Maintaining stabilization of the intestinal microbiota is important in preventing bacterial diseases in cultured fish. At present, there have been no reports on the composition and functional analysis of intestinal microbiota in Yunlong Grouper (Epinephelus moara♀ × Epinephelus lanceolatus♂). In this study we analyzed and compared the intestinal microbiota composition of healthy and diseased pond-reared fish to discern the functional profile of a healthy status. The richness and diversity of the intestinal microbiota did not differ significantly between diseased and healthy fish, yet the abundance of predominant phyla like the Proteobacteria were upregulated in the diseased Yunlong Grouper. At the genus level, a significant reduction of Cetobacterium was observed in the intestinal tracts of diseased fish, as Pseudomonas became the most dominant bacterium. To compare the intestinal microorganism abundances between the two health groups of fish, we first screened the gut bacteria and discerned 4 phyla and 12 genera to designate a healthy status in Yunlong Grouper. The environmental bacterial community influenced composition of the intestinal microbiota in Yunlong Grouper, and the intestinal microbiota of diseased fish was more susceptible to the influence of the culture water. In addition, the prediction of functional genes by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that the intestinal microbiota of Yunlong Grouper is related mainly to the terms “metabolism, environmental information processing, genetic information processing, human diseases, and cellular processing; moreover, the functions of the intestinal microbiota differed between the different health states of this fish. The overall results indicate that the occurrence of disease can affect the composition and function of the intestinal microbiota in a cultured fish.
Human host-associated microbial communities in body sites can reflect health status based on the population distribution and specific microbial properties in the heterogeneous community. Bacteria identification at the single-cell level provides a reliable biomarker and pathological information for clinical diagnosis. Nevertheless, biosamples obtained from some body sites cannot offer sufficient sample volume and number of target cells as required by most of the existing single-cell isolation methods such as flow cytometry. Herein we report a novel integrated microfluidic system, which consists of a microemulsion module for single-bacteria encapsulation and a sequential microdroplet capture and release module for selectively extracting only the single-bacteria encapsulated in microdroplets. We optimize the system for a success rate of the single-cell extraction to be > 38%. We further verify applicability of the system with prepared cell mixtures (Methylorubrum extorquens AM1 and Methylomicrobium album BG8) and biosamples collected from human skin, to quantify the population distribution of multiple key species in a heterogeneous microbial community. Results indicate perfect viability of the single-cell extracts and compatibility with downstream analyses such as PCR. Together, this research demonstrates that the reported single-bacteria extraction system can be applied in microbiome and pathology research and clinical diagnosis as a clinical or point-of-care device.
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