Deciphering Diversity Indices for a Better Understanding of Microbial Communities.
@article{Kim2017DecipheringDI, title={Deciphering Diversity Indices for a Better Understanding of Microbial Communities.}, author={Bo-Ra Kim and Jiwon Shin and Robin B Guevarra and Jun Hyung Lee and Doowan Kim and Kukhwan Seol and Ju-Hoon Lee and Hyeun bum Kim and Richard Isaacson}, journal={Journal of microbiology and biotechnology}, year={2017}, volume={27 12}, pages={ 2089-2093 } }
The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate…
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References
SHOWING 1-10 OF 30 REFERENCES
Robust estimation of microbial diversity in theory and in practice
- Environmental ScienceThe ISME Journal
- 2013
It is argued that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions, and recommended is the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.
The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.
- BiologyVeterinary microbiology
- 2015
High throughput sequencing methods for microbiome profiling: application to food animal systems
- BiologyAnimal Health Research Reviews
- 2012
Production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.
Microbial Population Structures in the Deep Marine Biosphere
- Environmental ScienceScience
- 2007
It is predicted that hundreds of thousands of sequences will be necessary to capture the vast diversity of microbial communities, and that different patterns of evenness for both high- and low-abundance taxa may be important in defining microbial ecosystem dynamics.
The commensal microbiology of the gastrointestinal tract.
- BiologyAdvances in experimental medicine and biology
- 2008
Characterizing the species composition of the healthy microbiota may be a key step in identifying bacterial or associated physiological conditions that are present or absent in an unhealthy microbiota.
Microbial diversity in the deep sea and the underexplored “rare biosphere”
- Environmental ScienceProceedings of the National Academy of Sciences
- 2006
It is shown that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment.
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria.
- Biology, MedicineJournal of microbiological methods
- 2007
The intestinal microbiome of the pig
- BiologyAnimal Health Research Reviews
- 2012
A review of the literature is consistent with many of the ecologic principles put forth by Rene Dubos, and there are clear and distinct differences in the composition of the pig intestinal microbiome moving from the proximal end of the intestinal tract to the distal end.
Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
- BiologyApplied and Environmental Microbiology
- 2005
A computer program, DOTUR, is developed, which assigns sequences to OTUs by using either the furthest, average, or nearest neighbor algorithm for each distance level, which addresses the challenge of assigning sequences to operational taxonomic units (OTUs) based on the genetic distances between sequences.
Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures
- Environmental ScienceApplied and Environmental Microbiology
- 2006
A computer program is presented, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.