Environment shapes the fecal microbiome of invasive carp species

Comparative analysis of gut microbiome in Pangasionodon hypopthalmus and Labeo catla during health and disease

The present study was conducted to study the composition of gut microbiome in the advanced fingerling and fingerling stage of striped pangasius catfish and catla during healthy and diseased conditions. Healthy pangasius and catla fishes were obtained from commercial farms and injected with the LD50 dose of A. hydrophila. The intestinal samples from the control and injected group were collected and pooled for 16 s metagenomic analysis. Community analysis was performed by targeting the 16 s rRNA gene to explore and compare the gut microbiota composition of these fishes. The operational taxonomic units (OTUs) consisted of four major phyla: Bacteroidia, Proteobacteria, Firmicutes, and Actinobacteria. Alpha and beta diversity indices were carried out to understand the diversity of microbes within and between a sample. While comparing the advanced fingerling and fingerling stage gut microbiome of Pangasius catfish, the dominance of Proteobacteria was found in fingerlings, whereas Firmicutes and Bacteroides were found in advanced fingerlings. In catla, Proteobacteria and Bacteroides were predominant. Taxonomic abundance of the microbiota in control and diseased Pangasius and catla fishes at phylum, class, order, family, genus, and species levels were also depicted. The present study is the first of its kind, and it will help to identify the diversity of novel potential bacterial species involved in disease protection of fishes. It can lead to the development of sustainable prophylactic measures against (re-)emerging bacterial diseases in aquaculture.

The early life microbiome of giant grouper (Epinephelus lanceolatus) larvae in a commercial hatchery is influenced by microorganisms in feed

Fish health, growth and disease is intricately linked to its associated microbiome. Understanding the influence, source and ultimately managing the microbiome, particularly for vulnerable early life-stages, has been identified as one of the key requirements to improving farmed fish production. One tropical fish species of aquaculture importance farmed throughout the Asia-Pacific region is the giant grouper (Epinephelus lanceolatus). Variability in the health and survival of E. lanceolatus larvae is partially dependent on exposure to and development of its early microbiome. Here, we examined the development in the microbiome of commercially reared giant grouper larvae, its surrounding environment, and that from live food sources to understand the type of bacterial species larvae are exposed to, and where some of the sources of bacteria may originate. We show that species richness and microbial diversity of the larval microbiome significantly increased in the first 4 days after hatching, with the community composition continuing to shift over the initial 10 days in the hatchery facility. The dominant larval bacterial taxa appeared to be predominantly derived from live cultured microalgae and rotifer feeds and included Marixanthomonas, Candidatus Hepatincola, Meridianimaribacter and Vibrio. In contrast, a commercial probiotic added as part of the hatchery's operating procedure failed to establish in the larvae microbiome. Microbial source tracking indicated that feed was the largest influence on the composition of the giant grouper larvae microbiome (up to 55.9%), supporting attempts to modulate fish microbiomes in commercial hatcheries through improved diets. The marked abundances of Vibrio (up to 21.7% of 16S rRNA gene copies in larvae) highlights a need for rigorous quality control of feed material.

Protective effects of dietary additive quercetin: Nephrotoxicity and ferroptosis induced by avermectin pesticide

In recent years, contamination of aquatic systems with Avermectin (AVM) has emerged as a significant concern. This contamination poses substantial challenges to freshwater aquaculture. Plant-derived Quercetin (QUE), known for its anti-inflammatory, antioxidant, and ferroptosis-inhibiting properties, is commonly employed as a supplement in animal feed. However, its protective role against chronic renal injury in freshwater carp induced by AVM remains unclear. This study assesses the influence of dietary supplementation with QUE on the consequences of chronic AVM exposure on carp renal function. The carp were subjected to a 30-day exposure to AVM and were provided with a diet containing 400 mg/kg of QUE. Pathological observations indicated that QUE alleviated renal tissue structural damage caused by AVM. RT-QPCR study revealed that QUE effectively reduced the increased expression levels of pro-inflammatory factors mRNA produced by AVM exposure, by concurrently raising the mRNA expression level of the anti-inflammatory factor. Quantitative analysis using DHE tests and biochemical analysis demonstrated that QUE effectively reduced the buildup of ROS in the renal tissues of carp, activity of antioxidant enzymes CAT, SOD, and GSH-px, which were inhibited by AVM, and increased the content of GSH, which was induced by prolonged exposure to AVM. QUE also reduced the levels of MDA, a marker of oxidative damage. Furthermore, assays for ferroptosis markers indicated that QUE increased the mRNA expression levels of gpx4 and slc7a11, which were reduced due to AVM induction, and it caused a reduction in the mRNA expression levels of ftl, ncoa4, and cox2, along with a drop in the Fe2+ concentration. In summary, QUE mitigates chronic AVM exposure-induced renal inflammation in carp by inhibiting the transcription of pro-inflammatory cytokines. By blocking ROS accumulation, renal redox homeostasis is restored, thereby inhibiting renal inflammation and ferroptosis. This provides a theoretical basis for the development of freshwater carp feed formula.

Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha)

Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.

Evaluation of quercetin in alleviating the negative effects of high soybean meal diet on spotted sea bass Lateolabrax maculatus

The aim of this study was to investigate the effects of quercetin (QUE) on alleviating the negative effects of high soybean meal diet for spotted sea bass Lateolabrax maculatus. A healthy control group fed a 44% fishmeal diet was used, while the induction control group replaced 50% fishmeal with soybean meal. Subsequently, QUE was added at concentrations of 0.25, 0.50, 0.75, and 1.00 g/kg in the experimental groups. A total of 540 tailed spotted sea bass were randomly divided into 6 groups and fed the corresponding diet for 56 days. The results showed that 40% soybean meal significantly decreased the growth performance and immunity, increased the intestinal mucosal permeability, and caused damage to the intestinal tissue morphology; moreover, there were alterations observed in the composition of the intestinal microbiota, accompanied by detectable levels of saponins in the metabolites. However, the addition of QUE did not yield significant changes in growth performance; instead, it notably reduced the permeability of the intestinal mucosa, improved the body's immunity and the structural integrity of the intestinal tissue, increased the proportion of Proteobacteria, and enhanced the richness and diversity of intestinal microorganisms to a certain extent. In addition, QUE up-regulate the metabolism of amino acids and their derivatives and energy-related metabolites such as uridine and guanosine; furthermore, it appears to regulate transporters through the ABC transporters pathway to promote the absorption and utilization of QUE by enterocytes.

Feeding strategy and feed protein level affect the gut microbiota of common carp (Cyprinus carpio)

Common carp (Cyprinus carpio) were fed food with different protein concentrations following different feeding regimes, which were previously shown to affect growth, nitrogen excretion and amino acid catabolism. 16S rRNA gene amplicon sequencing was performed to investigate the gut microbiota of these fish. Lower dietary protein content increased microbial richness, while the combination of demand feeding and dietary protein content affected the composition of the gut microbiota. Hepatic glutamate dehydrogenase (GDH) activity was correlated to the composition of the gut microbiota in all dietary treatments. We found that demand-fed carp fed a diet containing 39% protein had a significantly higher abundance of Beijerinckiaceae compared to other dietary groups. Network analysis identified this family and two Rhizobiales families as hubs in the microbial association network. In demand-fed carp, the microbial association network had significantly fewer connections than in batch-fed carp. In contrast to the large effects of the feeding regime and protein content of the food on growth and nitrogen metabolism, it had only limited effects on gut microbiota composition. However, correlations between gut microbiota composition and liver GDH activity showed that host physiology and gut microbiota are connected, which warrants functional studies into the role of the gut microbiota in fish physiology.

Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research

The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.

Vertical habitat preferences shape the fish gut microbiota in a shallow lake

Understanding the interactions between fish gut microbiota and the aquatic environment is a key issue for understanding aquatic microorganisms. Environmental microorganisms enter fish intestines through feeding, and the amount of invasion varies due to different feeding habits. Traditional fish feeding habitat preferences are determined by fish morphology or behavior. However, little is known about how the feeding behavior of fish relative to the vertical structure in a shallow lake influences gut microbiota. In our study, we used nitrogen isotopes to measure the trophic levels of fish. Then high-throughput sequencing was used to describe the composition of environmental microbiota and fish gut microbiota, and FEAST (fast expectation-maximization for microbial source tracking) method was used to trace the source of fish gut microbiota. We investigated the microbial diversity of fish guts and their habitats in Lake Sanjiao and verified that the sediments indeed played an important role in the assembly of fish gut microbiota. Then, the FEAST analysis indicated that microbiota in water and sediments acted as the primary sources in half of the fish gut microbiota respectively. Furthermore, we classified the vertical habitat preferences using microbial data and significant differences in both composition and function of fish gut microbiota were observed between groups with distinct habitat preferences. The performance of supervised and unsupervised machine learning in classifying fish gut microbiota by habitat preferences actually exceeded classification by fish species taxonomy and fish trophic level. Finally, we described the stability of fish co-occurrence networks with different habitat preferences. Interestingly, the co-occurrence network seemed more stable in pelagic fish than in benthic fish. Our results show that the preferences of fish in the vertical structure of habitat was the main factor affecting their gut microbiota. We advocated the use of microbial interactions between fish gut and their surrounding environment to reflect fish preferences in vertical habitat structure. This approach not only offers a novel perspective for understanding the interactions between fish gut microbiota and environmental factors, but also provides new methods and ideas for studying fish habitat selection in aquatic ecosystems.

Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice

Symbiotic microbial communities affect the host immune system and produce molecules contributing to the odor of an individual. In many mammalian species, saliva and vaginal fluids are important sources of chemical signals that originate from bacterial metabolism and may act as honest signals of health and reproductive status. In this study, we aimed to define oral and vaginal microbiomes and their dynamics throughout the estrous cycle in wild house mice. In addition, we analyzed a subset of vaginal proteomes and metabolomes to detect potential interactions with microbiomes. 16S rRNA sequencing revealed that both saliva and vagina are dominated by Firmicutes and Proteobacteria but differ at the genus level. The oral microbiome is more stable during the estrous cycle and most abundant bacteria belong to the genera Gemella and Streptococcus, while the vaginal microbiome shows higher bacterial diversity and dynamics during the reproductive cycle and is characterized by the dominance of Muribacter and Rodentibacter. These two genera cover around 50% of the bacterial community during estrus. Proteomic profiling of vaginal fluids revealed specific protein patterns associated with different estrous phases. Highly expressed proteins in estrus involve the keratinization process thus providing estrus markers (e.g., Hrnr) while some proteins are downregulated such as immune-related proteins that limit bacterial growth (Camp, Clu, Elane, Lyz2, and Ngp). The vaginal metabolome contains volatile compounds potentially involved in chemical communication, for example, ketones, aldehydes, and esters of carboxylic acids. Data integration of all three OMICs data sets revealed high correlations, thus providing evidence that microbiomes, host proteomes, and metabolomes may interact.IMPORTANCEOur data revealed dynamic changes in vaginal, but not salivary, microbiome composition during the reproductive cycle of wild mice. With multiple OMICs platforms, we provide evidence that changes in microbiota in the vaginal environment are accompanied by changes in the proteomic and metabolomics profiles of the host. This study describes the natural microbiota of wild mice and may contribute to a better understanding of microbiome-host immune system interactions during the hormonal and cellular changes in the female reproductive tract. Moreover, analysis of volatiles in the vaginal fluid shows particular substances that can be involved in chemical communication and reproductive behavior.

Comparative Microbiome Analysis of Artemia spp. and Potential Role of Microbiota in Cyst Hatching

Brine shrimp (Artemia spp.) is a significant factor in determining aquaculture production. Since the microbiota of Artemia can colonize the gut in larvae, various microorganisms transmitted from Artemia can affect host larval health. Although the microbiota composition of Artemia would be essential in determining aquaculture productivity, our understanding on microbiome of Artemia is still insufficient. Through our study, we identified the species of Artemia cysts supplied by three different manufacturers (P1, P2, and P3) with investigation of size and hatching efficiency. The species of Artemia from P1 was identified as A. tibetiana, and P2 and P3 was A. franciscana. A. tibetiana hatched from the P1 cysts had the largest body size with the lowest hatching rate. Furthermore, we conducted a comprehensive analysis of the microbiome present in the rearing water and the nauplius whole body from each product. We observed specific microbiota compositions, both beneficial and harmful, depending on the product types and the sample types. Additionally, we found that the microbiota composition in the rearing water was associated with the manufacturing environment, while the compositions in the nauplius whole body were species-specific. Notably, we discovered that an extract containing microbiota from the nauplius sample of P3 increased the hatching rate of A. tibetiana, indicating a positive role in Artemia culture. These findings demonstrate that the microbial communities present in Artemia vary according to the product and/or species, underscoring their significance in aquaculture production.

Aedes aegypti gut transcriptomes respond differently to microbiome transplants from field-caught or laboratory-reared mosquitoes

The mosquito microbiome is critical for host development and plays a major role in many aspects of mosquito biology. While the microbiome is commonly dominated by a small number of genera, there is considerable variation in composition among mosquito species, life stages, and geography. How the host controls and is affected by this variation is unclear. Using microbiome transplant experiments, we asked whether there were differences in transcriptional responses when mosquitoes of different species were used as microbiome donors. We used microbiomes from four different donor species spanning the phylogenetic breadth of the Culicidae, collected either from the laboratory or the field. We found that when recipients received a microbiome from a donor reared in the laboratory, the response was remarkably similar regardless of donor species. However, when the donor had been collected from the field, many more genes were differentially expressed. We also found that while the transplant procedure did have some effect on the host transcriptome, this is likely to have had a limited effect on mosquito fitness. Overall, our results highlight the possibility that variation in mosquito microbiome communities is associated with variability in host-microbiome interactions and further demonstrate the utility of the microbiome transplantation technique for investigating host-microbe interactions in mosquitoes.

Growth, Survival, and Intestinal Health Alterations in Mediterranean Yellowtail (Seriola dumerili) Due to Alternatives to Fishmeal and Fish Oil

Fishmeal and fish oil substitution in aquafeeds might have adverse effects on fish growth and health, mainly in carnivorous species, such as Mediterranean yellowtail (Seriola dumerili). Mediterranean yellowtail shows great potential as an alternative aquaculture species due to its fast growth and high price on the market, but the need for high-quality protein and fatty acid content in its diets is limiting its production. In order to improve the sustainability of its production, this study was conducted with 360 fish of 35 g to evaluate the effects on fish growth and health. Six diets were used: one control diet without replacement, three with FM replacement (FM66, FM33, and FM0) (33%, 66%, and 100% FM replacement), and two with FO replacement (FO50 and FO0) (50% and 100% FO replacement). The substitution of FM was with vegetable (VM) (corn gluten) and animal (AM) (krill and meat meal) meals. The reductions in FM and FO of up to 33 and 0%, respectively, did not affect the growth and survival of S. dumerili at the intestinal morphology level, except for the anterior intestine regarding the lower villi length and width and the posterior intestine regarding the lower width of the lamina propria. On the other hand, the substitution of fish ingredients in the diet affects liver morphology, indicating alterations in the major diameter of hepatocytes or their nuclei. Finally, diet did not affect the gut microbiota with respect to the control, but significant differences were found in alpha and beta diversity when FO and FM microbiota were compared. A 66% FM replacement and total FO replacement would be possible without causing major alterations in the fish.

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats

IMPORTANCE

Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.

Seaweed and Seaweed-Based Functional Metabolites as Potential Modulators of Growth, Immune and Antioxidant Responses, and Gut Microbiota in Fish

Seaweed, also known as macroalgae, represents a vast resource that can be categorized into three taxonomic groups: Rhodophyta (red), Chlorophyta (green), and Phaeophyceae (brown). They are a good source of essential nutrients such as proteins, minerals, vitamins, and omega-3 fatty acids. Seaweed also contains a wide range of functional metabolites, including polyphenols, polysaccharides, and pigments. This study comprehensively discusses seaweed and seaweed-derived metabolites and their potential as a functional feed ingredient in aquafeed for aquaculture production. Past research has discussed the nutritional role of seaweed in promoting the growth performance of fish, but their effects on immune response and gut health in fish have received considerably less attention in the published literature. Existing research, however, has demonstrated that dietary seaweed and seaweed-based metabolite supplementation positively impact the antioxidant status, disease resistance, and stress response in fish. Additionally, seaweed supplementation can promote the growth of beneficial bacteria and inhibit the proliferation of harmful bacteria, thereby improving gut health and nutrient absorption in fish. Nevertheless, an important balance remains between dietary seaweed inclusion level and the resultant metabolic alteration in fish. This review highlights the current state of knowledge and the associated importance of continued research endeavors regarding seaweed and seaweed-based functional metabolites as potential modulators of growth, immune and antioxidant response, and gut microbiota composition in fish.

Physiological differences between wild and captive animals: a century-old dilemma

Laboratory-based research dominates the fields of comparative physiology and biomechanics. The power of lab work has long been recognized by experimental biologists. For example, in 1932, Georgy Gause published an influential paper in Journal of Experimental Biology describing a series of clever lab experiments that provided the first empirical test of competitive exclusion theory, laying the foundation for a field that remains active today. At the time, Gause wrestled with the dilemma of conducting experiments in the lab or the field, ultimately deciding that progress could be best achieved by taking advantage of the high level of control offered by lab experiments. However, physiological experiments often yield different, and even contradictory, results when conducted in lab versus field settings. This is especially concerning in the Anthropocene, as standard laboratory techniques are increasingly relied upon to predict how wild animals will respond to environmental disturbances to inform decisions in conservation and management. In this Commentary, we discuss several hypothesized mechanisms that could explain disparities between experimental biology in the lab and in the field. We propose strategies for understanding why these differences occur and how we can use these results to improve our understanding of the physiology of wild animals. Nearly a century beyond Gause's work, we still know remarkably little about what makes captive animals different from wild ones. Discovering these mechanisms should be an important goal for experimental biologists in the future.

The role of diet and host species in shaping the seasonal dynamics of the gut microbiome

The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.

Deterministic processes dominate microbial community assembly in artificially bred Schizothorax wangchiachii juveniles after being released into wild

Fish artificial breeding and release is an important method to restore wild populations of endemic fish species around the world. Schizothorax wangchiachii (SW) is an endemic fish in the upper Yangtze River and is one of the most important species for the artificial breeding and release program implemented in the Yalong River drainage system in China. It is unclear how artificially bred SW adapts to the changeable wild environment post-release, after being in a controlled and very different artificial environment. Thus, the gut samples were collected and analyzed for food composition and microbial 16S rRNA in artificially bred SW juveniles at day 0 (before release), 5, 10, 15, 20, 25, and 30 after release to the lower reaches of the Yalong River. The results indicated that SW began to ingest periphytic algae from the natural habitat before day 5, and this feeding habit is gradually stabilized at day 15. Prior to release, Fusobacteria are the dominant bacteria in the gut microbiota of SW, while Proteobacteria and Cyanobacteria generally are the dominant bacteria after release. The results of microbial assembly mechanisms illustrated that deterministic processes played a more prominent role than stochastic processes in the gut microbial community of artificially bred SW juveniles after releasing into the wild. Overall, the present study integrates the macroscopic and microscopic methods to provide an insight into the food and gut microbial reorganization in the released SW. This study will be an important research direction to explore the ecological adaptability of artificially bred fish after releasing into the wild.

Comparison of exoskeleton microbial communities of co-occurring native and invasive crayfish species

Host-associated microbial communities are an important determinant of individual fitness and have recently been highlighted as one of the factors influencing the success of invasive species. Invasive hosts introduce their microbes into the new environment, and then both the host and its associated microbes enter into a series of interactions with the native macroscopic and microscopic biota. As these processes are largely unexplored, we aimed to compare the exoskeletal microbial communities of co-occurring and phylogenetically related crayfish: the native narrow-clawed crayfish Pontastacus leptodactylus and the invasive signal crayfish Pacifastacus leniusculus from the recently invaded Korana River, Croatia. The results of high-throughput 16S rRNA sequencing showed that the exoskeletal microbiome of both species is very diverse, significantly influenced by the local environment and dominated by low abundance bacterial families from the phylum Proteobacteria. Furthermore, the exoskeletal microbiomes of the crayfish species differed significantly in the composition and abundance of Amplicon Sequence Variants (ASVs), suggesting that they are to some extent shaped by species-specific intrinsic factors, despite sharing a common habitat. However, over 95% of the bacterial genera associated with the exoskeleton were detected in the exoskeleton samples of both native and invasive crayfish. We paid particular attention to two known crayfish pathogens, Aphanomyces astaci and Saprolegnia parasitica, and find that both species carry low amounts of both pathogens. On the side, we find that a non-standard ddPCR protocol outperforms standard qPCR test for A. astaci under low concentration conditions. Taken together, our results indicate the possibility of bidirectional mixing and homogenisation of exoskeleton microbiome. As such, they can serve as a baseline in future detangling of the processes that act together to shape the microbiomes of co-occuring native and invasive congeners during biological invasions.

Riverine pollution influences the intraspecific variation in the gut microbiome of an invasive fish, Cyprinus carpio (Linn., 1758)

Humans are significantly impacting riverine systems worldwide, prompting us to investigate the effects of water pollution on the gut microbiome of Cyprinus carpio (common carp). Using 16S rRNA gene sequencing, we compared the gut microbiomes of common carp from two sites along river Yamuna with different pollution levels. Water pollution significantly altered the fish gut microbiome structure and microbial composition. Proteobacteria dominated in both sampling sites, while Bacteroidota prevailed in polluted water samples, indicating sewage and fecal contamination. Less polluted samples exhibited Verrucomicrobiae and Planctomycetes, negatively correlated with pollution levels. The polluted site had higher prevalence of potentially pathogenic and heavy metal-resistant bacteria, as well as microbial communities associated with wastewater treatment systems. Functional prediction highlighted the significant role of the gut microbiome in digestion and metabolism, with active enzymes for breaking down various organic substances. Biosynthetic pathways for leucine, valine, and isoleucine were present in both sites, known to be involved fish immunity. The host maintained a stable and diverse bacterial consortium, while microbial diversity became more specialized due to human activities, adapting to anthropogenic stress and selection pressures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03747-0.

The Gut Microbiota of Farmed and Wild Brook Trout (Salvelinus fontinalis): Evaluation of Feed-Related Differences Using 16S rRNA Gene Metabarcoding

The gut microbiota has become a topic of increasing importance in various fields, including aquaculture. Several fish species have been the subject of investigations concerning the intestinal microbiota, which have compared different variables, including the intestinal portions, the environment, and diet. In this study, the microbiota of farmed and wild brook trout (Salvelinus fontinalis) were analyzed, in which the wall and content of the medial portion of the intestine were considered separately. A total of 66 fish (age class 2+) were sampled, of which 46 were wild and 20 were farmed brook trout, in two different years. Microbiota data were obtained using a 16S metabarcoding approach by analyzing the V3-V4 hypervariable regions of the corresponding 16S rRNA. The data showed that the core microbiota of these species consist of Proteobacteria (Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes (Bacilli and Clostridia), and, only for farmed animals, Fusobacteria. The latter taxon's presence is likely related to the fishmeal-based diet administered to farmed brook trout. Indeed, alpha and beta diversity analysis showed differences between wild and farmed fish. Finally, statistically significant differences in the microbiota composition were observed between the intestinal walls and contents of wild fish, while no differences were detected in reared animals. Our work represents the first study on the intestinal microbiota of brook trout with respect to both farmed and wild specimens. Future studies might focus on the comparison of our data with those pertaining to other fish species and on the study of other portions of the brook trout intestine.

Effect of Purslane (Portulaca oleracea L.) on Intestinal Morphology, Digestion Activity and Microbiome of Chinese Pond Turtle (Mauremys reevesii) during Aeromonas hydrophila Infection

Large-scale mortality due to Aeromonas hydrophila (A. hydrophila) infection has considerably decreased the yield of the Chinese pond turtle (Mauremys reevesii). Purslane is a naturally active substance with a wide range of pharmacological functions, but its antibacterial effect on Chinese pond turtles infected by A. hydrophila infection is still unknown. In this study, we investigated the effect of purslane on intestinal morphology, digestion activity, and microbiome of Chinese pond turtles during A. hydrophila infection. The results showed that purslane promoted epidermal neogenesis of the limbs and increased the survival and feeding rates of Chinese pond turtles during A. hydrophila infection. Histopathological observation and enzyme activity assay indicated that purslane improved the intestinal morphology and digestive enzyme (α-amylase, lipase and pepsin) activities of Chinese pond turtle during A. hydrophila infection. Microbiome analysis revealed that purslane increased the diversity of intestinal microbiota with a significant decrease in the proportion of potentially pathogenic bacteria (such as Citrobacter freundii, Eimeria praecox, and Salmonella enterica) and an increase in the abundance of probiotics (such as uncultured Lactobacillus). In conclusion, our study uncovers that purslane improves intestinal health to protect Chinese pond turtles against A. hydrophila infection.

Integrated analysis of how gender and body weight affect the intestinal microbial diversity of Gymnocypris chilianensis

Intestinal microorganisms that living in the mucosa and contents of the gastrointestinal tract of animals, have close links with their hosts over a long evolutionary history. The community structure of the fish intestinal microbiota is associated with food, living environment, and the growth stage. To screen for potential probiotics that can be used for regulating breeding behaviors, this study focused on the diversity of fish intestinal microorganisms. This study aimed to investigate the effects of sex and body weight on the intestinal microbial diversity of Gymnocypris chilianensis in the wild. The results showed that the significant high diversity and richness of intestinal microbiota were fould in heavier individuals, and males. The dominant bacterial phyla of G. chilianensis were Proteobacteria, Firmicutes, and Bacteroidetes. In addition, the abundance of Firmicutes varied significantly among different body weights. The genus profile revealed that small individuals were dominated by Weissella, while females were dominated by Aeromonas, and both large individuals and males were dominated by other genera. Phylogenetic relationships and UPGMA clustering analysis showed significant differences among the groups. In general, the two main factors that have an effect on the intestinal microbiota diversity of wild G. chilianensis are sex and body weight.

The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats

BACKGROUND

Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.

RESULTS

The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.

CONCLUSIONS

This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.

Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels (Anguilla bicolor bicolor McClelland, 1844)

This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.

The mycobiome of a successful crayfish invader and its changes along the environmental gradient

BACKGROUND

The microbiome plays an important role in biological invasions, since it affects various interactions between host and environment. However, most studies focus on the bacteriome, insufficiently addressing other components of the microbiome such as the mycobiome. Microbial fungi are among the most damaging pathogens in freshwater crayfish populations, colonizing and infecting both native and invasive crayfish species. Invading crayfish may transmit novel fungal species to native populations, but also, dispersal process and characteristics of the novel environment may affect the invaders' mycobiome composition, directly and indirectly affecting their fitness and invasion success. This study analyzes the mycobiome of a successful invader in Europe, the signal crayfish, using the ITS rRNA amplicon sequencing approach. We explored the mycobiomes of crayfish samples (exoskeletal biofilm, hemolymph, hepatopancreas, intestine), compared them to environmental samples (water, sediment), and examined the differences in fungal diversity and abundance between upstream and downstream segments of the signal crayfish invasion range in the Korana River, Croatia.

RESULTS

A low number of ASVs (indicating low abundance and/or diversity of fungal taxa) was obtained in hemolymph and hepatopancreas samples. Thus, only exoskeleton, intestine, sediment and water samples were analyzed further. Significant differences were recorded between their mycobiomes, confirming their uniqueness. Generally, environmental mycobiomes showed higher diversity than crayfish-associated mycobiomes. The intestinal mycobiome showed significantly lower richness compared to other mycobiomes. Significant differences in the diversity of sediment and exoskeletal mycobiomes were recorded between different river segments (but not for water and intestinal mycobiomes). Together with the high observed portion of shared ASVs between sediment and exoskeleton, this indicates that the environment (i.e. sediment mycobiome) at least partly shapes the exoskeletal mycobiome of crayfish.

CONCLUSION

This study presents the first data on crayfish-associated fungal communities across different tissues, which is valuable given the lack of studies on the crayfish mycobiome. We demonstrate significant differences in the crayfish exoskeletal mycobiome along the invasion range, suggesting that different local environmental conditions may shape the exoskeletal mycobiome during range expansion, while the mycobiome of the internal organ (intestine) remained more stable. Our results provide a basis for assessing how the mycobiome contributes to the overall health of the signal crayfish and its further invasion success.

Aedes aegypti gut transcriptomes respond differently to microbiome transplants from field-caught or laboratory-reared mosquitoes

The mosquito microbiome is critical for host development and plays a major role in many aspects of mosquito biology. While the microbiome is commonly dominated by a small number of genera, there is considerable variation in composition among mosquito species, life stages, and geography. How the host controls and is affected by this variation is unclear. Using microbiome transplant experiments, we asked whether there were differences in transcriptional responses when mosquitoes of different species were used as microbiome donors. We used microbiomes from four different donor species spanning the phylogenetic breadth of the Culicidae, collected either from the laboratory or field. We found that when recipients received a microbiome from a donor reared in the laboratory, the response was remarkably similar regardless of donor species. However, when the donor had been collected from the field, far more genes were differentially expressed. We also found that while the transplant procedure did have some effect on the host transcriptome, this is likely to have had a limited effect on mosquito fitness. Overall, our results highlight the possibility that variation in mosquito microbiome communities are associated with variability in host-microbiome interactions and further demonstrate the utility of the microbiome transplantation technique.

Probiotics Mediate Intestinal Microbiome and Microbiota-Derived Metabolites Regulating the Growth and Immunity of Rainbow Trout (Oncorhynchus mykiss)

Emerging evidence confirms using probiotics in promoting growth and immunity of farmed fish. However, the molecular mechanisms underlying the host-microbiome interactions mediated by probiotics are not fully understood. In this study, we used rainbow trout (Oncorhynchus mykiss) as a model to investigate the internal mechanisms of host-microbiome interactions influenced by two probiotic bacteria, Bacillus velezensis and Lactobacillus sakei. We carried out experiments, including intestinal histology, serum physiology, and transcriptome and combined intestinal microbiome and metabolite profiling. Our results showed that both probiotics had a positive effect on growth, immunity, serum enzyme activity, the gut microbiome, and resistance to Aeromonas salmonicida in rainbow trout. Moreover, the intestinal microbial structure was reshaped with increased relative abundance of potential beneficial bacteria, such as Ruminococcus, Lachnospiraceae ucg-004, Leptotrichia, Bacillus coagulans, Porphyromonadaceae, Anaerococcus, and Photobacterium in the B. velezensis group and Paenibacillaceae and Eubacterium hallii in the L. sakei group. Metabolomic profiling and transcriptome analysis revealed upregulated metabolites as biomarkers, i.e., sucrose and l-malic acid in the B. velezensis group, and N-acetyl-l-phenylalanine, N-acetylneuraminic acid, and hydroxyproline in the L. sakei group. Additionally, a multiomics combined analysis illustrated significant positive correlations between the relative abundance of microflora, metabolites, and gene expression associated with immunity and growth. This study highlights the significant role of probiotics as effectors of intestinal microbial activity and shows that different probiotics can have a species-specific effect on the physiological regulation of the host. These findings contribute to a better understanding of the complex host-microbiome interactions in rainbow trout and may have implications for the use of probiotics in aquaculture. IMPORTANCE Probiotics are kinds of beneficial live microbes that impart beneficial effects on the host. Recent studies have proven that when given supplementation with probiotics, farmed fish showed improved disease prevention and growth promotion. However, the underlying metabolic functions regarding their involvement in regulating growth phenotypes, nutrient utilization, and immune response are not yet well understood in the aquaculture field. Given the active interactions between the gut microbiota and fish immune and growth performance, we conducted the supplementation experiments with the probiotics Bacillus velezensis and Lactobacillus sakei. The results showed that probiotics mediated intestinal microbiome- and microbiota-derived metabolites regulating the growth and immunity of fish, and different probiotics participated in the species-specific physiological regulation of the host. This study contributed to a better understanding of the functional interactions associated with host health and gut microbiota species.

Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River

Fish represent a large part of the taxonomic diversity of vertebrates and are of high commercial value. However, the factors influencing the gut microbiota composition of freshwater fish over large spatial scales remain unclear. Therefore, this study explored gut microbiome diversity in 24 fish species from the Yellow River, which spans over 1500 km across China. The results showed that geographical distance, host phylogeny and diet significantly influenced gut microbial community diversity, whereas sex, body length and body weight had minimal influence. Geographical distance was the primary factor shaping gut microbiota, and dissimilarity in microbial community structure increased with an increase in geographical distance, which was mainly driven by dispersal limitation. The microbial communities were more homogeneous at higher host taxonomic resolutions due to the dominant role of homogeneous selection in community convergence. Phylosymbiosis was observed across all host species, with a stronger pattern in Cypriniformes, which harbour host-specific microbial taxa. Host diet explained little variation in gut microbiome diversity, although it was significant for all diversity metrics tested. These findings collectively suggest that the geographical and host-based patterns of fish gut microbiota tend to be shaped by different ecological forces across the Yellow River. The present work provides a robust assessment of multiple factors driving fish gut microbial community assembly and offers insight into the mechanisms underlying shifts in fish gut microbiota in rivers across large spatial scales.

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems

Gut microbiota play important roles in fish health and growth performance and the microbiome in fish has been shown to be a biomarker for stress. In this study, we surveyed the change of Chinook salmon (Oncorhynchus tshawytscha) gut and water microbiota in freshwater recirculating aquaculture systems (RAS) for 7 months and evaluated how gut microbial communities were influenced by fish health and growth performance. The gut microbial diversity significantly increased in parallel with the growth of the fish. The dominant gut microbiota shifted from a predominance of Firmicutes to Proteobacteria, while Proteobacteria constantly dominated the water microbiota. Photobacterium sp. was persistently the major gut microbial community member during the whole experiment and was identified as the core gut microbiota for freshwater farmed Chinook salmon. No significant variation in gut microbial diversity and composition was observed among fish with different growth performance. At the end of the trial, 36 out of 78 fish had fluid in their swim bladders. These fish had gut microbiomes containing elevated proportions of Enterococcus, Stenotrophomonas, Aeromonas, and Raoultella. Our study supports the growing body of knowledge about the beneficial microbiota associated with modern salmon aquaculture systems and provides additional information on possible links between dysbiosis and gut microbiota for Chinook salmon.

Using the Gut Microbiome to Assess Stocking Efforts of the Endangered Pallid Sturgeon, Scaphirhynchus albus

The endangered Pallid Sturgeon, Scaphirhynchus albus, has been actively managed to prevent population declines, including stocking of hatchery-raised fish. The gut microbiome plays an innate role in an organism's absorption of nutrients by increasing nutrient availability and can provide new insights for Pallid Sturgeon management. In this study, the Pallid Sturgeon's microbiome is dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. It was also determined that the gut bacterial diversity in hatchery-raised Pallid Sturgeon was not significantly different from wild Pallid Sturgeon, supporting that hatchery-raised Pallid Sturgeon are transitioning effectively to wild diets. There is also a high degree of intraspecific variation in the bacterial and eukaryotic sequences amongst individual Pallid Sturgeon microbiomes, suggesting the Pallid Sturgeon may be omnivorous. This study demonstrated that genetic markers may be used to effectively describe the dietary requirements for wild Pallid Sturgeon and provides the first genetic evidence that Pallid Sturgeons are effectively transitioning from hatchery-raised environments to the wild.

Distribution and influencing factors of antibiotic resistance genes of crayfish (Procambarus clarkii) intestine in main crayfish breeding provinces in China

The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO₃-N, pH and temperature), microbial alpha diversity and mobile genetic elements (MGEs) showed significant influence on ARGs profiles. Generally, our results illustrate that ARGs are prevalent in crayfish gut and may pose potential risk to human health, which will help develop targeted strategies for the risk management and assessment of ARGs in the aquaculture.

Starvation alters gut microbiome and mitigates off-flavors in largemouth bass (Micropterus salmoides)

The present study aimed to investigate the response of intestinal microbiota during 3 weeks' starvation of largemouth bass (Micropterus salmoides), an economically important freshwater fish, using 16S rRNA gene amplicon sequencing and PICRUSt2 predictive functional profiling. Overall, the microbiota was mainly represented by Mycoplasma, Pseudomonas, Acinetobacter, and Microbacterium in the initial group. This pattern contrasted with that of Cetobacterium and Aeromonas, which were major representative genera in the starved group. Significant differences in the richness and composition of intestinal microbial community induced by starvation were observed. Notably, earthy-musty off-flavor compounds (geosmin and 2-methylisoborneol) were significantly decreased during starvation, which were significantly correlated with the abundance of certain actinobacterial taxa, namely, Microbacterium and Nocardioides. Additionally, the functional pathways involved in synthesis of off-flavor compounds, protein digestion, fatty acid degradation, and biosynthesis of cofactors greatly decreased with starvation, indicating that microbiota modulated the specific metabolic pathway to adapt to food deprivation. These results emphasize that starvation can modulate diversity, community structure, and functions of the intestinal microbiota and mitigate the off-flavors, which has important implications for strategies to eliminate off-flavor odorants through the application of probiotics to manipulate the gut microbiome and ultimately enhance flesh quality of freshwater fish.

Rice flowering improves the muscle nutrient, intestinal microbiota diversity, and liver metabolism profiles of tilapia (Oreochromis niloticus) in rice-fish symbiosis

BACKGROUND

Rice-fish symbiosis, as an ecological and green aquaculture model, is an effective measure to relieve the environmental stress from intensive aquaculture. Compared with traditional aquaculture, the altered rearing pattern and environment will make differences in muscle nutrient and quality, intestinal microbiota, body metabolism, and even disease resistance in fish.

RESULTS

To investigate this, we explored the differences between rice-tilapia (aRT and bRT) and tank-tilapia (aTT and bTT) models at the periods before and after rice flowering using 16S rRNA sequencing and untargeted metabolomics. The results showed that compared with tilapia reared in the tank model, the fish body length and weight, the muscle total umami amino acid, and monounsaturated fatty acid content were obviously higher in the rice-fish model, especially after rice flowering. Compared with other groups, the intestinal microbiota diversity of fish in the bRT group was significantly higher; the dominant microbiota was Bacteroidetes and Firmicutes at the phylum level, Bacteroides and Turicibacter at the genus level, and the relative abundances of Gram-negative, potentially pathogenic, and stress-tolerant bacteria were the highest, lowest, and highest, respectively. Besides, the differential metabolite analysis indicated that rice-fish symbiosis improved the metabolic profiles and modulated the metabolic pathways in tilapia. Moreover, the correlation analysis of 16S sequencing and metabolomics showed that Bacteroides showed a positive correlation with many metabolites related to amino acid, fatty acid, and lipid metabolism. Video Abstract CONCLUSIONS: In summary, rice flowering improves the tilapia muscle nutrient, intestinal microbiota diversity, and disease resistance and modulates the host metabolism to acclimatize the comprehensive environment in rice-fish symbiosis. Specifically, rice flowering alters the microbiota abundance involved in amino acid, fatty acid, and lipid metabolism, resulting in improving the muscle nutrient and quality through the crosstalk of gut microbial and host metabolism. Our study will provide not only new insight into the gut microbiota-metabolism-phenotype axis, but also strong support for the promotion and application of rice-fish symbiosis in aquaculture.

Modulation of gut microbiota, blood metabolites, and disease resistance by dietary β-glucan in rainbow trout (Oncorhynchus mykiss)

BACKGROUND

Prebiotics are known to have a positive impact on fish health and growth rate, and β-glucans are among the most used prebiotics on the market. In this study, rainbow trout (Oncorhynchus mykiss) were treated with a β-1,3;1,6-glucan dietary supplement (at a dose of 0 g, 1 g, 10 g, and 50 g β-glucan per kg of feed). After 6 weeks, the effect of the β-glucan was evaluated by determining the changes in the microbiota and the blood serum metabolites in the fish. The impact of β-glucan on the immune system was evaluated through a challenge experiment with the bacterial fish pathogen Yersinia ruckeri.

RESULTS

The microbiota showed a significant change in terms of composition following β-glucan treatment, notably an increase in the relative abundance of members of the genus Aurantimicrobium, associated with a decreased abundance of the genera Carnobacterium and Deefgea. Furthermore, analysis of more than 200 metabolites revealed that the relative levels of 53 metabolites, in particular compounds related to phosphatidylcholines, were up- or downregulated in response to the dietary supplementation, this included the amino acid alanine that was significantly upregulated in the fish that had received the highest dose of β-glucan. Meanwhile, no strong effect could be detected on the resistance of the fish to the bacterial infection.

CONCLUSIONS

The present study illustrates the ability of β-glucans to modify the gut microbiota of fish, resulting in alteration of the metabolome and affecting fish health through the lipidome of rainbow trout.

The microbial community associated with Parascaris spp. infecting juvenile horses

Background

Parasitic nematodes, including large roundworms colloquially known as ascarids, affect the health and well-being of livestock animals worldwide. The equine ascarids, Parascaris spp., are important parasites of juvenile horses and the first ascarids to develop widespread anthelmintic resistance. The microbiota has been shown to be an important factor in the fitness of many organisms, including parasitic nematodes, where endosymbiotic Wolbachia have been exploited for treatment of filariasis in humans.

Methods

This study used short-read 16S rRNA sequences and Illumina sequencing to characterize and compare microbiota of whole worm small intestinal stages and microbiota of male and female intestines and gonads. Diversity metrics including alpha and beta diversity, and the differential abundance analyses DESeq2, ANCOM-BC, corncob, and metagenomeSeq were used for comparisons.

Results

Alpha and beta diversity of whole worm microbiota did not differ significantly between groups, but Simpson alpha diversity was significantly different between female intestine (FI) and male gonad (MG) (P= 0.0018), and Shannon alpha diversity was significantly different between female and male gonads (P = 0.0130), FI and horse jejunum (HJ) (P = 0.0383), and FI and MG (P= 0.0001). Beta diversity (Fig. 2B) was significantly different between female and male gonads (P = 0.0006), male intestine (MI) and FG (P = 0.0093), and MG and FI (P = 0.0041). When comparing organs, Veillonella was differentially abundant for DESeq2 and ANCOM-BC (p < 0.0001), corncob (P = 0.0008), and metagenomeSeq (P = 0.0118), and Sarcina was differentially abundant across four methods (P < 0.0001). Finally, the microbiota of all individual Parascaris spp. specimens were compared to establish shared microbiota between groups.

Conclusions

Overall, this study provided important information regarding the Parascaris spp. microbiota and provides a first step towards determining whether the microbiota may be a viable target for future parasite control options.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05533-y.

Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review

The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.

Dietary supplementation of two indigenous Bacillus spp on the intestinal morphology, intestinal immune barrier and intestinal microbial diversity of Rhynchocypris lagowskii

This study evaluated the effects of dietary administration of two indigenous Bacillus (A: basal control diet; B: 0.15 g/kg of Bacillus subtilis; C: 0.1 g/kg of Bacillus subtilis and 0.05 g/kg of Bacillus licheniformis; D: 0.05 g/kg of Bacillus subtilis and 0.1 g/kg of Bacillus licheniformis; E: 0.15 g/kg of Bacillus licheniformis) on the digestive enzyme activities, intestinal morphology, intestinal immune and barrier-related genes relative expression levels, and intestinal flora of Rhynchocypris lagowskii. The results showed that the fold height, lamina propria width, and muscle layer thickness of midgut and hindgut in group C were significantly higher than that of group A (P < 0.05). The activities of protease, amylase, and lipase in group C were significantly higher than those of group A (P < 0.05). The relative expression levels of IL-1β and IL-8 in the intestine of group C were significantly downregulated, and the relative expression levels of IL-10 and TGF-β were significantly upregulated (P < 0.05). The relative expression levels of Claudin-2 in group A significantly increased and the relative expression levels of Claudin-4 in group A significantly reduced compared with other groups (P < 0.05). The relative expression levels of ZO-1 in groups C and D were significantly higher than those of other groups (P < 0.05). The Bacillus in the intestine of group C has the highest relative abundance among all groups. Overall, it can generally be concluded that dietary supplementation of indigenous Bacillus subtilis and Bacillus licheniformis (group C) can improve the intestinal morphology, digestion, and absorption enzyme activities, enhance intestinal mucosal immunity and barrier function, and maintain the intestinal microbial balance of R. lagowskii.

Comparative analysis of the fecal bacterial communities of hawksbill sea turtles (Eretmochelys imbricata) and green sea turtles (Chelonia mydas)

Hawksbill sea turtles (Eretmochelys imbricata) are important for maintaining healthy coral reef ecosystems currently qualify as 'critically endangered' by the IUCN. Their gut microbiota is closely linked to host nutrition and health, however, the gut microbiota of hawksbill sea turtles from a natural reserve remains unclear. Therefore, exploring their microbial community structure in a natural reserve may provide valuable information on strategies for protecting this species. In this study, we investigated hawksbill sea turtle fecal microbial communities from a natural reserve using 16S metagenomics and compared the gut microbiota from fecal samples of hawksbill and green sea turtles (Chelonia mydas). The results indicated that the structure of fecal microbial communities was significantly different between hawksbill and green sea turtles. In hawksbill sea turtles, the three dominant phyla were Bacteroidetes, Firmicutes, and Fusobacteria, whereas the fecal microbial communities of green sea turtles were mainly composed of Firmicutes, Bacteroidetes, and Proteobacteria. Among the hawksbill sea turtle fecal microbes, the predominant genera were Cetobacterium and Rikenell, whereas in green sea turtles, the predominant genera were Bacteroides and Paludibacter. In addition, predictive metagenomic analysis indicated that sugar catabolism was enriched in green sea turtle fecal microbiota, whereas pathways related to secondary metabolite production were enriched in hawksbill sea turtle fecal microbiota. Our study provides preliminary data on the fecal microbiota features of sea turtles from the natural reserve which may contribute to the management of the food requirements and long-term conservation of hawksbill sea turtles.

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.

Does Exposure of Broodstock to Dietary Soybean Meal Affect Its Utilization in the Offspring of Zebrafish (Danio rerio)?

Simple Summary

Replacement of fishmeal in fish diets with plant protein has been an ongoing challenge. High-quality plant protein concentrates are widely used since their digestibility can be comparable to fishmeal. However, their price can exceed the cost of marine raw materials. Progress with utilization of lower-quality plant protein sources has been made but a number of concerns must be overcome to maintain acceptable growth rates at high fishmeal substitution levels. Nutritional programming represents a promising approach to offset the negative effects of dietary plant protein through its exposure in early life. We tested an unconventional programming strategy by exposing parental zebrafish to soybean meal diet to improve dietary soybean meal utilization in progeny fish. The study observed a strong trend showing better growth performance between progeny zebrafish fed soybean meal diet that originated from broodstock exposed to soybean meal as opposed to progeny fish fed soybean meal diet that originated from fishmeal diet fed broodstock. However, the study found no changes in the richness, diversity, or composition of gut microbial communities associated with progeny fish from fishmeal or soybean meal fed broodstock. Hence, the mechanism behind nutritional programming does not seem to be associated with modified gut microbiome.

Abstract

Nutritional programming (NP) is a concept in which early nutritional events alter the physiology of an animal and its response to different dietary regimes later in life. The objective of this study was to determine if NP via broodstock with dietary plant protein (PP) has any effect on the gut microbiome of the progeny fish and whether this modified gut microbiome leads to better utilization of PP diet. The experiment consisted of four different treatments as follows: (1) progeny that received FM diet obtained from fishmeal (FM)-fed broodstock (FMBS-FM, +control); (2) progeny that received PP diet obtained from FM-fed parents (FMBS-PP); (3) progeny that received PP diet obtained from “nutritionally programmed” parents (PPBS-PP; −control); and (4) progeny that received FM diet obtained from “nutritionally programmed” parents (PPBS-FM). Zebrafish was used as a model species. This study found that parental programming seems to have some positive effect on dietary PP utilization in progeny. However, the influence of NP with PP through broodstock on gut microbiota of the offspring fish was not detected.

Shift and homogenization of gut microbiome during invasion in marine fishes

Biological invasion is one of the main components of global changes in aquatic ecosystems. Unraveling how establishment in novel environments affects key biological features of animals is a key step towards understanding invasion. Gut microbiome of herbivorous animals is important for host health but has been scarcely assessed in invasive species. Here, we characterized the gut microbiome of two invasive marine herbivorous fishes (Siganus rivulatus and Siganus luridus) in their native (Red Sea) and invaded (Mediterranean Sea) ranges. The taxonomic and phylogenetic diversity of the microbiome increased as the fishes move away from the native range and its structure became increasingly different from the native microbiome. These shifts resulted in homogenization of the microbiome in the invaded range, within and between the two species. The shift in microbial diversity was associated with changes in its functions related with the metabolism of short-chain fatty acids. Altogether, our results suggest that the environmental conditions encountered by Siganidae during their expansion in Mediterranean ecosystems strongly modifies the composition of their gut microbiome along with its putative functions. Further studies should pursue to identify the precise determinants of these modifications (e.g. changes in host diet or behavior, genetic differentiation) and whether they participate in the ecological success of these species.

Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari)

Background

Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.

Results

Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.

Conclusion

For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00187-8.

Comparative Analysis of the Gut Microbiota of Mandarin Fish (Siniperca chuatsi) Feeding on Compound Diets and Live Baits

Siniperca chuatsi feeds on live fry throughout their life. The sustainable development of its farming industry has urgently necessitated the development of artificial diets to substitute live baits. It has been demonstrated that gut microbiota assists in feed adaptation and improves the feed conversion rate in fish. Therefore, this study aimed to understand the potential role of intestinal microorganisms in the domestication of S. chuatsi with a compound diet. Accordingly, we performed 16S rRNA sequencing of the gut microbial communities in S. chuatsi groups that were fed a compound diet (including large and small individuals) and live baits. A total of 2,471 OTUs were identified, and the large individual group possessed the highest number of unique OTUs. The α-diversity index of the gut microbiota in groups that were fed a compound diet was significantly higher (p < 0.05) than that in the live bait group. There were no significant differences in the α-diversity between the large and small individual groups. However, relatively higher numbers of Lactococcus, Klebsiella, and Woeseia were observed in the intestines of the large individual group. Prediction of the metabolic function of the microbiota among these three fish groups by Tax4Fun revealed that most metabolic pathways, such as glycan metabolism and amino acid metabolism, were typically more enriched for the larger individuals. The results indicated that certain taxa mentioned above exist in large individuals and may be closely related to the digestion and absorption of compound diets. The present study provides a basis for understanding the utilization mechanism of artificial feed by S. chuatsi.

Exploring the gut microbiota composition of Indian major carp, rohu (Labeo rohita), under diverse culture conditions

Gut microbiota of freshwater carps are often investigated for their roles in nutrient absorption, enzyme activities and probiotic properties. However, little is known about core microbiota, assembly pattern and the environmental influence on the gut microbiota of the Indian major carp, rohu. The gut microbial composition of rohu reared in different culture conditions was analysed by 16S rRNA amplicon sequencing. There was variation on gut microbial diversity and composition. A significant negative correlation between dissolved oxygen content (DO) and alpha diversity was observed, thus signifying DO content as one of the key environmental factors that regulated the diversity of rohu gut microbial community. A significant positive correlation was observed between phosphate concentration and abundance of Actinobacteria in different culture conditions. Two phyla, Proteobacteria and Actinobacteria along with OTU750868 (Streptomyces) showed significant (p < 0.05) differences in their abundance among all culture conditions. The Non-metric multidimensional scaling ordination (NMDS) analysis using Bray-Curtis distances, showed the presence of unique gut microbiota in rohu compared to other herbivorous fish. Based on niche breadth, 3 OTUs were identified as core generalists, persistent across all the culture conditions whereas the specialists dominated in the rohu gut microbiota assembly. Co-occurrence network analysis revealed positive interaction within core members while mutual exclusion between core and non-core members. Predicted microbiota function revealed that different culture conditions affected the metabolic capacity of gut microbiota of rohu. The results overall indicated the significant effect of different rearing environments on gut microbiota structure, assembly and inferred community function of rohu which might be useful for effective manipulation of gut microbial communities of rohu to promote better health and growth under different husbandry settings.

Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World's Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for 6 months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at the clade level, with the most geographically distant clades (A and D) being the most distinct, and the two overlapping clades (B and C) showing similarities. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters were. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying plastic changes and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group, at higher taxonomic scale, resembled that of other teleost fishes. Our results suggest that divergent natural environments giving rise to evolutionary novelties underlying host adaptations, also includes the microbiome of these fishes.

Key Performance Indicators of Common Carp (Cyprinus carpio L.) Wintering in a Pond and RAS under Different Feeding Schemes

Overwintering impacts common carp performance, yet the nature of changes is not known. The aim of the study was to compare the zootechnical and key performance indicators (KPI) of Cyprinus carpio wintering in a pond with no supplementary feeding (MCF), in a Recirculating Aquaculture System (RAS) fed typical (30% of protein and 8% of fat) carp diet (AFC), and in a RAS fed high protein (42%) and fat (12%) diet (ABF). The analysis showed that ABF fish had the highest final body weight and the Fulton’s condition factor, as well as the lowest food conversion rate compared with AFC and MCF fish. Histomorphological assessment revealed that MCF fish had thinner skin layers, a depleted population of mucous cells in skin, an excessive interlamellar mass in the gills, and no supranuclear vacuoles in the intestine compared to fish from RAS. At the molecular level, higher transcript levels of il-1β and il-6 transcripts were found in the gills of MCF than in fish from RAS. The transcript level of the intestinal muc5b was the highest in ABF fish. Relative expression of il-1β and il-6 in gills were presumably the highest due to lamellar fusions in MCF fish. Described KPIs may assist carp production to ensure sustainability and food security in the European Union.

Chronic Embryo-Larval Exposure of Fathead Minnows to the Pharmaceutical Drug Metformin: Survival, Growth, and Microbiome Responses

Metformin is a glucose-lowering drug commonly found in municipal wastewater effluents (MWWEs). The present study investigated the chronic effects of metformin in early-life stages of the fathead minnow (Pimephales promelas). Endpoints assessed were growth, survival, and deformities. The larval gut microbiome was also examined using 16 S ribosomal RNA gene amplicon sequencing to determine microbial community composition and alpha and beta diversity. Eggs and larvae were exposed to metformin measured concentrations (mean [standard deviation]) of 0.020 (0.017) μg/L (for controls) and 3.44 (0.23), 33.6 (1.6), and 269 (11) μg/L in a daily static-renewal setup, with 20 embryos per beaker. The low and middle metformin exposure concentrations represent river and MWWE concentrations of metformin. To detect small changes in growth, we used 18 replicate beakers for controls and 9 replicates for each metformin treatment. Over the 21-d exposure (5 d as embryos and 16 d posthatch [dph]), metformin did not affect survival or growth of larval fish. Hatch success, time to hatch, deformities in hatched fry, and survival were similar across all treatments. Growth (wet wt, length, and condition factor) assessed at 9 and 16 dph was also unaffected by metformin. Assessment of the microbiome showed that the larvae microbiome was dominant in Proteobacteria and Firmicutes, with small increases in Proteobacteria and decreases in Firmicutes with increasing exposure to metformin. No treatment effects were found for microbiome diversity measures. Control fish euthanized with the anesthetic tricaine methane sulfonate had decreased alpha diversity compared to those sampled by spinal severance. This experiment demonstrates that metformin at environmentally relevant concentrations (3.44 and 33.6 μg/L) and at 10 times MWWE concentrations (269 µg/L) does not adversely affect larval growth or gut microbiome in this ubiquitous freshwater fish species. Environ Toxicol Chem 2022;41:635-647. © 2021 Her Majesty the Queen in Right of Canada. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Environment and Climate Change Canada.

Comparison of the Intestinal Bacteria Between Black Seabass Centropristis striata Reared in Recirculating Aquaculture System and Net Pen

Determination of diversity and function of the bacteria in fish gut is essential to understanding the interaction between intestinal bacteria and their host organism. This study compared intestinal bacterial community of black seabass (Centropristis striata) hatched by the same breeding farm but reared in different aquaculture systems, an indoor recirculating aquaculture system (RAS) and an inshore net pen (INP). The fish were fed with formulated feed manufactured by same feed company. Bacteria in fish gut, formulated feed and seawater were identified by 16S rRNA high throughout sequencing (HTS). Total 1484 OTUs, which belonged to 34 phyla and 79 genera, were identified from fish gut, formulated feed and seawater. In fish gut, 24 phyla and 43 genera were identified. Proteobacteria, Fusobacteria, and Firmicutes dominated at the phylum level in fish gut in INP, while Proteobacteria and Firmicutes dominated in fish gut in RAS. Photobacterium, Vibrio, and Cetobacterium dominated at the genus level in fish gut in both INP and RAS. One OTU of Photobacterium occurred in all the fish gut samples, suggesting this bacterium might be the main component of the core microbiota. No significant difference was found in bacterial diversity in fish gut between INP and RAS, suggesting genetic background should be a primary factor determining intestinal bacterial community of black seabass. Bacterial diversity in seawater was high relative to that in fish gut and formulated feed, regardless in INP or RAS. The common OTU between fish gut and seawater was more than that between fish gut and formulated feed in INP, while the common OTU between fish gut and seawater was slightly less than that between fish gut and formulated feed in RAS. These results reveal that the bacteria in formulated feed and seawater could influence the bacteria in fish gut, and their priority in shaping intestinal bacterial community depended on the bacterial composition in feed and seawater. This study reveals that intestinal bacterial community of black seabass was influenced by both genetic background and environmental factors.

Solea senegalensis Bacterial Intestinal Microbiota Is Affected by Low Dietary Inclusion of Ulva ohnoi

The inclusion of macroalgae in the diets of farmed fish offers the opportunity for an added-value dietary ingredient to the nutraceutical feed. The composition of algae varies greatly among species. Several Ulva species have been considered in aquafeed formulations for different farmed fish, and Ulva ohnoi is being applied recently. However, the effects of seaweed dietary inclusion on the host must be evaluated. Considering the important role of the host intestinal microbiota, the potential effects of U. ohnoi dietary inclusion need to be studied. In this study, the characterization of the intestinal microbiome of Solea senegalensis, a flatfish with high potential for aquaculture in South Europe, receiving U. ohnoi (5%)-supplemented diet for 90 days has been carried out. In addition, the functional profiles of bacterial communities have been determined by using PICRUSt, a computational approach to predict the functional composition of a metagenome by using marker gene data and a database of reference genomes. The results show that long-term dietary administration of U. ohnoi (5%)-supplemented feed modulates S. senegalensis intestinal microbiota, especially in the posterior intestinal section. Increased relative abundance of Vibrio jointly with decreased Stenotrophomonas genus has been detected in fish receiving Ulva diet compared to control-fed fish. The influence of the diet on the intestinal functionality of S. senegalensis has been studied for the first time. Changes in bacterial composition were accompanied by differences in predicted microbiota functionality. Increased abundance of predicted genes involved in xenobiotic biodegradation and metabolism were observed in the microbiota when U. ohnoi diet was used. On the contrary, predicted percentages of genes associated to penicillin and cephalosporin biosynthesis as well as beta-lactam resistance were reduced after feeding with Ulva diet.

Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus

Environmental bacteria have a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to the disturbance from environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon the hindgut microbiota of cultured fugu. Consequently, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, implying a reduced stability upon bacterial disturbance from feed. Moreover, quantitative ecological analyses indicated that homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts in the context of lower degree of disturbance. While the disturbance peaked, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Our findings emphasized the intricate linkage between feed and gut microbiota and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.