Aims The aim of this work was to study the gut microbial diversity from eight species of wild fish with different feeding habits, digestive physiology (gastric vs. agastric) and provide comparative structural analysis of the microbial communities within their environment (food items, water, sediments, and macrophytes). Methods and Results The microbiota of fish gut and their prey items were studied using next generation high‐throughput sequencing of the 16S ribosomal RNA genes. A scatter plot based on PCoA scores demonstrated the microbiota formed three groups: 1) stomach and intestinal mucosa, 2) stomach and intestinal content, and 3) prey and environment. Comparisons using ANOSIM showed significant differences among intestinal content of omnivorous, zoobenthivorous, zooplanktivorous‐piscivorous fishes (p ≤ 0.1). No significant difference was detected for mucosa from the same groups (p > 0.1). Conclusions Neither the interspecies differences in fish diet nor their phylogenetic position had any effect on the microbiome of the intestinal mucosa, but diet did influence the composition of the microbiota of the intestinal content. Significance and Impact of Study The data demonstrate that fish harbored specific groups of bacteria that do not completely reflect the microbiota of the environment or prey.

The values of pH in the digestive tracts of 20 freshwater fish species inhabiting various Russian Federation waterbodies were studied. Only in six species (Coregonus lavaretus, Coregonus migratorius, Catostomus catostomus, Carassius gibelio, Rutilus rutilus, Leuciscus leuciscus) out of 20 species, the differences in pH values between different regions of the intestine were significant. Feeding habits, feeding frequency, and gut fullness in fish affected pH values. Temperature was one of the most important factors affecting pH values. During cold seasons (spring and fall; average water temperature: 8–10 and 5–6^○C, respectively), the pH values in fish guts were higher than that in the summer seasons(water temperature 22–25°C) for C. gibelio, Perca fluviatilis, Cyprinus carpio, L. leuciscus, and R. rutilus from the Chany Lake. Similar results (lower pH values in intestine at higher water temperatures) were also obtained for C. gibelio in warmer years in comparison to colder years in the same waterbody and in L. leuciscus and P. fluviatilis in the different waterbodies with different water temperatures. It is hypothesized that dependence of pH in fish gut on temperature may serve as a regulatory mechanism for maintaining the activities of hydrolytic enzymes at the required level for their successful functioning.

In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTUs, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species. Microbial diversity, community structure, proportions of read numbers derived from each OTU and the total number of OTU's obtained by different DNA extraction protocols could lead to a bias in results obtained in some cases, and therefore researchers should be conservative in conclusions about community structures.