Several species of Vibrio are the causative agent of gastroenteritis in humans. In aquaculture, Vibrio harveyi (Vh) and V. parahaemolyticus (Vp) have long been considered as shrimp pathogens in freshwater, brackish and marine environments. Here we show by using scanning electron microscopy (SEM) that Penaeus monodon orally inoculated with each of these two pathogens via an Artemia diet had numerous bacteria attached randomly across the stomach surface, in single and in large biofilm-like clusters 6 h post-infection. A subsequent marked proliferation in the number of V. harveyi within the biofilm-like formations resulted in the development of infections in the stomach, the upper and middle midgut, but neither in the posterior midgut nor the hindgut. SEM also revealed the induced production of peritrichous pili-like structures by the Vp attaching to the stomach lining, whilst only a single polar fibre was seen forming an apparent physical bridge between Vh and the host’s epithelium. In contrast to these observations, no such adherences or linkages were seen when trials were conducted with non-pathogenic Vibrio spp. or with Micrococcus luteus, with no obvious resultant changes to the host’s gut surface. In naive shrimp, the hindgut was found to be a favorable site for bacteria notably curved, short-rod shaped bacteria which probably belong to Vibrio spp. Data from the current study suggests that pathogens of P. monodon must be able to colonize the digestive tract, particularly the stomach, where chitin is present, and then they use an array of virulent factors and enzymes to infect their host resulting in disease. Oral infection is a better way of mimicking natural routes of infection; investigating the host-bacteria interactions occurring in the digestive tract may lead to new strategies for the prevention or control of bacterial infections in penaeids.

Despite their immense economic value as a key aquaculture species, the production of Pacific white shrimp ( Litopenaeus vannamei ) faces significant challenges from intensive farming practices and disease outbreaks. Routine microbial profiling for disease surveillance could be a promising approach to anticipate and control disease outbreaks. To achieve this, accuracy in microbial profiling in shrimp ponds is crucial for enabling targeted action and prevention. Extensive documentation emphasizes that, beyond biological factors (related to the host, diet, or health status during the rearing period), technical elements, including sequencing techniques significantly influence bacterial community profiling. This study investigated the influence of short- and long-read sequencing of 16S rRNA genes on the microbial profiles in shrimp intestines, water, and sediments. The origin of the samples (intestine or environmental) in shrimp culture ponds primarily drove the observed differences in core microbial species. The ecological niches accounted for 56% of bacterial community variations in culture ponds. Both sequencing approaches showed consistent results in identifying higher-rank taxa and assessing alpha and beta diversity. However, at the species level, full-length 16S rRNA gene sequences provided better resolution than V3–V4 sequences. For routine microbial profiling in shrimp culture ponds, our study suggests that short-read sequences were sufficient for determining overall bacterial community. IMPORTANCE: This interdisciplinary study investigated the influence of sequencing techniques on bacterial communities profiling within Pacific white shrimp ( Litopenaeus vannamei ) ponds. By integrating aquaculture, microbiology, and environmental science, we revealed the role of ecological niches and factors like salinity and pH on microbiota diversity and composition in shrimp intestines, pond water, and sediment. Additionally, we compared the taxonomic resolution using partial versus full-length 16S rRNA gene sequences, highlighting the value of longer amplicons for precise identification of key taxa. These findings provide novel insights into microbial dynamics underlying environmental effects in shrimp aquaculture. Comprehensive characterization of the pond microbiome could lead to management strategies that promote shrimp health and productivity. Furthermore, the potential of a multi-omics approach for integrating complementary data streams to elucidate environment-microbiome-host interactions was highlighted.

Prebiotics such as mannan-oligosaccharides (MOS) are a promising approach to improve performance and disease resistance in shrimp. To improve prebiotic utilization, we investigated the potential probiotics and their feasibility of synbiotic use in vitro. Two bacterial isolates, Man26 and Man122, were isolated from shrimp intestines and screened for mannanase, the enzyme for mannan digestion. The crude mannanase from both isolates showed optimal activities at pH 8 with optimum temperatures at 60 °C and 50 °C, respectively. The enzymes remained stable at pH 8–10 for 3 h (>70% relative activity). The thermostability range of Man26 was 20–40 °C for 20 min (>50%), while that of Man122 was 20–60 °C for 30 min (>50%). The V_max of Man122 against locust bean gum substrate was 41.15 ± 12.33 U·mg⁻¹, six times higher than that of Man26. The K_m of Man26 and Man122 were 18.92 ± 4.36 mg·mL⁻¹ and 34.53 ± 14.46 mg·mL⁻¹, respectively. With the addition of crude enzymes, reducing sugars of copra meal, palm kernel cake, and soybean meal were significantly increased (p < 0.05), as well as protein release. The results suggest that Man26 and Man122 could potentially be used in animal feeds and synbiotically with copra meal to improve absorption and utilization of feedstuffs.