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A Comparison Of Random Sequence Reads Versus 16S RDNA Sequences For Estimating The Biodiversity Of A Metagenomic Library
C. Manichanh, Charles E. Chapple, L. Frangeul, K. Gloux, Roderic Guigó, J. Doré
Published 2008 · Biology, Medicine
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The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10 010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.
This paper references
Comparative Metagenomics of Microbial Communities
S. Tringe (2005)
Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms
I. Head (1998)
Microbiome Metagenomic Analysis of the Human Distal Gut
S. R. Gill (2009)
Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut
A. Suau (1999)
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
H. Martín (2006)
Basic local alignment search tool.
S. Altschul (1990)
Genetic diversity in Sargasso Sea bacterioplankton
S. Giovannoni (1990)
The uncultured microbial majority.
M. Rappé (2003)
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
F. Warnecke (2007)
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
J. Cole (2009)
Metagenomics: Application of Genomics to Uncultured Microorganisms
J. Handelsman (2004)
Metagenomic Analysis of the Human Distal Gut Microbiome
S. Gill (2006)
Accurate phylogenetic classification of variable-length DNA fragments
A. McHardy (2007)
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
H. Teeling (2004)
Informatics for unveiling hidden genome signatures.
T. Abe (2003)
Metagenomics: DNA sequencing of environmental samples
S. Tringe (2005)
Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.
T. Abe (2005)
A quantitative map of nucleotide substitution rates in bacterial rRNA.
Y. Van de Peer (1996)
Diversity of the Human Intestinal Microbial Flora
P. Eckburg (2005)
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.
O. Béjà (2000)
Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles
R. Massana (2004)
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.
S. Acinas (2004)
Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms
M. R. Rondon (2000)
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
J. Cole (2007)
Prokaryotes: the unseen majority.
W. Whitman (1998)
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Venter (2004)
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
M. Kimura (2005)
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine
M. Claesson (2009)
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
D. J. Lane (1985)
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
C. Manichanh (2006)
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
J. Castresana (2000)
PHYLIP Phylogeny Inference Package version 3.5c. Seattle: Department of Genetics
J Felsenstein (1993)
Unsuspected diversity among marine aerobic anoxygenic phototrophs
O. Béjà (2002)
High diversity in DNA of soil bacteria.
V. Torsvik (1990)
MEGAN analysis of metagenomic data.
D. Huson (2007)
Phylogeny Inference Package version 3.5c
Microbial diversity in the deep sea and the underexplored “rare biosphere”
M. Sogin (2006)
The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis
P. McKenna (2008)
Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing.
T. M. Schmidt (1991)
Phylogenetic classification of short environmental DNA fragments
L. Krause (2008)
Dinucleotide relative abundance extremes: a genomic signature.
S. Karlin (1995)
Bacterial Community Variation in Human Body Habitats Across Space and Time
E. K. Costello (2009)
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
J. Thompson (1994)
rrndb: the Ribosomal RNA Operon Copy Number Database
J. A. Klappenbach (2001)
Fine-scale phylogenetic architecture of a complex bacterial community
S. Acinas (2004)
This paper is referenced by
Neisseria gonorrhoeae and humans perform an evolutionary LINE dance
M. T. Anderson (2011)
Comparison of Statistical Methods to Classify Environmental Genomic Fragments
G. Rosen (2010)
SSuMMo: rapid analysis, comparison and visualization of microbial communities
Alex L. B. Leach (2012)
When old metagenomic data meet newly sequenced genomes, a case study
X. Li (2018)
Gut-liver axis: role of inflammasomes.
Manan Bawa (2013)
THE HUMAN INTESTINAL MICROBIOTA ; FROM PHYLOGENETICS TO FUNCTIONAL METAGENOMICS
J. Doré (2010)
Le microbiote intestinal humain
J. Dore (2010)
Lower Gastrointestinal Microbiota in Health and Irritable Bowel Syndrome : Characterisation and Effect of Probiotic Intervention
L. Krogius-Kurikka (2011)
Comparative Genomics of Pathogens
E. Ivanova (2010)
i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets
M. H. Mohammed (2011)
Metagenomic Analyses: Past and Future Trends
Carola Simon (2010)
Metagenome Fragment Classification Using N-Mer Frequency Profiles
G. Rosen (2008)
Integrating Metagenomics and Geochemistry: Functional Evolution and Taxonomic Classification of Hot Spring Communities
Eric B. Alsop (2014)
[The human intestinal microbiota].
J. Doré (2010)
Exploring the influence of the gut microbiota and probiotics on health: a symposium report
L. Thomas (2014)
Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.
Samuel Jacquiod (2014)
R. Daniel (2011)
Flexible taxonomic assignment of ambiguous sequencing reads
J. C. Clemente (2010)
The Effect of Sequence Error and Partial Training Data on BLAST Accuracy
Steven D. Essinger (2010)
Culture-independent molecular tools for soil and rhizosphere microbiology
Vivian A. Rincon-Florez (2013)
Taxonomic Assignment in Metagenomics with TANGO
Daniel Alonso-Alemany (2011)
The Microbiome and Chronic Rhinosinusitis.
Do-Yeon Cho (2020)
Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real‐time PCR
S. Mieszkin (2010)
Metagenomics and future perspectives in virus discovery
John Mokili (2012)
Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials
N. Somboonna (2014)
Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces.
Nicolas Danylec (2018)
Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn’s disease
P. Ricanek (2012)
Metagenomic Analyses of Glacier Ice
Carola Simon (2009)
Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.
Magdalena Kröber (2009)
Nutrients , Enzyme Activities , and Microbial Communities of Major Soils used for Tobacco Production in Yunnan , China
Congming Zou (2018)
Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies.
Vincent Thomas (2015)
MICROBIOME OF TRADITIONAL CHINESE SOY SAUCE
K. Lumpur. (2014)See more