MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes

Abstract

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/.

The effect of high-fat diet on the composition of the gut microbiota in cloned and non-cloned pigs of lean and obese phenotype

“…The bands present in both duplicates were accepted as bacterial fragments and the duplicate with the best intensity was chosen for microbial profiling. T-RF profiles were subsequently identified in silico using the MiCA online software 30 and 16S rRNA gene sequences were assigned to their taxonomic names on the Ribosomal Database project. 31 All the data was transferred to Microsoft Excel for further analysis.…”

Effects of feeding finisher pigs with chicory or lupine feed for one week or two weeks before slaughter with respect to levels of Bifidobacteria and Campylobacter

“…The mean relative intensity of each T-RF within a sample was calculated by dividing the area of that individual peak with the total area of all peaks on the electropherogram. To identify possible bacterial genus corresponding to the individual T-RFs (61 bp) in this study, a virtual digest was made on a comprehensive published 16S rRNA gene bacterial clone library from pigs and mammals (Leser et al, 2002;Ley et al, 2008) by inserting the primer sequences and restriction enzymes used in this study into the online programme silico MiCA virtual digest (Shyu et al, 2007). All the potential 16S rRNA gene sequences that matched the detected T-RFs were aligned in RDP version 10 (http://rdp.cme.msu.edu) and assigned (if possible) to a bacterial class and genus.…”

The effect of a diet with fructan-rich chicory roots on intestinal helminths and microbiota with special focus on Bifidobacteria and Campylobacter in piglets around weaning

“…The mean relative intensity of each T-RF within a sample was calculated by dividing the area of that individual peak with the total area of all peaks on the electropherogram. To identify possible bacterial species corresponding to the individual T-RFs in this study, a virtual digest was done on a previously published 16S rRNA gene bacterial clone library from pigs (Leser et al, 2002) by inserting the primer sequences and restriction enzymes used in this study into the online program silico MiCA virtual digest (Shyu et al, 2007). The 16S rRNA gene sequences matching significant T-RFs for either treatment group were classified to bacterial groups by using the classifier function in RDP Release 10 (http:// rdp.cme.msu.edu/classifier/classifier.jsp).…”