Ecosyste.ms: Papers

10.1186/s40168-021-01100-2

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Cited by: 31
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Hanne Mordhorst, Marianne Ifversen, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 18
Published: over 3 years ago

10.1371/journal.pone.0195112

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats
Cited by: 43
Author(s): Edna Chiang, Marian L. Schmidt, Michelle A. Berry, Bopaiah A. Biddanda, Ashley M. Burtner, Thomas H. Johengen, Danna Palladino, Vincent J. Denef
Software Mentions: 16
Published: over 6 years ago

10.1186/s40168-020-00914-w

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
Cited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.pone.0242060

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types
Cited by: 3
Author(s): Elizaveta V. Evdokimova, Grigory Gladkov, Natalya I. Kuzina, Е. А. Иванова, Anastasiia K. Kimeklis, Aleksei Zverev, Arina Kichko, Tatyana S. Aksenova, А. Г. Пинаев, Evgeny Andronov
Software Mentions: 14
Published: about 4 years ago

10.1186/s40168-018-0569-2

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
Cited by: 107
Author(s): Joshua P. Earl, Nithin D. Adappa, Jarosław Król, Archana Bhat, Sergey Balashov, Rachel Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich, Joshua Chang Mell
Software Mentions: 13
Published: about 6 years ago

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: about 8 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

10.1371/journal.pcbi.1005404

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: over 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

10.7717/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

10.1093/gigascience/giz146

Systematic processing of ribosomal RNA gene amplicon sequencing data
Cited by: 45
Author(s): Julien Tremblay, Étienne Yergeau
Software Mentions: 10
Published: almost 5 years ago

10.1007/s00253-021-11449-x

Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota
Cited by: 6
Author(s): Alice Checcucci, Diana Luise, Monica Marianna Modesto, Federico Correa, Paolo Bosi, Paola Mattarelli, Paolo Trevisi
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

10.1128/mSystems.00571-21

Pathogenic <i>Vibrio</i> Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Cited by: 11
Author(s): Rachel E. Diner, Drishti Kaul, Ariel Rabines, Hong Zheng, Joshua A. Steele, John F. Griffith, Andrew E. Allen
Software Mentions: 10
Published: about 3 years ago

10.1111/1462-2920.14870

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys
Cited by: 23
Author(s): Laura Weber, Patricia González‐Díaz, Maickel Armenteros, Víctor Manuel Ferrer, Fernando Bretos, Erich Bartels, Alyson E. Santoro, Amy Apprill
Software Mentions: 9
Published: almost 5 years ago

10.1186/s40168-020-00887-w

Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate
Cited by: 73
Author(s): Nguyen K. Nguyen, Edward C. Deehan, Zhengxiao Zhang, Mingliang Jin, Nami Baskota, María Elisa Pérez-Muñoz, Janis Cole, Yunus E. Tunçil, Benjamin Seethaler, Ting Wang, Martine Laville, Nathalie M. Delzenne, Stephan C. Bischoff, Bruce R. Hamaker, Inés Martínez, Dan Knights, Jeffrey A. Bakal, Carla M. Prado, Jens Walter
Software Mentions: 9
Published: over 4 years ago

10.1155/2019/3717239

Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean
Cited by: 9
Author(s): Franziska Wemheuer, Avril Jean Elisabeth von Hoyningen-Huene, Marion Pohlner, Julius Degenhardt, Bert Engelen, Rolf Daniel, Bernd Wemheuer
Software Mentions: 9
Published: over 5 years ago

10.1038/s41396-019-0546-1

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus)
Cited by: 29
Author(s): Corey C. Holt, Mark van der Giezen, Carly L. Daniels, Grant D. Stentiford, David Bass
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0217804

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons
Cited by: 12
Author(s): Kirsten Grond, Julie Perreau, Wesley T. Loo, A. James Spring, Colleen M. Cavanaugh, Sarah M. Hird
Software Mentions: 8
Published: over 5 years ago

10.1128/Spectrum.00536-21

Mild and Severe SARS-CoV-2 Infection Induces Respiratory and Intestinal Microbiome Changes in the K18-hACE2 Transgenic Mouse Model
Cited by: 16
Author(s): Brittany Seibert, C. Joaquín Cáceres, Stivalis Cárdenas-García, Silvia Carnaccini, Ginger Geiger, Daniela S. Rajão, Elizabeth A. Ottesen, Daniel R. Pérez
Software Mentions: 8
Published: about 3 years ago

10.1038/s41598-020-80840-x

Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil
Cited by: 7
Author(s): Luciana de Sousa Lopes, Lucas William Mendes, Jadson Emanuel Lopes Antunes, Louise Melo de Souza Oliveira, Vânia Maria Maciel Melo, Arthur Prudêncio de Araújo Pereira, Antônio Félix da Costa, José de Paula Oliveira, Cosme Rafael Martínez, Márcia do Vale Barreto Figueiredo, Ademir Sérgio Ferreira de Araújo
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41598-021-92658-2

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP
Cited by: 10
Author(s): Abhijeet Singh, Bettina Müller, Anna Schnürer
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2020.01045

Effects of Intra- and Interspecific Plant Density on Rhizosphere Bacterial Communities
Cited by: 23
Author(s): Andrea Cavalieri, Friedhelm Bak, Adriana M. García-Lemos, Jacob Weiner, Mette Haubjerg Nicolaisen, Ole Nybroe
Software Mentions: 8
Published: over 4 years ago

10.3390/microorganisms9091873

Nutrient Enrichment Predominantly Affects Low Diversity Microbiomes in a Marine Trophic Symbiosis between Algal Farming Fish and Corals
Cited by: 5
Author(s): Adriana Messyasz, Rebecca L. Maher, Sonora S. Meiling, Rebecca Vega Thurber
Software Mentions: 8
Published: about 3 years ago

10.3390/microorganisms8060798

Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data
Cited by: 8
Author(s): Xiu Jia, Francisco Dini‐Andreote, Joana Falcão Salles
Software Mentions: 7
Published: over 4 years ago

10.3389/fpls.2019.01313

A Bioinformatics Guide to Plant Microbiome Analysis
Cited by: 45
Author(s): Rares Calin Lucaciu, Claus Pelikan, Samuel M. Gerner, Christos Zioutis, Stephan Köstlbacher, Harald Marx, Craig W. Herbold, Hannes Schmidt, Thomas Rattei
Software Mentions: 7
Published: about 5 years ago

10.3390/microorganisms9030557

The Composition and Diversity of the Gut Microbiota in Children Is Modifiable by the Household Dogs: Impact of a Canine-Specific Probiotic
Cited by: 10
Author(s): Carlos Gómez-Gallego, Mira Forsgren, Marta Selma‐Royo, Merja Nermes, María Carmen Collado, Seppo Salminen, Shea Beasley, Erika Isolauri
Software Mentions: 7
Published: over 3 years ago

10.3389/fpls.2020.602645

Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products
Cited by: 11
Author(s): Vinício Oliosi Favero, Rita Hilário de Carvalho, Victória Monteiro da Motta, Ana Beatriz Carneiro Leite, Márcia Reed Rodrigues Coelho, Gustavo Ribeiro Xavier, Norma Gouvêa Rumjanek, Segundo Urquiaga
Software Mentions: 7
Published: almost 4 years ago

10.1093/bioinformatics/btaa177

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: over 4 years ago

10.1098/rsos.210035

Local versus site-level effects of algae on coral microbial communities
Cited by: 4
Author(s): Amy A. Briggs, A. L. Brown, Craig W. Osenberg
Software Mentions: 7
Published: about 3 years ago

10.3389/fmicb.2020.536978

Repetitive Sampling and Control Threshold Improve 16S rRNA Gene Sequencing Results From Produced Waters Associated With Hydraulically Fractured Shale
Cited by: 2
Author(s): Jennifer L. Shelton, Elliott P. Barnhart, Leslie F. Ruppert, Aaron M. Jubb, Madalyn S. Blondes, Christina A. DeVera
Software Mentions: 7
Published: about 4 years ago

10.1093/gigascience/giaa022

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
Cited by: 28
Author(s): Haris Zafeiropoulos, Ha Quoc Viet, Katerina Vasileiadou, Antonis Potirakis, Christos Arvanitidis, Pantelis Topalis, Christina Pavloudi, Evangelos Pafilis
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-021-93918-x

Probiotic supplementation reduces inflammatory profiles but does not prevent oral immune perturbations during SIV infection
Cited by: 4
Author(s): Rhianna Jones, Kyle Kroll, Courtney Broedlow, Luca Schifanella, Scott Smith, Brady Hueber, Spandan V. Shah, Daniel R. Ram, Cordelia Manickam, Valerie Varner, Nichole R. Klatt, R. Keith Reeves
Software Mentions: 7
Published: over 3 years ago

10.3390/vetsci6040093

Influence of Colostrum and Vitamins A, D3, and E on Early Intestinal Colonization of Neonatal Holstein Calves Infected with Mycobacterium avium subsp. paratuberculosis
Cited by: 3
Author(s): Judith R. Stabel, Lucas A. Krueger, Caitlin J. Jenvey, Taylor L. T. Wherry, Jesse M. Hostetter, Donald C. Beitz
Software Mentions: 7
Published: about 5 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single <i>Ctena orbiculata</i> (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2020.536932

Hatching of Globodera pallida Induced by Root Exudates Is Not Influenced by Soil Microbiota Composition
Cited by: 5
Author(s): Camille Gautier, Lisa Martinez, Sylvain Fournet, Josselin Montarry, Jean-Claude Yvin, Éric Nguema-Ona, Anne‐Yvonne Guillerm‐Erckelboudt, Christophe Piriou, Juliette Linglin, Christophe Mougel, Lionel Lebreton
Software Mentions: 7
Published: about 4 years ago

10.3389/fmicb.2020.610009

Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease
Cited by: 28
Author(s): Citlalli A Aquino, Ryan M Besemer, Christopher M. DeRito, Jan Kocian, Ian Porter, Peter T. Raimondi, Jordan E Rede, Lauren M. Schiebelhut, Jed P. Sparks, John P. Wares, Ian Hewson
Software Mentions: 6
Published: almost 4 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

10.1186/s40168-017-0314-2

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis
Cited by: 61
Author(s): Fiona Whelan, Michael G. Surette
Software Mentions: 6
Published: over 7 years ago

10.1098/rstb.2019.0255

Dormancy dynamics and dispersal contribute to soil microbiome resilience
Cited by: 34
Author(s): Jackson W Sorensen, Ashley Shade
Software Mentions: 6
Published: over 4 years ago

10.18632/aging.103168

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis
Cited by: 103
Author(s): Jianquan He, Shuaimei Xu, Bangzhou Zhang, Chuanxing Xiao, Zhangran Chen, Fuyou Si, Jifan Fu, Xiaobo Lin, Guohua Zheng, Guangchuang Yu, Jian Chen
Software Mentions: 6
Published: over 4 years ago

10.3390/microorganisms9020252

Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model
Cited by: 7
Author(s): Robert Valeris-Chacín, Amanda Sponheim, Eduardo Fano, Richard E. Isaacson, Randall S. Singer, Joel Nerem, Fernando Leite, Maria Pieters
Software Mentions: 6
Published: almost 4 years ago

10.1128/mSphere.01261-20

Predominance of Atopobium vaginae at Midtrimester: a Potential Indicator of Preterm Birth Risk in a Nigerian Cohort
Cited by: 13
Author(s): Nkechi Martina Odogwu, Jun Chen, Chinedum Amara Onebunne, Patricio Jeraldo, Lu Yang, Stephen Johnson, Funmilola A. Ayeni, Marina Walther-Antonio, Oladapo Olayemi, Nicholas Chia, Akinyinka Omigbodun
Software Mentions: 6
Published: over 3 years ago

10.1186/s12866-017-1103-6

Ciliate diversity and distribution patterns in the sediments of a seamount and adjacent abyssal plains in the tropical Western Pacific Ocean
Cited by: 12
Author(s): Feng Zhao, Sabine Filker, Thorsten Stoeck, Kuidong Xu
Software Mentions: 6
Published: about 7 years ago

10.1128/mSystems.00232-18

Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems
Cited by: 31
Author(s): Sara F. Paver, Daniel Muratore, Ryan J. Newton, Maureen L. Coleman
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0064212

Differential Response of the Cynomolgus Macaque Gut Microbiota to Shigella Infection
Cited by: 52
Author(s): Anna M. Seekatz, Aruna Panda, David A. Rasko, Franklin R. Toapanta, Emiley A. Eloe‐Fadrosh, Abdul Qayyum Khan, Zhenqiu Liu, Steven T. Shipley, Louis J. DeTolla, Marcelo B. Sztein, Claire M. Fraser
Software Mentions: 6
Published: over 11 years ago

10.3390/microorganisms8070982

Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural Starter
Cited by: 10
Author(s): Lucas von Gastrow, Marie‐Noëlle Madec, Victoria Chuat, S. Lubac, Clémence Morinière, Sébastien Lê, Sylvain Santoni, Delphine Sicard, Florence Valence
Software Mentions: 6
Published: over 4 years ago

10.1186/s42523-020-00057-1

Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics
Cited by: 12
Author(s): Amy M. Van Cise, Paul R. Wade, Caroline E. C. Goertz, Kathleen A. Burek‐Huntington, Kim M. Parsons, Tonya M. Clauss, Roderick C. Hobbs, Amy Apprill
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-018-25450-4

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare
Cited by: 34
Author(s): Jessica Dittmer, Didier Bouchon
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0195534

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis
Cited by: 34
Author(s): Daniel Hagenfeld, Raphael Koch, Sebastian Jünemann, Karola Prior, Inga Harks, Peter Eickholz, Thomas Hoffmann, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Benjamin Ehmke, Dag Harmsen
Software Mentions: 6
Published: over 6 years ago

10.1111/1462-2920.14862

Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry
Cited by: 31
Author(s): Sara F. Paver, Ryan J. Newton, Maureen L. Coleman
Software Mentions: 5
Published: almost 5 years ago

10.1111/1462-2920.15484

Effect of salinity on cable bacteria species composition and diversity
Cited by: 19
Author(s): Ann‐Sofie Dam, Ian P. G. Marshall, Nils Risgaard‐Petersen, Laurine D. W. Burdorf, Ugo Marzocchi
Software Mentions: 5
Published: over 3 years ago

10.3389/fvets.2021.654927

Association of Broiler Litter Microbiome Composition and Campylobacter Isolation
Cited by: 7
Author(s): Robert Valeris-Chacín, Maria Pieters, Hyun Seok Hwang, Timothy J. Johnson, Randall S. Singer
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.00993

The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse
Cited by: 33
Author(s): Rose Kantor, Scott Miller, Kara L. Nelson
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2021.636405

Impact of Rocky Desertification Control on Soil Bacterial Community in Karst Graben Basin, Southwestern China
Cited by: 15
Author(s): Qiang Liu, Ang Song, Hui Yang, Wernér E.G. Müller
Software Mentions: 5
Published: over 3 years ago

10.1038/s41396-020-0625-3

Microbial symbionts and ecological divergence of Caribbean sponges: A new perspective on an ancient association
Cited by: 22
Author(s): Christopher Freeman, Cole G. Easson, Kenan O. Matterson, Robert Thacker, David M. Baker, Valerie J. Paul
Software Mentions: 5
Published: over 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

10.1186/s40168-020-00959-x

Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth
Cited by: 21
Author(s): Alexander Mahnert, Cyprien Verseux, Petra Schwendner, Kaisa Koskinen, Christina Kumpitsch, Marcus Blohs, Lisa Wink, Daniela Brunner, Theodora Goessler, Daniela Billi, Christine Moissl-Eichinger
Software Mentions: 5
Published: almost 4 years ago

10.1128/mSystems.00377-20

Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics
Cited by: 21
Author(s): Alexander Zaborin, Beatriz Peñalver Bernabé, Robert Keskey, Naseer Sangwan, Sanjiv Hyoju, Neil Gottel, Jack A. Gilbert, Olga Zaborina, John C. Alverdy
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2019.02118

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)
Cited by: 20
Author(s): Elizabeth M. Reinhart, Benjamin J. Korry, Aislinn D. Rowan-Nash, Peter Belenky
Software Mentions: 5
Published: about 5 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

10.3390/life11030246

Postoperative Complications Are Associated with Long-Term Changes in the Gut Microbiota Following Colorectal Cancer Surgery
Cited by: 7
Author(s): Felix C. F. Schmitt, Martin Schneider, William Mathejczyk, Markus A. Weigand, Jane C. Figueiredo, Christopher I. Li, David Shibata, Erin M. Siegel, Adetunji T. Toriola, Cornelia M. Ulrich, Alexis Ulrich, Sébastien Boutin, Biljana Gigic
Software Mentions: 5
Published: over 3 years ago

10.1128/mSystems.00093-19

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry
Cited by: 14
Author(s): Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon, Willem Waegeman, Vincent J. Denef
Software Mentions: 5
Published: about 5 years ago

10.1128/mSystems.00954-20

Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater
Cited by: 4
Author(s): Elizabeth A. Monaghan, Kelle C. Freel, Michael S. Rappé
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0089323

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
Cited by: 60
Author(s): Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu, Kang Ning
Software Mentions: 5
Published: over 10 years ago

10.3389/fmicb.2020.01110

Dietary Soluble and Insoluble Fiber With or Without Enzymes Altered the Intestinal Microbiota in Weaned Pigs Challenged With Enterotoxigenic E. coli F18
Cited by: 28
Author(s): Qingyun Li, Xiyu Peng, Eric Burrough, Orhan Şahin, Stacie A Gould, Nicholas K. Gabler, Crystal L. Loving, Karin S. Dorman, John F. Patience
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00003-15

Open-Source Sequence Clustering Methods Improve the State Of the Art
Cited by: 139
Author(s): Evguenia Kopylova, José A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Zhou Hong, Torbjørn Rognes, J. Gregory Caporaso, Rob Knight
Software Mentions: 5
Published: over 8 years ago

10.3390/microorganisms9050981

The Responses to Long-Term Water Addition of Soil Bacterial, Archaeal, and Fungal Communities in a Desert Ecosystem
Cited by: 5
Author(s): Ying Gao, Xiaotian Xu, Jingtao Ding, Fang Bao, Yashika G. De Costa, Wei-Qin Zhuang, Bo Wu
Software Mentions: 5
Published: over 3 years ago

10.1186/s42523-021-00104-5

Vertically transmitted microbiome protects eggs from fungal infection and egg failure
Cited by: 13
Author(s): Marie Bunker, Greg Elliott, H. Heyer-Gray, Michael R. Martin, A. Elizabeth Arnold, Stacey L. Weiss
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms9030606

Disproportionate CH4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community
Cited by: 1
Author(s): Marshall D. McDaniel, Marcela Hernández, Marc G. Dumont, Lachlan J. Ingram, Mark A. Adams
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-021-01037-6

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis
Cited by: 15
Author(s): Jessica Dittmer, Robert M. Brucker
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-90489-9

Auxiliary rapid identification of pathogenic and antagonistic microorganisms associated with Coptis chinensis root rot by high-throughput sequencing
Cited by: 7
Author(s): Hailang Liao, Ling Huang, Na Li, Wenjia Ke, Yiqing Xiang, Yuntong Ma
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2019.02999

Opioids Impair Intestinal Epithelial Repair in HIV-Infected Humanized Mice
Cited by: 37
Author(s): Jingjing Meng, Santanu Banerjee, Li Zhang, Gregory M. Sindberg, Shamsudheen Moidunny, Bin Li, David J. Robbins, Mohit Girotra, Bradley J. Segura, Sundaram Ramakrishnan, Sabita Roy
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-80557-x

Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)
Cited by: 33
Author(s): Esteban Góngora, Kyle H. Elliott, Lyle G. Whyte
Software Mentions: 5
Published: almost 4 years ago

10.3389/fcimb.2020.588155

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease
Cited by: 14
Author(s): Kai Bao, Xiaofei Li, Lucy Poveda, Weihong Qi, Nathalie Selevsek, Pınar Gümüş, Gülnur Emingil, Jonas Grossmann, Patricia I. Diaz, George Hajishengallis, Nagihan Bostancı, Georgios N. Belibasakis
Software Mentions: 5
Published: about 4 years ago

10.1186/s42523-020-00058-0

Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides
Cited by: 1
Author(s): Bianca R. P. Brown, Joaquin C. B. Nunez, David M. Rand
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-021-83524-2

Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures
Cited by: 37
Author(s): Shashank Gupta, Malini Shariff, Gaura Chaturvedi, Arpit Sharma, Nitin Goel, Monika Yadav, Martin Steen Mortensen, Søren J. Sørensen, Mitali Mukerji, Nar Singh Chauhan
Software Mentions: 5
Published: almost 4 years ago

10.1186/s40168-018-0430-7

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore
Cited by: 41
Author(s): Angélique Gobet, Laëtitia Mest, Morgan Perennou, Simon M. Dittami, Claire Caralp, Céline Coulombet, Sylvain Huchette, Sabine Roussel, Gurvan Michel, Catherine Leblanc
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-69672-x

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota
Cited by: 39
Author(s): Rodrigo Alegria Terrazas, Katharin Balbirnie-Cumming, Jenny Morris, Pete E. Hedley, Joanne Russell, Eric Paterson, Elizabeth M. Baggs, Eyal Fridman, Davide Bulgarelli
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0208917

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes
Cited by: 6
Author(s): Kara Tinker, Elizabeth A. Ottesen
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-017-11244-7

Methanogens predominate in natural corrosion protective layers on metal sheet piles
Cited by: 34
Author(s): Nardy Kip, Stefan Jansen, Márcio Fernandes Alves Leite, Mattias de Hollander, M. Afanasyev, Eiko E. Kuramae, Johannes A. van Veen
Software Mentions: 5
Published: about 7 years ago

10.3390/microorganisms8060906

Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature
Cited by: 23
Author(s): Francisco Luis Massello, Chia Sing Chan, Kok Gan Chan, Kian Mau Goh, Edgardo R. Donati, María Sofía Urbieta
Software Mentions: 5
Published: over 4 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: almost 7 years ago

10.1371/journal.pone.0215797

Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed
Cited by: 12
Author(s): Suzanne L. Ishaq, Medora Lachman, B.A. Wenner, Amy Baeza, Molly Butler, Emily A. Gates, Sarah K. Olivo, Julie Buono Geddes, P. G. Hatfield, Carl J. Yeoman
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-459

Structured RNAs and synteny regions in the pig genome
Cited by: 19
Author(s): Christian Anthon, Hakim Tafer, Jakob Hull Havgaard, Bo Thomsen, Jakob Hedegaard, Stefan E. Seemann, Sachin Pundhir, Stephanie Kehr, Sebastian Bartschat, Marie Konge Nielsen, Rasmus Oestergaard Nielsen, Merete Fredholm, Peter F. Stadler, Jan Gorodkin
Software Mentions: 5
Published: over 10 years ago

10.3389/fmicb.2019.01427

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
Cited by: 11
Author(s): Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe‐Fadrosh, Paul Dijkstra, Brian P. Hedlund
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0244341

Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children
Cited by: 9
Author(s): Christine Niemeier‐Walsh, Patrick Ryan, Jarosław Meller, Nicholas J. Ollberding, Atin Adhikari, Tiina Reponen
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-94761-w

Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica
Cited by: 3
Author(s): Lavinia Iancu, Iulia Roxana Angelescu, Victoria Ioana Paun, Carlos Henríquez‐Castillo, Paris Lavín, Cristina Purcărea
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.1758

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon
Cited by: 7
Author(s): Florent E. Angly, Olga Pantos, Thomas C. Morgan, V. I. Rich, Hemerson Tonin, David G. Bourne, Philip Mercurio, Andrew P. Negri, Gene W. Tyson
Software Mentions: 4
Published: over 8 years ago

10.3390/biom11091286

Lipocalin 2 Deficiency Restrains Aging-Related Reshaping of Gut Microbiota Structure and Metabolism
Cited by: 2
Author(s): Xing‐Biao Qiu, Chi Chen, Xiaoli Chen
Software Mentions: 4
Published: about 3 years ago

10.1186/s40104-020-00459-w

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens
Cited by: 33
Author(s): Joel J. Maki, Elizabeth Bobeck, Matthew J. Sylte, Torey Looft
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-018-4457-8

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon
Cited by: 10
Author(s): Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 4
Published: over 6 years ago

10.6026/97320630016567

Bacterial community dynamics with rhizosphere of Calotropis procera and Senna alexandrina desert plants in Saudi Arabia
Cited by: 4
Author(s): Diana A. Al-Quwaie
Software Mentions: 4
Published: about 4 years ago

10.1093/bioinformatics/btaa1096

MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes
Cited by: 8
Author(s): Maria K. Sobczyk, Tom R. Gaunt, Lavinia Paternoster
Software Mentions: 4
Published: almost 4 years ago

10.1093/bioinformatics/bty767

Methods for automatic reference trees and multilevel phylogenetic placement
Cited by: 35
Author(s): Lucas Czech, Pierre Barbera, Alexandros Stamatakis
Software Mentions: 4
Published: about 6 years ago

10.1016/j.wroa.2020.100056

Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households
Cited by: 5
Author(s): Erica R. Fuhrmeister, Ayşe Ercümen, Jessica A. Grembi, Mahfuza Islam, Amy J. Pickering, Kara L. Nelson
Software Mentions: 4
Published: almost 4 years ago

10.1111/1462-2920.13706

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir
Cited by: 21
Author(s): A. J. Freedman, BoonFei Tan, Janelle R. Thompson
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2019.00169

Biogeographic Patterns and Assembly Mechanisms of Bacterial Communities Differ Between Habitat Generalists and Specialists Across Elevational Gradients
Cited by: 43
Author(s): Luo Zhengming, Jinxian Liu, Pengyu Zhao, Tong Jia, Cui Li, Bo Chai
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.6403

Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean
Cited by: 28
Author(s): Masao Higo, Yuya Tatewaki, Kento Gunji, Akari Kaseda, Katsunori Isobe
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2019.00170

Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater
Cited by: 18
Author(s): Florian Trigodet, Nicolas Larché, Hilary G. Morrison, Mohamed Jebbar, Dominique Thierry, Loïs Maignien
Software Mentions: 4
Published: almost 6 years ago