Literature DB >> 21984239

Evaluation of subsampling-based normalization strategies for tagged high-throughput sequencing data sets from gut microbiomes.

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

Abstract

Several subsampling-based normalization strategies were applied to different high-throughput sequencing data sets originating from human and murine gut environments. Their effects on the data sets' characteristics and normalization efficiencies, as measured by several β-diversity metrics, were compared. For both data sets, subsampling to the median rather than the minimum number appeared to improve the analysis.

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Mesh：

Year:  2011        PMID： 21984239      PMCID： PMC3233110          DOI： 10.1128/AEM.05491-11

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


  8 in total

1.  Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.

Authors:  J Kirk Harris; Jason W Sahl; Todd A Castoe; Brandie D Wagner; David D Pollock; John R Spear
Journal:  Appl Environ Microbiol       Date:  2010-04-23       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.  A taxa-area relationship for bacteria.

Authors:  M Claire Horner-Devine; Melissa Lage; Jennifer B Hughes; Brendan J M Bohannan
Journal:  Nature       Date:  2004-12-09       Impact factor: 49.962

4.  Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale.

Authors:  Christian L Lauber; Micah Hamady; Rob Knight; Noah Fierer
Journal:  Appl Environ Microbiol       Date:  2009-06-05       Impact factor: 4.792

5.  Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples.

Authors:  Christian L Lauber; Nicholas Zhou; Jeffrey I Gordon; Rob Knight; Noah Fierer
Journal:  FEMS Microbiol Lett       Date:  2010-03-25       Impact factor: 2.742

6.  Microbial community resemblance methods differ in their ability to detect biologically relevant patterns.

Authors:  Justin Kuczynski; Zongzhi Liu; Catherine Lozupone; Daniel McDonald; Noah Fierer; Rob Knight
Journal:  Nat Methods       Date:  2010-09-05       Impact factor: 28.547

7.  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

8.  UniFrac: a new phylogenetic method for comparing microbial communities.

Authors:  Catherine Lozupone; Rob Knight
Journal:  Appl Environ Microbiol       Date:  2005-12       Impact factor: 4.792
  8 in total
  36 in total

1.  CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis.

Authors:  Sebastian Hupfauf; Mohammad Etemadi; Marina Fernández-Delgado Juárez; María Gómez-Brandón; Heribert Insam; Sabine Marie Podmirseg
Journal:  PLoS One       Date:  2020-12-02       Impact factor: 3.240

2.  Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests.

Authors:  Karita Saravesi; Sami Aikio; Piippa R Wäli; Anna Liisa Ruotsalainen; Maarit Kaukonen; Karoliina Huusko; Marko Suokas; Shawn P Brown; Ari Jumpponen; Juha Tuomi; Annamari Markkola
Journal:  Microb Ecol       Date:  2015-02-17       Impact factor: 4.552

Review 3.  Maternal microbiomes in preterm birth: Recent progress and analytical pipelines.

Authors:  Lindsay A Parnell; Catherine M Briggs; Indira U Mysorekar
Journal:  Semin Perinatol       Date:  2017-08-18       Impact factor: 3.300

4.  Ballast Water Exchange and Invasion Risk Posed by Intracoastal Vessel Traffic: An Evaluation Using High Throughput Sequencing.

Authors:  John A Darling; John Martinson; Yunguo Gong; Sara Okum; Erik Pilgrim; Katrina M Pagenkopp Lohan; Katharine J Carney; Gregory M Ruiz
Journal:  Environ Sci Technol       Date:  2018-08-21       Impact factor: 9.028

5.  Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge.

Authors:  Jan C Plaizier; Shucong Li; Anne Mette Danscher; Hooman Derakshani; Pia H Andersen; Ehsan Khafipour
Journal:  Microb Ecol       Date:  2017-02-08       Impact factor: 4.552

6.  Unique vaginal microbiota that includes an unknown Mycoplasma-like organism is associated with Trichomonas vaginalis infection.

Authors:  David H Martin; Marcela Zozaya; Rebecca A Lillis; Leann Myers; M Jacques Nsuami; Michael J Ferris
Journal:  J Infect Dis       Date:  2013-03-12       Impact factor: 5.226

7.  Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand.

Authors:  Laetitia Herrmann; Didier Lesueur; Lambert Bräu; John Davison; Teele Jairus; Henri Robain; Agnès Robin; Martti Vasar; Wanpen Wiriyakitnateekul; Maarja Öpik
Journal:  Mycorrhiza       Date:  2016-07-23       Impact factor: 3.387

8.  The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles.

Authors:  Joseph A Hakim; Hyunmin Koo; Ranjit Kumar; Elliot J Lefkowitz; Casey D Morrow; Mickie L Powell; Stephen A Watts; Asim K Bej
Journal:  FEMS Microbiol Ecol       Date:  2016-07-01       Impact factor: 4.194

9.  Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome.

Authors:  Lukasz Krych; Camilla H F Hansen; Axel K Hansen; Frans W J van den Berg; Dennis S Nielsen
Journal:  PLoS One       Date:  2013-05-01       Impact factor: 3.240

Review 10.  Bioinformatic approaches for functional annotation and pathway inference in metagenomics data.

Authors:  Carlotta De Filippo; Matteo Ramazzotti; Paolo Fontana; Duccio Cavalieri
Journal:  Brief Bioinform       Date:  2012-11       Impact factor: 11.622
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