Literature DB >> 20804791

V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.

Martin Hartmann1, Charles G Howes, Kessy Abarenkov, William W Mohn, R Henrik Nilsson.   

Abstract

V-Xtractor (http://www.cmde.science.ubc.ca/mohn/software.html) uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences. With a detection efficiency of 99.6% and low susceptibility to false-positives, this tool refines data reliability and facilitates subsequent analysis in community assays.
Copyright © 2010. Published by Elsevier B.V.

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Year:  2010        PMID： 20804791     DOI： 10.1016/j.mimet.2010.08.008

Source DB:  PubMed          Journal:  J Microbiol Methods        ISSN： 0167-7012            Impact factor:   2.363


  39 in total

1.  Resistance and resilience of the forest soil microbiome to logging-associated compaction.

Authors:  Martin Hartmann; Pascal A Niklaus; Stephan Zimmermann; Stefan Schmutz; Johann Kremer; Kessy Abarenkov; Peter Lüscher; Franco Widmer; Beat Frey
Journal:  ISME J       Date:  2013-09-12       Impact factor: 10.302

2.  Primer Design for an Accurate View of Picocyanobacterial Community Structure by Using High-Throughput Sequencing.

Authors:  Paula Huber; Francisco M Cornejo-Castillo; Isabel Ferrera; Pablo Sánchez; Ramiro Logares; Sebastián Metz; Vanessa Balagué; Silvia G Acinas; Josep M Gasol; Fernando Unrein
Journal:  Appl Environ Microbiol       Date:  2019-03-22       Impact factor: 4.792

3.  Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma.

Authors:  Shannon L Russell; Matthew J Gold; Martin Hartmann; Benjamin P Willing; Lisa Thorson; Marta Wlodarska; Navkiran Gill; Marie-Renée Blanchet; William W Mohn; Kelly M McNagny; Brett B Finlay
Journal:  EMBO Rep       Date:  2012-05-01       Impact factor: 8.807

4.  Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests.

Authors:  Martin Hartmann; Charles G Howes; David VanInsberghe; Hang Yu; Dipankar Bachar; Richard Christen; Rolf Henrik Nilsson; Steven J Hallam; William W Mohn
Journal:  ISME J       Date:  2012-08-02       Impact factor: 10.302

5.  How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

Authors:  Luis M Rodriguez-R; Juan C Castro; Nikos C Kyrpides; James R Cole; James M Tiedje; Konstantinos T Konstantinidis
Journal:  Appl Environ Microbiol       Date:  2018-03-01       Impact factor: 4.792

6.  Novel primers for 16S rRNA gene-based archaeal and bacterial community analysis in oceanic trench sediments.

Authors:  Na Yang; Chen Tian; Yongxin Lv; Jialin Hou; Zhifeng Yang; Xiang Xiao; Yu Zhang
Journal:  Appl Microbiol Biotechnol       Date:  2022-03-29       Impact factor: 4.813

7.  Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors.

Authors:  Ines Krohn-Molt; Bernd Wemheuer; Malik Alawi; Anja Poehlein; Simon Güllert; Christel Schmeisser; Andreas Pommerening-Röser; Adam Grundhoff; Rolf Daniel; Dieter Hanelt; Wolfgang R Streit
Journal:  Appl Environ Microbiol       Date:  2013-08-02       Impact factor: 4.792

8.  Unravelling soil fungal communities from different Mediterranean land-use backgrounds.

Authors:  Alberto Orgiazzi; Erica Lumini; R Henrik Nilsson; Mariangela Girlanda; Alfredo Vizzini; Paola Bonfante; Valeria Bianciotto
Journal:  PLoS One       Date:  2012-04-20       Impact factor: 3.240

9.  Distinct soil microbial diversity under long-term organic and conventional farming.

Authors:  Martin Hartmann; Beat Frey; Jochen Mayer; Paul Mäder; Franco Widmer
Journal:  ISME J       Date:  2014-10-31       Impact factor: 10.302

10.  Neutrophil elastase alters the murine gut microbiota resulting in enhanced Salmonella colonization.

Authors:  Navkiran Gill; Rosana B R Ferreira; L Caetano M Antunes; Benjamin P Willing; Inna Sekirov; Fatimah Al-Zahrani; Martin Hartmann; B Brett Finlay
Journal:  PLoS One       Date:  2012-11-14       Impact factor: 3.240
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