Phylogenetic Analysis of Intestinal Microflora Indicates a Novel Mycoplasma Phylotype in Farmed and Wild Salmon

Abstract

All studies of the microbial community of the gastrointestinal tract of salmon to date have employed culture-based approaches, typically on pond- or tank-raised, freshwater animals. We present a phylogenetic survey of the bacterial populations present in the distal intestine of salmon from three different marine locations in Europe. This was accomplished through PCR amplification, cloning, and sequencing of partial 16S rDNA genes from microbial community DNA isolated from the contents of the GI tract distal to the pyloric ceca. Using this approach, the intestinal microbial communities of wild salmon from Scotland and pen-raised salmon from Scotland and Norway were compared. The predominating bacterial populations detected were Acinetobacter junii and a novel Mycoplasma phylotype. This Mycoplasma phylotype apparently comprised approximately 96% of the total microbes in the distal intestine of wild salmon. Substantial differences in intestinal microbial community composition and diversity were observed between the two groups of pen-raised salmon, which, in addition to geographical separation, were raised on different feeds. The microbial profiles found in this study were substantially different from those indicated in earlier culture-based studies for several species of fish, presumably because of the culture-independent techniques employed. Further, analysis of short-chain fatty acids in the digestive tract indicated that the decreasing redox gradient from proximal to distal reaches common to homeothermic animals was absent in salmon, and that the bacterial fermentation levels were much lower than are reported in homeothermic animals.

Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

“…The presence of large numbers of Tenericutes in the gut microbiome is in agreement with multiple studies with vertebrate animals, including studies of the porcine gut (57) and oyster gut (58). The distal gut microbiome of farmed and wild salmon is dominated by Mycoplasma as well (59). However, our results differ from previous studies with rainbow trout (18,19,21,43), in which Proteobacteria, Firmicutes, and Actinobacteria represented the majority of phyla.…”

The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874)

“…Genus Mycoplasma is reported as pathogens for human, animals and plants [40]. However, Holben et al [41] detected a novel Mycoplasma phylotype which comprised for approximately 96 % of the total microbes in the distal intestine of wild Atlantic salmon ( Salmo salar L.), which were substantially different from those indicated in pen-raised salmon from Scotland and Norway. Moreover, the authors speculate the Mycoplasma species could utilize cytoplasmic secretions from the host and produce lactic and acetic acids which subsequently utilized by other bacteria in wild salmon intestine.…”

Characterization of Intestinal Bacteria in Wild and Domesticated Adult Black Tiger Shrimp (Penaeus monodon)

“…Although there have been several studies on bacterial diversity in commonly cultured aquatic species animals from the wild such as P. merguiensis (banana shrimp) [25], Salmo salar L (Atlantic salmon) [26], Gadus morhua L (Atlantic cod) [27], and Danio rerio (zebrafish) [2], there are limited findings on the intestinal bacteria of P. monodon. It was only recently that studies of bacterial diversities in the intestines of P. monodon post-larval and juvenile stages were reported [28], [29], yet there has been no report on the intestinal bacteria of wild-caught P. monodon , which feed on slow-moving benthic animals such as small crabs, shrimp, mollusks, and polychaetes [30].…”