Literature DB >> 21764953

Strategy for modular tagged high-throughput amplicon sequencing.

Daniel Aguirre de Cárcer1, Stuart E Denman, Chris McSweeney, Mark Morrison.   

Abstract

The use and validation of a strategy that allows a universal set of bar-coded sequencing primers to be appended to an amplified PCR product is described. The strategy allows a modular approach, in that the same bar code can be used with two or more target-specific primer sets, even simultaneously.

Mesh：

Substances：

Year:  2011        PMID： 21764953      PMCID： PMC3165417          DOI： 10.1128/AEM.05146-11

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  10 in total

1.  Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization.

Authors:  A Sghir; G Gramet; A Suau; V Rochet; P Pochart; J Dore
Journal:  Appl Environ Microbiol       Date:  2000-05       Impact factor: 4.792

Review 2.  Comparing microarrays and next-generation sequencing technologies for microbial ecology research.

Authors:  Seong Woon Roh; Guy C J Abell; Kyoung-Ho Kim; Young-Do Nam; Jin-Woo Bae
Journal:  Trends Biotechnol       Date:  2010-04-08       Impact factor: 19.536

3.  Diversity of the human intestinal microbial flora.

Authors:  Paul B Eckburg; Elisabeth M Bik; Charles N Bernstein; Elizabeth Purdom; Les Dethlefsen; Michael Sargent; Steven R Gill; Karen E Nelson; David A Relman
Journal:  Science       Date:  2005-04-14       Impact factor: 47.728

4.  Adaptor polymerase chain reaction for single molecule amplification.

Authors:  Michihiko Nakano; Jun Komatsu; Hirofumi Kurita; Hachiro Yasuda; Shinji Katsura; Akira Mizuno
Journal:  J Biosci Bioeng       Date:  2005-08       Impact factor: 2.894

Review 5.  Sequencing technologies - the next generation.

Authors:  Michael L Metzker
Journal:  Nat Rev Genet       Date:  2009-12-08       Impact factor: 53.242

6.  Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils.

Authors:  A Felske; H Rheims; A Wolterink; E Stackebrandt; A D Akkermans
Journal:  Microbiology (Reading)       Date:  1997-09       Impact factor: 2.777

7.  Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited.

Authors:  Thomas D Leser; Joanna Z Amenuvor; Tim K Jensen; Rikke H Lindecrona; Mette Boye; Kristian Møller
Journal:  Appl Environ Microbiol       Date:  2002-02       Impact factor: 4.792

8.  Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria.

Authors:  K Daly; R J Sharp; A J McCarthy
Journal:  Microbiology       Date:  2000-07       Impact factor: 2.777

9.  QIIME allows analysis of high-throughput community sequencing data.

Authors:  J Gregory Caporaso; Justin Kuczynski; Jesse Stombaugh; Kyle Bittinger; Frederic D Bushman; Elizabeth K Costello; Noah Fierer; Antonio Gonzalez Peña; Julia K Goodrich; Jeffrey I Gordon; Gavin A Huttley; Scott T Kelley; Dan Knights; Jeremy E Koenig; Ruth E Ley; Catherine A Lozupone; Daniel McDonald; Brian D Muegge; Meg Pirrung; Jens Reeder; Joel R Sevinsky; Peter J Turnbaugh; William A Walters; Jeremy Widmann; Tanya Yatsunenko; Jesse Zaneveld; Rob Knight
Journal:  Nat Methods       Date:  2010-04-11       Impact factor: 28.547

10.  A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing.

Authors:  Poornima Parameswaran; Roxana Jalili; Li Tao; Shadi Shokralla; Baback Gharizadeh; Mostafa Ronaghi; Andrew Z Fire
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971
  10 in total
  12 in total

1.  Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes.

Authors:  Carly P Rosewarne; Phillip B Pope; Jane L Cheung; Mark Morrison
Journal:  J Ind Microbiol Biotechnol       Date:  2014-01-22       Impact factor: 3.346

2.  Burn Injury Alters the Intestinal Microbiome and Increases Gut Permeability and Bacterial Translocation.

Authors:  Zachary M Earley; Suhail Akhtar; Stefan J Green; Ankur Naqib; Omair Khan; Abigail R Cannon; Adam M Hammer; Niya L Morris; Xiaoling Li; Joshua M Eberhardt; Richard L Gamelli; Richard H Kennedy; Mashkoor A Choudhry
Journal:  PLoS One       Date:  2015-07-08       Impact factor: 3.240

3.  From benchtop to desktop: important considerations when designing amplicon sequencing workflows.

Authors:  Dáithí C Murray; Megan L Coghlan; Michael Bunce
Journal:  PLoS One       Date:  2015-04-22       Impact factor: 3.240

4.  Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches.

Authors:  Stefan J Green; Raghavee Venkatramanan; Ankur Naqib
Journal:  PLoS One       Date:  2015-05-21       Impact factor: 3.240

5.  Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau.

Authors:  Xiao Dan Huang; Gonzalo Martinez-Fernandez; Jagadish Padmanabha; Ruijun Long; Stuart E Denman; Christopher S McSweeney
Journal:  Archaea       Date:  2016-04-28       Impact factor: 3.273

6.  Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome.

Authors:  Daniel Aguirre de Cárcer; Bruno Hernáez; Alberto Rastrojo; Antonio Alcamí
Journal:  PLoS One       Date:  2017-03-10       Impact factor: 3.240

7.  Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women.

Authors:  Supriya D Mehta; Ashish K Pradhan; Stefan J Green; Ankur Naqib; Elijah Odoyo-June; Charlotte A Gaydos; Sheila Barry; Alan Landay; Robert C Bailey
Journal:  Sci Rep       Date:  2017-11-13       Impact factor: 4.379

8.  Ecosystem function decays by fungal outbreaks in Antarctic microbial mats.

Authors:  David Velázquez; Alberto López-Bueno; Daniel Aguirre de Cárcer; Asunción de los Ríos; Antonio Alcamí; Antonio Quesada
Journal:  Sci Rep       Date:  2016-03-14       Impact factor: 4.379

9.  Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones.

Authors:  Aguirre de Cárcer Daniel; Carlos Pedrós-Alió; David A Pearce; Antonio Alcamí
Journal:  Front Microbiol       Date:  2016-03-18       Impact factor: 5.640

10.  Harvesting Mango Fruit with a Short Stem-End Altered Endophytic Microbiome and Reduce Stem-End Rot.

Authors:  Ortal Galsurker; Sonia Diskin; Danielle Duanis-Assaf; Adi Doron-Faigenboim; Dalia Maurer; Oleg Feygenberg; Noam Alkan
Journal:  Microorganisms       Date:  2020-04-13
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