Abstract
BackgroundGiven the lack of genetic background, the source tracking unknown individuals of fish species with both farmed and wild populations often cannot be robustly achieved. The gut microbiome, which is shaped by both deterministic and stochastic processes, can serve as a molecular marker of fish host source tracking, particularly as an alternative to the yet-to-be-established host genetic marker. A candidate for testing the feasibility is the large yellow croaker, Larimichthys crocea, which is carnivorous and ranks the top mariculture fish in China. Wild resource of this fish was depleted decades ago and might have potential problematic estimation because of escaping of farmed individuals.ResultsThe rectums of wild (n = 212) and farmed (n = 79) croakers from multiple batches were collected for the profiling of their gut bacterial communities. The farmed individuals had a higher alpha diversity and lower bacterial load than the wild individuals. The gut microbiota of the two sources exhibited divergence and high inter-batch variation, as featured by the dominance of Psychrobacter spp. in the wild group. Predicted functional capacity of the gut microbiome and representative isolates showed differences in terms of host source. This difference can be linked to the potential diet divergence between farmed and wild fishes. The non-stochastic distribution pattern of the core gut microbiota of the wild and farmed individuals supports the feasibility of microbiota-based host source tracking via the machine learning algorithm. A random forest classifier based on the divergence and non-stochastic assembly of the gut microbiome was robust in terms of host source tracking the individuals from all batches of croaker, including a newly introduced batch.ConclusionsOur study revealed the divergence of gut microbiota and related functional profiles between wild and farmed croakers. For the first time, with representative datasets and non-stochastic patterns, we have verified that gut microbiota can be robustly applied to the tracking of host source even in carnivorous fish.-VfFipfewh2ysdDNC2-2i-Video abstract
Highlights
Microbes living in animal gastrointestinal tracts play important roles in the nutrition and health of their hosts through extensive metabolic and immune interactions [1,2,3,4]
A variety of factors, such as source, habitat, diet, size, life-stage or age, and geographic origin, have a strong impact on the microbiomes in fish gut [5, 8,9,10] herbivorous and omnivorous fishes usually have higher selectivity in their intestine compared with carnivorous fish [11, 12], while host selectivity in certain microbial taxa has been reported for carnivorous Atlantic salmon [13]
The results further indicate that non-stochastic processes dominate the assembly of the major and core taxa in the guts of croaker, especially (See figure on page.) Fig. 4 Distribution of the core Operational taxonomic unit (OTU) and the goodness-of-fit to neutral model for the gut microbiota
Summary
Microbes living in animal gastrointestinal tracts play important roles in the nutrition and health of their hosts through extensive metabolic and immune interactions [1,2,3,4]. Core microbial taxa, which can be detected in most or all host individuals, can help to elucidate the patterns of physiological interactions and evolutionary relationships between microbes and hosts [6, 12, 14, 15]. In most of those studies, the core taxa were proposed on the basis of limited sampling batches despite the high dynamics of fish gut microbiota. A candidate for testing the feasibility is the large yellow croaker, Larimichthys crocea, which is carnivorous and ranks the top mariculture fish in China Wild resource of this fish was depleted decades ago and might have potential problematic estimation because of escaping of farmed individuals
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
