Ecosyste.ms: Papers

10.1371/journal.pone.0243241

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
Cited by: 15
Author(s): Sebastian Hupfauf, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandòn, Heribert Insam, Sabine Marie Podmirseg
Software Mentions: 13
Published: almost 4 years ago

10.3390/microorganisms9010092

Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems
Cited by: 23
Author(s): Joel F. Swift, Megan E. Hall, Zachary N. Harris, Misha T. Kwasniewski, Allison J. Miller
Software Mentions: 13
Published: over 3 years ago

10.1186/s40168-020-00861-6

Reservoirs of antimicrobial resistance genes in retail raw milk
Cited by: 41
Author(s): Jinxin Liu, Yongxu Zhu, Michele Jay-Russell, Danielle G. Lemay, David A. Mills
Software Mentions: 13
Published: about 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

10.1038/s41396-020-00862-1

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

10.1186/s40168-021-01089-8

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
Cited by: 28
Author(s): Alexander S. F. Berry, Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, Kevin T. O’Brien, Ying Chen, Samuel Murray, Lydia A. Ramharack, Robert N. Baldassano, Thomas D. Parsons, Daniel P. Beiting
Software Mentions: 9
Published: about 3 years ago

10.3389/fpls.2019.00910

Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms
Cited by: 57
Author(s): Giovanni Del Frari, Alex Gobbi, Marie Rønne Aggerbeck, Helena Oliveira, Lars Hestbjerg Hansen, Ricardo B. Ferreira
Software Mentions: 9
Published: about 5 years ago

10.7717/peerj.9017

Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon
Cited by: 10
Author(s): Jake Ivan P. Baquiran, Michael Angelou L. Nada, Niño Posadas, Dana P. Manogan, Patrick C. Cabaitan, Cecilia Conaco
Software Mentions: 9
Published: over 4 years ago

10.1111/mec.15735

Phylogenetic and geographical analysis of a retrovirus during the early stages of endogenous adaptation and exogenous spread in a new host
Cited by: 11
Author(s): Bonnie Chaban, Faye Wedrowicz, Fiona Hogan, Peter Timms
Software Mentions: 9
Published: over 3 years ago

10.3389/fmicb.2020.556793

Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt
Cited by: 3
Author(s): Antonios Michas, Mourad Harir, Marianna Lucio, Gisle Vestergaard, Anne M. Himmelberg, Philippe Schmitt‐Kopplin, Tillmann Lueders, Dimitris G. Hatzinikolaou, Anne Schöler, Ralf Rabus, Michael Schloter
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-021-92648-4

Transmitting silks of maize have a complex and dynamic microbiome
Cited by: 5
Author(s): Eman M. Khalaf, Anuja Shrestha, Jeffrey Rinne, Michael D. J. Lynch, Charles Shearer, Victor Limay-Rios, L. M. Reid, Manish N. Raizada
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pone.0231875

Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador
Cited by: 10
Author(s): M. V. Rao, Robert A. Rice, Robert C. Fleischer, Carly R. Muletz‐Wolz
Software Mentions: 8
Published: over 4 years ago

10.1002/ece3.6305

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

10.1111/mec.14860

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
Cited by: 43
Author(s): Robert Hooper, Jaelle C. Brealey, Tom van der Valk, Antton Alberdi, John W. Durban, Holly Fearnbach, Kelly M. Robertson, Robin W. Baird, M. Bradley Hanson, Paul R. Wade, M. Thomas P. Gilbert, Phillip A. Morin, Jochen B. W. Wolf, Andrew D. Foote, Katerina Guschanski
Software Mentions: 7
Published: almost 6 years ago

10.1128/mBio.03396-20

Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes
Cited by: 21
Author(s): Rozlyn C.T. Boutin, Hind Sbihi, Ryan J. McLaughlin, Aria S. Hahn, Kishori M. Konwar, Rachelle Loo, Darlene Dai, Charisse Petersen, Fiona S. L. Brinkman, Geoffrey L. Winsor, Malcolm R. Sears, Theo J. Moraes, Allan B. Becker, Meghan B. Azad, Piush J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 7
Published: about 3 years ago

10.1002/1873-3468.13278

The gut microbiome participates in transgenerational inheritance of low‐temperature responses in <i>Drosophila melanogaster</i>
Cited by: 23
Author(s): Aman Zare, Anna-Mia Johansson, Edvin Karlsson, Nicolas Delhomme, Per Stenberg
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0255012

Hierarchical modelling of immunoglobulin coated bacteria in dogs with chronic enteropathy shows reduction in coating with disease remission but marked inter-individual and treatment-response variability
Cited by: 0
Author(s): Lina María Martínez-López, Alexis Perez‐Gonzalez, Elizabeth A. Washington, Andrew Woodward, Alexandra J. Roth‐Schulze, Julien Dandrieux, Thurid Johnstone, Nathalee Prakash, Aaron R. Jex, Caroline Mansfield
Software Mentions: 7
Published: about 3 years ago

10.1111/mec.13891

Genomic epidemiology of <i>Cryptococcus</i> yeasts identifies adaptation to environmental niches underpinning infection across an African <scp>HIV</scp>/<scp>AIDS</scp> cohort
Cited by: 51
Author(s): Mathieu Vanhove, Mathew A. Beale, Johanna Rhodes, Duncan Chanda, Shabir Lakhi, Geoffrey Kwenda, Síle F. Molloy, Natasha Karunaharan, Neil Stone, Thomas S. Harrison, Tihana Bicanic, Matthew C. Fisher
Software Mentions: 7
Published: almost 8 years ago

10.3389/fmicb.2018.02364

Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking
Cited by: 16
Author(s): Moa Hägglund, Stina Bäckman, Anna Macellaro, Petter Lindgren, Emmy Borgmästars, Karin Jacobsson, Rikard Dryselius, Per Stenberg, Andreas Sjödin, Mats Forsman, Jon Ahlinder
Software Mentions: 6
Published: almost 6 years ago

10.3390/ijms22115981

Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract
Cited by: 8
Author(s): Adrian Low, Melissa Soh, Sou Miyake, Vanessa Zhi Jie Aw, Jian Feng, Adeline Wong, Henning Seedorf
Software Mentions: 6
Published: over 3 years ago

10.3389/fvets.2021.664318

Longitudinal Survey of Fecal Microbiota in Healthy Dogs Administered a Commercial Probiotic
Cited by: 3
Author(s): Susan Ciaravolo, Lina María Martínez-López, Richard Allcock, Andrew Woodward, Caroline Mansfield
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-021-86100-w

Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
Cited by: 11
Author(s): Andrew G. Farrer, Sterling L. Wright, Emily Skelly, Raphael Eisenhofer, Keith Dobney, Laura S. Weyrich
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-020-00809-w

Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases
Cited by: 15
Author(s): Eden Zhang, L Thibaut, Aleks Terauds, Mark Raven, Mark M. Tanaka, Josie van Dorst, Sin Yin Wong, Sally Crane, Belinda C. Ferrari
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2016.00563

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
Cited by: 21
Author(s): Jeffrey J. Marlow, Connor T. Skennerton, Li Zhou, Karuna Chourey, Robert L. Hettich, Chongle Pan, Victoria J. Orphan
Software Mentions: 6
Published: over 8 years ago

10.3390/nu13092983

Supplementation of 1-Kestose Modulates the Gut Microbiota Composition to Ameliorate Glucose Metabolism in Obesity-Prone Hosts
Cited by: 10
Author(s): Ayako Watanabe, Takumi Tochio, Yasuhiro Kadota, Motoki Takahashi, Yasuyuki Kitaura, H. Ishikawa, Takanori Yasutake, Masahiro Nakano, Hiroe Shinohara, Toru Kudo, Yuichiro Nishimoto, Yoshinori Mizuguchi, Akihito Endo, Yoshiharu Shimomura
Software Mentions: 6
Published: about 3 years ago

10.3389/fmicb.2019.01347

Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture
Cited by: 194
Author(s): Chrats Melkonian, Willi Gottstein, Sonja Blasche, Yongkyu Kim, Martin Abel-Kistrup, Hentie Swiegers, Sofie Saerens, Nathalia Edwards, Kiran R. Patil, Bas Teusink, Douwe Molenaar
Software Mentions: 6
Published: about 5 years ago

10.3390/ani10112020

Vaginal Microbiota Is Stable throughout the Estrous Cycle in Arabian Mares
Cited by: 19
Author(s): Marta Barba, Rebeca Martínez-Boví, J.J. Quereda, M. L. Mocé, María Plaza-Dávila, E. Jiménez-Trigos, Ángel Gómez-Martín, Pedro González-Torres, Belén Carbonetto, E. García-Roselló
Software Mentions: 5
Published: almost 4 years ago

10.3389/fpls.2020.00203

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar
Cited by: 19
Author(s): Andrea Firrincieli, Mahsa Khorasani, A. Carolin Frank, Sharon L. Doty
Software Mentions: 5
Published: over 4 years ago

10.3389/fvets.2020.00371

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers
Cited by: 29
Author(s): J.J. Quereda, Marta Barba, M. L. Mocé, J. Gomis, E. Jiménez-Trigos, Ángel García-Muñoz, Ángel Gómez-Martín, Pedro González-Torres, Belén Carbonetto, E. García-Roselló
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-021-02401-3

Detection of cell-free microbial DNA using a contaminant-controlled analysis framework
Cited by: 18
Author(s): Enrique Zozaya‐Valdés, Stephen Q. Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T. Papenfuss, Shahneen Sandhu, Mark A. Dawson, Sarah‐Jane Dawson
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.ppat.1009487

Lipocalin 2 modulates dendritic cell activity and shapes immunity to influenza in a microbiome dependent manner
Cited by: 6
Author(s): Martin L. Watzenboeck, Barbara Drobits, Sophie Zahalka, Anna-Dorothea Gorki, Asma Farhat, Federica Quattrone, Anastasiya Hladik, Karin Lakovits, Gabriel Richard, Therese Lederer, Birgit Strobl, Gijs A. Versteeg, Louis Boon, Philipp Starkl, Sylvia Knapp
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-72460-2

Dental black plaque: metagenomic characterization and comparative analysis with white-plaque
Cited by: 4
Author(s): Verónica Veses, Pedro González-Torres, Belén Carbonetto, MÂa del Mar Jovani-Sancho, Raquel González-Martínez, Isidoro Cortell-Ballester, Chirag C. Sheth
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-64393-7

Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study
Cited by: 13
Author(s): Manuela de Oliveira Ramalho, Christophe Duplais, Jérôme Orivel, Alain Déjean, Joshua C. Gibson, Andrew V. Suarez, Corrie S. Moreau
Software Mentions: 5
Published: over 4 years ago

10.1186/s42523-021-00074-8

Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)
Cited by: 10
Author(s): Sesilje Weiss, David A. Taggart, Ian Smith, Kristofer M. Helgen, Raphael Eisenhofer
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms8060875

Recovery of Vaginal Microbiota after Standard Treatment for Bacterial Vaginosis Infection: An Observational Study
Cited by: 16
Author(s): Liisa Lehtoranta, Ashley A. Hibberd, Jenni Reimari, Jouni Junnila, Nicolas Yeung, Johanna Maukonen, G. Crawford, Arthur C. Ouwehand
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00477-21

Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs
Cited by: 11
Author(s): Xiaofan Wang, Samantha Howe, Xiaoyuan Wei, Feilong Deng, Tsung‐Ting Tsai, Jianmin Chai, Yingping Xiao, Hua Yang, C. V. Maxwell, Ying Li, Jiangchao Zhao
Software Mentions: 5
Published: about 3 years ago

10.12688/f1000research.17706.3

Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia
Cited by: 5
Author(s): Li-Fang Yeo, Farhang Aghakhanian, J. Tan, Han Ming Gan, Maude E. Phipps
Software Mentions: 5
Published: over 5 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: over 3 years ago

10.1128/mSphere.00327-18

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

10.1186/s42523-021-00095-3

Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning
Cited by: 19
Author(s): Nida Amin, Sarah Schwarzkopf, Asako Kinoshita, Johanna Tröscher-Mußotter, Sven Dänicke, Amélia Camarinha‐Silva, Korinna Huber, Jana Frahm, Jana Seifert
Software Mentions: 5
Published: over 3 years ago

10.1111/1751-7915.13485

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits
Cited by: 19
Author(s): Shouguo Fang, Xuan Chen, Liwen Zhou, Chongchong Wang, Qiaohui Chen, Ruiyi Lin, Tianfang Xiao, Qianfu Gan
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-021-95789-8

Effect of black ginseng and silkworm supplementation on obesity, the transcriptome, and the gut microbiome of diet-induced overweight dogs
Cited by: 10
Author(s): Miey Park, Ki‐Hyun Kim, Varun Jaiswal, Jihee Choi, Ju Lan Chun, Kangmin Seo, Mi-Jin Lee, Hae‐Jeung Lee
Software Mentions: 5
Published: about 3 years ago

10.1038/s12276-021-00627-6

Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy
Cited by: 36
Author(s): Jong-Hwa Kim, Ki‐Young Kim, Wonyong Kim
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0200979

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR
Cited by: 19
Author(s): Alex Gobbi, Rui G. Santini, Elisa Filippi, Lea Ellegaard-Jensen, Carsten Suhr Jacobsen, Lars H. Hansen
Software Mentions: 4
Published: over 5 years ago

10.1186/s13099-014-0039-8

Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs
Cited by: 44
Author(s): Husen Zhang, Haifeng Wang, Megan Shepherd, Ke Wen, Guohua Li, Xing-Dong Yang, Jacob Kocher, Ernawati Arifin Giri-Rachman, Allan W. Dickerman, Robert E. Settlage, Lijuan Yuan
Software Mentions: 4
Published: about 10 years ago

10.1111/1574-6941.12362

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska
Cited by: 100
Author(s): Hye Min Kim, Jae Chang Jung, Étienne Yergeau, Chung Yeon Hwang, L. D. Hinzman, Sang Heon Nam, Soon Gyu Hong, Ok-Sun Kim, Jongsik Chun, Yoo Kyung Lee
Software Mentions: 4
Published: about 10 years ago

10.1128/mSphere.01044-20

Gut Bacteria Shared by Children and Their Mothers Associate with Developmental Level and Social Deficits in Autism Spectrum Disorder
Cited by: 5
Author(s): Yu Chen, Hui Fang, Chunyan Li, Guojun Wu, Ting Xu, Xin Yang, Liping Zhao, Xiaoyan Ke, Chenhong Zhang
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2020.01192

Behçet's Disease Under Microbiotic Surveillance? A Combined Analysis of Two Cohorts of Behçet's Disease Patients
Cited by: 21
Author(s): Tim B. van der Houwen, Jan A. M. van Laar, Jasper H Kappen, P. Martin van Hagen, Marcel R. de Zoete, Guus H. van Muijlwijk, Roos-Marijn Berbers, Ad C. Fluit, Malbert R. C. Rogers, James Groot, C. Marijn Hazelbag, Clarissa Consolandi, Marco Severgnini, Clelia Peano, Mario Milco D’Elios, Giacomo Emmi, Helen L. Leavis
Software Mentions: 4
Published: over 4 years ago

10.1080/19490976.2021.1927635

Engraftment of strictly anaerobic oxygen-sensitive bacteria in irritable bowel syndrome patients following fecal microbiota transplantation does not improve symptoms
Cited by: 8
Author(s): Patrick Browne, Frederik Cold, Andreas Munk Petersen, Sofie Ingdam Halkjær, Alice Højer Christensen, Stig Günther, Lars Hestbjerg Hansen
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.00198

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development
Cited by: 7
Author(s): Adriana M. García-Lemos, Alex Gobbi, Mette Haubjerg Nicolaisen, Lars Hansen, Thomas Roitsch, Bjarke Veierskov, Ole Nybroe
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.58999

Does diversity beget diversity in microbiomes?
Cited by: 28
Author(s): Naïma Madi, Michiel Vos, Carmen Lía Murall, Pierre Legendre, B. Jesse Shapiro
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2019.00346

Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera
Cited by: 56
Author(s): Brooke L. Weigel, Catherine A. Pfister
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.666584

Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation
Cited by: 63
Author(s): Anna Christine Trego, Paul G. McAteer, Corine Nzeteu, Thérèse Mahony, Florence Abram, Umer Zeeshan Ijaz, Vincent O’Flaherty
Software Mentions: 4
Published: over 3 years ago

10.1128/mSphere.00731-20

Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India
Cited by: 20
Author(s): Samantha L Huey, Lingjing Jiang, Marcus W. Fedarko, Daniel McDonald, Cameron Martino, Farhana Ali, David G. Russell, Shobha Udipi, Aparna Thorat, Varsha Thakker, Padmini Ghugre, Ramesh Potdar, Harsha Chopra, Kripa Rajagopalan, Jere D. Haas, Julia L. Finkelstein, Rob Knight, Saurabh Mehta
Software Mentions: 4
Published: almost 4 years ago

10.7717/peerj.8492

Influence of host phylogeny, geographical location and seed harvesting diet on the bacterial community of globally distributed<i> Pheidole</i> ants
Cited by: 9
Author(s): Carla Braga Martins, Corrie S. Moreau
Software Mentions: 4
Published: over 4 years ago

10.1111/1751-7915.12751

The dynamics of the bacterial communities developed in maize silage
Cited by: 66
Author(s): Javad Gharechahi, Zohreh Akhavan Kharazian, Sajjad Sarikhan, Gholamreza Salehi Jouzani, Mahnaz Aghdasi, Ghasem Hosseini Salekdeh
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0257961

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India
Cited by: 15
Author(s): T.J. Sushmitha, Meora Rajeev, P. Sriyutha Murthy, Sangita Ganesh, Subba Rao Toleti, Shunmugiah Karutha Pandian
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12884-021-03855-w

Association between premature ovarian insufficiency and gut microbiota
Cited by: 15
Author(s): Jiaman Wu, Yuanyuan Zhuo, Yu-Lei Liu, Yan Chen, Yan Ning, Jilong Yao
Software Mentions: 4
Published: over 3 years ago

10.1111/1751-7915.12308

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co‐fermentation with sugar beet silage
Cited by: 29
Author(s): Susanne Langer, Sharif Ahmed, Daniel Einfalt, Frank R. Bengelsdorf, Marian Kazda
Software Mentions: 4
Published: about 9 years ago

10.7717/peerj.9326

Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea
Cited by: 2
Author(s): Yukino Mizutani, Tetsushi Mori, Taeko Miyazaki, Satoshi Fukuzaki, Reiji Tanaka
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-019-6427-1

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences
Cited by: 44
Author(s): Narayan Nicole, Thomas Weinmaier, Emilio J Laserna-Mendieta, Marcus J. Claesson, Fergus Shanahan, Karim Dabbagh, Shoko Iwai, Todd Z. DeSantis
Software Mentions: 4
Published: over 4 years ago

10.1128/mSystems.00857-19

Depletion of <i>Blautia</i> Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening
Cited by: 165
Author(s): Alfonso Benı́tez-Páez, Eva M. Gómez del Pugar, Inmaculada López-Almela, Ángela Moya-Pérez, Pilar Codoñer‐Franch, Yolanda Sanz
Software Mentions: 4
Published: over 4 years ago

10.3390/microorganisms9081737

Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli
Cited by: 8
Author(s): Karla Vasco, Brian Nohomovich, Pallavi Singh, Cristina Venegas-Vargas, Rebekah E. Mosci, S. R. Rust, Paul C. Bartlett, Bo Norby, Daniel L. Grooms, Lixin Zhang, Shannon D. Manning
Software Mentions: 4
Published: about 3 years ago

10.1111/1751-7915.13393

Black soldier fly larvae (<i>Hermetia illucens</i>) strengthen the metabolic function of food waste biodegradation by gut microbiome
Cited by: 107
Author(s): Cheng-Liang Jiang, Wei-Zheng Jin, Xin-Hua Tao, Qian Zhang, Jun Zhu, Shiyun Feng, Xinhua Xu, Hongyi Li, Zehua Wang, Zhijian Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/2049-2618-2-15

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
Cited by: 707
Author(s): Andrew D. Fernandes, Jennifer Reid, Jean M. Macklaim, T.A. McMurrough, David R. Edgell, Gregory B. Gloor
Software Mentions: 4
Published: over 10 years ago

10.3390/microorganisms7100393

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?
Cited by: 15
Author(s): Léa Siegwald, Ségolène Caboche, Gaël Even, Éric Viscogliosi, Christophe Audebert, Magali Chabé
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSphere.00227-21

Microbiome Analysis Reveals Diversity and Function of <i>Mollicutes</i> Associated with the Eastern Oyster, <i>Crassostrea virginica</i>
Cited by: 16
Author(s): Zachary T. Pimentel, Keith Dufault‐Thompson, Kayla T. Russo, Abigail K. Scro, Roxanna Smolowitz, Marta Gómez-Chiarri, Ying Zhang
Software Mentions: 4
Published: about 3 years ago

10.3390/microorganisms7020035

The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence
Cited by: 17
Author(s): Joseph A. Hakim, Julie B. Schram, Aaron W. E. Galloway, Casey D. Morrow, Michael R. Crowley, Stephen A. Watts, Asim K. Bej
Software Mentions: 4
Published: over 5 years ago

10.3390/jof5040095

9th Trends in Medical Mycology Held on 11–14 October 2019, Nice, France, Organized under the Auspices of EORTC-IDG and ECMM
Cited by: 14
Author(s): Jean Pierre Gangneux, Olivier Lortholary, Oliver A. Cornely, Livio Pagano
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.00285

The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient
Cited by: 27
Author(s): Dayu Zou, Jie Pan, Zongbao Liu, Chuanlun Zhang, Hongbin Liu, Meng Li
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-021-01065-2

Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration
Cited by: 73
Author(s): Yuanyuan Lei, Li Tang, Shuang Liu, Shiping Hu, Ling-Yi Wu, Yaojiang Liu, Min Ye, Shengjie Huang, Xuefeng Tang, Tao Tang, Xiao‐Fan Zhao, Israël Vlodavsky, Shuo Zeng, Bo Tang, Shiming Yang
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-016-0209-7

Microbiota fingerprints lose individually identifying features over time
Cited by: 72
Author(s): David E. Wilkins, Marcus H. Y. Leung, Patrick K. H. Lee
Software Mentions: 3
Published: over 7 years ago

10.1186/s12885-021-08296-4

Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome
Cited by: 10
Author(s): Lito E. Papanicolas, Sarah Sims, Steven Taylor, Sophie J. Miller, Christos S. Karapetis, Steve Wesselingh, David L. Gordon, Geraint B. Rogers
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-019-0621-x

Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection
Cited by: 46
Author(s): Vanessa Las Heras, Adam G. Clooney, Feargal J. Ryan, Raúl Cabrera‐Rubio, Pat G. Casey, Cara M. Hueston, Jorge Pinheiro, Justine Rudkin, Silvia Melgar, Paul D. Cotter, Colin Hill, Cormac G. M. Gahan
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-016-1380-3

ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons
Cited by: 24
Author(s): Giovanni Scala, Ornella Affinito, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti, Sérgio Cocozza
Software Mentions: 3
Published: almost 8 years ago

10.1111/mec.15225

Comparative proteomics of stenotopic caddisfly <i>Crunoecia irrorata</i> identifies acclimation strategies to warming
Cited by: 13
Author(s): Joshua Niklas Ebner, Danilo Ritz, Stefanie von Fumetti
Software Mentions: 3
Published: almost 5 years ago

10.1111/mec.15592

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved
Cited by: 75
Author(s): Luna M. van der Loos, Reindert Nijland
Software Mentions: 3
Published: about 4 years ago

10.1038/srep45012

Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice
Cited by: 29
Author(s): Jeffrey D. Galley, Amy R. Mackos, Vanessa A. Varaljay, Michael T. Bailey
Software Mentions: 3
Published: over 7 years ago

10.1111/1755-0998.13002

Bioaerosol biomonitoring: Sampling optimization for molecular microbial ecology
Cited by: 46
Author(s): Robert Ferguson, Sonia García-Alcega, Frédéric Coulon, Alex J. Dumbrell, Corinne Whitby, I. Colbeck
Software Mentions: 3
Published: over 5 years ago

10.1186/s42523-020-00064-2

Oregano essential oil improves piglet health and performance through maternal feeding and is associated with changes in the gut microbiota
Cited by: 19
Author(s): Heidi Hall, Daniel J. Wilkinson, M Le Bon
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-84660-5

Supplementation of tuna hydrolysate and insect larvae improves fishmeal replacement efficacy of poultry by-product in Lates calcarifer (Bloch, 1790) juveniles
Cited by: 28
Author(s): Reaz Chaklader, Janet Howieson, Muhammad A.B. Siddik, Javed Foysal, Ravi Fotedar
Software Mentions: 3
Published: over 3 years ago

10.3390/jcm8050693

Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis
Cited by: 57
Author(s): Yunju Jeong, Ji-Won Kim, Hyun Ju You, Sangjun Park, Jennifer Lee, Ji Hyeon Ju, Myeong Soo Park, Hui Jin, Mi‐La Cho, Bin Kwon, Sung-Hwan Park, Geun Eog Ji
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.50918

Comparison of clinicopathological parameters, prognosis, micro-ecological environment and metabolic function of Gastric Cancer with or without Fusobacterium sp. Infection
Cited by: 15
Author(s): Siru Nie, Ang Wang, Yuan Yuan
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.48479

High fat diet induces microbiota-dependent silencing of enteroendocrine cells
Cited by: 68
Author(s): Lihua Ye, Olaf Mueller, Jennifer Bagwell, Michel Bagnat, Rodger A. Liddle, John F. Rawls
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0248371

Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
Cited by: 30
Author(s): Massab Umair, Aamer Ikram, Muhammad Salman, Adnan Khurshid, Masroor Alam, Nazish Badar, R. Suleman, Faheem Tahir, Salman Sharif, Joel M. Montgomery, Shannon Whitmer, John D. Klena
Software Mentions: 3
Published: over 3 years ago

10.1186/s42523-020-00043-7

Does solar irradiation drive community assembly of vulture plumage microbiotas?
Cited by: 4
Author(s): Gary R. Graves, Kenan O. Matterson, Christopher M. Milensky, Brian K. Schmidt, Michael O’Mahoney, Sergei V. Drovetski
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0242396

Microbial population shift and metabolic characterization of silver diamine fluoride treatment failure on dental caries
Cited by: 8
Author(s): Benjamin C. Paul, Maria A. Sierra, Fangxi Xu, Yasmi O. Crystal, Xin Li, Deepak Saxena, Ryan Richard Ruff
Software Mentions: 3
Published: over 3 years ago

10.1111/1751-7915.13702

Network analysis and functional estimation of the microbiome reveal the effects of cashew nut shell liquid feeding on methanogen behaviour in the rumen
Cited by: 9
Author(s): Koki Maeda, Van Thu Nguyen, Tomoyuki Suzuki, Keita Yamada, Kushi Kudo, Chie Hikita, Van Phong Le, Minh Chon Nguyen, Naohiro Yoshida
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers12061642

The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B
Cited by: 13
Author(s): Jaideep Chakladar, Lauren Wong, Selena Z. Kuo, Wei Tse Li, Michael Yu, Eric Y. Chang, Xiao Qi Wang, Weg M. Ongkeko
Software Mentions: 3
Published: about 4 years ago

10.1016/j.cub.2021.03.056

Stable high-density and maternally inherited Wolbachia infections in Anopheles moucheti and Anopheles demeilloni mosquitoes
Cited by: 40
Author(s): Thomas Walker, Shannon Quek, Claire L. Jeffries, Janvier Bandibabone, Vishaal Dhokiya, Roland Bamou, Mojca Kristan, Louisa A. Messenger, Alexandra Gidley, Emily A. Hornett, Enyia R Anderson, Cintia Cansado-Utrilla, Shivanand Hegde, Bantuzeko Chimanuka, Jennifer Stevenson, Neil F. Lobo, Simon C. Wagstaff, Christophe Antonio-Nkondjio, Seth R. Irish, Eva Heinz, Grant L. Hughes
Software Mentions: 3
Published: over 3 years ago

10.1186/s13099-021-00447-z

Microbiome diversity declines while distinct expansions of Th17, iNKT, and dendritic cell subpopulations emerge after anastomosis surgery
Cited by: 3
Author(s): Emilie E. Vomhof-DeKrey, Allie D. Stover, Marc D. Basson
Software Mentions: 3
Published: about 3 years ago

10.1002/ece3.6814

Jumping the green wall: The use of PNA‐DNA clamps to enhance microbiome sampling depth in wildlife microbiome research
Cited by: 3
Author(s): Luis Víquez-R, Ramona Fleischer, Kerstin Wilhelm, Marco Tschapka, Simone Sommer
Software Mentions: 3
Published: almost 4 years ago

10.1111/1751-7915.12298

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure
Cited by: 181
Author(s): Li Sun, Phillip B. Pope, Vincent G. H. Eijsink, Anna Schnürer
Software Mentions: 3
Published: about 9 years ago

10.1186/s12936-021-03606-4

Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota
Cited by: 24
Author(s): Diana Omoke, Mathew Kipsum, Solomon Otieno, Edward Esalimba, Mili Sheth, Audrey Lenhart, Ezekiel Mugendi Njeru, Eric Ochomo, Nsa Dada
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2019.01746

Gut Microbiota Analysis in Postoperative Lynch Syndrome Patients
Cited by: 20
Author(s): Giorgia Mori, Béatrice Silvia Orena, Ilenia Cultrera, Giulia Barbieri, Alessandra M. Albertini, G N Ranzani, Ileana Carnevali, Maria Grazia Tibiletti, Maria Rosalia Pasca
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2019.01706

A Novel Animal Model for Regional Microbial Dysbiosis of the Pioneer Microbial Community
Cited by: 3
Author(s): Nilusha Malmuthuge, Philip Griebel
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22062784

Urinary Exosomes Identify Inflammatory Pathways in Vancomycin Associated Acute Kidney Injury
Cited by: 12
Author(s): Linda Awdishu, Amy Le, Jordan Amato, Vidhyut Jani, Soma Bal, Robert H. Mills, Marvic Carrillo-Terrazas, David J. Gonzalez, Ashita J. Tolwani, Anjali Acharya, Jorge Cerdá, Melanie S. Joy, Paola Nicoletti, Etienne Macedo, Sucheta M. Vaingankar, Ravindra L. Mehta, Satish P. RamachandraRao
Software Mentions: 3
Published: over 3 years ago

10.1111/1751-7915.13693

Effects of growth‐promoting rhizobacteria on maize growth and rhizosphere microbial community under conservation tillage in Northeast China
Cited by: 38
Author(s): La Chen, Zhanhong Hao, Keke Li, Ye Sha, En Tao Wang, Xinhua Sui, Guohua Mi, Chang Fu Tian, Wenxin Chen
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2019.02408

Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica
Cited by: 14
Author(s): Yang Li, Qian‐Qian Cha, Yan-Ru Dang, Xiu-Lan Chen, Min Wang, Andrew McMinn, Giannina Espina, Yuzhong Zhang, Jenny M. Blamey, Qi‐Long Qin
Software Mentions: 3
Published: almost 5 years ago