HOST MICROBE INTERACTIONS Bacterial Community Associated with the Intestinal Tract of P. monodon in Commercial Farms Sage Chaiyapechara & Wanilada Rungrassamee & Ittipon Suriyachay & Yanin Kuncharin & Amornpan Klanchui & Nitsara Karoonuthaisiri & Pikul Jiravanichpaisal Received: 6 May 2011 /Accepted: 26 August 2011 /Published online: 14 September 2011 # Springer Science+Business Media, LLC 2011 Abstract The potentially important roles of intestinal bacteria on immune response, disease resistance, and nutrition for the black tiger shrimp Penaeus monodon have been increasingly investigated. However, so far, little is known about the intestinal bacterial community of the shrimp in the commercial aquaculture settings. In this study, the intestinal bacterial communities of juvenile P. monodon (70 individuals) from eight commercial farms in Thailand were examined using 16S rDNA PCR-DGGE, and seven 16S rDNA clone libraries from representative DGGE profiles were constructed. Bacteria in the γ- Proteobacteria class were the only common bacteria group found in the intestinal tracts of shrimp from all farms. The dominant bacterial genera in the intestinal population of each shrimp varied among different farms, and these genera were Vibrio, Photobacterium, Aeromonas, or Propionige- nium (phylum Fusobacteria). Other commonly found genera included Actinomyces, Anaerobaculum, Halospiru- lina, Pseudomonas, Mycoplasma, and Shewanella. Twelve phyla of bacteria including Proteobacteria, Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria, Teneri- cutes, Deinococcus-Thermus, Planctomycetes, Spiro- chaetes, Synergistetes, Thermotogae, and Verrucomicrobia were represented in the sequences. Additionally, strictly anaerobic bacteria such as Propionigenium and Fusibacter were found. These intestinal bacterial communities varied significantly among different commercial farms and were distinct from their rearing water. The results provide descriptive structures of the intestinal bacterial communities of P. monodon in commercial farms, which can further be applied to areas of research on the immunity, disease resistance, and nutrition of shrimp to improve aquaculture of the black tiger shrimp. Introduction Black tiger shrimp (Penaeus monodon) is a major agricul- tural product of high economic values for Thailand in the past decade [11]. However, in recent years, the industry has faced several major challenges such as a lack of suitable captive broodstocks and management of diseases [60]. There are considerable interests in maintaining a healthy and reliable aquaculture production of this native species in Thailand. The interaction between bacteria and their hosts has been recognized as a crucial element in the host animal’s well-being. Bacteria in the gastrointestinal tract of an aquatic animal have increasingly been determined to play a unique part to in host animal gastrointestinal tract development, nutrition, immune responses, and disease resistance [3, 24, 45, 49]. Previous studies in shrimp and other aquatic species suggested that this group of bacteria could also have some beneficial roles in shrimp [15, 24, 49]. The presence of intestinal bacteria in aquatic inverte- brates including crustaceans has been reported, but the roles and the factors affecting these bacteria are not well understood [24, 59]. Aquatic organisms constantly come S. Chaiyapechara (*) : I. Suriyachay : P. Jiravanichpaisal Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, 113 Paholyothin Rd., Klong Luang, Pathumthani 12120, Thailand e-mail: sage.cha@biotec.or.th W. Rungrassamee : Y. Kuncharin : A. Klanchui : N. Karoonuthaisiri Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, 113 Paholyothin Rd., Klong Luang, Pathumthani 12120, Thailand Microb Ecol (2012) 63:938–953 DOI 10.1007/s00248-011-9936-2