Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata)

Abstract

We compared the gut prokaryotic communities in wild, organically-, and conventionally reared sea bream (Sparus aurata) individuals. Gut microbial communities were identified using tag pyrosequencing of the 16S rRNA genes. There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. Most of the Bacteria belonged to the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The number of bacterial operational taxonomic units (OTUs) was reduced from the wild to the conventionally reared fish, implying a response of the gut microorganisms to the supplied food and possibly alterations in food assimilation. The dominant bacterial OTU in all examined fish was closely related to the genus Diaphorobacter. This is the first time that a member of the β-Proteobacteria, which dominate in freshwaters, are so important in a marine fish gut. In total the majority of the few Archaea OTUs found, were related to methane metabolism. The inferred physiological roles of the dominant prokaryotes are related to the metabolism of carbohydrates and nitrogenous compounds. This study showed the responsive feature of the sea bream gut prokaryotic communities to their diets and also the differences of the conventional in comparison to the organic and wild sea bream gut microbiota.

Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi

“…Because of the multitude of different DNA extraction methods and analytical methods for investigating these samples, there is no universal method to evaluate the bacterial diversity of fish guts. However, Proteobacteria, Firmicutes, and Bacteroidetes were identified as the major phyla in the gut microbiota of the koi carp, which is similar to the results obtained for sea bream ( Sparus aurata ) (Kormas, Meziti, Mente, & Frentzos, ). Previous studies also revealed a core microbiome from the intestines of fish dominated by Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria (Smriga, Sandin, & Azam, ; Sullam et al., ; Ye, Amberg, Chapman, Gaikowski, & Liu, ).…”

The fish microbiome and its interactions with mucosal tissues

“…Information on the archaeal communities associated with the fish gut is scarce, but Archaea have been detected in fecal or intestinal samples of European flounder Platichthys flesus (van der Maarel et al, 1998(van der Maarel et al, , 1999, gray mullet (van der Maarel et al, 1998Maarel et al, , 1999, gilthead seabream Sparus aurata (Kormas et al, 2014), and grass carp Ctenopharyngodon idella (Ni et al, 2014;Xia et al, 2014). Although information is not available for archaeal abundance, the archaeal diversity appears considerably lower than that of the bacterial communities in the fish GI tract (Li et al, 2014;Ni et al, 2014).…”

“…This core community consisted of 52 bacterial lineages and was dominated by members of the class Bacilli, followed by members of the Alphaproteobacteria and Gammaproteobacteria. Further, the comparison of the gut microbiomes of wild and reared individuals of the same species display a great deal of similarity and common community components (Roeselers et al, 2011;Kormas et al, 2014;Rodiles, Waines, Saoud and Merrifield, unpublished date).…”

“…In contrast however, no Archaea products were detected in two spotted red snapper Lutjanus bohar, whitecheek surgeonfish Acanthurus nigricans, daisy parrotfish Chlorurus sordidus, or zebra-perch sea chub Hermosilla azurea (Fidopiastis et al, 2006;Smriga et al, 2010) when using Archaea targeted approaches. No information is presently available on archaeal functionality or their impacts on host mucosal responses but the majority of archaeal OTUs detected in the seabream gut were anaerobic methanotrophs (Kormas et al, 2014).…”

Probiotics and Other Microbial Manipulations in Fish Feeds

“…Besides bacteria, yeasts are frequently isolated from fish gut, more especially in freshwater (Gatesoupe, 2007;Raggi et al, 2014). Archaea have been also reported in very few studies (van der Maarel et al, 1998(van der Maarel et al, , 1999Ni et al, 2014;Kormas et al, 2014), but methanogens would need further attention, as methane production was reported in fish intestine (Oremland, 1979). Very little is known about bacteriophages in fish intestine (e.g.…”