 |
|
Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community
Sang-Cheol Park, Sungho Won
Genomics Inform. 2018;16(4):e24 Published online 2018 Dec 28 DOI: https://doi.org/10.5808/GI.2018.16.4.e24
|
|
Citations to this article as recorded by
 Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome
Christopher J. Sweeney, Rishabh Kaushik, Melanie Bottoms
Integrated Environmental Assessment and Management.2024; 20(2): 337. CrossRef Drivers and human impacts on topsoil bacterial and fungal community biogeography across Australia
Peipei Xue, Budiman Minasny, Alexandre M. J.‐C. Wadoux, Mercedes Román Dobarco, Alex McBratney, Andrew Bissett, Patrice de Caritat
Global Change Biology.2024;[Epub] CrossRef Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Aubrey R. Odom, Tyler Faits, Eduardo Castro-Nallar, Keith A. Crandall, W. Evan Johnson
Scientific Reports.2023;[Epub] CrossRef Combination of poly-γ-glutamic acid and galactooligosaccharide improves intestinal microbiota, defecation status, and relaxed mood in humans: a randomized, double-blind, parallel-group comparison trial
Kentaro UMEDA, Atsuko IKEDA, Ryo UCHIDA, Ikuko SASAHARA, Tomoyuki MINE, Hitoshi MURAKAMI, Keishi KAMEYAMA
Bioscience of Microbiota, Food and Health.2023; 42(1): 34. CrossRef Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies
Francesco Mugnai, Federica Costantini, Anne Chenuil, Michèle Leduc, José Miguel Gutiérrez Ortega, Emese Meglécz
PeerJ.2023; 11: e14616. CrossRef The Contribution of the Human Oral Microbiome to Oral Disease: A Review
Austin Gregory Morrison, Soumyadev Sarkar, Shahid Umar, Sonny T. M. Lee, Sufi Mary Thomas
Microorganisms.2023; 11(2): 318. CrossRef Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems
Jessica Rieder, Adamandia Kapopoulou, Claudia Bank, Irene Adrian-Kalchhauser
Environmental Microbiome.2023;[Epub] CrossRef Isolation of Alginate-Degrading Bacteria from the Human Gut Microbiota and Discovery of Bacteroides xylanisolvens AY11-1 as a Novel Anti-Colitis Probiotic Bacterium
Tianyu Fu, Yamin Wang, Mingfeng Ma, Wei Dai, Lin Pan, Qingsen Shang, Guangli Yu
Nutrients.2023; 15(6): 1352. CrossRef Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required
Márton Szoboszlay, Laetitia Schramm, David Pinzauti, Jeanesse Scerri, Anna Sandionigi, Manuele Biazzo
Microorganisms.2023; 11(3): 804. CrossRef Geographical subdivision of Alviniconcha snail populations in the Indian Ocean hydrothermal vent regions
Sook-Jin Jang, Soo-Yeon Cho, Chuyu Li, Yadong Zhou, Hui Wang, Jin Sun, Ajit Kumar Patra, Yong-Jin Won
Frontiers in Marine Science.2023;[Epub] CrossRef Genomic analysis of lignocellulolytic enzyme producing novel Streptomyces sp.MS2A for the bioethanol applications
J. Ashwini John, Ethiraj Selvarajan
International Journal of Biological Macromolecules.2023; 250: 126138. CrossRef Microbiome depiction through user-adapted bioinformatic pipelines and parameters
Eric I. Nayman, Brooke A. Schwartz, Fantaysia C. Polanco, Alexandra K. Firek, Alayna C. Gumabong, Nolan J. Hofstee, Giri Narasimhan, Trevor Cickovski, Kalai Mathee
Journal of Medical Microbiology
.2023;[Epub] CrossRef Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach
Hugo Roume, Stanislas Mondot, Adrien Saliou, Sophie Le Fresne-Languille, Joël Doré
Scientific Reports.2023;[Epub] CrossRef The Clinical Utility of Two High-Throughput 16S rRNA Gene Sequencing Workflows for Taxonomic Assignment of Unidentifiable Bacterial Pathogens in Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Hiu-Yin Lao, Timothy Ting-Leung Ng, Ryan Yik-Lam Wong, Celia Sze-Ting Wong, Lam-Kwong Lee, Denise Sze-Hang Wong, Chloe Toi-Mei Chan, Stephanie Hoi-Ching Jim, Jake Siu-Lun Leung, Hazel Wing-Hei Lo, Ivan Tak-Fai Wong, Miranda Chong-Yee Yau, Jimmy Yiu-Wing L
Journal of Clinical Microbiology.2022;[Epub] CrossRef Bacterial keratitis: identifying the areas of clinical uncertainty
Stephen Tuft, Tobi F. Somerville, Ji-Peng Olivia Li, Timothy Neal, Surjo De, Malcolm J. Horsburgh, Joanne L. Fothergill, Daniel Foulkes, Stephen Kaye
Progress in Retinal and Eye Research.2022; 89: 101031. CrossRef Characteristics of the gut microbiome in women with gestational diabetes mellitus: A systematic review
Louise Søndergaard Rold, Caspar Bundgaard-Nielsen, Julie Niemann Holm-Jacobsen, Per Glud Ovesen, Peter Leutscher, Søren Hagstrøm, Suzette Sørensen, Chun Wie Chong
PLOS ONE.2022; 17(1): e0262618. CrossRef Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research
Meganathan P. Ramakodi
Biotechnology Letters.2022; 44(3): 523. CrossRef
Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within
Euryspongia arenaria
Cells
Qi Yang, Jackson K. B. Cahn, Jörn Piel, Yue-Fan Song, Wei Zhang, Hou-Wen Lin, Konstantinos Aristomenis Kormas
Microbiology Spectrum.2022;[Epub] CrossRef Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era
Dina G. Moussa, Paras Ahmad, Tamer A. Mansour, Walter L. Siqueira
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef BERT contextual embeddings for taxonomic classification of bacterial DNA sequences
Marwah A. Helaly, Sherine Rady, Mostafa M. Aref
Expert Systems with Applications.2022; 208: 117972. CrossRef
Pelagibacterium xiamenense sp. nov., isolated from intertidal sediment
Yufei He, Lina Lyu, Chunming Dong, Wanpeng Wang, Zhiqiang Yu, Zongze Shao
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing
Elisa Banchi, Vincenzo Manna, Viviana Fonti, Cinzia Fabbro, Mauro Celussi
Environmental Science and Pollution Research.2022; 29(44): 67466. CrossRef The gut microbiota and depressive symptoms across ethnic groups
Jos A. Bosch, Max Nieuwdorp, Aeilko H. Zwinderman, Mélanie Deschasaux, Djawad Radjabzadeh, Robert Kraaij, Mark Davids, Susanne R. de Rooij, Anja Lok
Nature Communications.2022;[Epub] CrossRef
Gordonia tangerina sp. nov., isolated from seawater
Yufei He, Lina Lyu, Ziyan Hu, Zhiqiang Yu, Zongze Shao
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef gcType: a high-quality type strain genome database for microbial phylogenetic and functional research
Wenyu Shi, Qinglan Sun, Guomei Fan, Sugawara Hideaki, Ohkuma Moriya, Takashi Itoh, Yuguang Zhou, Man Cai, Song-Gun Kim, Jung-Sook Lee, Ivo Sedlacek, David R Arahal, Teresa Lucena, Hiroko Kawasaki, Lyudmila Evtushenko, Bevan S Weir, Sarah Alexander, Dlauch
Nucleic Acids Research.2021; 49(D1): D694. CrossRef Probing periodontal microbial dark matter using metataxonomics and metagenomics
Purnima S. Kumar, Shareef M. Dabdoub, Sukirth M. Ganesan
Periodontology 2000.2021; 85(1): 12. CrossRef Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis
Liying Low, Pablo Fuentes-Utrilla, James Hodson, John D. O’Neil, Amanda E. Rossiter, Ghazala Begum, Kusy Suleiman, Philip I. Murray, Graham R. Wallace, Nicholas J. Loman, Saaeha Rauz
PeerJ.2021; 9: e10778. CrossRef Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis
Miguel Fernández-Niño, María Juliana Rodríguez-Cubillos, Fabio Herrera-Rocha, Juan Manuel Anzola, Martha Lucia Cepeda-Hernández, Jenny Lorena Aguirre Mejía, María José Chica, Héctor Hugo Olarte, Claudia Rodríguez-López, Dayana Calderón, Adan Ramírez-Rojas
Scientific Reports.2021;[Epub] CrossRef Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment
Megan S. Beaudry, Jincheng Wang, Troy J. Kieran, Jesse Thomas, Natalia J. Bayona-Vásquez, Bei Gao, Alison Devault, Brian Brunelle, Kun Lu, Jia-Sheng Wang, Olin E. Rhodes, Travis C. Glenn
Frontiers in Microbiology.2021;[Epub] CrossRef Sustaining Rice Production through Biofertilization with N2-Fixing Cyanobacteria
Macarena Iniesta-Pallarés, Consolación Álvarez, Francisco M. Gordillo-Cantón, Carmen Ramírez-Moncayo, Pilar Alves-Martínez, Fernando P. Molina-Heredia, Vicente Mariscal
Applied Sciences.2021; 11(10): 4628. CrossRef Establishment and assessment of an amplicon sequencing method targeting the 16S-ITS-23S rRNA operon for analysis of the equine gut microbiome
Yuta Kinoshita, Hidekazu Niwa, Eri Uchida-Fujii, Toshio Nukada
Scientific Reports.2021;[Epub] CrossRef Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing
Isabel Abellan-Schneyder, Monica S. Matchado, Sandra Reitmeier, Alina Sommer, Zeno Sewald, Jan Baumbach, Markus List, Klaus Neuhaus, Susannah Green Tringe
mSphere.2021;[Epub] CrossRef Analysis of Microbiota and Mycobiota in Fungal Ball Rhinosinusitis: Specific Interaction between Aspergillus fumigatus and Haemophilus influenza?
Sarah Dellière, Eric Dannaoui, Maxime Fieux, Pierre Bonfils, Guillaume Gricourt, Vanessa Demontant, Isabelle Podglajen, Paul-Louis Woerther, Cécile Angebault, Françoise Botterel
Journal of Fungi.2021; 7(7): 550. CrossRef Combining Imaging Flow Cytometry and Molecular Biological Methods to Reveal Presence of Potentially Toxic Algae at the Ural River in Kazakhstan
Yersultan Mirasbekov, Aigerim Abdimanova, Kuanysh Sarkytbayev, Kanat Samarkhanov, Aidyn Abilkas, Daria Potashnikova, Galina Arbuz, Zhanpeis Issayev, Ivan A. Vorobjev, Dmitry V. Malashenkov, Natasha S. Barteneva
Frontiers in Marine Science.2021;[Epub] CrossRef Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing
Carter Hoffman, Nazema Y. Siddiqui, Ian Fields, W. Thomas Gregory, Holly M. Simon, Michael A. Mooney, Alan J. Wolfe, Lisa Karstens, Nicholas Chia
mSystems.2021;[Epub] CrossRef Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement
Daniel Roush, Ana Giraldo-Silva, Ferran Garcia-Pichel
Scientific Data.2021;[Epub] CrossRef RESCRIPt: Reproducible sequence taxonomy reference database management
Michael S. Robeson, Devon R. O’Rourke, Benjamin D. Kaehler, Michal Ziemski, Matthew R. Dillon, Jeffrey T. Foster, Nicholas A. Bokulich, Mihaela Pertea
PLOS Computational Biology.2021; 17(11): e1009581. CrossRef ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples
Isabel Abellan-Schneyder, Andrea Janina Schusser, Klaus Neuhaus
BMC Microbiology.2021;[Epub] CrossRef Phylogenetic tree-based microbiome association test
Kang Jin Kim, Jaehyun Park, Sang-Chul Park, Sungho Won, Russell Schwartz
Bioinformatics.2020; 36(4): 1000. CrossRef Computational methods for 16S metabarcoding studies using Nanopore sequencing data
Andres Santos, Ronny van Aerle, Leticia Barrientos, Jaime Martinez-Urtaza
Computational and Structural Biotechnology Journal.2020; 18: 296. CrossRef A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes
Anders B. Nygaard, Hege S. Tunsjø, Roger Meisal, Colin Charnock
Scientific Reports.2020;[Epub] CrossRef Gut microbiota profiles of autism spectrum disorder and attention deficit/hyperactivity disorder: A systematic literature review.
Caspar Bundgaard-Nielsen, Julie Knudsen, Peter D. C. Leutscher, Marlene B. Lauritsen, Mette Nyegaard, Søren Hagstrøm, Suzette Sørensen
Gut Microbes.2020; 11(5): 1172. CrossRef MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding
Vanessa Arranz, William S. Pearman, J. David Aguirre, Libby Liggins
Scientific Data.2020;[Epub] CrossRef Secretion dynamics of soyasaponins in soybean roots and effects to modify the bacterial composition
Teruhisa Fujimatsu, Keiji Endo, Kazufumi Yazaki, Akifumi Sugiyama
Plant Direct.2020;[Epub] CrossRef Changes in Vaginal Microbiome in Pregnant and Nonpregnant Women with Bacterial Vaginosis: Toward Microbiome Diagnostics?
Ibrahim Mohamed, Samira Zakeer, Marwa Azab, Amro Hanora
OMICS: A Journal of Integrative Biology.2020; 24(10): 602. CrossRef Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform
Po-Li Wei, Ching-Sheng Hung, Yi-Wei Kao, Ying-Chin Lin, Cheng-Yang Lee, Tzu-Hao Chang, Ben-Chang Shia, Jung-Chun Lin
International Journal of Molecular Sciences.2020; 21(19): 7110. CrossRef Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country
Nurnabila Syafiqah Muhamad Rizal, Hui-min Neoh, Ramliza Ramli, Petrick @ Ramesh A/L K Periyasamy, Alfizah Hanafiah, Muttaqillah Najihan Abdul Samat, Toh Leong Tan, Kon Ken Wong, Sheila Nathan, Sylvia Chieng, Seow Hoon Saw, Bee Yin Khor
Diagnostics.2020; 10(10): 816. CrossRef A New Benchmark to Determine What Healthy Western Skin Looks Like in Terms of Biodiversity Using Standardised Methodology
Christopher Wallen-Russell, Sam Wallen-Russell
Cosmetics.2020; 7(4): 79. CrossRef Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis
Paul E. Smith, Sinead M. Waters, Ruth Gómez Expósito, Hauke Smidt, Ciara A. Carberry, Matthew S. McCabe
Frontiers in Microbiology.2020;[Epub] CrossRef
|