Microbial communities in dairy processing environment floor-drains are dominated by product-associated bacteria and yeasts

•Analysis of floor drain water and biofilm bacterial and eukaryotic communities.•Floor drain communities are dominated by product-associated microbes.•Only moderate overlap between drain water and drain biofilm communities was found.

Floor-drains in food production environments harbour diverse microbes and can be contamination sources. To prevent cross-contamination with spoilage organisms or pathogens, sanitation protocols are regularly applied in food processing facilities. Along with product-associated samples, floor-drain water serves as an important indicator in hygiene monitoring in food processing facilities. However, knowledge about the microbial communities in floor-drains is still low. In this study, the microbial communities in floor-drain water and biofilm samples from an Austrian dairy plant were analysed and revealed that floor-drain microbial communities are dominated by product-associated microbes. DNA was extracted of drain water and drain biofilm samples from three different areas (n = 6) of an Austrian cheese production facility. To characterise the bacterial and eukaryotic communities, 16S rRNA gene pyrosequencing as well as cloning and sequencing of 18S rRNA genes were used. Floor-drain communities were dominated by product-associated bacterial (e.g. Lactobacillus kefiranofaciens, Streptococcus thermophilus) and eukaryotic phylotypes (e.g. Debaryomyces hansenii, Saccharomyces unisporus). In addition, putative drain water-derived phylotypes (e.g. Psychrilyobacter atlanticus, Cobetia marina) and ciliates were identified.