Ecosyste.ms: Papers

10.3390/microorganisms7110547

Linking Soil Fungal Generality to Tree Richness in Young Subtropical Chinese Forests
Cited by: 9
Author(s): Christina Weißbecker, Anna Heintz‐Buschart, Helge Bruelheide, François Buscot, Tesfaye Wubet
Software Mentions: 19
Published: about 5 years ago

10.1128/mBio.01054-19

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures
Cited by: 28
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Simon Lax
Software Mentions: 18
Published: over 5 years ago

10.3389/fimmu.2020.00082

Fc Receptor-Like 6 (FCRL6) Discloses Progenitor B Cell Heterogeneity That Correlates With Pre-BCR Dependent and Independent Pathways of Natural Antibody Selection
Cited by: 7
Author(s): Kazuhito Honjo, Woong-Jai Won, R. Glenn King, Lara Ianov, David K. Crossman, Juliet Easlick, Mikhail A. Shakhmatov, Mohamed Khass, André M. Vale, Robert P. Stephan, Ran Li, Randall S. Davis
Software Mentions: 15
Published: almost 5 years ago

10.3389/fmicb.2019.01775

Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect Seasonality
Cited by: 23
Author(s): Hannah E. Epstein, Hillary A. Smith, Neal E. Cantin, Véronique J. L. Mocellin, Gergely Torda, Madeleine J. H. van Oppen
Software Mentions: 14
Published: over 5 years ago

10.3389/fpls.2020.01206

Similar Arbuscular Mycorrhizal Fungal Communities in 31 Durum Wheat Cultivars (Triticum turgidum L. var. durum) Under Field Conditions in Eastern Canada
Cited by: 16
Author(s): Franck Stefani, Sarah Dupont, Mario Laterrière, Ron Knox, Yuefeng Ruan, Chantal Hamel, Mohamed Hijri
Software Mentions: 13
Published: over 4 years ago

10.3389/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2018.02312

Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests
Cited by: 26
Author(s): Christina Weißbecker, Tesfaye Wubet, Guillaume Lentendu, Peter Kühn, Thomas Scholten, Helge Bruelheide, François Buscot
Software Mentions: 12
Published: about 6 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: over 4 years ago

10.1128/mSystems.00541-20

Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis
Cited by: 17
Author(s): Luis A. Ibarra-Juárez, Maureen Burton, Peter H. W. Biedermann, Luisa F. Cruz, Damaris Desgarennes, Enrique Ibarra-Laclette, Amparo Latorre, Alexandro Alonso-Sánchez, Emanuel Villafán, Greta Hanako-Rosas, Loredana Lopez, Mirna Vázquez-Rosas-Landa, Gloria Carrión, Daniel Carrillo, Andrés Moya, Araceli Lamelas
Software Mentions: 10
Published: about 4 years ago

10.3389/fmicb.2019.01702

Experimental Inoculation of Coral Recruits With Marine Bacteria Indicates Scope for Microbiome Manipulation in Acropora tenuis and Platygyra daedalea
Cited by: 47
Author(s): Katarina Damjanovic, Madeleine Jh van Oppen, Patricia Menéndez, Linda L. Blackall
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-57760-x

Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems
Cited by: 8
Author(s): Ricardo Schöps, Kezia Goldmann, Lotte Korell, Helge Bruelheide, Tesfaye Wubet, François Buscot
Software Mentions: 10
Published: almost 5 years ago

10.1002/ece3.7907

Inventory of the benthic eukaryotic diversity in the oldest European lake
Cited by: 2
Author(s): Benjamin Wilden, Walter Traunspurger, Stefan Geisen
Software Mentions: 10
Published: over 3 years ago

10.1002/ece3.6594

A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
Cited by: 36
Author(s): Devon O’Rourke, Nicholas A. Bokulich, Michelle A. Jusino, Matthew D. MacManes, Jeffrey T. Foster
Software Mentions: 10
Published: over 4 years ago

10.1038/s41396-020-00862-1

Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
Cited by: 21
Author(s): Sundy Maurice, Gontran Arnault, Jenni Nordén, Synnøve Smebye Botnen, Otto Miettinen, Håvard Kauserud
Software Mentions: 10
Published: almost 4 years ago

10.3389/fmicb.2020.00917

Changes in Faecal Microbiota Profiles Associated With Performance and Birthweight of Piglets
Cited by: 23
Author(s): Clare H. Gaukroger, Christopher J. Stewart, Sandra Edwards, John Walshaw, Ian Adams, Ι. Kyriazakis
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-020-62186-6

Site-specific molecular analysis of the bacteriota on worn spectacles
Cited by: 4
Author(s): Birgit Fritz, Melanie März, Severin Weis, Siegfried Wahl, Focke Ziemssen, Markus Egert
Software Mentions: 9
Published: over 4 years ago

10.1002/aps3.11344

A basic dd <scp>RAD</scp> seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
Cited by: 20
Author(s): Ingrid E. Jordon‐Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2018.02452

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter
Cited by: 52
Author(s): Umer Zeeshan Ijaz, Lojika Sivaloganathan, Aaron McKenna, Anne Richmond, Carmel Kelly, Mark Linton, Alexandros Ch. Stratakos, Ursula Lavery, Abdi Elmi, Brendan W. Wren, Nick Dorrell, Nicolae Corcionivoschi, Ozan Gundogdu
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-020-74952-7

Characterising the effect of crop species and fertilisation treatment on root fungal communities
Cited by: 6
Author(s): Liina Soonvald, Kaire Loit, Eve Runno-Paurson, Alar Astover, Leho Tedersoo
Software Mentions: 9
Published: about 4 years ago

10.1038/s41598-021-96431-3

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs
Cited by: 7
Author(s): Kathryn A. Uckele, Joshua P. Jahner, Eric J. Tepe, Lora A. Richards, Lee A. Dyer, Kaitlin M. Ochsenrider, Casey S. Philbin, Massuo Jorge Kato, Lydia F. Yamaguchi, Matthew L. Forister, Angela M. Smilanich, Craig D. Dodson, Christopher S. Jeffrey, Thomas L. Parchman
Software Mentions: 9
Published: over 3 years ago

10.15252/msb.20188190

High‐throughput discovery of functional disordered regions: investigation of transactivation domains
Cited by: 121
Author(s): Charles N. J. Ravarani, Tamara Y. Erkina, Greet De Baets, Daniel C Dudman, Alexandre M. Erkine, M. Madan Babu
Software Mentions: 9
Published: over 6 years ago

10.3390/microorganisms9061326

Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer
Cited by: 5
Author(s): Thijs Van Gerrewey, Christophe El‐Nakhel, Stefania De Pascale, Jolien De Paepe, Peter Clauwaert, Frederiek‐Maarten Kerckhof, Nico Boon, Danny Geelen
Software Mentions: 8
Published: over 3 years ago

10.1038/s41418-021-00817-9

Prolonged SARS-CoV-2 RNA virus shedding and lymphopenia are hallmarks of COVID-19 in cancer patients with poor prognosis
Cited by: 27
Author(s): Anne-Gaëlle Goubet, Agathe Dubuisson, Arthur Géraud, F-X. Danlos, Safae Terrisse, Carolina Alves Costa Silva, Damien Drubay, Lea Touri, Marion Picard, Marine Mazzenga, Aymeric Silvin, Garett Dunsmore, Yacine Haddad, Eugénie Pizzato, Pierre Ly, Caroline Flament, Cléa Melenotte, Éric Solary, Michaëla Fontenay, Gabriel Garcia, Corinne Balleyguier, Nathalie Lassau, Markus Maeurer, Claudia Grajeda‐Iglesias, Nitharsshini Nirmalathasan, Fanny Aprahamian, Sylvère Durand, Oliver Kepp, Gladys Ferrere, Cassandra Thelemaque, Imran Lahmar, Jean Eudes Fahrner, Lydia Meziani, Abdelhakim Ahmed–Belkacem, Nadia Saïdani, Bernard La Scola, Didier Raoult, Stéphanie Gentile, Sébastien Cortaredona, Giuseppe Ippolito, Benjamin Lelouvier, Alain Roulet, Fabrice André, Fabrice Barlési, Jean Charles Soria, Caroline Pradon, Emmanuelle Gallois, Fanny Pommeret, Emeline Colomba, Florent Ginhoux, Suzanne Kazandjian, Arielle Elkrief, Bertrand Routy, Makoto Miyara, Guy Gorochov, Éric Deutsch, Laurence Albigès, Annabelle Stoclin, Bertrand Gachot, Anne Florin, Mansouria Merad, Florian Scotté, Souad Assaad, Guido Kroemer, Jean Yves Blay, Aurélien Marabelle, Frank Griscelli, Laurence Zitvogel, Lisa Derosa
Software Mentions: 8
Published: over 3 years ago

10.1093/dnares/dsaa017

A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform
Cited by: 0
Author(s): Yuu Hirose, Takuhei Shiozaki, Itsuki Hamano, Shizue Yoshihara, Hayato Tokumoto, Toshihiko Eki, Naomi Harada
Software Mentions: 8
Published: over 4 years ago

10.1111/1365-2656.13065

Host genetics and geography influence microbiome composition in the sponge <i>Ircinia campana</i>
Cited by: 48
Author(s): Sarah M. Griffiths, Rachael E. Antwis, Luca Lenzi, Anita Lucaci, Donald C. Behringer, Mark J. Butler, Richard F. Preziosi
Software Mentions: 8
Published: over 5 years ago

10.3389/fmicb.2019.02736

Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding
Cited by: 14
Author(s): Simona Armeli Minicante, Roberta Piredda, Grazia Marina Quero, Stefania Finotto, Fabrizio Bernardi Aubry, Mauro Bastianini, Alessandra Pugnetti, Adriana Zingone
Software Mentions: 8
Published: about 5 years ago

10.1038/s41396-019-0563-0

Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere
Cited by: 11
Author(s): Matti O. Ruuskanen, Stéphane Aris‐Brosou, Alexandre J. Poulain
Software Mentions: 8
Published: about 5 years ago

10.1111/mec.15484

Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone
Cited by: 43
Author(s): Olivier Laroche, Oliver Kersten, Craig R. Smith, Erica Goetze
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.62208

A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
Cited by: 30
Author(s): David E. Cook, Holger Kramer, David E Torres, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0187758

Habitat- and soil-related drivers of the root-associated fungal community of Quercus suber in the Northern Moroccan forest
Cited by: 20
Author(s): Fatima Zahra Maghnia, Younes Abbas, Frédéric Mahe, Benaissa Kerdouh, Estelle Tournier, Mohamed Ouadji, Pierre Tisseyre, Yves Prin, Naïma El Ghachtouli, Salah Eddine Bakkali Yakhlef, Robin Duponnois, Hervé Sanguin
Software Mentions: 8
Published: about 7 years ago

10.1186/s40168-018-0468-6

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate
Cited by: 44
Author(s): Pål Trosvik, Eric J. de Muinck, Eli Knispel Rueness, Peter J. Fashing, Evan C. Beierschmitt, Kadie R. Callingham, Jacob B. Kraus, Thomas H. Trew, Amera Moges, Addisu Mekonnen, Vivek V. Venkataraman, Nga Nguyen
Software Mentions: 8
Published: over 6 years ago

10.1002/ece3.6305

Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (<i>Loxodonta africana</i>) and forest elephants (<i>L. cyclotis</i>)
Cited by: 16
Author(s): Kris Budd, Joe C. Gunn, Tabitha Finch, Katy E. Klymus, Noah Sitati, Lori S. Eggert
Software Mentions: 8
Published: over 4 years ago

10.1111/mec.15160

Impacts of long‐term elevated atmospheric CO₂ concentrations on communities of arbuscular mycorrhizal fungi
Cited by: 19
Author(s): Irena Maček, Dave R. Clark, Nataša Šibanc, Gerald M. Moser, Dominik Vodnik, Christoph Müller, Alex J. Dumbrell
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2021.719486

Compositional Shift of Bacterial, Archaeal, and Fungal Communities Is Dependent on Trophic Lifestyles in Rice Paddy Soil
Cited by: 5
Author(s): Hyun Kim, Jongbum Jeon, Kiseok Keith Lee, Yong-Hwan Lee
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2020.00423

The Relationships Between the Free-Living and Particle-Attached Bacterial Communities in Response to Elevated Eutrophication
Cited by: 26
Author(s): Yang Hu, Guobo Xie, Xingyu Jiang, Kwang‐Tsao Shao, Xiangming Tang, Guang Gao
Software Mentions: 7
Published: over 4 years ago

10.1007/s00248-019-01426-3

Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes
Cited by: 45
Author(s): Edward C. Rojas, Rumakanta Sapkota, Birgit Jensen, Henning Jørgensen, Tina Henriksson, Lise Nistrup Jørgensen, Mogens Nicolaisen, David B. Collinge
Software Mentions: 7
Published: over 5 years ago

10.1128/mSystems.00086-17

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota
Cited by: 8
Author(s): Eric J. de Muinck, Knut E.A. Lundin, Pål Trosvik
Software Mentions: 7
Published: about 7 years ago

10.3390/microorganisms9071368

Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)
Cited by: 0
Author(s): Qianqian Li, Rebecca E. Cooper, Carl‐Eric Wegner, Martin Taubert, Nico Jehmlich, Martin von Bergen, Kirsten Küsel
Software Mentions: 7
Published: over 3 years ago

10.1186/s40168-019-0677-7

Maize synthesized benzoxazinoids affect the host associated microbiome
Cited by: 160
Author(s): Enoch Narh Kudjordjie, Rumakanta Sapkota, Stine K. Steffensen, Inge S. Fomsgaard, Mogens Nicolaisen
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2018.02520

Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms
Cited by: 63
Author(s): Claire Bertelli, Sophie Courtois, Marta Rosikiewicz, P. Piriou, Sébastien Aeby, Robert Salais, Jean-François Loret, Gilbert Greub
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0238405

Persistent El Niño driven shifts in marine cyanobacteria populations
Cited by: 7
Author(s): Alyse A. Larkin, Allison R. Moreno, Adam Fagan, Alyssa Fowlds, Alani Ruiz, Adam C. Martiny
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-017-18435-2

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys
Cited by: 32
Author(s): Pål Trosvik, Eli Knispel Rueness, Eric J. de Muinck, Amera Moges, Addisu Mekonnen
Software Mentions: 7
Published: almost 7 years ago

10.1093/gigascience/giaa135

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology
Cited by: 33
Author(s): Christina Weißbecker, Beatrix Schnabel, Anna Heintz‐Buschart
Software Mentions: 7
Published: about 4 years ago

10.3389/fmicb.2020.577474

Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin
Cited by: 25
Author(s): Lisa Miclotte, Kim De Paepe, Leen Rymenans, Chris Callewaert, Jeroen Raes, Andreja Rajković, John Van Camp, Tom Van de Wiele
Software Mentions: 7
Published: about 4 years ago

10.12688/f1000research.18866.2

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data
Cited by: 12
Author(s): Mike W.C. Thang, Xin-Yi Chua, Gareth Price, D. Gorse, Matthew A. Field
Software Mentions: 7
Published: about 5 years ago

10.1111/1755-0998.13022

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring
Cited by: 64
Author(s): Jérôme Morinière, Michael Balke, Dieter Doczkal, Matthias F. Geiger, Laura A. Hardulak, Gerhard Haszprunar, Axel Hausmann, Lars Hendrich, Ledis Regalado, Björn Rulik, Stefan Schmidt, Johann‐Wolfgang Wägele, Paul D. N. Hebert
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2021.647709

The Effects of Host Plant Genotype and Environmental Conditions on Fungal Community Composition and Phosphorus Solubilization in Willow Short Rotation Coppice
Cited by: 7
Author(s): Piotr Koczorski, Bliss Ursula Furtado, Marcin Gołębiewski, Piotr Hulisz, Christel Baum, Martin Weih, Katarzyna Hrynkiewicz
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-019-5914-8

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products
Cited by: 36
Author(s): Marco Meola, Étienne Rifa, Noam Shani, Céline Delbès, Hélène Berthoud, Christophe Chassard
Software Mentions: 6
Published: over 5 years ago

10.1128/mBio.02634-20

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study
Cited by: 22
Author(s): Nastassia V. Patin, Angela Peña-Gonzalez, Janet K. Hatt, Christine L. Moe, Amy Kirby, Konstantinos T. Konstantinidis
Software Mentions: 6
Published: about 4 years ago

10.7150/thno.55946

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome
Cited by: 28
Author(s): Xiaomin Hu, Hanyu Li, Xinyue Zhao, Ronggang Zhou, Honghong Liu, Yiting Sun, Yue Fan, Yanan Shi, Shushan Qiao, Shuang‐Jiang Liu, Hongwei Liu, Shuyang Zhang
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-021-89950-6

Metabarcoding Malaise traps and soil eDNA reveals seasonal and local arthropod diversity shifts
Cited by: 15
Author(s): Ameli Kirse, Sarah J. Bourlat, Kathrin Langen, Vera G. Fonseca
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-92042-0

Socioeconomic position links circulatory microbiota differences with biological age
Cited by: 12
Author(s): Hannah Craven, Dagmara McGuinness, Sarah Buchanan, Norman Galbraith, David McGuinness, Brian Jones, Emilie Combet, Denise Mafra, Peter Bergman, Anne Ellaway, Peter Stenvinkel, Umer Zeeshan Ijaz, Paul G. Shiels
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2018.00651

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?
Cited by: 53
Author(s): Dominika Thiem, Marcin Gołębiewski, Piotr Hulisz, Agnieszka Piernik, Katarzyna Hrynkiewicz
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0249944

Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity
Cited by: 16
Author(s): Yu-Chi Chiu, Shih‐Wei Lee, Chen‐Wuing Liu, Rebecca Chou-Jui Lin, Yung‐Chia Huang, Tsuo-Hung Lan, Lawrence Shih Hsin Wu
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0217050

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
Cited by: 61
Author(s): Lucas Czech, Alexandros Stamatakis
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-70535-8

Bacterial microbiota diversity and composition in red and white wines correlate with plant-derived DNA contributions and botrytis infection
Cited by: 16
Author(s): Alena M. Bubeck, Lena C. Preiss, Anna Jung, Elisabeth Dörner, Daniel Podlesny, Marija Kulis, Cynthia Maddox, Cesar Arze, Christian Zörb, Nikolaus Merkt, W. Florian Fricke
Software Mentions: 6
Published: over 4 years ago

10.1080/19490976.2021.1902771

The intestinal microbiota and metabolites in patients with anorexia nervosa
Cited by: 44
Author(s): Petra Procházková, Radka Roubalová, Jiří Dvořák, Jakub Kreisinger, Martin Hill, Helena Tlaskalová‐Hogenová, Petra Tomášová, Helena Pelantová, M Cermáková, Marek Kuzma, Josef Bulant, Martin Bilej, Kvido Smitka, Alena Lambertová, Petra Holanová, Hana Papežová
Software Mentions: 6
Published: almost 4 years ago

10.3389/fmicb.2019.02278

Assessment of Artificial and Natural Transport Mechanisms of Ice Nucleating Particles in an Alpine Ski Resort in Obergurgl, Austria
Cited by: 4
Author(s): Philipp Baloh, Nora Els, Robert O. David, Catherine Larose, Karin Whitmore, Birgit Sattler, Hinrich Grothe
Software Mentions: 6
Published: about 5 years ago

10.1080/19490976.2020.1814120

Analysis of 16S rRNA genes reveals reduced Fusobacterial community diversity when translocating from saliva to GI sites
Cited by: 10
Author(s): Miles Richardson, Ji‐Chang Ren, Mara Roxana Rubinstein, Jamila A Taylor, Richard A. Friedman, Bo Shen, Yiping W. Han
Software Mentions: 6
Published: about 4 years ago

10.1111/1462-2920.14516

Differential ratio amplicons (<i>R</i>_amp) for the evaluation of RNA integrity extracted from complex environmental samples
Cited by: 12
Author(s): Fabien Cholet, Umer Zeeshan Ijaz, Cindy J. Smith
Software Mentions: 6
Published: almost 6 years ago

10.3389/fmicb.2021.675693

Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities
Cited by: 10
Author(s): Jialin Hu, Jonathan D. Richwine, Patrick D. Keyser, Lidong Li, Fei Yao, Sindhu Jagadamma, Jennifer M. DeBruyn
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2021.723682

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon)
Cited by: 13
Author(s): Ying Zhu, Yudong Li, Hai-Qiong Yang, Ke He, Keyi Tang
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.3730

Uncovering unseen fungal diversity from plant DNA banks
Cited by: 16
Author(s): Erin M. Datlof, Anthony S. Amend, Kamala Earl, J. Hayward, Clifford W. Morden, Rachael Wade, Geoffrey Zahn, Nicole A. Hynson
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0244616

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia
Cited by: 11
Author(s): Jan Niklas Macher, Martina Prazeres, Sarah Taudien, Jamaluddin Jompa, Aleksey Sadekov, Willem Renema
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13073-021-00951-6

Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus
Cited by: 10
Author(s): Nandan P. Deshpande, Stephen M. Riordan, Claire J. Gorman, Shaun Nielsen, Tonia Russell, Carolina Correa-Ospina, Samitha Fernando, Shafagh A. Waters, Natalia Castaño‐Rodríguez, Si Ming Man, Nicodemus Tedla, Marc R. Wilkins, Nadeem O. Kaakoush
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giz037

GenPipes: an open-source framework for distributed and scalable genomic analyses
Cited by: 107
Author(s): Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Létourneau, Joël Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, François Lefebvre, Gary Leveque, Eloi Mercier, David Bujold, Pascale Marquis, Patrick Tran Van, David Anderson de Lima Morais, Julien Tremblay, Xiaojian Shao, Édouard Henrion, Emmanuel González, Pierre-Olivier Quirion, B. Caron, Guillaume Bourque
Software Mentions: 6
Published: over 5 years ago

10.1002/ece3.7453

High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally
Cited by: 7
Author(s): Marjorie Couton, Aurélien Baud, Claire Daguin‐Thiébaut, Erwan Corre, Thierry Comtet, Frédérique Viard
Software Mentions: 6
Published: almost 4 years ago

10.3389/fnbeh.2020.581296

A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats
Cited by: 6
Author(s): Valérie Daugé, Catherine Philippe, Mahendra Mariadassou, Olivier Rué, Jean‐Charles Martin, Marie Rossignol, Nathalie Dourmap, Ljubica Svilar, Franck Tourniaire, Magali Monnoye, Déborah Jardet, Marie Bangratz, Sophie Holowacz, Sylvie Rabot, Laurent Naudon
Software Mentions: 6
Published: about 4 years ago

10.1186/s12866-019-1464-0

Statistical evaluation of diet-microbe associations
Cited by: 12
Author(s): Xiang Zhang, Max Nieuwdorp, Albert K. Groen, A. H. Zwinderman
Software Mentions: 6
Published: over 5 years ago

10.1038/s41396-021-00987-x

Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria
Cited by: 14
Author(s): François Thomas, Nolwen Le Duff, Ting-Di Wu, Aurélie Cébron, Stéphane Uroz, Pascal Riera, Cédric Leroux, Gwenn Tanguy, Erwan Legeay, Jean‐Luc Guerquin‐Kern
Software Mentions: 6
Published: over 3 years ago

10.3389/fneur.2020.528056

Oral Health, Oral Microbiota, and Incidence of Stroke-Associated Pneumonia—A Prospective Observational Study
Cited by: 14
Author(s): Fabian Cieplik, Alma Maria Wiedenhofer, Verena Pietsch, Karl‐Anton Hiller, Andreas Hiergeist, Andrea Wagner, Dobri Baldaranov, Ralf A. Linker, Jonathan Jantsch, Wolfgang Buchalla, Felix Schlachetzki, André Gessner
Software Mentions: 5
Published: about 4 years ago

10.3389/fpls.2019.01018

Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks
Cited by: 17
Author(s): Daniel Revillini, Gail W. T. Wilson, R. M. Miller, Ryan C. Lancione, Nancy Collins Johnson
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.00579-19

Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies
Cited by: 48
Author(s): Cecilia Noecker, Hsuan-Chao Chiu, Christopher A. McNally, Elhanan Borenstein
Software Mentions: 5
Published: about 5 years ago

10.1099/mgen.0.000199

Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity
Cited by: 10
Author(s): Amy C. Fleshman, Kristin Mullins, Jason W. Sahl, Crystal M. Hepp, Nathan C. Nieto, Kristin Wiggins, Heidie Hornstra, Daryl J. Kelly, Teik Chye Chan, Rattanaphone Phetsouvanh, Sabine Dittrich, Phonepasith Panyanivong, Daniel Paris, Paul N. Newton, Allen L. Richards, Talima Pearson
Software Mentions: 5
Published: over 6 years ago

10.3390/microorganisms9010064

Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap
Cited by: 8
Author(s): Maija Nuppunen-Puputti, Riikka Kietäväinen, Lotta Purkamo, Pauliina Rajala, Merja Itävaara, Ilmo Kukkonen, Malin Bomberg
Software Mentions: 5
Published: almost 4 years ago

10.1128/mSphere.00327-18

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
Cited by: 57
Author(s): Robin R Rohwer, Joshua J. Hamilton, Ryan J. Newton, Katherine D. McMahon
Software Mentions: 5
Published: about 6 years ago

10.3390/microorganisms8081134

Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome
Cited by: 10
Author(s): Elena Biagi, Carlo Mengucci, Monica Barone, Gianfranco Picone, Alex Lucchi, Pietro Celi, Gilberto Litta, Marco Candela, Gerardo Manfreda, Patrizia Brigidi, Francesco Capozzi, Alessandra De Cesare
Software Mentions: 5
Published: over 4 years ago

10.1186/s42523-020-00040-w

The microbiome of captive hamadryas baboons
Cited by: 6
Author(s): Xuanji Li, Urvish Trivedi, Asker Brejnrod, Gisle Vestergaard, Martin Steen Mortensen, Mads F. Bertelsen, Søren J. Sørensen
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.01306-20

Cultivating the Bacterial Microbiota of <i>Populus</i> Roots
Cited by: 12
Author(s): Dana L. Carper, David J. Weston, Aditya Barde, Collin M. Timm, Tse-Yuan S. Lu, Leah H. Burdick, Sara Jawdy, Dawn M. Klingeman, Michael S. Robeson, Allison M. Veach, Melissa Cregger, Udaya C. Kalluri, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.02372

Phylogeography and Ecological Niche Shape the Cichlid Fish Gut Microbiota in Central American and African Lakes
Cited by: 25
Author(s): Laura Baldo, Joan Lluís Riera, Walter Salzburger, Marta Barluenga
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-020-70249-x

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study
Cited by: 5
Author(s): Tereza Matějková, Petra Hájková, Romana Stopková, Michał Stanko, Jean‐François Martin, Jakub Kreisinger, Pavel Stopka
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-017-17150-2

Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact
Cited by: 98
Author(s): Judith Bakker, Owen S. Wangensteen, Demian D. Chapman, Germain Boussarie, Dayne Buddo, Tristan L. Guttridge, Heidi Hertler, David Mouillot, Laurent Vigliola, Stefano Mariani
Software Mentions: 5
Published: about 7 years ago

10.3390/microorganisms9020346

Gut Microbiota Profile and Changes in Body Weight in Elderly Subjects with Overweight/Obesity and Metabolic Syndrome
Cited by: 13
Author(s): Alessandro Atzeni, Serena Galiè, Jananee Muralidharan, Nancy Babió, Francisco J. Tinahones, Jesús Vioque, Dolores Corella, Olga Castañer, Josep Vidal, Isabel Moreno-Indias, Laura Torres-Collado, Rebeca Fernández-Carrión, Montserrat Fitó, Romina Olbeyra, Miguel Ángel Martínez‐González, Mònica Bulló, Jordi Salas‐Salvadó
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2020.603234

Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors
Cited by: 13
Author(s): Patricia Bovio-Winkler, Angela Cabezas, Claudia Etchebehere
Software Mentions: 5
Published: almost 4 years ago

10.7717/peerj.12198

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
Cited by: 16
Author(s): Nicholas D. Youngblut, Ruth E. Ley
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-017-16375-5

Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico
Cited by: 45
Author(s): Adrien Vigneron, Eric Alsop, Perrine Cruaud, Gwenaelle Philibert, Benjamin L. King, Leslie Baksmaty, D. A. Lavallée, Bart P. Lomans, Nikos C. Kyrpides, Ian M. Head, Nicolas Tsesmetzis
Software Mentions: 5
Published: about 7 years ago

10.1002/ece3.5691

Metabolically similar cohorts of bacteria exhibit strong cooccurrence patterns with diet items and eukaryotic microbes in lizard guts
Cited by: 7
Author(s): Iris Holmes, Ivan V. Monagan, Daniel L. Rabosky, Alison R. Davis Rabosky
Software Mentions: 5
Published: about 5 years ago

10.1186/s40168-020-00980-0

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut
Cited by: 33
Author(s): Jason W. Arnold, Jeffery Roach, Salvador Fabela, Emily Moorfield, Shengli Ding, R. Eric Blue, Sue F. Dagher, Scott T. Magness, Rita Tamayo, José M. Bruno-Bárcena, M. Andrea Azcárate-Peril
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0182869

Active microorganisms thrive among extremely diverse communities in cloud water
Cited by: 94
Author(s): Pierre Amato, Muriel Joly, Ludovic Besaury, Anne Oudart, Najwa Taïb, Anne Moné, Laurent Deguillaume, Anne-Marie Delort, Didier Debroas
Software Mentions: 5
Published: over 7 years ago

10.1093/gigascience/giy054

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
Cited by: 82
Author(s): Alexandre Almeida, Alex L. Mitchell, Aleksandra Tarkowska, Alex Bateman
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-017-0279-1

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
Cited by: 79
Author(s): Eric J. de Muinck, Pål Trosvik, Gregor D. Gilfillan, Johannes R. Hov, Arvind Sundaram
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.10539

Composition and distribution of fish environmental DNA in an Adirondack watershed
Cited by: 2
Author(s): Robert S. Cornman, James E. McKenna, Jennifer A. Fike
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0254556

Simple mapping-based quantification of a mock microbial community using total RNA-seq data
Cited by: 4
Author(s): Shigeharu Moriya
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2018.01138

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada
Cited by: 43
Author(s): Matti O. Ruuskanen, Kyra A. St. Pierre, Vincent L. St. Louis, Stéphane Aris‐Brosou, Alexandre J. Poulain
Software Mentions: 5
Published: over 6 years ago

10.1002/ece3.6482

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area
Cited by: 46
Author(s): Natalia Fraija-Fernández, Marie-Catherine Bouquieaux, Anaïs Rey, Iñaki Mendibil, Unai Cotano, Xabier Irigoien, M.B. Santos, Naiara Rodríguez-Ezpeleta
Software Mentions: 5
Published: over 4 years ago

10.1186/s12866-016-0885-2

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories
Cited by: 41
Author(s): François-Joël Gatesoupe, Christine Huelvan, Nicolas Le Bayon, Hervé Le Delliou, Lauriane Madec, Olivier Mouchel, Patrick Quazuguel, David Mazurais, José‐Luis Zambonino-Infante
Software Mentions: 5
Published: about 8 years ago

10.3390/v13081647

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner
Cited by: 25
Author(s): Devon A. Gregory, Chris G. Wieberg, Jeff Wenzel, Chung‐Ho Lin, Marc C. Johnson
Software Mentions: 5
Published: over 3 years ago

10.1111/1462-2920.15114

Heterogeneity of the rice microbial community of the Chinese centuries‐old Honghe Hani rice terraces system
Cited by: 8
Author(s): Pascal Alonso, Laurence Blondin, Pierre Gladieux, Frédéric Mahe, Hervé Sanguin, Romain Ferdinand, Denis Filloux, Érick Desmarais, Frédérique Cerqueira, Baocheng Jin, Huichuan Huang, Xiahong He, Jean-Benoît Morel, Darren P. Martin, Philippe Roumagnac, Christian Vernière
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0244666

On genetic diversity in caraway: Genotyping of a large germplasm collection
Cited by: 2
Author(s): Daniel von Maydell, Heike Lehnert, Thomas Berner, Evelyn Klocke, Wolfram Junghanns, Jens Keilwagen, Frank Marthe
Software Mentions: 5
Published: almost 4 years ago

10.1038/s42003-021-01659-4

Amynthas corticis genome reveals molecular mechanisms behind global distribution
Cited by: 4
Author(s): Xing Wang, Yi Zhang, Yufeng Zhang, Mingming Kang, Yuanbo Li, Samuel W. James, Yang Yang, Yang Bi, Hao Jiang, Yi Zhao, Zhenjun Sun
Software Mentions: 5
Published: almost 4 years ago