The gut microbiota of aquatic animals plays a crucial role in host health through nutrient acquisition and outcompetition of pathogens. In this study, on the basis of the high-throughput sequencing of 16S rRNA gene amplicons, we examined the bacterial communities in the gut of freshwater shrimp (Mac...
The gut microbiota of aquatic animals plays a crucial role in host health through nutrient acquisition and outcompetition of pathogens. In this study, on the basis of the high-throughput sequencing of 16S rRNA gene amplicons, we examined the bacterial communities in the gut of freshwater shrimp (Macrobrachium nipponense) and in their living environments (sediment and pond water) and analyzed the effects of abiotic and biotic factors on the shrimp gut bacterial communities. High bacterial heterogeneity was observed in the freshwater shrimp gut samples, and the result indicated that both the surrounding bacterial community and water quality factors (particularly dissolved oxygen and temperature) could affect the shrimp gut bacterial community. Despite the observed heterogeneity, 57 genera, constituting 38-99% of the total genera in each of the 40 shrimp gut samples, were identified as the main bacterial population in the gut of M. nipponense. In addition, a high diversity and abundance of lactic acid bacteria (26 genera), which could play significant roles in the digestion process in shrimp, were observed in the shrimp gut samples. Overall, this study provides insights into the gut bacterial communities of freshwater shrimp and basic information for shrimp farming regarding the application of probiotics and disease prevention.
The gut microbiota of aquatic animals plays a crucial role in host health through nutrient acquisition and outcompetition of pathogens. In this study, on the basis of the high-throughput sequencing of 16S rRNA gene amplicons, we examined the bacterial communities in the gut of freshwater shrimp (Macrobrachium nipponense) and in their living environments (sediment and pond water) and analyzed the effects of abiotic and biotic factors on the shrimp gut bacterial communities. High bacterial heterogeneity was observed in the freshwater shrimp gut samples, and the result indicated that both the surrounding bacterial community and water quality factors (particularly dissolved oxygen and temperature) could affect the shrimp gut bacterial community. Despite the observed heterogeneity, 57 genera, constituting 38-99% of the total genera in each of the 40 shrimp gut samples, were identified as the main bacterial population in the gut of M. nipponense. In addition, a high diversity and abundance of lactic acid bacteria (26 genera), which could play significant roles in the digestion process in shrimp, were observed in the shrimp gut samples. Overall, this study provides insights into the gut bacterial communities of freshwater shrimp and basic information for shrimp farming regarding the application of probiotics and disease prevention.
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문제 정의
The animal gut is considered a main route of pathogen transmission [53]; therefore, understanding which pathogenic bacteria is of great importance for shrimp farming. In this study, the investigation of opportunistic pathogens revealed certain potential health risks in shrimp and their living environment. Ten potentially pathogenic genera that have been reported in the previous literature are shown in Table S4.
가설 설정
It is widely accepted that lactic acid bacteria (LAB) are important to the digestion systems of animals, and these bacteria have been intensively applied as probiotic supplements to enhance immunity and disease resistance in aquaculture [46-48]. In this study, we investigated the diversity and abundance of LAB in the shrimp gut samples. Fig.
제안 방법
In this study, the microbial communities in the shrimp guts, pond water, and sediment were analyzed on the basis of 4,452,347 quality-filtered, non-chimeric 16S rRNA gene sequences. Fig.
Therefore, it is difficult to define a core bacterial population shared by all shrimp guts owing to the heterogeneity of the microbial community. In this study, to characterize the dominant bacteria in shrimp guts, we identified the main bacterial genera on the basis of the OTU abundance and frequency.
Bacterial communities in shrimp guts and the surrounding environment (water and sediment) at different sampling times. Sampling was performed separately six times at different sites, in March, April, May, June, July, and September of 2016.
대상 데이터
In this study, freshwater shrimps (M. nipponense) were collected from 25 shrimp ponds at six shrimp farms located in Liyang (LY), Yangzhong (YZ), Wuxi (WX), Suzhou (SZ), Xinghua (XH), and Pukou (PK) of Jiangsu Province, China, between March and September of 2016. Information about the sampling sites and shrimp is summarized in Table S1.
The purified PCR products were sent to Jiangsu Zhongyijinda Analytical & Testing Co., Ltd. (China) for library preparation and high-throughput sequencing on the MiSeq platform (Illumina, USA).
이론/모형
On the basis of the relative abundance of OTUs, the NMDS plot (Fig. 2), a nonparametric method that provides graphical ordination of the experimental data [37], was employed to compare the similarity of the microbial community composition among different samples. As expected, the three kinds of samples were clearly separated and formed three distinct clusters owing to the significantly different bacterial communities.
The taxonomy of the representative sequence of each OTU was assigned with the RDP Classifier [30]. The differences in the microbial community among different samples were analyzed by nonmetric multidimensional scaling (NMDS) based on Bray-Curtis distance. In addition, redundancy analysis (RDA) was used to reveal the relationships between the water quality parameters and the abundance of the major OTUs.
The distances were determined using the Bray-Curtis method on the basis of OTU relative abundance.
3) with the “gplots” and “vegan” packages. The significantly different taxa in different groups of samples were determined and visualized using linear discriminant analysis effect size (LEfSe), a statistical tool designed to find biomarkers from the data with default parameters [31].
성능/효과
4C). At the phylum level, the four most abundant taxa were Proteobacteria, Firmicutes, Bacteroidetes, and Acidobacteria, which showed an abundance ranging from 2.44-95.07%, 0.18-65.02%, 0.01-35.76%, and 0.01- 10.49%, respectively.
In addition, Clostridium XlVb (5.10 ± 0.19%), Aeromonas (4.52 ± 1.17%), Citrobacter (4.00 ± 0.36%), and Bacillariophyta (1.95 ± 0.54%) were other major genera in the shrimp gut samples.
In conclusion, the results of this study revealed high bacterial heterogeneity in freshwater shrimp guts, and Proteobacteria was found to be the most abundant bacterial group in freshwater gut samples (accounting for 51.40 ±1.92% on average), which significantly differs from the results reported in seawater shrimp.
In the pond water samples, the dominant OTUs were assigned to Bacillariophyta (4.57 ± 0.09%), Aeromonas (3.57 ± 0.12%), GpI (1.79 ± 0.23%), Acinetobacter (1.76 ± 0.32%), and GpIIa (1.67 ± 0.43%).
4C). It was found that the potential pathogenic bacteria belonging to Yersinia and Lawsonia accounted for 92.01% and 81.97% of these two samples, respectively (Fig. 4C). At the phylum level, the four most abundant taxa were Proteobacteria, Firmicutes, Bacteroidetes, and Acidobacteria, which showed an abundance ranging from 2.
The most abundant OTU (representing 10.45 ± 1.46% of all bacterial sequences on average) was assigned to the genus Dongia.
후속연구
In summary, an ecological perspective may greatly contribute to disease prevention and control in aquaculture animal production. Further studies are needed to investigate the detailed underlying mechanisms and to develop practical approaches.
Moreover, some potentially pathogenic genera were identified. Future research should focus on the functions of the bacteria in the shrimp gut to provide information for establishing sustainable microbial management strategies for shrimp farming.
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