Funding supports Chulalongkorn University Systems Biology, Research Affair,

Faculty of Medicine, Chulalongkorn University, Thailand

Copyright © 2015 Witthaya Poomipak, E-mail: Witthaya.p@chula.ac.th

Witthaya Poomipak1, Kesmanee Praianantathavorn2, Jarika Makkoch2, Ukrit Thongphoom2, Trairak Pisitkul1, Sunchai Payungporn1, 2 1Chulalongkorn University Systems Biology Center, Research affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand

2Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand

Background: Generally, Thai traditional fermented foods contain both non-pathogenic and pathogenic bacterial communities. These pathogenic bacteria may cause symptoms in persons who consume raw fermented foods. However, little is known about bacterial strains in Thai traditional fermented foods. In this study, high-throughput sequencing and metagenomic analyses were perform to identify bacteria communities from Thai traditional fermented foods. Material/methods: Six fermented foods (n=18) including pickled fish, pickled crab, pickled mussel, shrimp paste, fermented lettuce and fermented shoot were collected from three big markets in Bangkok, Thailand. Total DNA was extracted by phenol-chloroform extraction and QIAmp DNA mini kit (QIAGEN). The 16S ribosomal DNA was amplified by using specific primers within a V3/V4 region and then followed by DNA libraries preparation. After that DNA libraries with different indexes were pooled together with equal concentration and pair-end sequenced (250x2) by a MiSeq platform (Illumina®). CLC Genomics Workbench (version 8.0) was applied to identify bacterial species and analyze the metagenomic data. Table1: The table show the name of Top10 common bacteria strain in Thai-fermented foods.

Determination of bacterial communities in Thai fermented foods based on high-throughput DNA sequencing of 16S ribosomal DNA

Results: Metagenomic analysis among 6 fermented foods revealed that different bacterial communities were observed in different fermented foods. Firstly, Klebsiella pneumonia and Weissella hellenica were the predominant bacteria found in fermented lettuce whereas Lactobacillus plantarum and Lactobacillus fermentum were commonly detected in fermented shoot. In addition, Geomicrobium sediminis was the most common bacteria found in pickled crab while Spirochaeta litoralis and Lactococcus lactis were the majority of bacteria in pickled mussel. Moreover, Tetragenococcus muriaticus and Tetragenococcus halophilus were the main bacteria identified in pickled fish however Lentibacillus salinarum and Alkalibacillus halophilus were the most prevalence species in shrimp paste. Conclusions: This study is the first report for identification of bacterial communities in Thai fermented foods based on 16S ribosomal DNA high-throughput sequencing. However, further study should be confirmed for the characteristics of each bacterial strain observed in Thai fermented foods. Top10 Common bacteria were found in 3 markets

fermented lettuce fermented shoot pickled crab pickled fish pickled mussel shrimp paste

K. pneumoniae L. plantarum G. sediminis T. muriaticus S. litoralis L. salinarum

W. hellenica L. fermentum S. soli T. halophilus L. lactis A. halophilus

P. atrosepticum W. hellenica I. calvum H. praevalens V. alginolyticus G. halotolerans

L. lactis L. fuchuensis T. omphalii H. fermentans S. parauberis S. album

A. soli L. paralimentarius R. tesquicola S. sharmensis L. sakei S. salsiraiae

L.acetotolerans L. acetotolerans I. fluminis V. alginolyticus L. raffinolactis H. thailandensis

P. putida L. namurensis S. biformata T. osmophilus N. capsulatum L. halodurans

S. pavanii N. capsulatum C. stylophorae L. acidipiscis S. asiatica H. halophilus

P. stali L. mudanjiangensis M. cryptomonadis L. salivarius P. maris T. muriaticus

X. axonopodis L. composti M. gallinaceum C. haemolyticum V. parahaemolyticus V. alginolyticus

Figure1: Six venn diagram show number of bacteria strain that found in Thai-fermented foods.