Determination of microbial diversity in environmental samples: pitfalls of PCR‐based rRNA analysis
2.2K
TL;DR: Specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis are covered.
read more
Abstract: After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation.
Wilfred F. M. Röling,Michael G. Milner,D. Martin Jones,Kenneth Lee,Fabien Daniel,Richard J. P. Swannell,Ian M. Head +6 more
TL;DR: The extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally, rather than N and P limited degradation over the concentration range tested.
Extracellular DNA in soil and sediment: fate and ecological relevance.
Giacomo Pietramellara,Judith Ascher,Federica Borgogni,Maria Teresa Ceccherini,G. Guerri,Paolo Nannipieri +5 more
TL;DR: The characterisation of extracellular DNA can integrate information on the composition of the microbial community of soil and sediments obtained by analysing intracellular DNA.
538
Species divergence and the measurement of microbial diversity
Catherine A. Lozupone,Rob Knight +1 more
TL;DR: Divergence-based methods are providing new insights into microbial community structure and function because microorganisms in a community differ dramatically in sequence similarity, which also often correlates with phenotypic similarity in key features such as metabolic capabilities.
522
•Journal Article
Metagenomics: DNA sequencing of environmental samples
TL;DR: Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest.
A Bioinformatician's Guide to Metagenomics
TL;DR: In this article, the authors describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step, and provide recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies.
References
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
12K
16S ribosomal DNA amplification for phylogenetic study.
TL;DR: A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described in this paper.
11.6K
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
TL;DR: Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.
9.3K
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Fleischmann Rd,Adams,Owen White,Rebecca A. Clayton,Ewen F. Kirkness,Anthony R. Kerlavage,Carol J. Bult,J F Tomb,Brian Dougherty,Merrick Jm +9 more
TL;DR: An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence of the genome from the bacterium Haemophilus influenzae Rd.
6.2K
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.
TL;DR: Fluorescent oligonucleotide hybridization probes were used to label bacterial cells for analysis by flow cytometry and the intensity of fluorescence was increased additively by the combined use of two or three fluorescent probes complementary to different regions of the same 16S rRNA.
4.3K