Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

Abstract

Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.

The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota

“…Porphyromonadaceae (Bacteroidetes; Bacteroidia; Bacteroidales) is negatively associated with cognitive decline, affective disorders and anxiety-like behavior in aged mice ( Scott et al, 2017 ). Fusobacteriaceae (Fusobacteria; Fusobacteriia; Fusobacteriales) is involved in the fermentative progress of a variety of carbohydrates, amino acids and peptides ( Md Zoqratt et al., 2018 ). Therefore, we hypothesized that the difference in gene function between C. reevesii and T. scripta elegans may be related to their absorption and utilization of food resources.…”

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

“…Also importantly, the V3V4 region was far more diverse, and the top 50 represented~90% of the total families. Other families with intra-group variability include Fusobacteriaceae, more abundant in the intestine, which is dedicated to extract energy through the fermentation of a variety of carbohydrates, amino acids and peptides [64], and the chemo-organotrophic Caulobacteraceae family, more prominent in hepatopancreas with a characteristic alkaline phosphatase activity [65], consistent with the organ function.…”

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

“…Since ASVs are supposed to be consistent biological entities, they provide high levels of reproducibility and comparability across independent studies (Callahan et al ., , ; Amir et al ., ). Initial studies comparing ASVs against OTUs obtained by global clustering approaches from the same samples support these and other advantages of ASVs (Callahan et al ., ; Utter et al ., ; Allali et al ., ; Needham et al ., ; Nearing et al ., ; Zoqratt et al ., ). One congruent finding of all these studies was that distinctively fewer ASVs than OTUs were produced from the same samples, regardless of the sampled habitat.…”