Quantitative PCR Analysis of Gut Disease-Discriminatory Phyla for Determining Shrimp Disease Incidence

Abstract

There is evidence that gut microbial signatures are indicative of host health status. However, few efforts have been devoted to establishing an applicable technique for determining disease incidence by using gut microbial signatures. Herein, we established a quantitative PCR (qPCR)-based approach to detect the relative abundances of gut disease-discriminatory phyla, which in turn afforded independent variables for quantitatively determining the incidence of shrimp disease. Given the temporal dynamics of gut bacterial communities as healthy shrimp aged, we identified disease-discriminatory phyla after ruling out age-discriminatory phyla. The top 10 disease-discriminatory phyla contributed to an overall 93.2% accuracy in diagnosis ( = 103 samples from shrimp that were determined with high confidence to be healthy or that exhibited apparent disease symptoms and subsequent death), with 70% diagnosis accuracy at the disease onset stage, when symptoms or signs of disease were not apparent. 16S rRNA gene-targeted group-specific primers of five disease-discriminatory phyla were then designed according to their compositions within shrimp gut microbiota, and other primers were borrowed from previous studies. The relative abundances of the 10 disease-discriminatory phyla assayed by qPCR exhibited a high consistency ( = 0.946, < 0.001) with those detected by Illumina sequencing. Notably, using the profiles of disease-discriminatory phyla assayed by qPCR and the corresponding weight coefficients as independent variables, we were able to accurately estimate the incidences of future disease outcome. This work establishes an applicable technique to quantitatively determine the incidence and onset of shrimp disease, which is a valuable attempt to translate scientific research into a practical application. Current studies have identified gut microbial signatures of host health using high-throughput sequencing (HTS) techniques. However, HTS is still expensive and time-consuming and requires a high technical ability, thereby impeding its application in routine monitoring in aquaculture. Hence, it is necessary to seek an alternative strategy to overcome these shortcomings. Herein, we establish a qPCR-based approach to detect the relative abundances of gut disease-discriminatory phyla, which in turn afford independent variables to quantitatively determine the incidence and onset of shrimp disease. Notably, there is a high consistency between the accuracies of disease diagnosis achieved by qPCR and HTS. This applicable technique makes important progress toward defining a diseased state in shrimp and toward solving an important animal health management-driven economic problem.

Response of host–bacterial colonization in shrimp to developmental stage, environment and disease

“…Given the marked changes in gut microbiota in response to disease (Figure ), it is of great interest to identify the taxa that are indicative of shrimp disease. However, the stage‐specific gut microbiota impedes the identification of features characteristic of a “healthy” microbiome (Greenhalgh et al., ; Yu et al., ). As such, we ruled out the 24 taxa that were closely associated with shrimp developmental stages (Figure ).…”

“…However, there is increasing evidence of strong host filters on the symbiotic microbiota, where hosts of the same species living in different aquatic habitats share similar gut bacterial communities (Rungrassamee et al., ; Schmidt, Smith, Melvin, & Amaralzettler, ; Tzeng et al., ). Recently, it became clear that host diseases could attribute to dysbiosis (shifts in the microbial community that have a negative impact on the host [Petersen & Round, ]) in the gut microbiota (Dai, Yu, Xuan, Zhen, & Xiong, ; Nie, Zhou, Qiao, & Chen, ; Xiong et al., ; Yu, Cao, Dai, Qiu, & Xiong, ). In this regard, a better understanding of the route of transmission or acquisition of gut symbionts is indispensable, because it aids in designing better disease management strategies.…”

“…diseases could attribute to dysbiosis (shifts in the microbial community that have a negative impact on the host [Petersen & Round, 2014]) in the gut microbiota (Dai, Yu, Xuan, Zhen, & Xiong, 2018a;Nie, Zhou, Qiao, & Chen, 2017;Xiong et al, 2015a;Yu, Cao, Dai, Qiu, & Xiong, 2018). In this regard, a better understanding of the route of transmission or acquisition of gut symbionts is indispensable, because it aids in designing better disease management strategies.…”

“…Given the functional importance of gut microbiota in preventing pathogen colonization (Inohara, 2013;McFall-Ngai et al, 2013;Xiong, 2018), digestion and energy acquisition (Dai et al, 2018b;Pereira & Berry, 2017;Xiong et al, 2017a), and other conditions, extensive studies have shown that the gut microbiota compositions of aquatic animals are affected by factors such as developmental stage (Xiong et al, 2017b;Yan et al, 2016), health status (Nie et al, 2017;Yu et al, 2018;Zhu et al, 2016), rearing water quality and planktonic microbes (Giatsis et al, 2015). From an ecological perspective, the gut can be considered an "island" for colonizing bacteria within a "sea" of surrounding (e.g., rearing water) environments (Delong, 2014;Yan et al, 2016).…”

Surface structure of cobalt, palladium, and mixed oxide‐based catalysts and their activity in methane combustion studied by means of micro‐Raman spectroscopy

“…A similar situation can be observed in the presence of a toxin such as sulfur oxide. [15,16] Thus, the development of suitable catalysts that overcome some of the drawbacks of palladium is still crucial. [17] One promising direction of development is to use palladium metal only as a dope, compared to the other metals in the proposed catalyst, as shown in our previous studies.…”