Chryseobacterium mulctrae sp. nov., isolated from raw cow's milk

Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets

BACKGROUND

Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made to evaluate novel feed formulations, focusing especially on the effects on the fish gut microbiome. Few studies have explored host-environment interactions. In the present study, we evaluated the influence of novel insect-based (Tenebrio molitor) fish diets on the microbiome at the water-fish interface in an engineered rainbow trout (Oncorhynchus mykiss) farming ecosystem. Using 16S rRNA gene metabarcoding, we comprehensively analyzed the microbiomes of water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples.

RESULTS

Core microbiome analysis revealed the presence of a highly reduced core shared by all sample sources, constituted by Aeromonas spp., in both the control and novel feed test groups. Network analysis showed that samples were clustered based on the sample source, with no significant differences related to the feed formulation tested. Thus, the different diets did not seem to affect the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. To disentangle the contribution of feed at a finer scale, we performed a differential abundance analysis and observed differential enrichment/impoverishment in specific taxa, comparing the samples belonging to the control diet group and the insect-based diet group.

CONCLUSIONS

Omic exploration of the water-fish interface exposes patterns that are otherwise undetected. These data demonstrate a link between the environment and fish and show that subtle but significant differences are caused by feed composition. Thus, the research presented here is a step towards positively influencing the aquaculture environment and its microbiome.

Chryseobacterium endalhagicum sp. nov., isolated from seed of leguminous plant

A Gram-stain-negative, yellow-pigmented bacterium, designated as L7^T, was isolated from seeds of Alhagi sparsifolia Shap., a leguminous plant that grows in northwest PR China. Strain L7^T was found to be non-flagellated, non-spore forming rods which can grow at 10–37 °C, pH 6.0–8.5 and in 0–3 % (v/w) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain L7^T belongs to the genus Chryseobacterium with sequence similarities to Chryseobacterium vietnamense GIMN1.005^T (98.1%), C. bernardetii NCCTC13530^T (98.0%), C. vrystaatense LMG 22846^T (97.9%), C. nakagawai NCTC13529^T (97.7%), C. shigense DSM 17126^T (97.6%) and C. rhizosphaerae RSB3-1^T (97.5%). The average nucleotide identity of strain L7^T to 31 reference strains were 78.6–85.6 %, lower than the species delineation threshold of 95 %. MK-6 was the only respiratory quinone of L7^T and major fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH, C_16 : 1 ω7c and/or C_16 : 1 ω6c, isoC_17 : 1 ω9c and/or C_16 : 0 10-methyl. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, two unidentified aminolipids, three unidentified glycolipids and two unidentified lipids. The G+C content of the genome was 38.58 mol%. On the basis of polyphasic taxonomy analyses in this study, strain L7^T is considered to represent a novel species in the genus Chryseobacterium, for which the name Chryseobacterium endalhagicum sp. nov. is proposed. The type strain is L7^T (=MCCC 1K05687^T=JCM 34506^T)