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.

Among emerging zoonotic pathogens, mosquito-borne viruses (MBVs) circulate between vertebrate animals and mosquitoes and represent a serious threat to humans via spillover from enzootic cycles to the human community. Active surveillance of MBVs in their vectors is therefore essential to better understand and prevent spillover and emergence, especially at the human–animal interface. In this study, we assessed the presence of MBVs using molecular and phylogenetic methods in mosquitoes collected along an ecological gradient ranging from rural urbanized areas to highland forest areas in northern Thailand. We have detected the presence of insect specific flaviviruses in our samples, and the presence of the emerging zoonotic Tembusu virus (TMUV). Reported for the first time in 1955 in Malaysia, TMUV remained for a long time in the shadow of other flaviviruses such as dengue virus or the Japanese encephalitis virus. In this study, we identified two new TMUV strains belonging to cluster 3, which seems to be endemic in rural areas of Thailand and highlighted the genetic specificities of this Thai cluster. Our results show the active circulation of this emerging flavivirus in Thailand and the need for continuous investigation on this poorly known but threatening virus in Asia.

Fipronil was evaluated as a systemic control agent for the rat flea Xenopsylla cheopis (Rothschild), the main vector of Yersinia pestis (Yersin), the causative agent of plague, in Madagascar. The effectiveness of fipronil as a systemic control agent against X. cheopis was assessed by determining the toxicity values of the "Lethal Dose 50" (LD50). Two techniques were used to evaluate the systemic action of the insecticide on the vector: 1) an artificial feeding device filled with blood-fipronil mixture from which X. cheopis was fed and 2) rodent hosts, Rattus norvegicus (Berkenhout) and Rattus rattus (L.), which fed on fipronil-treated bait. As a standardized control method, the susceptibility of X. cheopis to fipronil was evaluated by exposure to impregnated paper within World Health Organization (WHO) insecticide test protocol to compare its effect to the systemic activity of the studied insecticide. Results showed that when administered in a systemic way, fipronil appears to be more effective: the toxicity level was evaluated to be ninefold higher compared with the WHO test. Compared with other methods, which require indiscriminate dusting of rodent burrows and human dwellings, fipronil applied in a systemic way enables the direct targeting of the plague vector. Thus, this method appears to be a superior alternative to fipronil-dusting for the control of the main plague vector in Madagascar. However, subsequent tests in the field are necessary to confirm the suitability of fipronil administration in a systemic way on large scales.