cran: vegan | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2019.00144

Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges
Cited by: 70
Author(s): Laura M. Carroll, Manjarí Mukherjee, David Nicholas, Lisa A. Mingle, Nellie B. Dumas, Jocelyn A. Cole, Jasna Kovač
Software Mentions: 12
Published: almost 6 years ago

10.1002/ece3.6784

Ecomorphology of the pectoral girdle in anurans (Amphibia, Anura): Shape diversity and biomechanical considerations
Cited by: 10
Author(s): Karolin Engelkes, Lena Kath, Thomas Kleinteich, Jörg U. Hammel, André Beerlink, Alexander Haas
Software Mentions: 12
Published: about 4 years ago

10.1093/conphys/coaa047

Changes in physiology and microbial diversity in larval ornate chorus frogs are associated with habitat quality
Cited by: 9
Author(s): Cory B. Goff, Susan C. Walls, David Rodríguez, Caitlin R. Gabor
Software Mentions: 12
Published: almost 5 years ago

10.1128/mSystems.00903-19

manta: a Clustering Algorithm for Weighted Ecological Networks
Cited by: 7
Author(s): Lisa Röttjers, Karoline Faust
Software Mentions: 12
Published: almost 5 years ago

10.1128/mSystems.00750-21

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies
Cited by: 11
Author(s): Christoph Ammer‐Herrmenau, Nina Pfisterer, T. van den Berg, Ivana Gavrilova, Ahmad Amanzada, Shiv K. Singh, Alaa Mohamed, Rohia Alili, Eugeni Belda, Karine Clément, Ahmed Abd El Wahed, ElSagad Eltayeb Gady, Martin Haubrock, Tim Beißbarth, Volker Ellenrieder, Albrecht Neeße
Software Mentions: 12
Published: about 3 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

10.3897/BDJ.4.e8357

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)
Cited by: 12
Author(s): Constantinos Varsos, Theodore Patkos, Anastasis Oulas, Christina Pavloudi, Alexandros Gougousis, Umer Zeeshan Ijaz, Irene Filiopoulou, Nikolaos Pattakos, E. Vanden Berghe, Antonio Fernàndez-Guerra, Sarah Faulwetter, Eva Chatzinikolaou, Evangelos Pafilis, Chryssoula Bekiari, Martin Doerr, Christos Arvanitidis
Software Mentions: 12
Published: about 8 years ago

10.1002/aps3.1227

Open‐source data reveal how collections‐based fungal diversity is sensitive to global change
Cited by: 24
Author(s): Carrie Andrew, Ulf Büntgen, Simon Egli, Béatrice Senn-Irlet, John‐Arvid Grytnes, Jacob Heilmann‐Clausen, Lynne Boddy, Claus Bässler, Alan C. Gange, Einar Heegaard, Klaus Høiland, Paul M. Kirk, Irmgard Krisai‐Greilhuber, Thomas W. Kuyper, Håvard Kauserud
Software Mentions: 12
Published: over 5 years ago

10.1111/gcb.14581

Structural and functional responses of invertebrate communities to climate change and flow regulation in alpine catchments
Cited by: 61
Author(s): Daniel Bruno, Óscar Belmar, Anthony Maire, Adrien Morel, Bernard Dumont, Thibault Datry
Software Mentions: 12
Published: over 5 years ago

10.12688/f1000research.14013.2

Taxa: An R package implementing data standards and methods for taxonomic data
Cited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: about 6 years ago

10.1186/s12915-016-0258-1

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model
Cited by: 283
Author(s): Philipp Dirksen, Sarah Arnaud Marsh, Ines Braker, Nele Heitland, Sophia Wagner, Rania Nakad, Sebastian Mäder, Carola Petersen, Vienna Kowallik, Philip Rosenstiel, Marie‐Anne Félix, Hinrich Schulenburg
Software Mentions: 12
Published: over 8 years ago

10.1371/journal.pone.0236305

Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance
Cited by: 7
Author(s): David J. Bradshaw, Nicholas J. Dickens, John H. Trefry, Peter J. McCarthy
Software Mentions: 12
Published: about 4 years ago

10.3389/fmicb.2017.01553

Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves
Cited by: 58
Author(s): Juliana Dias, Marcos Inácio Marcondes, Melline Fontes Noronha, Rafael Tassinari Resende, F. S. Machado, Hilário Cuquetto Mantovani, Kimberly A. Dill‐McFarland, Garret Suen
Software Mentions: 12
Published: over 7 years ago

10.3390/nu13082639

Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts
Cited by: 18
Author(s): Chiara-Maria Homann, Connor A J Rossel, Sara Dizzell, Liene Bervoets, Julia Simioni, Jenifer Li, Elizabeth Gunn, Michael G. Surette, Russell J. de Souza, Monique Mommers, Eileen K. Hutton, Katherine M. Morrison, John Penders, Niels van Best, Jennifer C. Stearns
Software Mentions: 12
Published: over 3 years ago

10.3389/fmicb.2020.01116

Crop Management Impacts the Soybean (Glycine max) Microbiome
Cited by: 41
Author(s): Reid Longley, Zachary A Noel, Gian Maria Niccolò Benucci, Martin I. Chilvers, Frances Trail, Gregory Bonito
Software Mentions: 12
Published: over 4 years ago

10.1371/journal.pone.0238219

Ground-dwelling arthropods of pinyon-juniper woodlands: Arthropod community patterns are driven by climate and overall plant productivity, not host tree species
Cited by: 6
Author(s): Derek A. Uhey, Hannah Lee Riskas, Aaron D. Smith, Richard W. Hofstetter
Software Mentions: 11
Published: about 4 years ago

10.1186/s42523-020-00045-5

Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)
Cited by: 4
Author(s): Emily Dodd, Melissa L. Pierce, Jonathan S. F. Lee, Rachel Poretsky
Software Mentions: 11
Published: over 4 years ago

10.3389/fmicb.2017.00682

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
Cited by: 314
Author(s): David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, Philip Hugenholtz
Software Mentions: 11
Published: over 7 years ago

10.3897/BDJ.8.e56876

Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout
Cited by: 5
Author(s): Akio Imamura, Kana Hayami, Masato Sakata, Toshifumi Minamoto
Software Mentions: 11
Published: about 4 years ago

10.1002/ece3.7515

Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes
Cited by: 4
Author(s): Primrose J. Boynton, Dominika Wloch‐Salamon, Doreen Landermann, Eva H. Stukenbrock
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0242331

Ocean warming affected faunal dynamics of benthic invertebrate assemblages across the Toarcian Oceanic Anoxic Event in the Iberian Basin (Spain)
Cited by: 4
Author(s): Veronica Piazza, Clemens V. Ullmann, Martin Aberhan
Software Mentions: 11
Published: almost 4 years ago

10.1038/s41598-019-47595-6

Coordinated community structure among trees, fungi and invertebrate groups in Amazonian rainforests
Cited by: 14
Author(s): Jason Vleminckx, Heidy Schimann, Thibaud Decaëns, Mélanie Fichaux, Vincent Vedel, Gaëlle Jaouen, Mélanie Roy, Emmanuel Lapied, Julien Engel, Aurélie Dourdain, Pascal Pétronelli, Jérôme Orivel, Christopher Baraloto
Software Mentions: 11
Published: over 5 years ago

10.1016/j.mex.2018.07.003

A practical method to control spatiotemporal confounding in environmental impact studies
Cited by: 4
Author(s): Rezvan Hatami
Software Mentions: 11
Published: almost 7 years ago

10.3389/fmicb.2019.01770

Gut Microbiota as an Objective Measurement for Auxiliary Diagnosis of Insomnia Disorder
Cited by: 55
Author(s): Bingdong Liu, Win Lin, Shujie Chen, Ting Xiang, Yifan Yang, Yulong Yin, Guohuan Xu, Zhihong Liu, Li Liu, Jiyang Pan, Liwei Xie
Software Mentions: 11
Published: over 5 years ago

10.1186/s12866-020-02075-0

Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments
Cited by: 11
Author(s): Zala Schmautz, Carlos Espinal, Andrea M. Bohny, Fabio Rezzonico, Ranka Junge, Emmanuel Frossard, Theo H. M. Smits
Software Mentions: 11
Published: almost 4 years ago

10.1038/s41598-021-86396-8

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Cited by: 15
Author(s): Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard‐Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud‐Haond, Daniela Zeppilli
Software Mentions: 11
Published: over 3 years ago

10.7717/peerj.5209

Distribution and ecological segregation on regional and microgeographic scales of the diploidCentaurea asperaL., the tetraploidC. seridisL., and their triploid hybrids (Compositae)
Cited by: 5
Author(s): Alfonso Garmendia, Hugo Merlé, Pablo L. Ruiz, M. Ferriol
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pone.0132783

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities
Cited by: 388
Author(s): Mads Albertsen, Søren Michael Karst, Anja Ziegler, Rasmus Hansen Kirkegaard, Per Halkjær Nielsen
Software Mentions: 11
Published: over 9 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

10.1186/s42523-020-00066-0

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary
Cited by: 16
Author(s): Rebecca J. Stevick, Anton F. Post, Marta Gómez-Chiarri
Software Mentions: 11
Published: almost 4 years ago

10.1371/journal.pntd.0009321

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature
Cited by: 15
Author(s): Camila Farias Amorim, Fernanda O. Novais, Ba Tiep Nguyen, Maurício T. Nascimento, Jamile Lago, Alexsandro S. Lago, Lucas P. Carvalho, Daniel P. Beiting, Phillip Scott
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0207451

Functional roles and redundancy of demersal Barents Sea fish: Ecological implications of environmental change
Cited by: 16
Author(s): Magnus Aune, Michaela Aschan, Michael Greenacre, Andrey V. Dolgov, Maria Fossheim, Raul Primicerio
Software Mentions: 11
Published: about 6 years ago

10.1128/mSphere.00481-19

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities
Cited by: 15
Author(s): Ryan B. Ghannam, Laura G. Schaerer, Timothy Butler, Stephen M. Techtmann
Software Mentions: 11
Published: over 4 years ago

10.3389/fmicb.2019.02291

Reduced Gut Microbiome Diversity and Metabolome Differences in Rhinoceros Species at Risk for Iron Overload Disorder
Cited by: 25
Author(s): Terri L. Roth, Alexandra D. Switzer, Miki Watanabe-Chailland, Elisabeth M. Bik, David A. Relman, Lindsey E. Romick-Rosendale, Nicholas J. Ollberding
Software Mentions: 11
Published: about 5 years ago

10.1002/ece3.7881

Conversion of rainforest into oil palm and rubber plantations affects the functional composition of litter and soil Collembola
Cited by: 4
Author(s): Winda Ika Susanti, Tamara Bartels, Valentyna Krashevska, Rahayu Widyastuti, Louis Deharveng, Stefan Scheu, Anton M. Potapov
Software Mentions: 11
Published: over 3 years ago

10.1098/rspb.2021.0616

Juvenile ecology drives adult morphology in two insect orders
Cited by: 4
Author(s): Peter T. Rühr, Thomas van de Kamp, Tomáš Faragó, Jörg U. Hammel, Fabian Wilde, Elena Borisova, Carina Edel, Melina Frenzel, Tilo Baumbach, Alexander Blanke
Software Mentions: 11
Published: over 3 years ago

10.1186/s40168-019-0658-x

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Cited by: 124
Author(s): Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Jesse Connell, Jung‐Jin Lee, Bryton Fett, Frederic D. Bushman, Kyle Bittinger
Software Mentions: 11
Published: over 5 years ago

10.3389/fpls.2020.588856

So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central Europe
Cited by: 16
Author(s): Andrea Melichárková, Marek Šlenker, Judita Zozomová‐Lihová, Katarína Skokanová, Barbora Šingliarová, Tatiana Kačmárová, Michaela Caboňová, Matúš Kempa, Gabriela Šrámková, Terezie Mandáková, Martin Lysák, Marek Svitok, Lenka Mártonfiová, Karol Marhold
Software Mentions: 11
Published: almost 4 years ago

10.3390/microorganisms8101619

Salt Marsh Elevation Drives Root Microbial Composition of the Native Invasive Grass Elytrigia atherica
Cited by: 6
Author(s): Edisa García Hernández, Elena Baraza, Christian Smit, Matty P. Berg, Joana Falcão Salles
Software Mentions: 11
Published: about 4 years ago

10.7717/peerj.4152

Population structure and phenotypic variation ofSclerotinia sclerotiorumfrom dry bean (Phaseolus vulgaris) in the United States
Cited by: 28
Author(s): Zhian N. Kamvar, Bimal S. Amaradasa, Rachana Jhala, Serena McCoy, James R. Steadman, Sydney E. Everhart
Software Mentions: 11
Published: almost 7 years ago

10.1371/journal.pone.0235283

Targeting the oral plaque microbiome with immobilized anti-biofilm peptides at tooth-restoration interfaces
Cited by: 18
Author(s): Dina G. Moussa, Conrado Aparicio
Software Mentions: 11
Published: over 4 years ago

10.1038/s41598-018-23518-9

The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ
Cited by: 47
Author(s): Na Wei, Tia‐Lynn Ashman
Software Mentions: 11
Published: over 6 years ago

10.3389/fmicb.2020.01391

Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland
Cited by: 31
Author(s): Tim Richter-Heitmann, Benjamin Hofner, Franz‐Sebastian Krah, Johannes Sikorski, Pia K. Wüst, Boyke Bunk, Sixing Huang, Kathleen M. Regan, Doreen Berner, Runa S. Boeddinghaus, Sven Marhan, Daniel Prati, Ellen Kandeler, Jörg Overmann, Michael W. Friedrich
Software Mentions: 11
Published: over 4 years ago

10.1371/journal.pone.0156825

Inundation and Fire Shape the Structure of Riparian Forests in the Pantanal, Brazil
Cited by: 32
Author(s): Wellinton de Sá Arruda, Jens Oldeland, Antônio Conceição Paranhos Filho, Arnildo Pott, Nicolay Leme da Cunha, Iria Hiromi Ishii, Geraldo Alves Damasceno
Software Mentions: 11
Published: over 8 years ago

10.3390/microorganisms8040550

Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering
Cited by: 22
Author(s): Micha Weil, Haitao Wang, Mia M. Bengtsson, Daniel Köhn, Anke Günther, Gerald Jurasinski, John Couwenberg, Wakene Negassa, Dominik Zak, Tim Urich
Software Mentions: 11
Published: over 4 years ago

10.3390/cancers12123800

Dynamics of Fecal Microbiota with and without Invasive Cervical Cancer and Its Application in Early Diagnosis
Cited by: 14
Author(s): Gi-Ung Kang, Da-Ryung Jung, Yoon Hee Lee, Se Young Jeon, Hyung Soo Han, Gun Oh Chong, Jae‐Ho Shin
Software Mentions: 11
Published: almost 4 years ago

10.1186/s40168-019-0714-6

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments
Cited by: 78
Author(s): Jiarui Chen, Shelby E. McIlroy, Anand Asundi, David M. Baker, Gianni Panagiotou
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-018-20825-z

Mosquito community influences West Nile virus seroprevalence in wild birds: implications for the risk of spillover into human populations
Cited by: 30
Author(s): Josué Martínez‐de la Puente, Martina Ferraguti, Santiago Ruíz, David Roiz, Francisco Rubio Llorente, Elisa Pérez‐Ramírez, Miguel Ángel Jiménez‐Clavero, Ramón C. Soriguer, Jordi Figuerola
Software Mentions: 11
Published: almost 7 years ago

10.1038/s41598-017-17728-w

Enclaves of genetic diversity resisted Inca impacts on population history
Cited by: 28
Author(s): Chiara Barbieri, José R. Sandoval, Jairo Valqui, Aviva Shimelman, Stefan Ziemendorff, Roland Schröder, Martin Geppert, Lutz Roewer, Russell D. Gray, Mark Stoneking, Ricardo Fujita, Paul Heggarty
Software Mentions: 11
Published: almost 7 years ago

10.3389/fmicb.2020.570985

Differently Pre-treated Rapeseed Meals Affect in vitro Swine Gut Microbiota Composition
Cited by: 8
Author(s): Long Cheng, S. de Vries, Koen Venema
Software Mentions: 11
Published: about 4 years ago

10.3389/fmicb.2018.02301

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach
Cited by: 38
Author(s): Wen Chen, Graham Wilkes, Izhar U. H. Khan, Katarina Pintar, Joseph P. Thomas, C. André Lévesque, Julie T. Chapados, Edward Topp, David R. Lapen
Software Mentions: 11
Published: about 6 years ago

10.1128/mSystems.00316-20

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
Cited by: 8
Author(s): Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia
Software Mentions: 11
Published: about 4 years ago

10.3389/fmicb.2021.633659

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast
Cited by: 14
Author(s): Maria Luis de Vilar Correia Brito Bôto, Catarina Magalhães, Rafaela Perdigão, Diogo A. M. Alexandrino, Joana P. Fernandes, Ana M. Bernabéu, Sandra Ramos, Maria F. Carvalho, Miguel Semedo, Julie LaRoche, C. Marisa R. Almeida, Ana P. Mucha
Software Mentions: 11
Published: over 3 years ago

10.1038/s42003-020-01166-y

Spatial patterns of microbial communities across surface waters of the Great Barrier Reef
Cited by: 28
Author(s): Pedro R. Frade, Bettina Glasl, Samuel A. Matthews, Camille Mellin, Ester Á. Serrão, Kennedy Wolfe, Peter J. Mumby, Nicole S. Webster, David G. Bourne
Software Mentions: 11
Published: over 4 years ago

10.1128/mSystems.00404-19

Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In Vitro
Cited by: 13
Author(s): Kaitlyn Oliphant, Kyla Cochrane, Kathleen Schroeter, Michelle Daigneault, Sandi Yen, Elena F. Verdú, Emma Allen‐Vercoe
Software Mentions: 11
Published: almost 5 years ago

10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: over 3 years ago

10.3390/microorganisms9081723

Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System
Cited by: 7
Author(s): Jacques Gonzalès, Justine Marchix, Laetitia Aymeric, Catherine Le Berre‐Scoul, Johanna Zoppi, Philippe Bordron, Marie Burel, Laetitia Davidovic, J. L. Richard, Alexandru Gaman, Florian Lejuste, Julie Z. Brouillet, Françoise Le Vacon, Samuel Chaffron, Marion Leboyer, Hélène Boudin, Michel Neunlist
Software Mentions: 10
Published: over 3 years ago

10.1038/s41396-021-00940-y

Locally adapted gut microbiomes mediate host stress tolerance
Cited by: 28
Author(s): Shira Houwenhuyse, Robby Stoks, Shinjini Mukherjee, Ellen Decaestecker
Software Mentions: 10
Published: over 3 years ago

10.1099/mgen.0.000552

Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen
Cited by: 6
Author(s): Josephine Grützke, Mayada Gwida, Carlus Deneke, Holger Brendebach, Michaela Projahn, Alexander Schattschneider, Dirk Hofreuter, Maged El-Ashker, Burkhard Malorny, Sascha Al Dahouk
Software Mentions: 10
Published: over 3 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

10.3390/microorganisms8121887

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function
Cited by: 13
Author(s): Laurin Christopher Gierse, Alexander Meene, Daniel Schultz, Theresa Schwaiger, Claudia Karte, Charlotte Schröder, Haitao Wang, Christine Wünsche, Karen Methling, Bernd Kreikemeyer, Stephan Fuchs, Jörg Bernhardt, Dörte Becher, Michael Lalk, Tim Urich, Katharina Riedel
Software Mentions: 10
Published: almost 4 years ago

10.1111/mec.15179

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem
Cited by: 25
Author(s): Elias Broman, Caroline Raymond, Christian Sommer, Jonas S. Gunnarsson, Simon Creer, Francisco J. A. Nascimento
Software Mentions: 10
Published: over 5 years ago

10.7717/peerj.10871

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula
Cited by: 2
Author(s): Anastasiia K. Kimeklis, Grigory Gladkov, Aleksei Zverev, Arina Kichko, Evgeny Andronov, E. I. Ergina, I. V. Kostenko
Software Mentions: 10
Published: almost 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/s41598-020-71663-x

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: about 4 years ago

10.3389/fmicb.2020.597745

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce
Cited by: 15
Author(s): Saskia Windisch, Loreen Sommermann, Doreen Babin, Soumitra Paul Chowdhury, Rita Grosch, Narges Moradtalab, Frank Walker, Birgit Höglinger, Abbas El‐Hasan, Wolfgang Armbruster, Joseph Nesme, Søren J. Sørensen, Ingo Schellenberg, Joerg Geistlinger, Kornelia Smalla, Michael Rothballer, Uwe Ludewig, Günter Neumann
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-020-60654-7

Pesticide pollution in freshwater paves the way for schistosomiasis transmission
Cited by: 25
Author(s): Jeremias Martin Becker, Akbar Ganatra, Faith Jebiwot Kandie, Lina Mühlbauer, Jörg Ahlheim, Werner Brack, Baldwyn Torto, Eric L. Agola, Francis McOdimba, Henner Hollert, Ulrike Fillinger, Matthias Liess
Software Mentions: 10
Published: over 4 years ago

10.3390/microorganisms9071487

Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
Cited by: 20
Author(s): Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja‐Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman‐Yassky, Tove Agner
Software Mentions: 10
Published: over 3 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

10.1038/s41598-017-09303-0

The impact of immigration on microbial community composition in full-scale anaerobic digesters
Cited by: 111
Author(s): Rasmus Hansen Kirkegaard, Simon Jon McIlroy, Jannie Munk Kristensen, Marta Nierychlo, Søren Michael Karst, Morten Simonsen Dueholm, Mads Albertsen, Per Halkjær Nielsen
Software Mentions: 10
Published: about 7 years ago

10.18632/aging.202174

Periodontitis in elderly patients with type 2 diabetes mellitus: impact on gut microbiota and systemic inflammation
Cited by: 18
Author(s): Jinyou Li, Haifeng Lü, Hengchao Wu, Shunmei Huang, Lufang Chen, Qifeng Gui, Wenjing Zhou, Yichen Yang, Yue Wu, Hua Zhang, Qin Zhang, Yunmei Yang
Software Mentions: 10
Published: almost 4 years ago

10.1186/s42523-021-00094-4

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales
Cited by: 23
Author(s): Connie A. Rojas, Santiago Ramírez‐Barahona, Kay E. Holekamp, Kevin R. Theis
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-021-03967-2

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R
Cited by: 7
Author(s): Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina Kechris, Miranda Kroehl
Software Mentions: 10
Published: almost 4 years ago

10.1111/eva.13143

Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus )
Cited by: 20
Author(s): Laura Benestan, Quentin Rougemont, Caroline Senay, Éric Normandeau, Éric Parent, Rick M. Rideout, Louis Bernatchez, Yvan Lambert, Céline Audet, Gérard Parent
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pbio.2005396

Gut microbiome transition across a lifestyle gradient in Himalaya
Cited by: 109
Author(s): Aashish R. Jha, Emily Davenport, Yoshina Gautam, Dinesh Bhandari, Sarmila Tandukar, Katharine M. Ng, Gabriela K. Fragiadakis, Susan Holmes, Guru Prasad Gautam, Jeff D. Leach, Jeevan Bahadur Sherchand, Carlos D. Bustamante, Justin L. Sonnenburg
Software Mentions: 10
Published: about 6 years ago

10.1186/s40168-021-01104-y

Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome
Cited by: 22
Author(s): Alexandra J. Roth‐Schulze, Megan A. S. Penno, Katrina Ngui, Helena Oakey, Esther Bandala‐Sanchez, Andrew C. Smith, Theo R. Allnutt, Rebecca L. Thomson, Peter Vuillermin, Maria E. Craig, William D. Rawlinson, Elizabeth A. Davis, Mark Harris, Georgia Soldatos, Peter Colman, John M. Wentworth, Aveni Haynes, Simon C. Barry, Richard Sinnott, Grant Morahan, Naiara G. Bediaga, Gordon K. Smyth, Anthony T. Papenfuss, Jennifer Couper, Leonard C. Harrison
Software Mentions: 10
Published: over 3 years ago

10.1186/s42523-019-0007-1

Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice
Cited by: 15
Author(s): Alireza Kashani, Asker Brejnrod, Chunyu Jin, Timo Kern, Andreas Nygaard Madsen, Louise Holm, Georg K. Gerber, Jens-Christian Holm, Torben Hansen, Birgitte Holst, Manimozhiyan Arumugam
Software Mentions: 10
Published: about 5 years ago

10.1186/s42523-020-00039-3

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata
Cited by: 20
Author(s): H. Pieter J. van Veelen, Joana Falcão Salles, Kevin D. Matson, Marco van der Velde, B. Irene Tieleman
Software Mentions: 10
Published: over 4 years ago

10.1186/s13073-021-00919-6

Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery
Cited by: 14
Author(s): Rima Chakaroun, Lucas Massier, Anna Heintz‐Buschart, Nedal Said, Jörg Fallmann, Alyce Crane, Tatjana Schütz, Arne Dietrich, Matthias Blüher, Michael Stümvoll, Niculina Musat, Peter Kovacs
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.11222

The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids
Cited by: 1
Author(s): Isaure Scavezzoni, Valentin Fischer
Software Mentions: 10
Published: over 3 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: almost 5 years ago

10.1186/s40168-020-00895-w

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota
Cited by: 32
Author(s): Shashank Gupta, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Xuanji Li, Martin Steen Mortensen, Jakob Russel, Urvish Trivedi, Morten Arendt Rasmussen, Jakob Stokholm, Hans Bisgaard, Søren J. Sørensen
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: over 3 years ago

10.1002/ece3.5599

Linking pollen foraging of megachilid bees to their nest bacterial microbiota
Cited by: 29
Author(s): Anna Voulgari‐Kokota, Markus J. Ankenbrand, Gudrun Grimmer, Ingolf Steffan‐Dewenter, Alexander Keller
Software Mentions: 10
Published: about 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

10.1186/s40168-019-0756-9

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling
Cited by: 174
Author(s): Jennifer E. Schmidt, Angela D. Kent, Vanessa Brisson, Amélie C. M. Gaudin
Software Mentions: 10
Published: about 5 years ago

10.3897/zookeys.1044.62340

Carabid beetle (Coleoptera, Carabidae) richness, diversity, and community structure in the understory of temporarily flooded and non-flooded Amazonian forests of Ecuador
Cited by: 2
Author(s): Kathryn N. Riley Peterson, Robert A. Browne, Terry L. Erwin
Software Mentions: 10
Published: over 3 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

10.1128/AEM.00880-20

Community Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy
Cited by: 7
Author(s): Alden C. Dirks, Randall D. Jackson
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0128124

Oceanographic Conditions Limit the Spread of a Marine Invader along Southern African Shores
Cited by: 57
Author(s): Jorge Assis, Mirta Zupan, Katy R. Nicastro, Gerardo I. Zardi, Christopher D. McQuaid, Ester Á. Serrão
Software Mentions: 10
Published: over 9 years ago

10.1534/g3.120.401309

CeMbio - TheCaenorhabditis elegansMicrobiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: about 4 years ago

10.3390/genes12040503

Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance
Cited by: 10
Author(s): Mathieu Anatole Tele Ayenan, Agyemang Danquah, Paterne A. Agre, Peter Hanson, Isaac Asante, Eric Danquah
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2021.643730

Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria
Cited by: 8
Author(s): Anneke Heins, Greta Reintjes, Rudolf Amann, Jens Harder
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-021-02337-8

Best practices on the differential expression analysis of multi-species RNA-seq
Cited by: 36
Author(s): Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol Shetty, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 3 years ago

10.1093/plankt/fbaa017

Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea
Cited by: 11
Author(s): Laura Käse, Alexandra Kraberg, Katja Metfies, Stefan Neuhaus, Pim Sprong, Bernhard M. Fuchs, Maarten Boersma, Karen Helen Wiltshire
Software Mentions: 10
Published: over 4 years ago

10.3389/fmicb.2021.642543

Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites
Cited by: 6
Author(s): Jorge Doña, Stephany Virrueta Herrera, Tommi Nyman, Mervi Kunnasranta, Kevin P. Johnson
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2021.657508

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas
Cited by: 3
Author(s): Fernando Igne Rocha, Thiago Gonçalves Ribeiro, Marcelo Antoniol Fontes, Stefan Schwab, Márcia Reed Rodrigues Coelho, J. F. Lumbreras, P. E. F. da Motta, W. G. Teixeira, James R. Cole, Ana Carolina Borsanelli, Iveraldo S. Dutra, Adina Howe, Aline Pacobahyba de Oliveira, Ederson da Conceição Jesus
Software Mentions: 10
Published: over 3 years ago

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