Composition of the microbial communities in the gastrointestinal tract of perch (Perca fluviatilis L. 1758) and cestodes parasitizing the perch digestive tract

Using the approach of sequencing the V3‐V4 region of the 16S rRNA gene, we have analysed the bacterial diversity associated with the distinct compartments of the gastrointestinal tract of perch (Perca fluviatilis) and cestodes (Proteocephalus sp.) parasitizing their digestive tract. The dominant microbiota associated with cestodes (Proteocephalus sp.) was represented by bacteria from the genera Serratia, Pseudomonas and Mycoplasma. By comparing the associated microbiota of perch and cestodes, a clear difference in bacterial composition and diversity was revealed between the community from the stomach content and other parts of the gastrointestinal tract of fish. Microbiota associated with cestodes was not significantly different in comparison with microbiota of different subcompartments of perch (mucosa and content of intestine and pyloric caeca) (ADONIS, p > .05) excluding microbiota of stomach content (ADONIS, p ≤ .05). PICRUSt‐based functional assessments of the microbial communities of perch and cestodes indicated that they mainly linked in terms of metabolism and environmental information processing and could play an important role in the nutrition and health of host.info:eu-repo/semantics/acceptedVersio

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish

Aims The aim of the present study was to investigate the composition of the intestinal microbiota during the acute stage of a bacterial infection to understand how dysbiosis of the gut may influence overall taxonomic hierarchy and diversity, and determine if there exists a bacterial taxon(s) that serve as markers for healthy or diseased rainbow trout (Oncorhynchus mykiss). Methods and Results From July to September 2015 29 specimens of three‐year‐old (an average weight from 240.9±37.7 to 850.7±70.1 g) rainbow trout Oncorhynchus mykiss were studied. Next‐generation high‐throughput sequencing of the 16S ribosomal RNA genes was applied to stomach and intestinal samples to compare the impact of infection status on the microbiota of rainbow trout Oncorhynchus mykiss (Walbaum) from the northwest part of Eurasia (Karelian region, Russia). The alpha diversity (Chao1, Simpson and Shannon index) of the microbial community of healthy rainbow trout was significantly higher than in unhealthy fish. The greatest contribution to the gut microbial composition of healthy fish was made by OTU's belonging to Bacillus, Serratia, Pseudomonas, Cetobacterium, and Lactobacillus. Microbiota of unhealthy fish in most cases was represented by the genera Serratia, Bacillus, and Pseudomonas. In microbiota of unhealthy fish there were also registered unique taxa such as bacteria from the family Mycoplasmataceae and Renibacterium. Analysis of similarities (ANOSIM test) revealed the significant dissimilarity between the microbiota of stomach and intestine (p≤0.05). Conclusions A substantial finding was the absence of differences between microbial communities of the stomach and intestine in the unhealthy groups if compared with healthy fish. Significance and Impact of Study These results demonstrated alterations of the gut microbiota of farmed rainbow trout, O. mykiss during co‐infections and can be useful for the development of new strategies for disease control programs.info:eu-repo/semantics/acceptedVersio

Microbial community structure in a host‐parasite system: the case of Prussian carp and its parasitic crustaceans

Aims. The aim of the study was to investigate the skin microbiota of Prussian carp infested by ectoparasites from the genus Argulus and Lernaea. Methods and Results. Associated microbiota of skin of Prussian carp and ectoparasites were investigated by sequencing of the V3, V4 hypervariable regions of 16S rRNA using Illumina MiSeq sequencing platform. Conclusions. According to the Spearman rank correlation test, the increasing load of ulcerations of the skin of Prussian carp was weakly negative correlated with reduction in the abundance of the following taxa: Acrobacter, bacteria C39 (Rhodocyclaceae), Rheinheimera, Comamonadaceae, Helicobacteraceae, and Vogesella. In the present study, the microbiota of ectoparasites from genus Lernaea and Argulus were characterized for the first time. The microbiota associated with L. cyprinacea was significantly different from microbial communities of intact skin mucosa of both infested and uninfested fish and skin ulcers (ADONIS, p≤0.05). The microbiota associated with parasitic crustaceans L. cyprinacea were dominated by unclassified bacteria from Comamonadaceae, Aeromonadaceae families, and Vogesella. The dominant microbiota of A. foliaceus were represented by Flavobacterium, Corynebacterium, and unclassified Comamonadaceae. Significance and Impact of Study. Results from these studies indicate that ectoparasites have the potential to alter skin microbiota, which can play a possible role in transmission of secondary bacterial infection in fish, caused by pathogenic bacteria.info:eu-repo/semantics/acceptedVersio

The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia)

Using the approach of sequencing the V3–V4 region of the 16S rRNA gene, we have analyzed the bacterial diversity associated with the gut and “body” (other parts of nematode after dissection: cuticle, epidermis and longitudinal muscles, etc) of Cystidicola farionis parasitizing the swim bladder of different morphotypes of the nosed charr. Comparisons of the gut microbiota of nematodes with their “body” has revealed that the associated microbiota are closely related to each other. Taxonomic analysis indicated that the relative abundances of the dominant nematode-associated bacteria varied with individual fish. The common dominant microbiota of the gut and “body” of nematodes were represented by Aeromonas, Pseudomonas, Shewanella, and Yersinia, while the associated microbiota of the swim bladder of the nosed charr was dominated by Acinetobacter, Cetobacterium, Pajaroellobacter, Paracoccus, Pseudomonas, Shewanella. By comparing the associated microbiota of nematode parasitizing the different morphotypes of the nosed charr the difference in richness estimates (number of OTU’s and Chao1) were revealed between the N1g and N2 morphs.info:eu-repo/semantics/publishedVersio