Katsoulis-Dimitriou, S. | Search bioRxiv

bioRxiv2026

Distinct Daphnia spp. whole-body bacterial microbiota in two contrasting Mediterranean lakes

The microbiota and microbiome associated with zooplankton remains rather understudied compared to other animal groups and/or taxa. The present study aimed at investigating the whole-body bacterial microbiota of Daphnia spp. in two contrasting Greek lakes, the shallow and hypertrophic Lake Koronia vs. the deep and mesotrophic Lake Vegoritida, including both egg-bearing and non-egg-bearing individuals. In both lakes, 2,060 bacterial operational taxonomic units (OTUs) were found, with 223 of them being conditionally rare (crOTUs) with low contribution even for the dominant phyla, with L. Vegoritida having more crOTUs than L. Koronia. The individuals microbiota had inconsiderable overlap with the surrounding water microbiota in both lakes. The two lakes showed significant differences in their Daphnia -associated microbiota. L. Koronia had richer OTUs and rather homogeneous bacterial communities, with higher occupancy. Overall, no significant differences in between the microbiota of egg-bearing and non-egg-bearing Daphnia individuals in both lakes. However, regarding the most important OTUs (miOTUs), the L. Koronia miOTUs were highly overlapped between the individuals with and without eggs, with only one missing from the individuals without eggs. In L. Vegoritida the individuals without eggs had only six miOTUs and while egg-bearing individuals had nine different ones; the two lakes had no shared miOTUs., considerable differences occurred.. A total of 27 miOTUs, was found and belonged to the Pseudomonadota, unclassified Bacteria, Cyanobacteria, Bacteroidota, Bacillota and Actinomycetota. Those miOTUs, where assignment to the genus level was possible, they were related to Cyanobium, Mucilaginibacter, Flavobacterium and Staphylococcus. This study showed that lake morphotype and ecological status can exert some impact on Daphnia-associated bacterial microbiota, with more pronounced effects on egg-bearing and non-egg-bearing individuals.

microbiology↗

bioRxiv2024

The effect of dietary fish oil replacement by microalgae on the gilthead sea bream midgut bacterial microbiota

It is well known that the gut microbiome and its interaction with the host influence several important factors for fish health such as nutrition and metabolism. Diet is one of the main factors influencing the composition of the gut microbiome in reared fish. Microalgae, due to their high fatty acid content, appear to be a promising alternative for replacing fish oil in aquafeed. Thus, the aim of this work was to evaluate the effects of dietary microalgae blends as fish oil replacers on the midgut bacterial microbiota of the gilthead sea bream (Sparus aurata). The control diet (FO) contained only fish oil as source of lipids, EPA and DHA fatty acids, while three experimental diets were used where fish oil was replaced at 67% by one of the following microalgae biomass blends: Microchloropsis gaditana and Isochrysis sp. (Tisochrysis lutea) (MI), Phaeodactylum tricornutum and Isochrysis sp. (PI) and Schizochytrium sp. and P. tricornutum (SP). The midgut bacterial community composition of the experimental diets was altered compared to the control diet. There were 11 operational taxonomic units (OTUs) which were highly abundant in FO compared to the three experimental diets (FO, MI, SP) and two OTUs that were found in high abundance in both FO and the experimental diets in all comparisons (FO-MI, FO-PI, FO-SP). Most of the highly abundant OTUs in the experimental diets were unique to each experimental diet, with two OTUs being found in common between FO-MI and FO-PI. Additional evidence from the presumptive bacterial functional metabolic pathways suggested that the microalgae-based diets resulted in one over-expressed and one under-expressed pathway. The overexpressed pathway was related to the metabolism of fucose, a major constituent of the polysaccharide content of several microalgal species. Peptidoglycan biosynthesis was the under-expressed metabolic pathway. This suggests that a new gut microbiota profile was selected due to the microalgae inclusion in the provided diet. This study showed that, with the absence of mortality in fish, the gilthead sea bream gut microbiome can smoothly adapt its function according to the metabolic capacity of the dietary microalgae combinations that were used. The MI feed seems to promote several beneficial bacteria with potential probiotic abilities in the fish gut, belonging to the Pseudoalteromonas, Pseudomonas, Bacillus and Rhodopseudomonas genera.

microbiology↗