ago

10.1186/s12898-019-0269-1

FACEPAI: a script for fast and consistent environmental DNA processing and identification
Cited by: 2
Author(s): Emma Wahlberg
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2019.02387

Dispersant Enhances Hydrocarbon Degradation and Alters the Structure of Metabolically Active Microbial Communities in Shallow Seawater From the Northeastern Gulf of Mexico
Cited by: 12
Author(s): Xiaoxu Sun, Lena Chu, Elisa Mercando, Isabel C. Romero, David J. Hollander, Joel E. Kostka
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.615102

Functional Profiling of Antibody Immune Repertoires in Convalescent Zika Virus Disease Patients
Cited by: 12
Author(s): Ahmed S. Fahad, Morgan R. Timm, Bharat Madan, Katherine E. Burgomaster, Kimberly A. Dowd, Erica Normandin, Matías Gutiérrez-González, Joseph M. Pennington, Matheus Oliveira de Souza, Amy R. Henry, Farida Laboune, Lingshu Wang, David R. Ambrozak, Ingelise J. Gordon, Daniel C. Douek, Julie E. Ledgerwood, Barney S. Graham, Leda R. Castilho, Theodore C. Pierson, John R. Mascola, Brandon J. DeKosky
Software Mentions: 2
Published: over 3 years ago

10.1099/ijsem.0.004806

Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales
Cited by: 12
Author(s): Fatmah O. Sefrji, Ramona Marasco, Grégoire Michoud, Kholoud Seferji, Giuseppe Merlino, Daniele Daffonchio
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-017-4260-y

Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections
Cited by: 75
Author(s): Anita Lerch, Cristian Koepfli, Natalie Hofmann, Camilla Messerli, Stephen Wilcox, Johanna Helena Kattenberg, Inoni Betuela, Liam O’Connor, Ivo Müeller, Ingrid Felger
Software Mentions: 2
Published: about 7 years ago

10.1093/femsec/fiaa021

Methanogenic response to long-term permafrost thaw is determined by paleoenvironment
Cited by: 22
Author(s): Stine Holm, Josefine Walz, Fabian Horn, Shuai Yang, Mikhail N. Grigoriev, Dirk Wagner, Christian Knoblauch, Susanne Liebner
Software Mentions: 2
Published: almost 5 years ago

10.1007/s11356-021-13885-8

Characterization of microbial response to petroleum hydrocarbon contamination in a lacustrine ecosystem
Cited by: 6
Author(s): Emilio D’Ugo, Marco Bruno, Arghya Mukherjee, Dhrubajyoti Chattopadhyay, Roberto Giuseppetti, Rita De Pace, Fabio Magurano
Software Mentions: 2
Published: over 3 years ago

10.1186/s40793-020-00358-7

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences
Cited by: 261
Author(s): Franziska Wemheuer, Jessica Averitt Taylor, Rolf Daniel, Emma L. Johnston, Peter Meinicke, Torsten Thomas, Bernd Wemheuer
Software Mentions: 2
Published: over 4 years ago

10.1111/1758-2229.12684

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
Cited by: 80
Author(s): Mohammad Bahram, Sten Anslan, Falk Hildebrand, Peer Bork, Leho Tedersoo
Software Mentions: 2
Published: about 6 years ago

10.3389/fvets.2021.732129

Identification of Multiple Blastocystis Subtypes in Domestic Animals From Colombia Using Amplicon-Based Next Generation Sequencing
Cited by: 49
Author(s): Adriana Higuera, Giovanny Herrera, Paula Andrea Jiménez, Diego García-Corredor, Martín Orlando Pulido-Medellín, Diana María Bulla-Castañeda, Juan Carlos Pinilla, Darwin A. Moreno-Pérez, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 2
Published: about 3 years ago

10.1002/ece3.7748

Metabarcoding options to study eukaryotic endoparasites of birds
Cited by: 7
Author(s): Vincent Bourret, Rafael Gutiérrez López, Martim Melo, Claire Loiseau
Software Mentions: 2
Published: over 3 years ago

10.3390/genes10110858

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions
Cited by: 58
Author(s): Henrik Krehenwinkel, Aaron Pomerantz, Stefan Prost
Software Mentions: 2
Published: about 5 years ago

10.1186/s13059-021-02419-7

STRONG: metagenomics strain resolution on assembly graphs
Cited by: 53
Author(s): Christopher Quince, Sergey Nurk, Sébastien Raguideau, Rob S. James, Orkun S. Soyer, J Kimberley Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi, Aaron E. Darling
Software Mentions: 2
Published: over 3 years ago

10.3389/fcimb.2018.00001

Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections
Cited by: 62
Author(s): Noa Ziklo, Miranda E. Vidgen, Kuong Taing, Wilhelmina M. Huston, Peter Timms
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2021.625562

Characterization and Functional Test of Canine Probiotics
Cited by: 12
Author(s): Hyun‐Jun Jang, Seung‐Woo Son, Jung-Ae Kim, Min Young Jung, Yun‐Sang Choi, Dae-Hyuk Kim, Hak Kyo Lee, Donghyun Shin, Yangseon Kim
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.02220-20

From People to <i>Panthera</i> : Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo
Cited by: 270
Author(s): Denise McAloose, Melissa Laverack, Leyi Wang, Mary Lea Killian, Leonardo Cardia Caserta, Fuh-Gwo Yuan, Patrick K. Mitchell, Krista Queen, Matthew R. Mauldin, Brittany D. Cronk, Susan L. Bartlett, John M. Sykes, Stephanie Zec, Tracy Stokol, Karen Ingerman, Martha A. Delaney, Richard Fredrickson, Marina Ivančić, Melinda Jenkins-Moore, Katie Mozingo, Kerrie Franzen, Nichole Hines Bergeson, Laura B. Goodman, Haibin Wang, Ying Fang, Colleen Olmstead, Colleen McCann, Patrick R. Thomas, Erin L. Goodrich, François Elvinger, David C. Smith, Suxiang Tong, Sally Slavinski, Paul P. Calle, Karen A. Terio, Mia Kim Torchetti, Diego G. Diel
Software Mentions: 1
Published: about 4 years ago

10.1093/femsec/fiy114

Metagenomic insights into diazotrophic communities across Arctic glacier forefields
Cited by: 31
Author(s): Maisie V. Nash, Alexandre M. Anesio, Gary Barker, Martyn Tranter, Gilda Varliero, Emiley A. Eloe‐Fadrosh, Torben Nielsen, Thomas Turpin-Jelfs, Liane G. Benning, Patricia Sánchez‐Baracaldo
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2020.596882

Unveiling the Biogeography and Potential Functions of the Intestinal Digesta- and Mucosa-Associated Microbiome of Donkeys
Cited by: 11
Author(s): Ruiyang Zhang, Junpeng Zhang, Wanyi Dang, David M. Irwin, Zhe Wang, Shuyi Zhang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpls.2021.719987

Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae
Cited by: 5
Author(s): Stéphane Boivin, Frédéric Mahé, Frederic Debellé, Marjorie Pervent, Mathilde Tancelin, Marc Tauzin, Jerzy Wielbo, Sylvie Mazurier, J. Peter W. Young, Marc Lepetit
Software Mentions: 1
Published: about 3 years ago

10.3389/fmicb.2019.02141

Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone
Cited by: 36
Author(s): Simone Muck, Daniele De Corte, Elisabeth L. Clifford, Barbara Bayer, Gerhard J. Herndl, Eva Sintes
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-38874-3

Faecal bacterial and short-chain fatty acids signature in hypercholesterolemia
Cited by: 113
Author(s): Ana Belén Granado-Serrano, Meritxell Martín-Gari, Virginia Sánchez, Marissa Riart Solans, Rebeca Berdún, Iziar A. Ludwig, Laura Rubió, Ester Vilaprinyó, Manuel Portero‐Otín, José C. E. Serrano
Software Mentions: 1
Published: almost 6 years ago

10.3390/microorganisms9050997

Mind the Gap: New Full-Length Sequences of Blastocystis Subtypes Generated via Oxford Nanopore Minion Sequencing Allow for Comparisons between Full-Length and Partial Sequences of the Small Subunit of the Ribosomal RNA Gene
Cited by: 48
Author(s): Jenny G. Maloney, Mónica Santı́n
Software Mentions: 1
Published: over 3 years ago

10.1002/ece3.4066

<i>Wolbachia</i> enhances insect‐specific flavivirus infection in <i>Aedes aegypti</i> mosquitoes
Cited by: 30
Author(s): Hilaria Esiawonam Kafui Abla Amuzu, Kirill Tsyganov, Cassandra Koh, Rosemarie I. Herbert, David Powell, Elizabeth A. McGraw
Software Mentions: 1
Published: over 6 years ago

10.6026/97320630014560

Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions
Cited by: 54
Author(s): Fauzul Mobeen, Vikas Sharma, Tulika Prakash
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.11619

Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding
Cited by: 10
Author(s): Jon Thomassen Hestetun, Anders Lanzén, Thomas G. Dahlgren
Software Mentions: 1
Published: over 3 years ago

10.1534/g3.117.300099

Selection Mapping Identifies Loci Underpinning Autumn Dormancy in Alfalfa (<i>Medicago sativa</i>)
Cited by: 10
Author(s): Gitanshu Munjal, Jingjie Hao, Larry R. Teuber, E. Charles Brummer
Software Mentions: 1
Published: almost 7 years ago

10.1155/2020/7086939

Half-Elemental Diet Shifts the Human Intestinal Bacterial Compositions and Metabolites: A Pilot Study with Healthy Individuals
Cited by: 0
Author(s): Jun Miyoshi, Daisuke Saito, Mio Nakamura, Miki Miura, Tatsuya Mitsui, Toru Kudo, S. Murakami, Minoru Matsuura, Tadakazu Hisamatsu
Software Mentions: 1
Published: over 4 years ago

10.1186/s40168-017-0355-6

Individual signatures and environmental factors shape skin microbiota in healthy dogs
Cited by: 35
Author(s): Anna Cuscó, Janelle M. Belanger, Liza C. Gershony, Alma Islas–Trejo, Kerinne Levy, Juan F. Medrano, Armand Sánchez, Anita M. Oberbauer, Olga Francino
Software Mentions: 1
Published: about 7 years ago

10.3390/genes12060886

Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics
Cited by: 5
Author(s): Sigitas Šulčius, Gediminas Alzbutas, Viktorija Juknevičiūtė, Eugenijus Šimoliūnas, Petras Venckus, Monika Šimoliūnienė, Ričardas Paškauskas
Software Mentions: 1
Published: over 3 years ago

10.1002/ece3.6655

Evaluating the link between predation and pest control services in the mite world
Cited by: 6
Author(s): Lise Roy, Adrien Taudière, Julien Papaïx, Rumsaïs Blatrix, Geoffrey Chiron, Ghais Zriki, Olivier Bonato, Jean‐Yves Barnagaud
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2021.640693

HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis
Cited by: 0
Author(s): Kodjovi D Mlaga, Alban Mathieu, Charles Joly Beauparlant, Alban Ott, Ahmad Khodr, Olivier Périn, Arnaud Droit
Software Mentions: 1
Published: over 3 years ago

10.3390/nu10070895

SunGold Kiwifruit Supplementation of Individuals with Prediabetes Alters Gut Microbiota and Improves Vitamin C Status, Anthropometric and Clinical Markers
Cited by: 28
Author(s): Renée Wilson, Jinny Willis, Richard B. Gearry, A.D. Hughes, Blair Lawley, Paula Skidmore, Chris Frampton, Elizabeth Fleming, Angie Anderson, Lizzie Jones, Gerald W. Tannock, Anitra C. Carr
Software Mentions: 1
Published: over 6 years ago

10.1186/s40168-020-00798-w

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans
Cited by: 19
Author(s): Samuel A. Vohsen, Kaitlin E. Anderson, Andrea M. Gade, Harald R. Gruber‐Vodicka, Richard P. Dannenberg, Eslam O. Osman, Nicole Dubilier, Charles R. Fisher, Iliana B. Baums
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2015.01321

The Community Structures of Prokaryotes and Fungi in Mountain Pasture Soils are Highly Correlated and Primarily Influenced by pH
Cited by: 27
Author(s): Anders Lanzén, Lur Epelde, Carlos Garbisu, Mikel Anza, Iker Martín-Sánchez, F. Blanco, Iker Mijangos
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13071-016-1427-3

Paratransgenesis to control malaria vectors: a semi-field pilot study
Cited by: 60
Author(s): Maria Vittoria Mancini, Roberta Spaccapelo, Claudia Damiani, Anastasia Accoti, Mario Tallarita, Elisabetta Petraglia, Paolo Rossi, Alessia Cappelli, Aida Capone, Giulia Peruzzi, Matteo Valzano, Matteo Picciolini, Abdoulaye Diabaté, Luca Facchinelli, Irene Ricci, Guido Favia
Software Mentions: 1
Published: over 8 years ago

10.1186/s13071-020-04484-6

Use of Oxford Nanopore MinION to generate full-length sequences of the Blastocystis small subunit (SSU) rRNA gene
Cited by: 14
Author(s): Jenny G. Maloney, Aleksey Molokin, Mónica Santı́n
Software Mentions: 1
Published: almost 4 years ago

10.3390/vetsci8090187

Relative Effects of Dietary Administration of a Competitive Exclusion Culture and a Synbiotic Product, Age and Sampling Site on Intestinal Microbiota Maturation in Broiler Chickens
Cited by: 4
Author(s): Nikoletta Such, Valéria Farkas, Gábor Csitári, László Pál, Alíz Márton, László Menyhárt, Károly Dublecz
Software Mentions: 1
Published: about 3 years ago

10.3390/vaccines9070779

Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants
Cited by: 88
Author(s): Vladimir A. Gushchin, Inna V. Dolzhikova, А. М. Щетинин, А. С. Одинцова, Andrei E. Siniavin, М. А. Никифорова, Andrei A. Pochtovyi, Elena V. Shidlovskaya, Nadezhda A. Kuznetsova, О. А. Бургасова, Л. В. Колобухина, Anna A. Iliukhina, Anna V. Kovyrshina, А. Г. Ботиков, Aleksandra V. Kuzina, Daria M. Grousova, Amir I. Tukhvatulin, Dmitry V. Shcheblyakov, Olga V. Zubkova, О.В. Карпова, Olga L. Voronina, Н. Н. Рыжова, Ekaterina I. Aksenova, Marina S. Kunda, Dmitry Lioznov, Daria Danilenko, Andrey Komissarov, Artem P. Tkachuck, Denis Y. Logunov, Alexander L. Gintsburg
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0171017

Microbiome sharing between children, livestock and household surfaces in western Kenya
Cited by: 47
Author(s): Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Cecilia Noecker, Ohad Manor, Sarah K Hilton, Samuel M. Thumbi, Clayton Onyango, Gemina Garland-Lewis, Douglas R. Call, M. Kariuki Njenga, Judith N. Wasserheit, Jennifer A. Zambriski, Judd L. Walson, Guy H. Palmer, Joel M. Montgomery, Elhanan Borenstein, Richard Omore, Peter Rabinowitz
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0197353

Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Cited by: 30
Author(s): Cassandra Soler, Tim Goossens, Alvaro Bermejo, Lourdes Migura-García, Anna Cuscó, Olga Francino, Lorenzo Fraile
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-78890-2

A highly sensitive method for the detection of recombinant PERV-A/C env RNA using next generation sequencing technologies
Cited by: 5
Author(s): Ken Kono, Kiyoko Kataoka, Yuzhe Yuan, Kosuke Yusa, Kazuaki Uchida, Yoji Sato
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0226930

Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion
Cited by: 34
Author(s): Tanvi P. Honap, Krithivasan Sankaranarayanan, Stephanie L. Schnorr, Andrew T. Ozga, Christina Warinner, Cecil M. Lewis
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.jhepr.2021.100299

Hepatic microbiome in healthy lean and obese humans
Cited by: 12
Author(s): Malte P. Suppli, Jonatan I. Bagger, Benjamin Lelouvier, Amandine Broha, Mia Demant, Merete Juhl Kønig, Charlotte Strandberg, Asger Lund, Tina Vilsbøll, Filip K. Knop
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.634025

Adaptation of Microbial Communities to Environmental Arsenic and Selection of Arsenite-Oxidizing Bacteria From Contaminated Groundwaters
Cited by: 10
Author(s): Sarah Zecchin, Simona Crognale, P. Zaccheo, Stefano Fazi, Stefano Amalfitano, Barbara Casentini, Matteo Callegari, R. Zanchi, Gian Attilio Sacchi, Simona Rossetti, L. Cavalca
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2018.02758

The Microbiome of the Cosmopolitan Diatom Leptocylindrus Reveals Significant Spatial and Temporal Variability
Cited by: 33
Author(s): Penelope Ajani, Tim Kahlke, Nachshon Siboni, Rick Carney, Shauna A. Murray, Justin R. Seymour
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2019.01497

Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov.
Cited by: 27
Author(s): Marianne Quéméneur, Gaël Erauso, Eléonore Frouin, Emna Zeghal, Céline Vandecasteele, Bernard Ollivier, Christian Tamburini, Marc Garel, Bénédicte Ménèz, Anne Postec
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.64774

Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities
Cited by: 39
Author(s): Lisa Mahler, Sarah P. Niehs, Karin Martin, Thomas Weber, Kirstin Scherlach, Christian Hertweck, Martin Roth, Miriam A. Rosenbaum
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1007039

The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito
Cited by: 231
Author(s): Andrew Hammond, Kyros Kyrou, Marco Bruttini, Ace North, Roberto Galizi, Xenia Karlsson, Nace Kranjc, Francesco M. Carpi, Romina D’Aurizio, Andrea Crisanti, Tony Nolan
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.53581

Respiratory tissue-associated commensal bacteria offer therapeutic potential against pneumococcal colonization
Cited by: 19
Author(s): Soner Yildiz, João P Pereira Bonifacio Lopes, Matthieu Bergé, Víctor González‐Ruiz, Damian Baud, Joachim Kloehn, Inês Boal-Carvalho, Olivier P. Schaeren, Michael Schotsaert, Lucy J. Hathaway, Serge Rudaz, Patrick H. Viollier, Siegfried Hapfelmeier, Patrice François, Mirco Schmolke
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-94209-1

Effects of different straw biochar combined with microbial inoculants on soil environment in pot experiment
Cited by: 8
Author(s): Yuqi Qi, Haolang Liu, Jihong Wang, Ying‐Ping Wang
Software Mentions: 1
Published: over 3 years ago

10.1038/srep35470

mdRNA-Seq analysis of marine microbial communities from the northern Red Sea
Cited by: 12
Author(s): Songjun Hou, Ulrike Pfreundt, Dan Miller, Ilana Berman‐Frank, Wolfgang R. Hess
Software Mentions: 1
Published: about 8 years ago

10.1038/srep45258

Genomic characterization of Nontuberculous Mycobacteria
Cited by: 146
Author(s): Tarcisio Fedrizzi, Conor J. Meehan, Antonella Grottola, Elisabetta Giacobazzi, Giulia Fregni Serpini, Sara Tagliazucchi, Anna Fabio, Clotilde Bettua, Roberto Bertorelli, Veronica De Sanctis, Fabio Rumpianesi, Monica Pecorari, Olivier Jousson, Enrico Tortoli, Nicola Segata
Software Mentions: 1
Published: over 7 years ago

10.3390/microorganisms7090335

A Glimpse into Genetic Diversity and Symbiont Interaction Patterns in Lichen Communities from Areas with Different Disturbance Histories in Białowieża Forest, Poland
Cited by: 12
Author(s): Garima Singh, Martin Kukwa, Francesco Dal Grande, Anna Łubek, Jürgen Otte, Imke Schmitt
Software Mentions: 1
Published: about 5 years ago

10.3390/biology9120436

The Foreign Oligochaete Species Quistadrilus multisetosus (Smith, 1900) in Lake Geneva: Morphological and Molecular Characterization and Environmental Influences on Its Distribution
Cited by: 0
Author(s): Régis Vivien, M. Lafont, Brigitte Lods-Crozet, Maria Holzmann, Laure Apothéloz-Perret-Gentil, Yaniss Guigoz, B. Ferrari
Software Mentions: 1
Published: almost 4 years ago

10.3390/microorganisms9010155

The Gut Microbiota Profile According to Glycemic Control in Type 1 Diabetes Patients Treated with Personal Insulin Pumps
Cited by: 14
Author(s): Sandra Mrozińska, Przemysław Kapusta, Tomasz Gosiewski, Agnieszka Sroka-Oleksiak, Agnieszka H. Ludwig-Słomczyńska, Bartłomiej Matejko, Beata Kieć‐Wilk, Małgorzata Bulanda, Maciej Małecki, Paweł Wołkow, Tomasz Klupa
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.4662

Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data
Cited by: 8
Author(s): Iris Holmes, Alison R. Davis Rabosky
Software Mentions: 1
Published: over 6 years ago