Fish Gut Microbiome Research Articles

Allium-Derived Compound Propyl Propane Thiosulfonate (PTSO) Reduces Vibrio Populations and Increases Body Weight of European Seabass (Dicentrarchus labrax) Juveniles.

The global demand for fish products is continuously increasing as the population grows, and aquaculture plays an important role in supplying this demand. However, industrial antibiotic misuse has contributed to the spread of antimicrobial resistance among pathogenic bacteria, therefore, several antibiotic alternatives have been proposed. In this study, we have analyzed the effects of Allium-derived propyl propane thiosulfonate (PTSO) in European seabass juveniles' growth and performance. These effects were tested by measuring the body weight and analyzing the gut microbiome of fish after 89 days of feeding trial. The relative abundance of potentially pathogenic Vibrio in the foregut and hindgut of supplemented fish decreased, while Pseudomonas and Kocuria increased significantly. Alpha diversity indices significantly decreased in both gut regions of fish fed with Allium-derived PTSO supplemented diet, as well as between bacterial community composition. These results may indicate a positive effect of the supplementation in the diet with Allium-derived PTSO, reducing potentially pathogenic Vibrio and increasing body weight at the end of the experiment (89 days). However, this supplementation with Allium-derived PTSO produces changes in the diversity and composition of microbial communities, so further experiments would be necessary to explore bacterial community composition and health relationship.

Gut Microbiota of Salmo trutta fario and Oncorhynchus mykiss: Implications for Fish Health and Aquaculture Management

This review compares the gut microbiota of two economically significant freshwater fish species from India’s Himalayas, Salmo trutta fario and Oncorhynchus mykiss. Knowing the composition and variety of gut microbiota in these two species is crucial to their health and productivity. Recent sequencing advances have helped to find and characterize different microbial communities in numerous habitats, including fish gut microbiota. The gut microbiota of these two fish has been compared using Himalayan literature. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria dominate both species’ gut microbiota, but their relative abundance differs. S. trutta fario has a more metabolically varied gut microbiota than O. mykiss. Scientific literature reveals that diet, water quality, seasonality, and host genetics influence the fish gut microbiome. Nutrition greatly affects the intestinal microbiome of animals. This study examines how the gut microbiota affects these fish’s immune systems and probiotics’ ability to boost their health and performance. This review reveals how changing the gut microbiota of these species might increase their health and production. In order to enhance the health of these commercially important fish species, there is a need for more research to understand the complex interaction between gut microbiota, host genetics, and environmental factors.

Integrative analysis of microbiome and metabolome reveals the linkage between gut microbiota and carp growth

Gut microbiota and their metabolites are increasingly recognized for their crucial role in regulating the health and growth of the host. The mechanism by which the gut microbiome affects the growth rate of fish (Cyprinus carpio) in the rice-fish coculture system, however, remains unclear. In this study, the gut contents of the fast-growing and slow-growing (FG and SG) carp were collected from the rice-fish coculture system for both the fish gut microbiome and metabolome analyses. High throughput 16 S rRNA gene sequencing showed that the overall gut microbiota of FG group was distinct from that of SG group. For example, the cyanobacteria were highly enriched in the guts of SG carp (18.61%), in contrast, they only represented a minor fraction of gut microbiota for FG group (<0.20%). The liquid chromatography-mass spectrometry (LC-MS)-based metabolomics analysis revealed that 191 identified metabolites mostly located in 18 KEGG pathways were differentially present between the two groups, of which more than 50% of these metabolites were involved in lipid and amino acids metabolism. Compared with the FG group, the gut microbiota of SG group significantly enriched the metabolic pathways involved in the steroid (hormone) biosynthesis, whereas reducing those associated with beta-alanine metabolism, biosynthesis of unsaturated fatty acids and bile secretion. The enrichment and depletion of these metabolic pathways resulted in an increase in steroid metabolites and a decrease in the concentration of spermidine, which may have a major impact on the growth rate of carp. The metabolome results were further supported by the predicated KEGG functions of the gut microbiomes of the two groups, pointing out that the gut microbiota could substantially affect the growth of fish via their unique metabolic functions. Together, our integrated fish gut microbiome and metabolome analysis has substantial implications for the development of engineered microbiome technologies in aquaculture.

Biotherapeutic microbial supplementation for ameliorating fish health: developing trends in probiotics, prebiotics, and synbiotics use in finfish aquaculture.

Nutrition demands in aquaculture can be realized through quality aquafeeds as compounded diets that contribute to the growth and health of aquaculture species. Functional additives in feed, notably probiotics, prebiotics, and their admixture synbiotics, have been recently recognized for their biotherapeutic role as immunostimulants capable of conferring disease resistance, stress tolerance, and gastrointestinal health; counteracting the negative effects of anti-nutrients, pathogenic prevalence, and antimicrobials in finfish aquaculture. Formulated diets based on probiotics, prebiotics, and as a supplemental combination for synbiotics can significantly influence fish gut microbiomes, establishing the modalities of microbial dynamics to maximize host-associated benefits. These microbial functional-feed supplements are acclaimed to be biocompatible, biodegradable, and safe for dietary consumption as well as the environment. In fed fish aquaculture, prebiotic appended probiotic diet 'synbiotic' has propounded larger attention for its additional health and nutritional benefits. Synbiotic, prebiotic, and probiotic usage as functional feeds for finfish aquaculture thus provides promising prospects. Developing trends in their intended application are reviewed here forth.

Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe, China)

Abstract Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large‐scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish‐farming lake in mid‐eastern China. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind‐mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally‐driven environmental variables including water temperature and nutrient availability.

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.

Legacy metal contamination is reflected in the fish gut microbiome in an urbanised estuary

Estuaries are critical habitats subject to a range of stressors requiring effective management. Microbes are gaining recognition as effective environmental indicators, however, the response of host associated communities to stressors remains poorly understood. We examined microbial communities from seawater, sediments and the estuarine fish Pelates sexlineatus, in Australia's largest urbanised estuary, and hypothesised that anthropogenic contamination would be reflected in the microbiology of these sample types. The human faecal markers Lachno3 and HF183 were not detected, indicating negligible influence of sewage, but a gradient in copy numbers of the class 1 integron (intI-1), which is often used as a marker for anthropogenic contamination, was observed in sediments and positively correlated with metal concentrations. While seawater communities were not strongly driven by metal contamination, shifts in the diversity and composition of the fish gut microbiome were observed, with statistical links to levels of metal contamination (F2, 21 = 1.536, p < 0.01). Within the fish gut microbiome, we further report increased relative abundance of amplicon sequence variants (ASVs; single inferred DNA sequences obtained in sequencing) identified as metal resistant and potentially pathogenic genera, as well as those that may have roles in inflammation. These results demonstrate that microbial communities from distinct habitats within estuarine systems have unique response to stressors, and alterations of the fish gut microbiome may have implications for the adaptation of estuarine fish to legacy metal contamination.

Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient.

The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.

Gut microbiomes of cyprinid fish exhibit host-species symbiosis along gut trait and diet.

Teleost omnivorous fish that coexist partially sharing resources are likely to modify their gut traits and microbiome as a feedback mechanism between ecological processes and evolution. However, we do not understand how the core gut microbiome supports the metabolic capacity of the host and regulates digestive functions in specialized omnivorous fish gut traits. Therefore, we evaluated the gut microbiome of eight omnivorous fish from a single family (i.e., Cyprinidae) in the current study. We examined the correlation between host phylogeny, diet composition, and intestinal morphological traits related to the intestinal microbiome. The results indicated that cyprinid fish with similar relative gut lengths had considerable gut microbiome similarity. Notably, the SL (short relative gut length) group, as zoobenthos and zooplankton specialists, was abundant in Proteobacteria and was less abundant in Firmicutes than in the ML (medium relative gut length) and LL (long relative gut length) groups. These fish could extract nutrients from aquatic plants and algae. Additionally, we found the relative abundance of Clostridium and Romboutsia to be positively correlated with host relative gut length but negatively correlated with the relative abundance of Cetobacterium, Plesiomonas, Bacteroides, and Lactobacillus, and host-relative gut length. We also show a positive linear relationship between host gut microbiome carbohydrate metabolism and relative gut length, while the amino acid and lipid metabolism of the gut microbiome was negatively correlated with host-relative gut length. In addition, omnivorous species competing for resources improve their ecological adaptability through the specialization of gut length, which is closely related to variation in the synergy of the gut microbiome. Above all, specialized gut microbiota and associated gut morphologies enable fish to variably tolerate resource fluctuation and improve the utilization efficiency of nutrient extraction from challenging food resources.

The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0–30%). Fish gut microbiomes were significantly more variable at degraded reefs, a pattern driven by changes in the relative abundance of the most common taxa potentially associated with stress. We also demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which may suggest a less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions may be vulnerable to severe coral degradation.

Feeding black soldier fly larvae (Hermetia illucens) reared on organic rest streams alters gut characteristics of Atlantic salmon (Salmo salar)

The Atlantic salmon (Salmo salar) aquaculture industry is growing, and with it, the need to source and optimise sustainable ingredients for aquafeeds. Black soldier fly (BSF) larvae (Hermetia illucens) have received increasing research attention since they are a good source of protein that can efficiently convert a wide range of low-value organic material into valuable resources. This study investigated the impact of three differently processed BSF meals, an untreated BSF diet (BSFC+), a dechitinated BSF diet (BSFC-) and a fermented BSF diet (BSFC+P+) at a 10% inclusion level replacing fish meal in a fish meal control (FM) and a marine and soy protein concentrate based control diet (SPC). Growth performance, gut microbiome and gut histology of salmon fry was assessed. The inclusion and processing methods of BSF showed no adverse impacts on either growth performance or gut histology. However, the gut microbiome of fish was significantly altered by both the protein source and the processing method of the BSF larvae. Fish fed BSFC+, had an increased diversity and evenness of the community compared with conventional protein sources alone, and compared with the other BSF processing methods. However, control diets had a greater presence of lactic acid bacteria and genera associated with faster growing hosts. Fish fed BSF had a high relative abundance of the genus, Exiguobacterium, a chitin-degrading bacterium and in BSFC+P+ fed fish this bacterium completely dominated the community, indicating the presence of dysbiosis. Future studies should determine, why Exiguobacterium has dominated the community for the BSFC+P+ diet, and if it provides a digestive function to the host and identify bacteria that are indicators of optimal host performance and resilience. The results confirmed that BSF is a promising fish meal replacement for salmon, and it demonstrated that BSFC+ has a potential prebiotic impact on the gut microbiome of Atlantic salmon.

Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer

The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.

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.

Dysbiosis and Restoration Dynamics of the Gut Microbiome Following Therapeutic Exposure to Florfenicol in Snubnose Pompano (Trachinotus blochii) to Aid in Sustainable Aquaculture Production Strategies.

Information on unintended effects of therapeutic exposure of antibiotics on the fish gut microbiome is a vital prerequisite for ensuring fish and environmental health during sustainable aquaculture production strategies. The present study forms the first report on the impact of florfenicol (FFC), a recommended antibiotic for aquaculture, on the gut microbiome of snubnose pompano (Trachinotus blochii), a high-value marine aquaculture candidate. Both culture-dependent and independent techniques were applied to identify the possible dysbiosis and restoration dynamics, pointing out the probable risks to the host and environment health. The results revealed the critical transient dysbiotic events in the taxonomic and functional metagenomic profiles and significant reductions in the bacterial load and diversity measures. More importantly, there was a complete restoration of gut microbiome density, diversity, functional metagenomic profiles, and taxonomic composition (up to class level) within 10–15 days of antibiotic withdrawal, establishing the required period for applying proper management measures to ensure animal and environment health, following FFC treatment. The observed transient increase in the relative abundance of opportunistic pathogens suggested the need to apply proper stress management measures and probiotics during the period. Simultaneously, the results demonstrated the inhibitory potential of FFC against marine pathogens (vibrios) and ampicillin-resistant microbes. The study pointed out the possible microbial signatures of stress in fish and possible probiotic microbes (Serratia sp., Methanobrevibacter sp., Acinetobacter sp., and Bacillus sp.) that can be explored to design fish health improvisation strategies. Strikingly, the therapeutic exposure of FFC neither caused any irreversible increase in antibiotic resistance nor promoted the FFC resistant microbes in the gut. The significant transient increase in the numbers of kanamycin-resistant bacteria and abundance of two multidrug resistance encoding genes (K03327 and K03585) in the treated fish gut during the initial 10 days post-withdrawal suggested the need for implementing proper aquaculture effluent processing measures during the period, thus, helps to reduce the spillover of antibiotic-resistant microbes from the gut of the treated fish to the environment. In brief, the paper generates interesting and first-hand insights on the implications of FFC treatment in the gut microbiome of a marine aquaculture candidate targeting its safe and efficient application in unavoidable circumstances. Implementation of mitigation strategies against the identified risks during the initial 15 days of withdrawal period is warranted to ensure cleaner and sustainable aquaculture production from aquatic animal and ecosystem health perspectives.

Appraisal of cytotoxicity and acrylamide mitigation potential of L-asparaginase SlpA from fish gut microbiome.

L-asparaginase catalyzes the hydrolysis of L-asparagine toL-aspartic acid and ammonia. It has application in the treatment of acute lymphoblastic leukemia in children, as well as in other malignancies, in addition to its role as a food processing aid for the mitigation of acrylamide formation in the baking industry. Its use in cancer chemotherapy is limited due to problems such as its intrinsic glutaminase activity and associated side effects, leading to anincreased interest in the search for novel L-asparaginases without L-glutaminase activity. This study reports the cloning and expression of an L-asparaginase contig obtained from whole metagenome shotgun sequencing of Sardinella longiceps gut microbiota. Purified recombinant glutaminase-free L-asparaginase SlpA was a 74kDa homodimer, with maximal activity at pH 8 and 30°C. Km and Vmax of SlpA were determined to be 3.008mM and 0.014mM/min, respectively. SlpA displayed cytotoxic activity against K-562 (chronic myeloid leukemia) and MCF-7 (breast cancer) cell lines with IC50 values of 0.3443 and 2.692 U/mL, respectively. SlpA did not show any cytotoxic activity against normal lymphocytes and was proved to be hemocompatible. Pre-treatment of biscuit and bread dough with different concentrations of SlpA resulted in a clear, dose-dependent reduction of acrylamide formation during baking. KEY POINTS: • Cloned and expressed L-asparaginase (SlpA) from fish gut microbiota • Purified SlpA displayed good cytotoxicity against K-562 and MCF-7 cell lines • SlpA addition caused a significant reduction of acrylamide formation during baking.

Gut Microbiome Analyses of Wild Migratory Freshwater Fish (Megalobrama terminalis) Through Geographic Isolation.

Gut microbiome is considered as a critical role in host digestion and metabolic homeostasis. Nevertheless, the lack of knowledge concerning how the host-associated gut microbiome underpins the host metabolic capability and regulates digestive functions hinders the exploration of gut microbiome variation in diverse geographic population. In the present study, we selected the black Amur bream (Megalobrama terminalis) that inhabits southern China drainage with multiple geographic populations and relatively high digestive plasticity as a candidate to explore the potential effects of genetic variation and environmental discrepancy on fish gut microbiome. Here, high-throughput 16S rRNA gene sequencing was utilized to decipher the distinct composition and diversity of the entire gut microbiota in wild M. terminalis distributed throughout southern China. The results indicated that mainland (MY and XR) populations exhibited a higher alpha diversity than that of the Hainan Island (WS) population. Moreover, a clear taxon shift influenced by water temperature, salinity (SA), and gonadosomatic index (GSI) in the course of seasonal variation was observed in the gut bacterial community. Furthermore, geographic isolation and seasonal variation significantly impacted amino acid, lipid, and carbohydrate metabolism of the fish gut microbiome. Specifically, each geographic population that displayed its own unique regulation pattern of gut microbiome was recognized as a specific digestion strategy to enhance adaptive capability in the resident environment. Consequently, this discovery suggested that long-term geographic isolation leads to variant environmental factors and genotypes, which made a synergetic effect on the diversity of the gut microbiome in wild M. terminalis. In addition, the findings provide effective information for further exploring ecological fitness countermeasures in the fish population.

Effects of in situ experimental selenium exposure on finescale dace (Phoxinus neogaeus) gut microbiome

Selenium (Se) is an environmental contaminant of global concern that can cause adverse effects in fish at elevated levels. Fish gut microbiome play essential roles in gastrointestinal function and host health and can be perturbed by environmental contaminants, including metals and metalloids. Here, an in-situ Se exposure of female finescale dace (Phoxinus neogaeus) using mesocosms was conducted to determine the impacts of Se accumulation on the gut microbiome and morphometric endpoints. Prior to this study, the gut microbiome of finescale dace, a widespread Cyprinid throughout North America, had not been characterized. Exposure to Se caused a hormetic response of alpha diversity of the gut microbiome, with greater diversity at the lesser concentration of 1.6 μg Se/L, relative to that of fish exposed to the greater concentration of 5.6 μg Se/L. Select gut microbiome taxa of fish were differentially abundant between aqueous exposure concentrations and significantly correlated with liver-somatic index (LSI). The potential effects of gut microbiome dysbiosis on condition of wild fish might be a consideration when assessing adverse effects of Se in aquatic environments. More research regarding effects of Se on field-collected fish gut microbiome and the potential adverse effects or benefits on the host is warranted.

Legacy Metal Contamination is Reflected in the Fish Gut Microbiome in an Urbanised Estuary

Legacy Metal Contamination is Reflected in the Fish Gut Microbiome in an Urbanised Estuary

Impact of early-life rearing history on gut microbiome succession and performance of Nile tilapia

BackgroundFish gut microbial colonisation starts during larval stage and plays an important role in host’s growth and health. To what extent first colonisation could influence the gut microbiome succession and growth in later life remains unknown. In this study, Nile tilapia embryos were incubated in two different environments, a flow-through system (FTS) and a biofloc system (BFS); hatched larvae were subsequently cultured in the systems for 14 days of feeding (dof). Fish were then transferred to one common recirculating aquaculture system (RAS1, common garden, 15–62 dof), followed by a growth trial in another RAS (RAS2, growth trial, 63–105 dof). In RAS2, fish were fed with two types of diet, differing in non-starch polysaccharide content. Our aim was to test the effect of rearing environment on the gut microbiome development, nutrient digestibility and growth performance of Nile tilapia during post-larvae stages.ResultsLarvae cultured in the BFS showed better growth and different gut microbiome, compared to FTS. After the common garden, the gut microbiome still showed differences in species composition, while body weight was similar. Long-term effects of early life rearing history on fish gut microbiome composition, nutrient digestibility, nitrogen and energy balances were not observed. Still, BFS-reared fish had more gut microbial interactions than FTS-reared fish. A temporal effect was observed in gut microbiome succession during fish development, although a distinct number of core microbiome remained present throughout the experimental period.ConclusionOur results indicated that the legacy effect of first microbial colonisation of the fish gut gradually disappeared during host development, with no differences in gut microbiome composition and growth performance observed in later life after culture in a common environment. However, early life exposure of larvae to biofloc consistently increased the microbial interactions in the gut of juvenile Nile tilapia and might possibly benefit gut health.

Investigating the Effect of an Oxytetracycline Treatment on the Gut Microbiome and Antimicrobial Resistance Gene Dynamics in Nile Tilapia (Oreochromis niloticus).

Antibiotics play a vital role in aquaculture where they are commonly used to treat bacterial diseases. However, the impact of antibiotic treatment on the gut microbiome and the development of antimicrobial resistance in Nile tilapia (Oreochromis niloticus) over time remains to be fully understood. In this study, fish were fed a single treatment of oxytetracycline (100 mg/kg/day) for eight days, followed by a 14-day withdrawal period. Changes in the distal gut microbiome were measured using 16S rRNA sequencing. In addition, the abundance of antimicrobial resistance genes was quantified using real-time qPCR methods. Overall, the gut microbiome community diversity and structure of Nile tilapia was resilient to oxytetracycline treatment. However, antibiotic treatment was associated with an enrichment in Plesiomonas, accompanied by a decline in other bacteria taxa. Oxytetracycline treatment increased the proportion of tetA in the distal gut of fish and tank biofilms of the treated group. Furthermore, the abundance of tetA along with other tetracycline resistance genes was strongly correlated with a number of microbiome members, including Plesiomonas. The findings from this study demonstrate that antibiotic treatment can exert selective pressures on the gut microbiome of fish in favour of resistant populations, which may have long-term impacts on fish health.