Analysis of bacterial and fungal communities in fermented fish (pla-ra) from Northeast Thailand

Our aim was to explore the microbial community composition (bacteria and fungi) of fermented fish (pla-ra) from Northeast Thailand. We also made functional predictions concerning these microbial communities. The association between the microbiota and odor intensity was also analyzed. Fourteen samples of 1-year fermented fish samples derived from seven local markets in Khon Kaen, Northeast Thailand were used. The microbial community composition of each was investigated by sequencing the V1–V9 regions of the 16S rRNA gene (bacteria) and the ITS gene (fungi) using an Illumina MiSeq platform. Functional prediction analysis was conducted through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the use of the bacterial 16S rRNA gene sequences. The bacterial communities were rich, comprising 402 genera from 28 phyla, including such genera as Tetragenococcus, Staphylococcus, Virgibacillus, Lactobacillus and Lentibacillus. The fungal communities comprised 7 phyla and 60 genera, such as Heterobasidion, Densospora, Exophiala and Monascus. The bacterial community functional analysis revealed an association with six biological metabolic pathway categories (e.g., metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases) with 17 subfunctions, showing the richness of bacterial community functions. Odor-association analysis revealed that Brevibacterium, Brachybacterium and Chromohalobacter were more abundant in the weak-odor group, while Noviherbaspirillum was more abundant in the strong-odor group. This study provides a preliminary analysis of pla-ra microbial community structure and function in popular traditional Thai foods. Functional prediction analysis might be helpful to improve our knowledge of the microbiota in fermented fish.