Quantifying the Colonization of Environmental Microbes in the Fish Gut: A Case Study of Wild Fish Populations in the Yangtze River

Exploring the gut microbiota and metabolome of Lateolabrax japonicus: A multi-omics approach

The intestinal microbiota plays a crucial role in the health and development of fish, engaging in intricate interactions with the host organism. As a significant species in aquaculture, Lateolabrax japonicus serves as an exemplary model for investigating these interactions and their subsequent effects on growth and health. This study utilized a multi-omics approach, incorporating metagenomic sequencing and non-targeted metabolomics, to delineate the gut microbiota and metabolome of L. japonicus throughout various developmental phases. Collected from a meticulously controlled aquaculture setting, the intestinal microbiota of L. japonicus underwent high-throughput sequencing to scrutinize microbial DNA and enumerate metabolites. The metagenomic analysis uncovered a heterogeneous gut microbiota in L. japonicus, predominantly composed of Proteobacteria and Firmicutes, with marked heterogeneity in microbial composition across developmental stages. A particularly noteworthy discovery was the prevalence of the genus Acinetobacter, which may significantly influence health and disease resistance. The metabolomic profiling discerned 4479 metabolites, each exhibiting pronounced stage-specific metabolic signatures, particularly within lipid, amino acid, and energy metabolism pathways. The correlation analysis between microbiota and metabolites highlighted the substantial impact of specific genera, such as Acinetobacter and Gaeumannomyces, on the metabolic milieu. This study provides a comprehensive overview of the dynamic shifts in the gut microbiota and metabolome of L. japonicus, highlighting stage-specific transitions that could be pivotal for refining aquaculture practices. The findings underscore the complex interdependence between microbiota composition and metabolic function, providing valuable insights into the modulation of fish health and growth.

Variable phylosymbiosis and cophylogeny patterns in wild fish gut microbiota of a large subtropical river

The persistence and specificity of fish host-microbial interaction during evolution is an important part of exploring the host-microbial symbiosis mechanism. However, it remains unclear how the environmental and host factors shape fish host-microbe symbiotic relationships in subtropical rivers with complex natural environments. Freshwater fish are important consumers in rivers and lakes and are considered keystone species in maintaining the stability of food webs there. In this study, patterns and mechanisms shaping gut microbiota community in 42 fish species from the Pearl River, in the subtropical zone of China, were investigated. The results showed that fish host specificity is a key driver of gut microbiota evolution and diversification. Different taxonomic levels of the host showed different degrees of contribution to gut microbiota variation. Geographical location and habitat type were the next most important factors in shaping gut microbiota across the 42 fishes, followed by diet and gut trait. Our results emphasized the contribution of stochastic processes (drift and homogenizing dispersal) in the gut microbial community assembly of freshwater fishes in the middle and lower reaches of the Pearl River. Phylosymbiosis is evident at both global and local levels, which are jointly shaped by complex factors including ecological or host physiological filtration and evolutionary processes. The core microbiota showed co-evolutionary relationships of varying degrees with different taxonomic groups. We speculate that host genetic isolation or habitat variation facilitates the heterogeneous selection (deterministic process), which occurs and results in different host-core bacterium specificity.

IMPORTANCE

Freshwater fish are regarded as the dominant consumers in rivers and lakes. Due to their diverse feeding modes, fish significantly enhance the trophic link and nutrient recycling/retention in aquatic habitats. For this, they are often considered keystone species in maintaining the stability of food webs in rivers and lakes. A significant part of fish nutrition is essentially mediated by their gut microbiota, which can enhance fish tolerance to fluctuations in external resources and improve the efficiency of nutrients extracted from various food sources. As gut bacterial symbionts have a profound impact on the nutrition and development of their hosts, as well as their overall fitness, it is critical to answer the question of how hosts maintain these benefits by procuring or inheriting these vital symbionts, which is still largely unanswered, especially for freshwater fish. Our study provides new insights into the co-evolutionary relationship between wild fish and their symbiotic microbiome, the hidden diversity of gut microbiome, and the ecological adaptation potential of wild freshwater fish.

Seasonal and Regional Dynamics of the Intestinal Microbiota in Schizothorax nukiangensis from the Nujiang River

The dynamic alterations in intestinal microbiota can provide insights into the adaptive relationships between these microorganisms and their hosts in response to environmental changes. Schizothorax nukiangensis is widely distributed throughout the Nujiang River and exhibits numerous unique adaptations. In this study, we collected samples of S. nukiangensis across different seasons and regions within the Nujiang River to comprehensively elucidate the diversity and composition of its intestinal microbiota using metagenomic technology. The results indicated that Firmicutes and Proteobacteria predominated at the phylum level, while Priestia, Bacillus, and Aeromonas were the most abundant genera identified. Notably, the relative abundance of these microorganisms varied significantly across different seasons and regions. From autumn through spring and into summer, the predominant microorganisms shifted from Firmicutes to Proteobacteria. Biomarker analysis revealed that Firmicutes (including the class bacilli and the genera Priestia and Bacillus) exhibited a higher relative abundance within the upstream group, where categories related to amino acid metabolism and carbohydrate metabolism were significantly enriched. Conversely, Proteobacteria (including several potential pathogens, such as Saezia, Pantoea, Lelliotia, and Aeromonas genera) showed an increased relative abundance within downstream groups, where disease-related categories exhibited significant enrichment. Our findings significantly enhance our understanding of how S. nukiangensis adapts to its environment, providing valuable data support for the conservation of S. nukiangensis and for ecological security assessment of the Nujiang River.

Gut microbes of a high-value marine fish, Snubnose Pompano (Trachinotus blochii) are resilient to therapeutic dosing of oxytetracycline

Trachinotus blochii is a high-value tropical mariculture species. The present study evaluated the gut microbial impact of therapeutic exposure (80 mg/day/kg biomass for 10 days) to oxytetracycline, the most common aquaculture antibiotic in T. blochii. The cultivable counts, α-diversity measures of taxonomic and functional metagenomics, microbial dysbiosis (MD) index, and microbial taxon abundances showed the resilience of gut microbiota at 16-26 days of treatment. A significant reduction in bacterial abundance, diversity measures, Firmicutes and Actinobacteria and an increase in γ-Proteobacteria was recorded on the 6th and 11th day of treatment. The increased metagenomic stress signatures, decreased beneficial bacterial abundances, decreased abundance of microbial pathways on energy metabolism, and MD index indicated short-term transient stress during the initial days of therapeutic withdrawal, warranting health management measures. Therapeutic exposure reduced the abundance of fish pathogens, including Vibrio spp., kanamycin and ampicillin-resistant bacteria. Strikingly, oxytetracycline treatment did not increase tetracycline-resistant bacterial counts and the predicted abundance of tetracycline resistance encoding genes in the gut, illustrating that therapeutic application would not pose a risk in the context of antimicrobial resistance in short term. Altogether, the present study provides a foundation for oxytetracycline treatment to develop suitable risk minimization tactics in sustainable aquaculture.

Microbiome and network analysis reveal potential mechanisms underlying Carassius auratus diseases: The interactions between critical environmental and microbial factors

Despite the rapid development of research on aquatic environment microbiota, limited attention has been paid to exploring the complex interactions between microbial communities and aquatic environments. Particularly, the mechanisms underlying fish diseases based on such dynamic interactions remain unknown. This study aimed to address the gap by conducting microbiome and co-occurrence network analyses on the typical freshwater aquaculture systems. High-throughput 16S rRNA gene sequencing results revealed significant differences in the microbiota between the disease and healthy groups. Notably, disease mortality varied consistently with the gradient of relative abundance of Proteobacteria (intestine, R2 = 0.46, p < 0.05) and Cyanobacteria (gill, R2 = 0.67, p < 0.01), indicating their potential use as diagnostic criteria. Furthermore, the elevated hepatosomatic index, NO3-N, COD and TC (sediment) were directly correlated with diseases (r > 0.54, p < 0.01). Mean concentrations of NO3-N, COD and TC were elevated by 78.87%, 25.63% and 44.2%, respectively, in ponds where diseases occurred. Quantitative analysis (qPCR) revealed that Aeromonas sobria infected hosts through a potential pathway of "sediment (4.4 × 105 copy number/g)-water (1.1 × 103 copy number/mL)-intestine (1.2 × 106 copy number/g)". Similarly, the potential route for Aeromonas veronii was sediment (4.9 × 106 copy number/g) to gill (5.1 × 105 copy number/g). Additionally, the complexity of microbial networks in the intestine, water, and sediment was significantly lower in the disease group, although no similar phenomenon was observed in the gill microbial network. In summary, these findings reveal that elevated concentrations of crucial environmental factors disrupt the linkages within microbiota, fostering the growth of opportunistic bacteria capable of colonizing fish gut or gills. This offers new insights into potential mechanisms by which environmental factors cause disease in fish.

Comparative microbial community occurrence pattern, growth attributes, and digestive enzyme indices of Puntius gonionotus (Bleeker, 1850), Pangasianodon hypophthalmus (Sauvage, 1878) and Heteropneustus fossilis (Bloch, 1794) under freshwater biofloc based polyculture system

BACKGROUND

The biofloc system (BFS) provides a sustainable aquaculture system through its efficient in situ water quality maintenance by the microbial biomass, besides continuous availability of these protein-rich microbes as feed to enhance growth and immunity of the reared organism. This study explores the gill architecture, growth performance, digestive enzyme activity, intestinal microbial composition, and histology of three freshwater fish species, Puntius gonionotus, Pangasianodon hypophthalmus, and Heteropneustus fossilis reared in biofloc based polyculture system.

RESULTS

The three species in T2 showed significantly higher WG and SGR, followed by T1 and T3. The wet mount of gill architecture showed smaller inter-filament gaps in gill arches of silver barb followed by stinging catfish and stripped catfish, but showed no correlation with the weight gain. However, silver barb being an omnivore and filter-feeder, accumulated a more diverse microbial community, both in T1 and BFS (T2 and T3), while the bottom feeder H. fossilis exhibited unique gut bacterial adaptability. The presence of floc in T2 and T3 enhanced bacterial abundance in water and fish gut, but their microbial diversities significantly reduced compared to T1 receiving only feed. Next-generation sequencing revealed that the Pseudomonas dominated in gut of P. gonionotus and P. hypophthalmus in T1, Enterobacterales and Fusobacterium prevailed in those of T2 and T3, respectively. In contrast, gut of H. fossilis had the highest proportion of Clostridium in T1, while Rhizobiaceae dominated in T3. Similarly in floc samples, Enterococcus dominated in T1 while Micrococcales and Rhizobiaceae dominated in T2 and T3, respectively. A positive correlation of enterobacteria, with the digestive enzyme activities and growth patterns was observed in all treatments.

CONCLUSION

The present study revealed feeding behaviour to play crucial role in distinguishing the gut microbial composition patterns in fishes reared in Biofloc System. Further it revealed the requirement of supplementary feed along with floc in these three species for higher growth in the biofloc system.

The piranha gut microbiome provides a selective lens into river water biodiversity

Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.

Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season

The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.

Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies

In the present study, we propose the use of swabs in non-lethal sampling procedures to collect the mucosa-adhered gut microbiota from the posterior intestine of fish, and therefore, we compare the bacterial communities collected by conventional scraping and by swabbing methods. For this purpose, samples of the posterior intestine of rainbow trout (Oncorhynchus mykiss) were collected first using the swabbing approach, and after fish euthanasia, by mucosa scraping. Finally, bacterial communities were compared by 16S rRNA gene Illumina sequencing. Results from the current study revealed that similar values of bacterial richness and diversity were found for both sampling procedures. Similarly, there were no differences between procedures when using qualitative metrics (Jaccard and unweighted UniFrac) for estimating inter-individual diversity, but the quantitative metrics (Bray-Curtis and weighted UniFrac) showed a higher dispersion when samples were obtained by swabbing compared to scraping. In terms of bacterial composition, there were differences in abundance for the phyla Firmicutes and Proteobacteria. The cause of these differential abundances may be the inability of the swab to access to certain areas, such as the basal region of the intestinal villi. Moreover, swabbing allowed a higher representation of low abundant taxa, which may also have an important role in host microbiome regardless of their low abundance. Overall, our results demonstrate that the sampling method is a factor to be considered in experimental design when studying gut bacterial communities to avoid potential biases in the interpretation or comparison of results from different studies. In addition, the advantages and disadvantages of each procedure (swabbing vs scraping) are discussed in detail, concluding that swabbing can be implemented as a reliable and non-lethal procedure for posterior gut microbiota studies, which is of particular interest for animal welfare and the 3Rs principle, and may offer a wide range of novel applications.

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 microbiota dynamics interacting with gastrointestinal evacuation of Apostichopus japonicus: novel insights into promising strategies for environmental improvement

As an important input of environmental micropollutants into aquaculture environment, feed is now considered to be a critical factor in shaping gastrointestinal evacuation characteristics of animals. We analyzed the gastrointestinal evacuation characteristics and gut bacteria of Apostichopus japonicus within 30 h after feeding in recirculating aquaculture system (RAS) and explored the evacuation mechanism interacting by bacteria. The Gauss model was the most precise gastrointestinal evacuation curve, and 80% of gastrointestinal evacuation time was 27.81 h after feeding. Linear discriminant analysis effect size analysis revealed that gut microbial abundance associated significantly with time (P < 0.05), and 42 biomarkers that could predict gastrointestinal evacuation were totally detected, such as Lutibacter and Vibrio. Biomarkers at 25 h after feeding were related to harmful bacteria. A dynamic response between gastrointestinal content ratio and gut microbial abundance was detected. Taken together, we could discharge sewage about 25 h after feeding and carry out the next round of feeding activities.

Effectiveness assessment of using water environmental microHI to predict the health status of wild fish

Aquatic wildlife health assessment is critically important for aquatic wildlife conservation. However, the health assessment of aquatic wildlife (especially aquatic wild animals) is difficult and often accompanied by invasive survey activities and delayed observability. As there is growing evidence that aquatic environmental microbiota could impact the health status of aquatic animals by influencing their symbiotic microbiota, we propose a non-invasive method to monitor the health status of wild aquatic animals using the environmental microbiota health index (microHI). However, it is unknown whether this method is effective for different ecotype groups of aquatic wild animals. To answer this question, we took a case study in the middle Yangtze River and studied the water environmental microbiota and fish gut microbiota at the fish community level, population level, and ecotype level. The results showed that the gut microHI of the healthy group was higher than that of the unhealthy group at the community and population levels, and the overall gut microHI was positively correlated with the water environmental microHI, whereas the baseline gut microHI was species-specific. Integrating these variations in four ecotype groups (filter-feeding, scraper-feeding, omnivorous, and carnivorous), only the gut microHI of the carnivorous group positively correlated with water environmental microHI. Alcaligenaceae, Enterobacteriaceae, and Achromobacter were the most abundant groups with health-negative-impacting phenotypes, had high positive correlations between gut sample group and environment sample group, and had significantly higher abundance in unhealthy groups than in healthy groups of carnivorous, filter-feeding, and scraper-feeding ecotypes. Therefore, using water environmental microHI to indicate the health status of wild fish is effective at the community level, is effective just for carnivorous fish at the ecotype level. In the middle Yangtze River, Alcaligenaceae, Enterobacteriaceae (family level), and Achromobacter (genus level) were the key water environmental microbial groups that potentially impacted wild fish health status. Of course, more data and research that test the current hypothesis and conclusion are encouraged.

Alterations of gut microbiota and short-chain fatty acids induced by Balantidium polyvacuolum in the hindgut of Xenocyprinae fishes providing new insights into the relationship among protozoa, gut microbiota and host

Introduction

Parasitic ciliates are protozoans with a global distribution. Along with the gut microbiota, they have formed a micro-ecosystem that affects the host's nutrition, metabolism, and immunity. The interactions and relationships among the three components of this microecosystem (protozoa, gut microbiota, and host) remain only partially understood. Xenocypris fish and the unique ciliate Balantidium polyvacuolum in its hindgut are good materials to study the interplay.

Methods

In this study, 16S rRNA gene amplicon sequencing and short-chain fatty acids (SCFAs) identification were used. Network was also constructed to understand their relationships.

Results

We found that the gut microbiota of B. polyvacuolum-infected X. davidi and X. argentea had higher diversity, richness, and evenness than uninfected ones. B. polyvacuolum could lead to an increase of Fusobacterium and Chloroflexi in both X. davidi and X. argentea, while significantly increase the abundance of genera Romboutsia and Clostridium in X. argentea. Besides, B. polyvacuolum could significantly increase the content of total SCFAs and acetic acid in X. davidi and increase the concentrations of propionic, isobutyric and butanoic acids in X. argentea. Furthermore, correlation analyses showed that B. polyvacuolum may alter SCFAs by affecting key SCFAs-producing bacteria such as Clostridium and Cetobacterium.

Discussion

This study greatly expands our understanding of relationships among B. polyvacuolum, gut microbiota and host Xenocypris fish, which sheds new insights into the mechanism of interaction among protozoa, gut microbiota and host.

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.

Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore (Asellus aquaticus)

Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.

Evaluation of phoxim toxicity on aquatic and zebrafish intestinal microbiota by metagenomics and 16S rRNA gene sequencing analysis

Phoxim is one of the main organophosphorus pesticides used in agricultural production. However, little information is known about how it affects the aquatic microbial community and the intestinal microbiota of fish. Herein, we utilized shotgun metagenomics and 16S rRNA gene sequencing to reveal the aquatic eco-risk of phoxim. Seven days of phoxim exposure significantly changed the composition of aquatic microbial community, obliterated the interactions between microorganisms, and thus reduced the complexity and stability of the microbial community. During long-time exposure (i.e., 14 days), most of the ecological functions were restored due to the redundancy of the microbial community. However, phoxim exposure promoted the dissemination of elfamycin resistance gene. The zebrafish gut microbial community also recovered from a temporary ecological disorder of aquatic microbiota, but phoxim continually affected zebrafish growth and swimming behavior. Overall, our results demonstrated that phoxim exposure significantly changed the structure and function of the microbial community and displayed a negative impact on freshwater ecosystems in a short exposure time.