Insights into the Gut Microbiota of Freshwater Shrimp and Its Associations with the Surrounding Microbiota and Environmental Factors

Abstract

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 highthroughput 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.

Spatiotemporal successions of shrimp gut microbial colonization: high consistency despite distinct species pool

“…Our SEM results showed that water salinity, temperature and DO are determinants in driving the successions in shrimp gut microbiota (Fig. 5), corroborating previous findings obtained in shrimp gut systems (Zhao et al, 2018;Xiong et al, 2018a). The noteworthy finding is that, when compared with bacterioplankton community, water variables shaped the shrimp gut microbiota by conjointly direct and indirect effects (Supporting Information Table S3).…”

“…The large proportion of 'unknown' source could be colonized into the gut from other environmental sources that we did not investigate, such as vertical transmission, sedimentary biofilm, food or shrimp care staff. However, ample evidence has shown that the bacterial communities in shrimp gut are significantly distinct from these in rearing water and sediment (Xiong et al, 2015;Cornejo-Granados et al, 2017;Hou et al, 2018;Zhao et al, 2018). Alternatively, these 'unknown' bacteria were present in the rearing water but undetected here.…”

“…1), with sampling location only contributing 5.3% variation in bacterial community (Table 1). However, ample evidence has shown that the bacterial communities in shrimp gut are significantly distinct from these in rearing water and sediment (Xiong et al, 2015;Cornejo-Granados et al, 2017;Hou et al, 2018;Zhao et al, 2018). In other words, the dominant taxa in shrimp gut do not share their niche preferences with these in rearing environment.…”

Assessment of the Dynamics of Microbial Community Associated with Tetraselmis suecica Culture under Different LED Lights Using Next-Generation Sequencing

“…The results of artificial conditions in the laboratory are essential to understanding the growth characteristics in outdoor cultures [27]. The culture was non-axenic, which is associated with bacteria present in the natural environment and cultured with algae [16]. Besides, the non-axenic microalgae cultures are applied in the green-water technique, and it is important to recognize the microbiota associated with the microalgae cultures [28].…”

“…However, since the bacterial communities are difficult to observe directly, they are first separated by isolation and then analyzed using methods such as clone libraries or RFLP [14,15], which requires a lot of time and effort. Next-generation sequencing (NGS) is a technique used to quickly analyze microbiota in detail without isolating the microorganism separately [16,17]. There are two ways; the first is a nucleotide sequence analysis targeting 16S rRNA and the second is a shotgun method.…”