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

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human

BACKGROUND

Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.

RESULTS

The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.

CONCLUSIONS

The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.

Responses of growth performance, immunity, disease resistance of shrimp and microbiota in Penaeus vannamei culture system to Bacillus subtilis BSXE-1601 administration: Dietary supplementation versus water addition

This study evaluated the effects of Bacillus subtilis BSXE-1601, applied either as dietary supplementation or water addition, on growth performance, immune responses, disease resistance of Penaeus vannamei, and microbiota in shrimp gut and rearing water. During the 42-day feeding experiment, shrimp were fed with basal diet (CO and BW group), basal diet supplemented with live strain BSXE-1601 at the dose of 1 × 109 CFU kg-1 feed (BD group) and 15 mg kg-1 florfenicol (FL group), and basal diet with strain BSXE-1601 added to water at the concentration of 1 × 107 CFU L-1 every five days (BW group). Results showed that dietary supplementation of strain BSXE-1601 significantly promoted growth performance of shrimp, both in the diet and water, enhanced disease resistance against Vibrio parahaemolyticus (P < 0.05). The BD and BW groups exhibited significant increases in acid phosphatase, alkaline phosphatase, lysozyme, peroxidase, superoxide dismutase activities, phenonoloxidase content in the serum of shrimp compared to the control (P < 0.05). Meanwhile, the expression of immune-related genes proPO, LZM, SOD, LGBP, HSP70, Imd, Toll, Relish, TOR, 4E-BP, eIF4E1α, eIF4E2 were significantly up-regulated compared to the control (P < 0.05). When added in rearing water, strain BSXE-1601 induced greater immune responses in shrimp than the dietary supplement (P < 0.05). Chao1 and Shannon indices of microbiota in rearing water were significantly lower in BD group than in the control. The microbiota in rearing water were significantly altered in BD, BW and FL groups compared to the control, while no significant impacts were observed on the microbiota of shrimp gut. When supplemented into the feed, strain BSXE-1601 obviously reduced the number of nodes, edges, modules in the ecological network of rearing water. The results suggested that dietary supplementation of BSXE-1601 could be more suitable than water addition in the practice of shrimp rearing when growth performance, non-specific immunity, disease resistance against V. parahaemolyticus in shrimp were collectively considered.

Effects of dietary fermented Saccharomyces cerevisiae extract (Hilyses) supplementation on growth, hematology, immunity, antioxidants, and intestinal health in Nile tilapia

This study investigated the effects of dietary supplementation with the product Hilyses on growth performance, feed utilization, nutrient composition, hematological parameters, serum biochemistry, immune function, antioxidant status, and digestive enzyme activity in juvenile Nile tilapia (Oreochromis niloticus, initial body weight 4.24 ± 0.01 g). The fish were fed diets supplemented with Hilyses at concentrations of 0, 1, 2, or 3 g/kg for a period of 8 weeks. The results showed that supplementation with Hilyses at levels up to 2 g/kg diet significantly improved final body weight, weight gain, specific growth rate, feed efficiency ratio, protein efficiency ratio, apparent protein utilization, and energy utilization compared to the control diet without Hilyses. Carcass crude protein content and moisture were significantly higher in Hilyses-fed groups, while crude lipid content decreased at the 3 g/kg supplementation level. Hilyses supplementation enhanced various hematological parameters, including increased red blood cell count, total leukocyte count, hemoglobin concentration, hematocrit, and mean corpuscular volume. Serum biochemistry and immune function markers like total protein, albumin, complement component C3, IgM, and IgG were significantly elevated in the 2 and 3 g/kg Hilyses groups. Antioxidant enzyme activities (catalase, glutathione peroxidase, total superoxide dismutase) were enhanced, and lipid peroxidation was reduced, in the 2 g/kg Hilyses group. Digestive enzyme activities, particularly protease and lipase, were also improved with Hilyses supplementation. Histological examination showed reduced lipid deposition in the liver and increased branching of intestinal villi at the 2 g/kg Hilyses level. Overall, these results indicated that dietary Hilyses supplementation at 2 g/kg diet optimizes growth, feed utilization, nutrient composition, hematology, immunity, antioxidant status, and digestive function in juvenile Nile tilapia.

A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea

BACKGROUND

Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.

RESULTS

The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.

CONCLUSION

Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.

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.

Gut microbiome play a crucial role in geographical and interspecies variations in mercury accumulation by fish

Mercury (Hg) contamination in fish has raised global concerns for decades. The Hg biotransformation can be manipulated by gut microbiome and it is found to have a substantial impact on the speciation and final fate of Hg in fish. However, the contribution of intestinal microbiota in geographical and interspecies variations in fish Hg levels has not been thoroughly understood. The present study compared the Hg levels in wild marine fish captured from two distinct regions in South China sea. We observed a quite "ironic" phenomenon that MeHg levels in carnivorous fish from a region with minimal human impacts (Xisha Islands, 92 ± 7.2 ng g-1 FW) were much higher than those from a region with severe human impacts (Daya Bay, 19 ± 0.41 ng g-1 FW). Furthermore, the results showed that gut microbiome determined Hg biotransformation and played a crucial role in the variances in fish Hg levels across different geographical locations and species. The intestinal methylators, rather than demethylators, were more significant in affecting Hg biotransformation in fish. The carnivorous species in Xisha Islands exhibited a higher abundance of intestinal methylators, leading to higher MeHg accumulation. Besides, the gut microbiome could be shaped in response to the elevated Hg levels in these fish, which may benefit their adaptation to Hg toxicity and overall health preservation. However, anthropogenic activities (particularly overfishing) in Daya Bay have severely affected the fish population, disrupting the reciprocal relationships between fish and intestinal microbiota and rendering them more susceptible to pathogenic microbes. Overall, this study provided a comprehensive understanding of the role of gut microbiome in Hg bioaccumulation in fish and offered valuable insights into the co-evolutionary dynamics between fish and gut microbiome in the presence of Hg exposure.

Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review

The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.

Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter

BACKGROUND

Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth.

RESULTS

We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and > 70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus.

CONCLUSION

Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.

Changes in pH and Nitrite Nitrogen Induces an Imbalance in the Oxidative Defenses of the Spotted Babylon (Babylonia areolata)

In order to reveal the acute toxicity and physiological changes of the spotted babylon (Babylonia areolata) in response to environmental manipulation, the spotted babylon was exposed to three pH levels (7.0, 8.0 and 9.0) of seawater and four concentrations of nitrite nitrogen (0.02, 2.7, 13.5 and 27 mg/L). The activities of six immunoenzymes, superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), catalase (CAT), acid phosphatase (ACP), alkaline phosphatase (AKP) and peroxidase (POD), were measured. The levels of pH and nitrite nitrogen concentrations significantly impacted immunoenzyme activity over time. After the acute stress of pH and nitrite nitrogen, the spotted babylon appeared to be unresponsive to external stimuli, exhibited decreased vigor, slowly climbed the wall, sank to the tank and could not stand upright. As time elapsed, with the extension of time, the spotted babylon showed a trend of increasing and then decreasing ACP, AKP, CAT and SOD activities in order to adapt to the mutated environment and improve its immunity. In contrast, POD and GSH-PX activities showed a decrease followed by an increase with time. This study explored the tolerance range of the spotted babylon to pH, nitrite nitrogen, and time, proving that external stimuli activate the body's immune response. The body's immune function has a specific range of adaptation to the environment over time. Once the body's immune system was insufficient to adapt to this range, the immune system collapsed and the snail gradually died off. This study has discovered the suitable pH and nitrite nitrogen ranges for the culture of the spotted babylon, and provides useful information on the response of the snail's immune system.

Relationship of environmental factors in pond water and dynamic changes of gut microbes of sea bass Lateolabrax japonicus

The effect of structure of gut microbes on the health of host has attracted increasing attention. Sea bass Lateolabrax japonicus is an important farmed fish in China. The relationship of the dynamic changes of intestinal bacterial communities in L. japonicus and the cultural water environment is very important for healthy culture. Here, the diversity and abundance of the gut microbial communities of L. japonicus were evaluated during the culture using 16S rRNA Illumina sequencing. Both the opportunistic pathogens Aeromonas (1.68%), Vibrio (1.59%), and Acinetobacter (1.22%); and the potential probiotics Lactobacillus (2.27%), Bacillus (1.16%), and Lactococcus (0.37%) were distributed in the gut of L. japonicus. The increasing concentration of nitrogen of water environments with the increase of culture time significantly correlated with shifts in the microbial community structure: 40.04% of gut microbial changes due to nitrogen concentration. Higher concentrations of nitrogen showed a significantly negative correlation with intestinal probiotics in L. japonicus. The results indicate that the abundance of intestinal bacteria of L. japonicus is mainly driven by the changes of environmental factors (e.g., nitrogen), and it’s very important that the linking environmental parameters with bacterial data of guts could be used as an early warning indicator in L. japonicus heath culture.

Transport Stress Induces Oxidative Stress and Immune Response in Juvenile Largemouth Bass (Micropterus salmoides): Analysis of Oxidative and Immunological Parameters and the Gut Microbiome

Transport is essential in cross-regional culturing of juvenile fish. Largemouth bass (Micropterus salmoides) often exhibit decreased vitality and are susceptible to disease after transportation. To study the effects of transport stress on juvenile largemouth bass, juveniles (average length: 8.42 ± 0.44 cm, average weight 10.26 ± 0.32 g) were subjected to a 12 h simulated transport, then subsequently, allowed to recover for 5 d. Liver and intestinal tissues were collected at 0, 6 and 12 h after transport stress and after 5 d of recovery. Oxidative and immunological parameters and the gut microbiome were analyzed. Hepatocytic vacuolization and shortened intestinal villi in the bass indicated liver and intestinal damage due to transport stress. Superoxide dismutase, lysozyme and complement C3 activities were significantly increased during transport stress (p < 0.05), indicating that transport stress resulted in oxidative stress and altered innate immune responses in the bass. With the transport stress, the malondialdehyde content first increased, then significantly decreased (p < 0.05) and showed an increasing trend in the recovery group. 16S rDNA analysis revealed that transport stress strongly affected the gut microbial compositions, mainly among Proteobacteria, Firmicutes, Cyanobacteria and Spirochaetes. The Proteobacteria abundance increased significantly after transport. The Kyoto Encyclopedia of Genes and Genomes functional analysis revealed that most gut microbes played roles in membrane transport, cell replication and repair. Correlation analyses demonstrated that the dominant genera varied significantly and participated in the measured physiological parameter changes. With 5 days of recovery after 12 h of transport stress, the physiological parameters and gut microbiome differed significantly between the experimental and control groups. These results provide a reference and basis for studying transport-stress-induced oxidative and immune mechanisms in juvenile largemouth bass to help optimize juvenile largemouth bass transportation.