Ecosyste.ms: Papers

10.12688/f1000research.10443.1

ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
Cited by: 7
Author(s): Espen Mikal Robertsen, Hubert Denise, Alex L. Mitchell, Alex Bateman, Lars Ailo Bongo, Nils Peder Willassen
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41597-021-01015-5

Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement
Cited by: 20
Author(s): Daniel Roush, Ana Giraldo-Silva, Ferrán García-Pichel
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-019-50730-y

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability
Cited by: 22
Author(s): Océane Nicolitch, Maureen Feucherolles, Jean-Louis Churin, Laure Fauchery, M.-P. Turpault, Stéphane Uroz
Software Mentions: 3
Published: about 5 years ago

10.1186/s12934-019-1265-z

Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)
Cited by: 31
Author(s): Chaoqun Li, Beili Zhang, Xin Wang, Xionge Pi, X Wang, Huihui Zhou, Kangsen Mai, Gang He
Software Mentions: 3
Published: almost 5 years ago

10.1002/ece3.5676

Evidence for host effect on the intestinal microbiota of whitefish (<i>Coregonus</i> sp.) species pairs and their hybrids
Cited by: 22
Author(s): Maelle Sevellec, Martin Laporte, Alex Bernatchez, Nicolas Derôme, Louis Bernatchez
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0091092

Evidence of a Putative Deep Sea Specific Microbiome in Marine Sponges
Cited by: 55
Author(s): Jonathan Kennedy, Burkhardt Flemer, Stephen A. Jackson, John P. Morrissey, Fergal O’Gara, Alan D. W. Dobson
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2018.01192

Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources
Cited by: 24
Author(s): Paula B. Matheus Carnevali, Craig W. Herbold, K. P. Hand, John C. Priscu, Alison E. Murray
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2020.586050

The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial
Cited by: 13
Author(s): Robin Raveau, Joël Fontaine, Mohamed Hijri, Anissa Lounès-Hadj Sahraoui
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12866-020-01859-8

How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies
Cited by: 11
Author(s): Barbora Bendová, Jaroslav Piálek, Ľudovít Ďureje, Lucie Schmiedová, Dagmar Čížková, Jean‐François Martin, Jakub Kreisinger
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.536535

Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer
Cited by: 7
Author(s): Sean W. Mullin, Greg Wanger, Brittany R. Kruger, Joshua D. Sackett, Scott D. Hamilton-Brehm, R. Bhartia, Jan P. Amend, Duane P. Moser, Victoria J. Orphan
Software Mentions: 2
Published: about 4 years ago

10.3390/microorganisms9040877

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan
Cited by: 3
Author(s): Herón Navarrete-Euan, Zuemy Rodríguez-Escamilla, Ernesto Pérez‐Rueda, Karla S. Escalante-Herrera, Mario Alberto Martínez-Núñez
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-885

Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae
Cited by: 23
Author(s): Yuriy Rebets, Bogdan Tokovenko, Igor Lushchyk, Christian Rückert, Nestor Zaburannyi, Andreas Bechthold, Jörn Kalinowski, Andriy Luzhetskyy
Software Mentions: 2
Published: about 10 years ago

10.3389/fmicb.2015.00818

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression
Cited by: 24
Author(s): Jia Yi Har, Tim Helbig, Jae S. Lim, Samodha C. Fernando, Adam M. Reitzel, Kevin Penn, Janelle R. Thompson
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2017.01078

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms
Cited by: 15
Author(s): Adam Šťovíček, Ani Azatyan, M. I. M. Soares, Osnat Gillor
Software Mentions: 2
Published: over 7 years ago

10.3390/microorganisms7110518

Metagenomic Characterization Reveals Pronounced Seasonality in the Diversity and Structure of the Phyllosphere Bacterial Community in a Mediterranean Ecosystem
Cited by: 11
Author(s): Despoina Vokou, Savvas Genitsaris, Katerina Karamanoli, Katerina Vareli, Marina Zachari, Despoina Voggoli, Nikolaos Monokrousos, John M. Halley, Ioannis Sainis
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-020-07048-1

Multiple omics analysis reveals that high fiber diets promote gluconeogenesis and inhibit glycolysis in muscle
Cited by: 8
Author(s): Jianghong Wu, Yang Ding, Husile Gong, Yunxia Qi, Huichao Sun, Yongbin Liu, Yahong Liu, Qiu Xiao
Software Mentions: 2
Published: about 4 years ago

10.3390/genes12010070

The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure
Cited by: 10
Author(s): Lore Bulteel, Shira Houwenhuyse, Steven Declerck, Ellen Decaestecker
Software Mentions: 2
Published: almost 4 years ago

10.3390/microorganisms7090324

Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils
Cited by: 16
Author(s): Rajneesh Jaswal, Ashish Pathak, Ashvini Chauhan
Software Mentions: 2
Published: about 5 years ago

10.1038/srep18206

The impact of rearing environment on the development of gut microbiota in tilapia larvae
Cited by: 194
Author(s): Christos Giatsis, Detmer Sipkema, Hauke Smidt, Hans G.H.J. Heilig, Giulia Benvenuti, J.A.J. Verreth, Marc Verdegem
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep31802

Soil bacterial and fungal community dynamics in relation to Panax notoginseng death rate in a continuous cropping system
Cited by: 115
Author(s): Lixin Dong, Jiang Xu, Feng Gao, Xiwen Li, Shilin Chen
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-017-03487-1

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome
Cited by: 30
Author(s): Eugeni Belda, Boubacar Coulibaly, Abdrahamane Fofana, Abdoul Habib Béavogui, Sékou F. Traorè, Daryl M. Gohl, Kenneth D. Vernick, Michelle M. Riehle
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-05241-z

Effects of suspended sediments on the sponge holobiont with implications for dredging management
Cited by: 36
Author(s): Mari Carmen Pineda, Brian Strehlow, Miriam Sternel, Alan Duckworth, Ross Jones, Nicole S. Webster
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-23437-9

Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge
Cited by: 28
Author(s): Laureen Crouzet, Muriel Derrien, Claire Cherbuy, Sandra Plancade, Mélanie Foulon, Benjamin Chalin, Johan E. T. van Hylckama Vlieg, Gianfranco Grompone, Lionel Rigottier-Gois, Pascale Serror
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9051088

Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae
Cited by: 4
Author(s): Susana C. Arcos, Felipe Lira, Lee Robertson, Miguel Ángel González Rebollo, Noelia Carballeda-Sangiao, Isabel Sánchez‐Alonso, Laura Zamorano, Mercedes Careche, Yolanda Jiménez‐Ruiz, Ricardo Ramos, Carlos Lloréns, Miguel González‐Muñoz, Antonio Oliver, José Luis Martínez, Andrés Navas
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-40347-6

Intensity of Nosema ceranae infection is associated with specific honey bee gut bacteria and weakly associated with gut microbiome structure
Cited by: 62
Author(s): Andrey Rubanov, Kaleigh A. Russell, Jason A. Rothman, James C. Nieh, Quinn S. McFrederick
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-59771-0

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

10.1038/s41598-020-60362-2

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots
Cited by: 14
Author(s): Fei Ren, Yuguang Zhang, Hai Yu, Yong-An Zhang
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms9020437

Characterization of the Habitat- and Season-Independent Increase in Fungal Biomass Induced by the Invasive Giant Goldenrod and Its Impact on the Fungivorous Nematode Community
Cited by: 3
Author(s): Paula Harkes, Lisa J. M. van Heumen, S.J.J. van den Elsen, P.J.W. Mooijman, M.T.W. Vervoort, Gerrit Gort, M.H.M. Holterman, Joris J.M. van Steenbrugge, Casper W. Quist, J. Helder
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-70141-8

Influence of 16S rRNA target region on the outcome of microbiome studies in soil and saliva samples
Cited by: 20
Author(s): Ana Soriano‐Lerma, Virginia Pérez-Carrasco, M. Sánchez‐Marañón, Matilde Ortiz-González, Victoria Sánchez-Martín, J Gijón, José María Navarro-Marí, José A. García‐Salcedo, Miguel Soriano
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-74678-6

Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study
Cited by: 16
Author(s): Deborah Traversi, Ivana Rabbone, Giacomo Scaioli, Camilla Vallini, Giulia Carletto, Irene Racca, Ugo Ala, Marilena Durazzo, Alessandro Collo, Arianna Ferro, Deborah Carrera, Silvia Savastio, Francesco Cadario, Roberta Siliquini, Fránco Cerutti
Software Mentions: 2
Published: about 4 years ago

10.1186/s12866-018-1304-7

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing
Cited by: 57
Author(s): Morgane Mailhe, Davide Ricaboni, Véronique Vitton, Jean-Michel González, Dipankar Bachar, Grégory Dubourg, F. Cadoret, Caroline Robert, Jérémy Delerce, Anthony Levasseur, Pierre‐Edouard Fournier, Emmanouil Angelakis, Jean-Christophe Lagier, Didier Raoult
Software Mentions: 2
Published: about 6 years ago

10.3390/microorganisms9051027

Bioinformatics Analysis of Oral, Vaginal, and Rectal Microbial Profiles during Pregnancy: A Pilot Study on the Bacterial Co-Residence in Pregnant Women
Cited by: 5
Author(s): Megumi Fudaba, Toshikazu Kamiya, Daisuke Tachibana, Masayasu Koyama, Naoko Ohtani
Software Mentions: 2
Published: over 3 years ago

10.3390/s21072514

A Review of Recent Deep Learning Approaches in Human-Centered Machine Learning
Cited by: 36
Author(s): Tharindu Kaluarachchi, Andrew Reis, Suranga Nanayakkara
Software Mentions: 2
Published: over 3 years ago

10.1186/s12866-020-01747-1

Characterisation of the gut microbial community of rhesus macaques in high-altitude environments
Cited by: 23
Author(s): Yuhan Wu, Yongfang Yao, Meichen Dong, Tianrui Xia, Diyan Li, Meng Xie, Jiayun Wu, Anxiang Wen, Qin Wang, Guangxiang Zhu, Qingyong Ni, Mingwang Zhang, Hengyong Xu
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.02975-19

Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria
Cited by: 32
Author(s): Jimmy H. Saw, Takuro Nunoura, Miho Hirai, Yoshihiro Takaki, Rachel Parsons, Michelle L. Michelsen, Krista Longnecker, Elizabeth B. Kujawinski, Ramunas Stepanauskas, Zachary C. Landry, Craig A. Carlson, Stephen J. Giovannoni
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.00023-16

<i>Thermus</i> and the Pink Discoloration Defect in Cheese
Cited by: 67
Author(s): Lisa Quigley, Daniel J. O’Sullivan, David F.M. Daly, Órla O’Sullivan, Zuzana Burdíková, Rostislav Váňa, Tom Beresford, R. Paul Ross, Gerald F. Fitzgerald, P.L.H. McSweeney, Linda Giblin, Jeremiah J. Sheehan, Paul D. Cotter
Software Mentions: 2
Published: over 8 years ago

10.3390/v9030047

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater
Cited by: 17
Author(s): Flavia Flaviani, Declan C. Schroeder, Cecilia Balestreri, Joanna L. Schroeder, Karen Moore, Konrad Paszkiewicz, Maya C. Pfaff, Edward P. Rybicki
Software Mentions: 2
Published: over 7 years ago

10.1038/s41396-021-00903-3

Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps
Cited by: 8
Author(s): Dalton J. Leprich, Beverly E. Flood, Peter R. Schroedl, Elizabeth Ricci, Jeffery J. Marlow, Peter R. Girguis, Jake V. Bailey
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12866-020-01768-w

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site
Cited by: 8
Author(s): Christen L. Grettenberger, J. R. Havig, Trinity L. Hamilton
Software Mentions: 2
Published: over 4 years ago

10.1155/2020/5036959

The Composition of Gut Microbiota in Patients Bearing Hashimoto’s Thyroiditis with Euthyroidism and Hypothyroidism
Cited by: 28
Author(s): Simo Liu, Yingli An, Bin Cao, Rongxin Sun, Jing Ke, Dong Zhao
Software Mentions: 2
Published: about 4 years ago

10.1186/s13071-020-04491-7

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

10.1186/1753-6561-7-S7-S4

Better primer design for metagenomics applications by increasing taxonomic distinguishability
Cited by: 20
Author(s): Melita Jaric, Jonathan Segal, Eugenia Silva-Herzog, Lisa Schneper, Kalai Mathee, Giri Narasimhan
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12989-021-00400-7

Diesel exhaust particles alter the profile and function of the gut microbiota upon subchronic oral administration in mice
Cited by: 15
Author(s): Sybille van den Brûle, Margaux Rappe, Jérôme Ambroise, Caroline Bouzin, Chantal Dessy, Adrien Paquot, Giulio G. Muccioli, Dominique Lison
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.11757

Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey
Cited by: 7
Author(s): Babett Günther, Jean‐Marc Fromentin, Luisa Métral, Sophie Arnaud‐Haond
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.11888

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms
Cited by: 302
Author(s): Hanno Teeling, Bernhard M. Fuchs, Christin M. Bennke, Karen Krüger, Meghan Chafee, Lennart Kappelmann, Greta Reintjes, Jost Waldmann, Christian Quast, Frank Oliver Glöckner, Judith Lucas, Antje Wichels, Gunnar Gerdts, Karen Helen Wiltshire, Rudolf Amann
Software Mentions: 2
Published: over 8 years ago

10.1186/s12890-019-0981-9

Longitudinal profiling of gut microbiome among tuberculosis patients under anti-tuberculosis treatment in China: protocol of a prospective cohort study
Cited by: 1
Author(s): Wenpei Shi, Yi Hu, Xubin Zheng, Zhu Ning, Wu M, Fan Xia, Stefanie Prast‐Nielsen, Yue Hu, Biao Xu
Software Mentions: 2
Published: about 5 years ago

10.1186/s12917-020-02318-2

Bacterial fecal microbiota is only minimally affected by a standardized weight loss plan in obese cats
Cited by: 8
Author(s): Moran Tal, J. Scott Weese, Diego E. Gómez, Myriam Hesta, Jöerg M. Steiner, Adronie Verbrugghe
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.11926

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition
Cited by: 1
Author(s): Laura Leonard, Eoin L. Brodie, Kenneth H. Williams, Jonathan O. Sharp
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.2006035

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution
Cited by: 30
Author(s): Aude Gilabert, Thomas D. Otto, Gavin G. Rutledge, Blaise Franzon, Benjamin Ollomo, Céline Arnathau, Patrick Durand, Nancy Diamella Moukodoum, Alain-Prince Okouga, Barthélémy Ngoubangoye, Boris Makanga, Larson Boundenga, Christophe Paupy, François Renaud, Franck Prugnolle, Virginie Rougeron
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1009530

Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea
Cited by: 20
Author(s): Yinnan Mu, Chao Bian, Ruoyu Liu, Yuguang Wang, Guangming Shao, Jia Li, Ying Qiu, Tianliang He, Wanru Li, Jingqun Ao, Qiong Shi, Xinhua Chen
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0232742

Surface runoff alters cave microbial community structure and function
Cited by: 8
Author(s): Madison Davis, Marianna Messina, Giuseppe Nicolosi, Salvatore Petralia, Melvin D. Baker, Christiana K. S. Mayne, Chelsea M. Dinon, Christina J. Moss, Bogdan P. Onac, James R. Garey
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0209857

Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary
Cited by: 12
Author(s): Deepa Varkey, Sophie Mazard, Thomas C. Jeffries, David Hughes, Justin R. Seymour, Ian T. Paulsen, Martin Ostrowski
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0087624

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers
Cited by: 330
Author(s): Kenan Hadziavdic, Katrine Lekang, Anders Lanzén, Inge Jonassen, Eric M. Thompson, Christofer Troedsson
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0180859

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome
Cited by: 31
Author(s): Marion Engel, David Endesfelder, Brigitte Schloter-Hai, Susanne Kublik, Michael S. Granitsiotis, Pierà Boschetto, Mariarita Stendardo, Imre Barta, Balázs Döme, Jean‐François Deleuze, Anne Boland, Joachim Müller–Quernheim, Antje Prasse, Tobias Welte, Jens M. Hohlfeld, Deepak Subramanian, David Parr, Marta Gut, Timm Greulich, Andreas Rembert Koczulla, Adam Nowiński, Dorota Górecka, Dave Singh, Sumit Gupta, Christopher E. Brightling, Harald Hoffmann, Marion Frankenberger, Thomas P. Hofer, Dorothe Burggraf, Marion Heiß-Neumann, Loems Ziegler-Heitbrock, Michael Schloter, Wolfgang zu Castell
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0222501

Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale
Cited by: 31
Author(s): Sarah Goertz, Alexandre B. de Menezes, Richard J. Birtles, Jonathan Fenn, Ann Lowe, Andrew D. C. MacColl, Benoit Poulin, Stuart Young, Janette E. Bradley, Christopher H. Taylor
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0150181

Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study
Cited by: 20
Author(s): Katrina Callender, Suzanne Roy, Damase P. Khasa, Lyle G. Whyte, Charles W. Greer
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0222449

Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients
Cited by: 18
Author(s): Solveig Tangedal, Rune Nielsen, Marianne Aanerud, Louise Jeanette Pauline Persson, Harald G. Wiker, Per Bakke, Pieter S. Hiemstra, Tomas Mikal Eagan
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0148824

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection
Cited by: 85
Author(s): Vijay C. Antharam, Daniel C. McEwen, Timothy J. Garrett, Aaron T. Dossey, Eric C. Li, Andrew Kozlov, Zhubene Mesbah, Gary P. Wang
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0214273

Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome
Cited by: 11
Author(s): Boris Le Nevé, Muriel Derrien, Julien Tap, Rémi Brazeilles, Stéphanie Cools Portier, Denis Guyonnet, Lena Öhman, Stine Störsrud, Hans Törnblom, Magnus Simrén
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0154642

Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows
Cited by: 44
Author(s): Jitka Kašparovská, Martina Pecinkova, Kateřina Dadáková, Ludmila Křížová, Sylvie Hadrová, Matej Lexa, Jan Lochman, Tomáš Kašparovský
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0254227

Nitrogen and phosphorus losses by surface runoff and soil microbial communities in a paddy field with different irrigation and fertilization managements
Cited by: 8
Author(s): Limin Wang, Dongfeng Huang
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0138837

Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem
Cited by: 62
Author(s): Susana Rodriguez‐Marconi, Rodrigo De la Iglesia, Beatriz Dı́ez, Cássio A. Fonseca, Eduardo Hajdu, Nicole Trefault
Software Mentions: 2
Published: about 9 years ago

10.3390/biomedicines9091246

Oral Capsaicinoid Administration Alters the Plasma Endocannabinoidome and Fecal Microbiota of Reproductive-Aged Women Living with Overweight and Obesity
Cited by: 6
Author(s): Claudia Manca, Sébastien Lacroix, F. Pérusse, Nicolas Flamand, Yvon C. Chagnon, Vicky Drapeau, Angelo Tremblay, Vincenzo Di Marzo, Cristoforo Silvestri
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0090785

Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?
Cited by: 102
Author(s): Amy Apprill, Jooke Robbins, A. Murat Eren, Adam A. Pack, Julie Réveillaud, David K. Mattila, Michael J. Moore, Misty Niemeyer, Kathleen Moore, Tracy J. Mincer
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0047075

Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project
Cited by: 147
Author(s): Sean Conlan, Heidi H. Kong, Julia A. Segre
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0237975

A multi-omics approach to solving problems in plant disease ecology
Cited by: 43
Author(s): Sharifa G. Crandall, Kaitlin M. Gold, María del Mar Jiménez-Gasco, Camila C. Filgueiras, Denis S. Willett
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0036740

The Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips
Cited by: 85
Author(s): Daniël van der Lelie, Safiyh Taghavi, Sean McCorkle, Luen Luen Li, Stephanie Malfatti, Denise C. Monteleone, Bryon S. Donohoe, Shi You Ding, William S. Adney, Michael E. Himmel, Susannah G. Tringe
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0082705

New Insights into the Phylogeny and Molecular Classification of Nicotinamide Mononucleotide Deamidases
Cited by: 7
Author(s): Guiomar Sánchez-Carrón, Ana Belén Martínez-Moñino, Agustín Sola-Carvajal, Hideto Takami, Francisco García-Carmona, Álvaro Sánchez‐Ferrer
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0084210

Soil Bacterial Communities Respond to Mowing and Nutrient Addition in a Steppe Ecosystem
Cited by: 47
Author(s): Ximei Zhang, Quansheng Chen, Xingguo Han
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-018-2399-4

PQ, a new program for phylogeny reconstruction
Cited by: 0
Author(s): Dmitry Penzar, Mikhail Krivozubov, Sergei A. Spirin
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0226159

Low-diversity bacterial microbiota in Southern Ocean representatives of lanternfish genera Electrona, Protomyctophum and Gymnoscopelus (family Myctophidae)
Cited by: 10
Author(s): Alison Gallet, Philippe Koubbi, Nelly Léger, Mathilde Scheifler, Magdalena Ruiz‐Rodríguez, Marcelino T. Suzuki, Yves Desdevises, Sébastien Duperron
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-015-0858-8

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data
Cited by: 14
Author(s): Claudia Sala, Silvia Vitali, Enrico Giampieri, Ítalo Faria do Valle, Daniel Remondini, Paolo Garagnani, Matteo Bersanelli, Ettore Mosca, Luciano Milanesi, Gastone Castellani
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0035294

Novel Bacterial Taxa in the Human Microbiome
Cited by: 85
Author(s): Kristine M. Wylie, Rebecca Truty, Thomas J. Sharpton, Kathie A. Mihindukulasuriya, Yanjiao Zhou, Hongyu Gao, Erica Sodergren, George M. Weinstock, Katherine S. Pollard
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0163178

Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice
Cited by: 29
Author(s): Yoshiaki Ueda, Katharina Frindte, Claudia Knief, Md. Ashrafuzzaman, Michael Frei
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0211271

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon
Cited by: 19
Author(s): Pablo de Jesús Suárez-Moo, Andrew P. Vovides, M. Patrick Griffith, Francisco Barona‐Gómez, Angélica Cibrián-Jaramillo
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-11-317

Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences
Cited by: 32
Author(s): Amber Hartman, Sean Riddle, Timothy M. McPhillips, Bertram Ludäscher, Jonathan A. Eisen
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0063139

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome
Cited by: 169
Author(s): Kelvin Li, Monika Bihan, Barbara A. Methé
Software Mentions: 2
Published: over 11 years ago

10.3390/md19070397

Metabolomic Characterization of a cf. Neolyngbya Cyanobacterium from the South China Sea Reveals Wenchangamide A, a Lipopeptide with In Vitro Apoptotic Potential in Colon Cancer Cells
Cited by: 5
Author(s): Lijian Ding, Rinat Bar-Shalom, Dikla Aharonovich, Naoaki Kurisawa, Gaurav Patial, Shuang Li, Shan He, Xiaojun Yan, Arihiro Iwasaki, Kiyotake Suenaga, Cheng-Cong Zhu, Haixi Luo, Fuli Tian, Fuad Fares, C. Benjamin Naman, Tal Luzzatto-Knaan
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0184371

Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean
Cited by: 12
Author(s): P. Jackson Gainer, Helena L. Pound, Alyse A. Larkin, Gary R. LeCleir, Jennifer M. DeBruyn, Erik R. Zinser, Zackary I. Johnson, Steven W. Wilhelm
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0143795

Evolution of the Northern Rockweed, Fucus distichus, in a Regime of Glacial Cycling: Implications for Benthic Algal Phylogenetics
Cited by: 12
Author(s): Haywood Dail Laughinghouse, Kirsten M. Müller, Walter H. Adey, Yannick Lara, Reginald H.F. Young, Gabriel Johnson
Software Mentions: 2
Published: almost 9 years ago

10.1111/1751-7915.13622

Fish growth enhances microbial sulfur cycling in aquaculture pond sediments
Cited by: 16
Author(s): Keke Zhang, Xiaoming Zheng, Zhili He, Tony Yang, Longfei Shu, Fanshu Xiao, Yongjie Wu, Binhao Wang, Li Zhou, Pubo Chen, Qingyun Yan
Software Mentions: 2
Published: over 4 years ago

10.15252/emmm.201911917

Zinc inhibits lethal inflammatory shock by preventing microbe‐induced interferon signature in intestinal epithelium
Cited by: 11
Author(s): Jolien Souffriau, Steven Timmermans, Tineke Vanderhaeghen, Charlotte Wallaeys, Kelly Van Looveren, Lindsy Aelbrecht, Sylviane Dewaele, Jolien Vandewalle, Evy Goossens, Serge Verbanck, Filip Boyen, Melanie Eggermont, Lindsey De Commer, Riet De Rycke, Michiel De Bruyne, Raúl Y. Tito, Marlies Ballegeer, Sofie Vandevyver, Tiago Velho, Luís F. Moita, Tino Hochepied, Karolien De Bosscher, Jeroen Raes, Filip Van Immerseel, Rudi Beyaert, Claude Libert
Software Mentions: 2
Published: about 4 years ago

10.29219/fnr.v64.3672

Green tea leaf powder prevents dyslipidemia in high-fat diet-fed mice by modulating gut microbiota
Cited by: 26
Author(s): Jin Wang, Ping Li, Shuang Liu, Bowei Zhang, Yaozhong Hu, Hui Ma, Shuo Wang
Software Mentions: 2
Published: about 4 years ago

10.1099/mgen.0.000159

The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping
Cited by: 35
Author(s): Stefanie Lutz, Jenine McCutcheon, James B. McQuaid, Liane G. Benning
Software Mentions: 2
Published: over 6 years ago

10.3389/fbioe.2019.00010

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability
Cited by: 28
Author(s): Felipe Rodríguez Maza, Jonathan Maldonado, Javiera Vásquez-Dean, Dinka Mandaković, Alexis Gaete, Verónica Cambiazo, Maurício González
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40168-018-0575-4

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries
Cited by: 198
Author(s): Jacob S. Leiby, Kevin McCormick, Scott Sherrill-Mix, Erik L. Clarke, Lyanna R. Kessler, Louis J. Taylor, Casey E. Hofstaedter, Aoife M. Roche, Lisa M. Mattei, Kyle Bittinger, Michal A. Elovitz, Rita Leite, Samuel Parry, Frederic D. Bushman
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2017.00593

Microbial and Isotopic Evidence for Methane Cycling in Hydrocarbon-Containing Groundwater from the Pennsylvania Region
Cited by: 26
Author(s): Adrien Vigneron, Andrew N. Bishop, Eric Alsop, Kellie Hull, Ileana Rhodes, R. C. Hendricks, Ian M. Head, Nicolas Tsesmetzis
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.01985

Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository
Cited by: 45
Author(s): Alexey Safonov, Т. Л. Бабич, Д. Ш. Соколова, Denis S. Grouzdev, T. P. Tourova, А. Б. Полтараус, Еlena V. Zakharova, Alexander Y. Merkel, А. П. Новиков, Т. Н. Назина
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2018.01152

Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface
Cited by: 16
Author(s): Zachary C. Landry, Kevin L. Vergin, Christopher Mannenbach, Stephen Block, Yingjie Qiao, Paul C. Blainey, Craig A. Carlson, Stephen J. Giovannoni
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2017.01649

The Microbial Community Dynamics during the Vitex Honey Ripening Process in the Honeycomb
Cited by: 21
Author(s): Yue Wen, Lin Wang, Jin Yugan, Jinzhen Zhang, Lei Su, Xiaoling Zhang, Jinhui Zhou, Yi Li
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-016-0153-6

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
Cited by: 42
Author(s): Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J. Gregory Caporaso, Scott T. Kelley
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-019-0665-y

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data
Cited by: 68
Author(s): Krithika Arumugam, Caner Bağcı, Irina Bessarab, Sina Beier, Benjamin Buchfink, Anna Górska, Guanglei Qiu, Daniel H. Huson, Rohan B. H. Williams
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2015.00495

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time
Cited by: 26
Author(s): Cody S. Sheik, Emily Stevenson, Paul A. Den Uyl, Carli A. Arendt, S. Aciego, Gregory J. Dick
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2019.02978

Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish
Cited by: 23
Author(s): Chun-Ang Lian, Guoyong Yan, Junzhe Huang, Antoine Danchin, Yong Wang, Lisheng He
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2019.02296

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments
Cited by: 12
Author(s): Stefanie Böhnke, Katharina Saß, Giorgio Gonnella, Alexander Diehl, Charlotte Kleint, Wolfgang Bach, Rebecca Zitoun, Andrea Koschinsky, Daniela Indenbirken, Sylvia G. Sander, Stefan Kurtz, Mirjam Perner
Software Mentions: 2
Published: about 5 years ago

10.1186/s40168-021-01038-5

Urban wastewater bacterial communities assemble into seasonal steady states
Cited by: 27
Author(s): Emily Lou LaMartina, Aurash Mohaimani, Ryan J. Newton
Software Mentions: 2
Published: over 3 years ago

10.1186/s40168-016-0216-8

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease
Cited by: 121
Author(s): Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Andrew Nelson, Bashi̇r Abdulkadi̇r, Tom Skeath, Joseph F. Petrosino, John D. Perry, Janet Berrington, Stephen Cummings
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-015-2265-y

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
Cited by: 111
Author(s): Jarmo Ritari, Jarkko Salojärvi, Leo Lahti, Willem M. de Vos
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2013.00182

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities
Cited by: 37
Author(s): Barbara J. Campbell, Shawn W. Polson, Lisa Zeigler Allen, Shannon J. Williamson, Charles K. Lee, K. Eric Wommack, S. Craig Cary
Software Mentions: 2
Published: almost 12 years ago

10.3390/nu12010241

Gut Microbiota Modulation by Dietary Barley Malt Melanoidins
Cited by: 26
Author(s): Nesreen Aljahdali, Pascale Gadonna‐Widehem, Pauline M. Anton, Franck Carbonero
Software Mentions: 1
Published: almost 5 years ago