Quantifying the Importance of Abiotic and Biotic Factors Governing the Succession of Gut Microbiota Over Shrimp Ontogeny

Abstract

Intensive studies have evaluated abiotic factors in shaping host gut microbiota. In contrast, little is known on how and to what extent abiotic (geochemical variables) and biotic (i.e., surrounding microbes, younger shrimp, and age) factors assemble the gut microbiota over shrimp ontogeny. Considering the functional importance of gut microbiota in improving host fitness, this knowledge is fundamental to sustain a desirable gut microbiota for a healthy aquaculture. Here, we characterized the successional rules of both the shrimp gut and rearing water bacterial communities over the entire shrimp farming. Both the gut and rearing water bacterial communities exhibited the time decay of similarity relationship, with significantly lower temporal turnover rate for the gut microbiota, which were primarily governed by shrimp age (days postlarval inoculation) and water pH. Gut commensals were primary sourced (averaged 60.3%) from their younger host, rather than surrounding bacterioplankton (19.1%). A structural equation model revealed that water salinity, pH, total phosphorus, and dissolve oxygen directly governed bacterioplankton communities but not for the gut microbiota. In addition, shrimp gut microbiota did not simply mirror the rearing bacterioplankton communities. The gut microbiota tended to be governed by variable selection over shrimp ontogeny, while the rearing bacterioplankton community was shaped by homogeneous selection. However, the determinism of rare and stochasticity of abundant subcommunities were consistent between shrimp gut and rearing water. These findings highlight the importance of independently interpreting host-associated and free-living communities, as well as their rare and abundant subcommunities for a comprehensive understanding of the ecological processes that govern microbial successions.

A meta‐analysis study of the robustness and universality of gut microbiota–shrimp diseases relationship

“…The gut microbial communities of shrimp are highly temporal dynamics over shrimp ontogeny, which are differed significantly even between an interval of a few days (Xiong et al ., 2017a; Zhang et al ., 2021). Similar pattern has also been observed in fishes (Yan et al ., 2012).…”

“…Similar pattern has also been observed in fishes (Yan et al ., 2012). Indeed, shrimp age is the most powerful predictor for the gut bacterial community, resulting in predictable assembly of the gut microbiota as shrimp aged (Xiong et al ., 2020; Zhang et al ., 2021). Thus, a key challenge is how to untangle the deviations of the gut microbiota between health status from these over host lifetime (Greenhalgh et al ., 2016).…”

Microbiota in monocultured Litopenaeus vannamei vs. polyculture with Trachinotus ovatus

“…Hence, this made the structure of the intestinal flora similar to that of the water but different from that of the sediment. It has also been suggested that the feed composition (He et al, 2017), environmental factors (Zhang et al, 2021), individual genetic development (Garibay-Valdez et al, 2020), and disease and season (Li et al, 2019) all influence the diversity of intestinal flora in L. vannamei. The specific factors influencing this warrant further exploration.…”

In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling

“…P. vannamei farming has increased rapidly to meet the growing edible high-quality protein demand. Despite this, P. vannamei farming is constantly hampered by abiotic and biotic factors [ 58 ]. One of the challenges faced by P. vannamei farming relates to emerging diseases caused by bacteria, viruses, and fungi affecting the sustainability of shrimp [ 1 , 31 , 32 ].…”