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Comparison of three methods to enumerate gut microbiota of weanling piglets fed insoluble dietary fibre differing in lignin content

SUMMARY The aim of the current study was to compare three methods for determining the influence of different feeding strategies on the gut microbiota of piglets. Forty-eight weanling piglets were fed four different diets enriched with insoluble dietary fibre (wheat bran and pollen from Pinus massoniana). Starting from ileal and colonic samples, the total microbial DNA was isolated and bacterial parameters (lactobacilli, bifidobacteria, Bacteroides vulgatus and total bacterial counts) were quantified using real-time polymerase chain reaction (PCR). The results for lactobacilli, bifidobacteria and total bacterial counts were compared with those obtained by fluorescence in situ hybridization (FISH) and cultivation method. No significant differences could be observed between dietary treatments with real-time PCR and FISH for all investigated parameters. Comparing the applied three methods no consistent results were achieved, whereas FISH usually showed lower values. It was shown that real-time PCR can be regarded as an alternative to conventional techniques and also as a complement to results obtained from conventional culture method.