Integration of microbial ecology and statistics: a test to compare gene libraries

Applied and Environmental Microbiology
Patrick D SchlossJo Handelsman

Abstract

Libraries of 16S rRNA genes provide insight into the membership of microbial communities. Statistical methods help to determine whether differences in library composition are artifacts of sampling or are due to underlying differences in the communities from which they are derived. To contribute to a growing statistical framework for comparing 16S rRNA libraries, we present a computer program, integral -LIBSHUFF, which calculates the integral form of the Cramér-von Mises statistic. This implementation builds upon the LIBSHUFF program, which uses an approximation of the statistic and makes a number of modifications that improve precision and accuracy. Once integral -LIBSHUFF calculates the P values, when pairwise comparisons are tested at the 0.05 level, the probability of falsely identifying a significant P value is 0.098 for a study with two libraries, 0.265 for three libraries, and 0.460 for four libraries. The potential negative effects of making the multiple pairwise comparisons necessitate correcting for the increased likelihood that differences between treatments are due to chance and do not reflect biological differences. Using integral -LIBSHUFF, we found that previously published 16S rRNA gene libraries constructed from...Continue Reading

References

Mar 6, 1999·Current Opinion in Microbiology·D M Ward
Aug 30, 2001·Applied and Environmental Microbiology·D R SingletonW B Whitman
Sep 26, 2001·Applied and Environmental Microbiology·J B HughesB J Bohannan
Jun 1, 2002·Applied and Environmental Microbiology·John DunbarCheryl R Kuske
Jul 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Thomas P CurtisJack W Scannell
Jul 31, 2002·Applied and Environmental Microbiology·Andrew P Martin
Dec 4, 2002·Environmental Microbiology·Jennifer E BrofftLawrence J Shimkets
Feb 7, 2003·Applied and Environmental Microbiology·Shaheen B HumayounJames T Hollibaugh
Apr 26, 2003·Environmental Microbiology·Olga PantosJohn C Bythell
May 7, 2003·Applied and Environmental Microbiology·John P Bowman, Robert D McCuaig
May 7, 2003·Applied and Environmental Microbiology·Mark R LilesRobert M Goodman
Aug 7, 2003·Applied and Environmental Microbiology·Jonathan L SebatRonald L Crawford
Oct 9, 2003·Applied and Environmental Microbiology·James E M StachAlan T Bull
Apr 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·John F RawlsJeffrey I Gordon
Jul 1, 2003·FEMS Microbiology Ecology·Shane M PowellJonathan S Stark

❮ Previous
Next ❯

Citations

Jan 20, 2010·Archives of Microbiology·Chandra Shekhar NautiyalPuneet Singh Chauhan
Mar 17, 2007·Microbial Ecology·David M NelsonRoderick I Mackie
Oct 5, 2010·Microbial Ecology·Thiago BruceFabiano L Thompson
Jun 25, 2009·Applied Microbiology and Biotechnology·Juliana Cardinali-RezendeAndrea M A Nascimento
Feb 3, 2012·Applied Microbiology and Biotechnology·D I Kurtböke
Jan 13, 2010·Extremophiles : Life Under Extreme Conditions·Catherine LaroseTimothy M Vogel
Jan 20, 2012·Extremophiles : Life Under Extreme Conditions·Katerina KatsaveliKostas Bourtzis
Jun 20, 2012·Extremophiles : Life Under Extreme Conditions·Angel ValverdeDon A Cowan
Aug 22, 2013·Extremophiles : Life Under Extreme Conditions·A R LuchetaM R Lambais
Dec 4, 2009·Marine Biotechnology·Mona RadwanRussell T Hill
Feb 7, 2012·Antonie van Leeuwenhoek·J Félix Aguirre-GarridoHugo C Ramírez-Saad
Feb 18, 2011·Applied Biochemistry and Biotechnology·Fredy MoralesHumberto Hernández-Sánchez
Dec 19, 2008·The ISME Journal·Christopher M DeRito, Eugene L Madsen
Feb 27, 2009·The ISME Journal·Delphine RivièreAbdelghani Sghir
Mar 27, 2009·The ISME Journal·Debora F RodriguesJames M Tiedje
Jul 9, 2010·The ISME Journal·Pia K WüstHarold L Drake
Jun 3, 2005·Nature Reviews. Microbiology·Rolf Daniel
Feb 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Min LiLiping Zhao
Dec 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Frank ScheckenbachHartmut Arndt
Sep 20, 2012·Environmental Technology·Kelly ChoSonia M Tiquia
Apr 16, 2005·Science·Paul B EckburgDavid A Relman
Jun 9, 2009·Applied and Environmental Microbiology·Matthew T Cottrell, David L Kirchman
Jul 6, 2006·Applied and Environmental Microbiology·Daniel H BuckleyJanice E Thies
Apr 12, 2011·Applied and Environmental Microbiology·Sindy HungerHarold L Drake
Jul 22, 2008·Applied and Environmental Microbiology·Jason M Smith, Andrew Ogram
May 13, 2008·Applied and Environmental Microbiology·Naglaa M MohamedRussell T Hill
Jun 17, 2008·Applied and Environmental Microbiology·Pedro A DimitriuMelanie R Mormile
Jun 26, 2007·Applied and Environmental Microbiology·J Michael BemanChristopher A Francis
Oct 6, 2006·Applied and Environmental Microbiology·Patrick D Schloss, Jo Handelsman

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.