Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae)

Differences in the bacterial communities along the intestinal tract of juvenile channel (Ictalurus punctatus) and hybrid (I. punctatus× I. furcatus) catfish

Hybrid catfish (Ictalurus punctatus × I. furcatus) is the preferred catfish for US aquaculture due to the heterosis exhibited in many production traits. Improvements in fry production protocols have enabled widespread adoption of these hybrids, with producers using management practices optimized for channel catfish. Research to consider differences, outside of production traits, which may exist between hybrids and their parent species is lacking. Utilizing management practices specifically designed for hybrids may improve production efficiency. The gut microbiome plays critical roles in host development and health and, thus, is relevant to production. In the present study, the microbiota in the anterior, middle, and posterior segments of the intestinal tract were compared between channel and hybrid catfish using high-throughput 16S rRNA gene sequencing. Bacterial community structure was different between channels and hybrids across all intestinal segments (P < 0.05) despite a lack of difference in community diversity. Cetobacterium spp. were found in higher abundances in the middle intestinal segment of hybrids compared with channels (q = 0.02) and found to have a trend of increasing abundance with increasingly distal segments in both channels and hybrids (q < 0.05). Vibrio spp., a low-abundance taxon, was similarly found in higher abundances in the anterior segment of hybrids. These results provide evidence of differences in the gut microbiomes of channels and hybrids and insight into the bacterial communities along the catfish intestinal tract. Additional research will be valuable in understanding why do differences between channel and hybrid catfish exist and how they may contribute to variation in gut microbiome-related production traits.NEW & NOTEWORTHY Hybrid and channel catfish are inhabited by gut bacterial communities of similar overall diversity but of significantly different structure and composition. Cetobacterium spp., a genus previously shown to confer benefits in other hosts, was found in higher abundances in the middle intestinal segment of hybrids and was found to have increasing abundance along the intestinal tract of both channels and hybrids.

Effects of Different Preservation Methods on the Structure and Diversity of Intestinal Microbiota of Marine Fishes

The fish intestine is a complex ecosystem where microbial communities are dynamic and influenced by various factors. Preservation conditions during field collection can introduce biases affecting the microbiota amplified during sequencing. Therefore, establishing effective, standardized methods for sampling fish intestinal microbiota is crucial. This study used hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) to examine the effects of six preservation methods: dry ice (1 day), dry ice (1 day) followed by - 80 °C storage (5 days), liquid nitrogen (1 day), liquid nitrogen (1 day) with subsequent - 80 °C storage (5 days), refrigeration at 4 °C (3 days), and freezing at - 20 °C (3 days), with fresh samples as controls. High-throughput 16S rRNA sequencing assessed microbial diversity, community structure, dominant species, and OTU abundance across treatments. Results indicated that dry ice and liquid nitrogen methods, especially with - 80 °C storage, had minimal impact on microbial diversity and structure. Compared to other preservation methods, refrigeration at 4 °C and freezing at - 20 °C may result in suboptimal reproducibility and altered community structure, particularly affecting rare microbial taxa. This study underscores the need for standardized preservation techniques to ensure accurate fish intestinal microbiota analysis and provides a foundation for future research.

Heterogeneity of the rearing environment enhances diversity of microbial communities in intensive farming

Heterogeneity of the rearing environment in farmed animals can improve welfare and stocking success by enhancing natural behaviours, reducing stress, and decreasing pathogen occurrence. Although microbial diversity is often associated with well-being, their direct and indirect effects on health of farmed animals remain underexplored. We examined the impact of structural heterogeneity of aquaculture tanks on microbial communities in tank biofilm and fish gut microbiome. Enrichment (stones and shelters) significantly promoted microbial diversity and community homogeneity in tank biofilm. However, diversity of gut microbiome did not depend on rearing treatment or microbial composition of the environment. Fish in enriched tanks exhibited greater compositional variation in gut microbiome than those in standard tanks. Tanks without enrichments had higher occurrence of potentially pathogenic bacterial families (Corynebacteriaceae and Staphylococcaceae), while enriched tanks had more beneficial gut microbes (Lactobacillus). Microbial diversity in tank biofilm was negatively associated with fish mortality during a natural epidemic of Flavobacterium columnare, suggesting a protective effect of diverse microbial communities. These findings support environmental enrichment in mitigating disease outbreaks through enhanced microbial diversity, providing important implications for disease control and sustainable health management in aquaculture.

Sex-Specific Effects of Environmental Exposure to the Antimicrobial Agents Benzalkonium Chloride and Triclosan on the Gut Microbiota and Health of Zebrafish (Danio rerio)

The use of disinfectants containing benzalkonium chloride (BAC) has become increasingly widespread in response to triclosan (TCS) restrictions and the COVID-19 pandemic, leading to the increasing presence of BAC in aquatic ecosystems. However, the potential environmental health impacts of BAC on fish remain poorly explored. In this study, we show that BAC and TCS can induce the gut dysbiosis in zebrafish (Danio rerio), with substantial effects on health. Breeding pairs of adult zebrafish were exposed to environmentally relevant concentrations of BAC and TCS (0.4-40 μg/L) for 42 days. Both BAC and TCS exposure perturbed the gut microbiota, triggering the classical NF-κB signaling pathway and resulting in downstream pathological toxicity associated with inflammatory responses, histological damage, inhibited ingestion, and decreased survival. These effects were dose-dependent and sex-specific, as female zebrafish were more susceptible than male zebrafish. Furthermore, we found that BAC induced toxicity to a greater extent than the restricted TCS at environmentally relevant concentrations, which is particularly concerning. Our results suggest that environmental exposure to antimicrobial chemicals can have ecological consequences by perturbing the gut microbiota, a previously underappreciated target of such chemicals. Rigorous ecological analysis should be conducted before widely introducing replacement antimicrobial compounds into disinfecting products.

A metagenomic comparison of clearwater, probiotic, and Rapid BFTTM on Pacific whiteleg shrimp, Litopenaeus vannamei cultures

Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFTTM with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFTTM and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified-V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFTTM) in shrimp culture.

Hatchery tanks induce intense reduction in microbiota diversity associated with gills and guts of two endemic species of the São Francisco River

The São Francisco River (SFR), one of the main Brazilian rivers, has suffered cumulative anthropogenic impacts, leading to ever-decreasing fish stocks and environmental, economic, and social consequences. Rhinelepis aspera and Prochilodus argenteus are medium-sized, bottom-feeding, and rheophilic fishes from the SFR that suffer from these actions. Both species are targeted for spawning and restocking operations due to their relevance in artisanal fisheries, commercial activities, and conservation concerns. Using high-throughput sequencing of the 16S rRNA gene, we characterized the microbiome present in the gills and guts of these species recruited from an impacted SFR region and hatchery tanks (HT). Our results showed that bacterial diversity from the gill and gut at the genera level in both fish species from HT is 87% smaller than in species from the SFR. Furthermore, only 15 and 29% of bacterial genera are shared between gills and guts in R. aspera and P. argenteus from SFR, respectively, showing an intimate relationship between functional differences in organs. In both species from SFR, pathogenic, xenobiont-degrading, and cyanotoxin-producer bacterial genera were found, indicating the critical pollution scenario in which the river finds itself. This study allowed us to conclude that the conditions imposed on fish in the HT act as important modulators of microbial diversity in the analyzed tissues. It also raises questions regarding the effects of these conditions on hatchery spawn fish and their suitability for restocking activities, aggravated by the narrow genetic diversity associated with such freshwater systems.