Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts

The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes

Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ13C and δ15N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.

Identifying macroplastic pathobiomes and antibiotic resistance in a subtropical fish farm

Macroplastics are ubiquitous in aquaculture ecosystems. However, to date the potential role of plastics as a support for bacterial biofilm that can include potential human pathogenic bacteria (PHPB) and antibiotic-resistant bacteria (ARB) has been largely overlooked. In this study, we used a combination of metabarcoding and standard antibiotic susceptibility testing to study the pathobiome and resistome of macroplastics, fish guts and the environment in a marine aquaculture farm in Mauritius. Aquaculture macroplastics were found to be higher in PHPB, dominated by the Vibrionaceae family (0.34 % of the total community), compared with environmental samples. Moreover, isolates from aquaculture plastics showed higher significant multiple antibiotic resistance (MAR) compared to non-plastic samples of seawater, sediment and fish guts. These results suggest that plastics act as a reservoir and fomite of PHPB and ARB in aquaculture, potentially threatening the health of farmed fish and human consumers.

Comparative analysis of intestinal microbiota composition and transcriptome in diploid and triploid Carassius auratus

Polyploidy and the microbiome are crucial factors in how a host organism responds to disease. However, little is known about how triploidization and microbiome affect the immune response and disease resistance in the fish host. Therefore, this study aims to identify the relationship between intestinal microbiota composition, transcriptome changes, and disease resistance in triploid Carassius auratus (3nCC). In China's central Dongting lake water system, diploid (2nCC) and triploid Carassius auratus were collected, then 16S rRNA and mRNA sequencing were used to examine the microbes and gene expression in the intestines. 16S rRNA sequencing demonstrated that triploidization altered intestinal richness, as well as the diversity of commensal bacteria in 3nCC. In addition, the abundance of the genus Vibrio in 3nCC was increased compared to 2nCC (P < 0.05). Furthermore, differential expression analysis of 3nCC revealed profound up-regulation of 293 transcripts, while 324 were down-regulated. Several differentially expressed transcripts were related to the immune response pathway in 3nCC, including NLRP3, LY9, PNMA1, MR1, PELI1, NOTCH2, NFIL3, and NLRC4. Taken together, triploidization can alter bacteria composition and abundance, which can in turn result in changes in expression of genes. This study offers an opportunity for deciphering the molecular mechanism underlying disease resistance after triploidization.

Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast)

Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.

Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River

The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.