MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes
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A web-based resource, Microbial Community Analysis (MiCA), has been developed to facilitate studies on microbial community ecology that use analyses of terminal-restriction fragment length polymorphisms (T-RFLP) of 16S and 18S rRNA genes. MiCA provides an intuitive web interface to access two specialized programs and a specially formatted database of 16S ribosomal RNA sequences. The first program performs virtual polymerase chain reaction (PCR) amplification of rRNA genes and restriction of the amplicons using primer sequences and restriction enzymes chosen by the user. This program, in silico PCR and Restriction (ISPaR), uses a binary encoding of DNA sequences to rapidly scan large numbers of sequences in databases searching for primer annealing and restriction sites while permitting the user to specify the number of mismatches in primer sequences. ISPaR supports multiple digests with up to three enzymes. The number of base pairs between the 5′ and 3′ primers and the proximal restriction sites can be reported, printed, or exported in various formats. The second program, APLAUS, infers a plausible community structure(s) based on T-RFLP data supplied by a user. APLAUS estimates the relative abundances of populations and reports a listing of phylotypes that are consistent with the empirical data. MiCA is accessible at http://mica.ibest.uidaho.edu/.
KeywordsTerminal Restriction Fragment Length Polymorphism Enzyme Combination Terminal Restriction Fragment Length Polymorphism Analysis Microbial Community Analysis Terminal Restriction Fragment Length Polymorphism Profile
This research was supported by a grant from Procter and Gamble to J.A.F. and L.J.F. and by a grant from the National Institutes of Health (NIH NCRR IP20 RR16448) to L.J.F.
- 4.Cole, JR, Chai, B, Marsh, TL, Farris, RJ, Wang, Q, Kulam, SA, Chandra, S, McGarrell, DM, Schmidt, TM, Garrity, GM, Tiedje, JM (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442–443PubMedCrossRefGoogle Scholar
- 8.Ercolini, D, Moschetti, G, Blaiotta, G, Coppola, S (2001) The potential of a polyphasic PCR-DGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo mozzarella cheese production: bias of culture-dependent and culture-independent analysis. Syst Appl Microbiol 24: 610–617PubMedCrossRefGoogle Scholar
- 18.Michel Jr, FC, Sciarini, SM (2004) Fragsort 4.0, a tool for multiple restriction digestion T-RFLP analysis based on in silico amplification and digestion of 16S ribosomal RNA gene sequences. In: Proceedings of the 10th International Symposium on Microbial Ecology (ISME-10), Poster Session P03CGoogle Scholar
- 22.Schuler, GD (1997) Sequence mapping by electronic PCR. Genomic Methods 7: 541–550Google Scholar
- 28.Wise, MJ, Osborn, AM (2001) TRUFFLER: programs to study microbial community composition and flux from fluorescent DNA fingerprinting data. Proceedings of 2nd IEEE International Symposium on Bioinformatics and Bioengineering (BIBE '01), p 129Google Scholar