The application of rarefaction techniques to molecular inventories of microbial diversity

Methods in Enzymology
Jennifer B Hughes, Jessica J Hellmann

Abstract

With the growing capacity to inventory microbial community diversity, the need for statistical methods to compare community inventories is also growing. Several approaches have been proposed for comparing the diversity of microbial communities: some adapted from traditional ecology and others designed specifically for molecular inventories of microbes. Rarefaction is one statistical method that is commonly applied in microbial studies, and this chapter discusses the procedure and its advantages and disadvantages. Rarefaction compares observed taxon richness at a standardized sampling effort using confidence intervals. Special emphasis is placed here on the need for precise, rather than unbiased, estimation methods in microbial ecology, but precision can be judged only with a very large sample or with multiple samples drawn from a single community. With low sample sizes, rarefaction curves also have the potential to lead to incorrect rankings of relative species richness, but this chapter discusses a new method with the potential to address this problem. Finally, this chapter shows how rarefaction can be applied to the comparison of the taxonomic similarity of microbial communities.

Citations

Mar 14, 2007·Applied and Environmental Microbiology·Jonathan P AllenSilvia Rossbach
Apr 5, 2014·PLoS Computational Biology·Paul J McMurdie, Susan Holmes
Apr 16, 2015·MAbs·Bernardo Cortina-CeballosJesús Martínez-Barnetche
Jun 12, 2014·Frontiers in Microbiology·Lindsay E DarjanyJesse G Dillon
Nov 1, 2017·Nature Communications·Tobias Guldberg FrøslevAnders Johannes Hansen
Apr 19, 2015·Applied and Environmental Microbiology·Yan YanJohannes A van Veen
Sep 12, 2015·Circulation Research·Jingyuan FuAlexandra Zhernakova
May 30, 2008·Nature·Cara M SantelliKatrina J Edwards
Jul 22, 2008·Environmental Microbiology·Allison K ShawJennifer B H Martiny
Aug 13, 2009·Antonie van Leeuwenhoek·M C PortilloJ M Gonzalez
Aug 19, 2010·Microbial Ecology·M C Portillo, J M Gonzalez
May 22, 2009·The Journal of Eukaryotic Microbiology·David A Caron
May 6, 2019·The ISME Journal·Mario E MuscarellaJay T Lennon
Nov 12, 2019·Environmental Microbiology·Katarina DamjanovicMadeleine J H van Oppen
Jul 2, 2020·Environmental Microbiology·David R Johnson, Francesco Pomati
Aug 8, 2020·Molecular Ecology·Christopher C M BakerCorina E Tarnita
Jul 25, 2018·Ecology and Evolution·Amruta Varudkar, Uma Ramakrishnan
Sep 11, 2018·Frontiers in Microbiology·Chuanshang ChengJian Peng
Jul 5, 2017·The Journal of Antimicrobial Chemotherapy·Johan Bengtsson-PalmeErik Kristiansson
Apr 22, 2018·BMC Genomics·Mariana Buongermino PereiraErik Kristiansson
Nov 27, 2020·Environmental Science and Pollution Research International·Chengyu YuanXinqiang Liang
Dec 4, 2020·NPJ Biofilms and Microbiomes·Huang Lin, Shyamal Das Peddada
Jan 9, 2021·BMC Veterinary Research·Xiaoxing YeShaoming Fang

Related Concepts

Bionomics
Environmental Microbiology

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.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Pediculosis pubis

Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.

Rh Isoimmunization

Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.

Enzyme Evolution

This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.

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.

Pharmacology of Proteinopathies

This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.