Evaluation of biodiversity of lactic acid bacteria microbiota in the calf intestinal tracts

Amplified fragment length polymorphism (AFLPs) were used to analyse the naturally occurring flora of lactic acid bacteria (LAB) in gastrointestinal tracts of two healthy 65-day-old calves. More than 1,000 of presumptive LAB were collected and cultured from the gastrointestinal tracts and, among the isolated colonies, a total of 311 strains were analysed and separated into eight clusters based on AFLP banding patterns. To precisely determine the species inside the clusters, partial sequences of fragments of the 16S ribosomal DNA gene were determined, and sequence homology searches were conducted through GenBank on few strains per cluster. The most representative genera of LAB were Lactobacillus (169 isolates, 54% of total) and Streptococcus (99 isolates, 32% of total), while the most frequent species was identified as L. mucosae with 86 different isolates (51% of the Lactobacillus spp. and 28% of the total). This report gives a first characterization of LAB strain biodiversity recovered directly from calf intestine and is the first account of the presence of the L. mucosae species in calves. Moreover it demonstrates that the AFLP is a robust and useful technique for characterizing the strain level of LAB microflora.