The intestinal bacterial community of healthy and diseased animals and its association with the aquaculture environment

Temporal variations of bacterial and eukaryotic community in coastal waters-implications for aquaculture

Despite increased attention to the aquaculture environment, there is still a lack of understanding regarding the significance of water quality. To address this knowledge gap, this study utilized high-throughput sequencing of 16S rRNA and 18S rRNA to examine microbial communities (bacteria and eukaryotes) in coastal water over different months through long-term observations. The goal was to explore interaction patterns in the microbial community and identify potential pathogenic bacteria and red tide organisms. The results revealed significant differences in composition, diversity, and richness of bacterial and eukaryotic operational taxonomic units (OTUs) across various months. Principal coordinate analysis (PCoA) demonstrated distinct temporal variations in bacterial and eukaryotic communities, with significant differences (P = 0.001) among four groups: F (January-April), M (May), S (June-September), and T (October-December). Moreover, a strong association was observed between microbial communities and months, with most OTUs showing a distinct temporal preference. The Kruskal-Wallis test (P < 0.05) indicated significant differences in dominant bacterial and eukaryotic taxa among months, with each group exhibiting unique dominant taxa, including potential pathogenic bacteria and red tide organisms. These findings emphasize the importance of monitoring changes in potentially harmful microorganisms in aquaculture. Network analysis highlighted positive correlations between bacteria and eukaryotes, with bacteria playing a key role in network interactions. The key bacterial genera associated with other microorganisms varied significantly (P < 0.05) across different groups. In summary, this study deepens the understanding of aquaculture water quality and offers valuable insights for maintaining healthy aquaculture practices. KEY POINTS: • Bacterial and eukaryotic communities displayed distinct temporal variations. • Different months exhibited unique potential pathogenic bacteria and red tide organisms. • Bacteria are key taxonomic taxa involved in microbial network interactions.

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.

Differences in Physiological Performance and Gut Microbiota between Deep-Sea and Coastal Aquaculture of Thachinotus Ovatus: A Metagenomic Approach

Aquaculture has become the fastest growing sector in global agriculture. The environmental degradation, diseases, and high density of mariculture has made for an inevitable shift in mariculture production from coastal to deep-sea areas. The influence that traditional coastal and emerging deep-sea farming environments exert on aquatic growth, immunity and gut microbial flora is unclear. To address this question, we compared the growth performance, physiological indicators and intestinal microbiological differences of deep-sea and coastal aquaculture in the Guangxi Beibu Gulf of China. The results showed that the growth performance and the complement of C3 and C4 (C3, C4), superoxide dismutase (SOD), and lysozyme (LYS), these physiological and biochemical indicators in the liver, kidney, and muscle of Trachinotus ovatus (T. ovatus), showed significant differences under different rearing conditions. Metagenome sequencing analysis showed Ascomycota, Pseudomonadota, and Bacillota were the three dominant phyla, accounting for 52.98/53.32 (coastal/deep sea), 24.30/22.13, and 10.39/11.82%, respectively. Aligned against the CARD database, a total of 23/2 (coastal/deep-sea) antibiotic resistance genes were screened and grouped into 4/2 genotypes. It indicated that compared with deep-sea fish, higher biological oxygen levels (3.10 times), inorganic nitrogen (110.00 times) and labile phosphate levels (29.00 times) in coastal waters might contributed to the existence of eutrophication with antibiotic resistance. The results of the study can provide complementary data on the study of the difference between deep-sea farming and traditional coastal farming, serving as a reference to future in-depth work on the transformation of fisheries development and scientific standardization of deep-sea farming.

Analysis of the mechanism of action of quercetin in the treatment of hyperlipidemia based on metabolomics and intestinal flora

Hyperlipidemia (HLP) is one of the main factors leading to cardiovascular diseases. Quercetin (QUE) is a naturally occurring polyhydroxy flavonoid compound that has a wide range of pharmacological effects. However, the potential mechanism for treating HLP remains unclear. Thus, the study aimed to investigate the role of QUE in HLP development and its underlying mechanisms in HLP rats based on the analysis of gut microbiota and plasma metabolomics. Following the establishment of an HLP model in rats, QUE was orally administered. Plasma samples and fecal samples were collected from HLP rats for microbiome 16S rDNA sequencing and metabolic UPLC-Q-Exactive-MS analysis. The results suggested that QUE could regulate dyslipidemia and inhibit the levels of TC, TG, and LDL-c. Additionally, histopathological findings revealed that QUE could reduce lipid deposition, ameliorate hepatic injury and steatosis in HFD-induced rats, and have a protective effect on the liver. The analysis and identification of plasma metabolomics showed that the intervention effect of QUE on HLP rats was related to 60 differential metabolites and signal pathways such as lactosamine, 11b-hydroxyprogesterone, arachidonic acid, glycerophospholipid, sphingolipid, glycerolipid, and linoleic acid metabolism. Combined with fecal microbiological analysis, it was found that QUE could significantly change the composition of intestinal flora in HLP rats, increase beneficial bacteria, and reduce the composition of harmful bacteria, attenuating the Firmicutes/Bacteroidetes ratio. The results of correlation analysis showed that the relative abundance level of Firmicutes, Deironobacterium, Fusobacterium, Bacteroides, and Escherichia coli was closely related to the change of differential metabolites. In summary, combined with metabolomics and gut microbiota studies, it is found that QUE can reduce lipid levels and improve liver function. The potential mechanism may be the regulation of metabolism and intestinal flora that play a role in reducing lipid levels, to achieve the purpose of treatment of HLP.

Inputs don't equal outputs: bacterial microbiomes of the ingesta, gut, and feces of the keystone deposit feeder Ilyanassa obsoleta

Bacteria drive energy fluxes and geochemical processes in estuarine sediments. Deposit-feeding invertebrates alter the structure and activity of microbial communities through sediment ingestion, gut passage, and defecation. The eastern mud snail, Ilyanassa obsoleta, is native to estuaries of the northwestern Atlantic, ranging from Nova Scotia, Canada, to Florida in the USA. Given extremely high densities, their deposit-feeding and locomotory activities exert ecological influence on other invertebrates and microbes. Our aim was to characterize the bacterial microbiome of this 'keystone species' and determine how its feeding alters the native bacterial microbiota. We gathered snails from both mudflat and sandflat habitats and collected their fresh fecal pellets in the laboratory. Dissection of these same snails allowed us to compare bacterial assemblages of ingested sediments, shell surfaces, gut sections (esophagus, stomach, intestine), and feces using DNA metabarcoding. Our findings indicate a diverse, resident gut microbiota. The stomach and intestines were dominated by bacteria of the genus Mycoplasma. Comparison of ingesta and feces revealed digestion of several bacterial taxa, introduction of gut residents during passage, in addition to unique bacterial taxa within the feces of unknown provenance. Our results demonstrate that I. obsoleta has the potential to modify microbial community structure in estuarine sediments.

Characterization and Dynamics of the Gut Microbiota in Rice Fishes at Different Developmental Stages in Rice-Fish Coculture Systems

The rice-fish system (RFS), a traditional coculture farming model, was selected as a "globally important agricultural heritage system." Host-associated microbiota play important roles in development, metabolism, physiology, and immune function. However, studies on the gut microbiota of aquatic animals in the RFS are scarce, especially the lack of baseline knowledge of the dynamics of gut microbial communities in rice fish during different developmental stages. In this study, we characterized the microbial composition, community structure, and functions of several sympatric aquatic animals (common carp (Cyprinus carpio), crucian carp (Carassius carassius), and black-spotted frogs (Pelophylax nigromaculatus)), and the environment (water) in the RFS using 16S rRNA gene sequencing. Moreover, we investigated stage-specific signatures in the gut microbiota of common carp throughout the three developmental stages (juvenile, sub-adult, and adult). Our results indicated that the Fusobacteriota, Proteobacteria, and Firmicutes were dominant gut microbial phyla in rice fish. The differences in gut microbial compositions and community structure between the three aquatic species were observed. Although no significant differences in alpha diversity were observed across the three developmental stages, the microbial composition and community structure varied with development in common carp in the RFS, with an increase in the relative abundance of Firmicutes in sub-adults and a shift in the functional features of the community. This study sheds light on the gut microbiota of aquatic animals in the RFS. It deepens our understanding of the dynamics of gut microflora during common carp development, which may help improve aquaculture strategies in the RFS.

Bacterial communities in co-cultured fish intestines and rice field soil irrigated with aquaculture wastewater

In some regions, integrated rice-fish farms have been developed to balance the needs of aquaculture wastewater discharge and rice field irrigation. In this type of aqua-agriculture system, soil is irrigated with aquaculture wastewater, and intestinal bacteria in cultured fish species likely impact soil bacteria through irrigation. However, little is known about the relationship between soil bacteria and intestinal bacteria in some carp species commonly co-cultured in some Asian regions. Therefore, we co-cultured five carp species in aquaculture ponds and used the aquaculture wastewater to irrigate rice fields for over 5 years, and then compared carp intestinal bacterial communities with rice field soil bacterial communities. The results from analysis of similarity and SourceTracker analysis showed that a low similarity (R = 0.7908, P = 0.001) and contribution (an average of 9.9% of bacterial genera) of intestinal bacteria to soil bacterial communities although 77.5% of soil bacterial genera were shared by intestinal bacteria. Our results also indicated that intestinal bacteria in the numerically dominant fish species in the co-culture system do not necessarily impact soil bacteria more significantly than those of less abundant carp species, and that intestinal bacterial communities in one single fish species may impact certain soil bacterial phyla more significantly than others. Our results provide a better understanding of the impact of aquaculture wastewater on rice fields and will be helpful for the development of this type of aqua-agriculture system.

Bacterial community in Sinonovacula constricta intestine and its relationship with culture environment

Although the importance of intestinal microbes to aquaculture animals has been recognized, the intestinal bacteria of Sinonovacula constricta and its culture environment are rarely studied. In this study, high-throughput sequencing was used to explore the intestinal bacterial communities of pond water, sediment, and S. constricta intestine. Significance analysis and principal coordinates analysis (PCoA) showed that there were significant differences in bacterial communities among animals' intestine, pond water, and sediment (p < 0.05). Venn analysis showed that intestinal bacteria shared a considerable number of OTUs (operational taxonomic units) with the sediment and water. SourceTracker analysis suggested that the contribution of sediment to the intestinal bacteria of S. constricta was much larger than that of rearing water. The Kruskal-Wallis test showed that the dominant bacterial taxa differed significantly between animals' intestines and the pond environment, and each of them has a unique bacterial composition. A network diagram indicated the complex positive and negative interactions between intestinal bacteria at the OTU level. Furthermore, BugBase analysis indicated that the bacterial contribution to potential pathogens in the animals' intestines is similar to that in sediments, suggesting that sediment was the main source of potential pathogens in S. constricta intestine. This study provided a theoretical basis for environmental regulation and disease prevention of S. constricta in aquaculture. KEY POINTS: • Culture environment had a significant effect on the intestinal bacterial community in S. constricta. • Sediment was a major source of intestinal bacteria and potentially pathogenic bacteria. • Complex positive and negative interactions existed between intestinal bacteria.

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

In aquatic animals, gut microbial communities shift with host development and living environments. Understanding the mechanism by which the environment impacts the gut microbial communities of aquatic animals is crucial for assessing and managing aquatic ecosystem health. Here, we proposed a simplified framework for the colonization and dynamics of gut microbial communities. Then, to quantify the colonization of environmental microbes in the wild fish gut, the current study used 16S rRNA gene amplicon sequencing to obtain the structure of the water environmental microbial community and the gut microbial community in 10 wild fish populations (Leiocassis crassilabris, Leiocassis longirostris, Pelteobagrus vachelli, Silurus asotus, Siniperca chuatsi, Coilia brachygnathus, Aristichthys nobilis, Hypophthalmichthys molitrix, Coreius heterodon, and Xenocypris argentea) from the Wuhan section of the Yangtze River, and the relationship of these microbial communities was analyzed. The results identified that in most individuals, approximately 80% of gut microbes [at the operational taxonomic unit (OTU) level] were shared with the water environmental microbial community (except for individuals of Siniperca chuatsi and Coilia brachygnathus, approximately 74%). In approximately 80% of individuals, more than 95% of microbial species (OTUs) in the gut were transient. For fish species, more than 99% of microbial species (OTUs) that were introduced into the gut were transient. Nearly 79% of OTUs and 89% of species of water environmental microbes could be introduced into the fish gut. Driven by the introduction of transient microbes, fishes with similar feeding habits had similar gut microbial communities. The results indicated that for adult wild fishes, most gut microbiota were transient from the environmental microbiota that were related to fish feeding habits. We therefore encourage future research to focus on environmental microbiota monitoring and management to promote the better conservation of aquatic animals. It was important to note that, because of various influence factors, interspecific differences and individual variations on gut microbial community characteristics, the quantification of gut microbes in the current work was approximate rather than accurate. We hope that more comparable research could be conducted to outline the quantitative characteristics of the relationship between gut microbial community and aquatic environment microbial community as soon as possible.

Comparison of planktonic bacterial communities indoor and outdoor of aquaculture greenhouses

AIMS

Greenhouses are widely used in agriculture systems to shield crops from unfavourable weather to achieve a year-round food supply. In recent years, aquaculture ponds have been placed in greenhouses in many regions. The impacts of the greenhouses on planktonic bacterial communities should be uncovered.

METHODS AND RESULTS

In this study, two polyolefin film greenhouses accommodating aquaculture ponds were established and planktonic bacterial communities were compared from samples taken in aquaculture ponds inside and outside the greenhouses, using Illumina 16S rRNA sequencing.

CONCLUSIONS

The results showed there were significant variations in bacterial community structure between indoor and outdoor samples. Obvious differences were also found between two greenhouses, whereas the differences in indoor samples were weaker than outdoor samples. Significantly higher temperature (in summer), pH and permanganate index were found in the outdoor pond samples. Results of redundancy analysis showed that Proteobacteria and Bacteroidota were positively related to the dissolved oxygen, total nitrogen and total phosphorus, and Actinobacteriota were positively related to pH, temperature and permanganate index, whereas Cyanobacteria were positively related to the salinity, conductivity, total dissolved solids and ammonia nitrogen.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study revealed that greenhouses significantly influenced planktonic bacterial communities in aquaculture ponds. This study is expected to provide a scientific basis for aquaculture in greenhouses.

Significant Differences in Intestinal Microbial Communities in Aquatic Animals from an Aquaculture Area

While much attention has been given to the role of animal intestinal microbes, few studies have focused on microbial communities and associated functions in cultured aquatic animals. In this study, high–throughput sequencing was used to analyze intestinal microbial communities and functions in fish, shrimp, crab and razor clams. Alpha diversity analyses showed significant differences in intestinal microbial diversity amongst these aquatic animals, and that shrimp intestines harbored the highest diversity and species numbers. T–test analyses (p < 0.05) showed significant differences in dominant microbial operational taxonomic units (OTUs) between all aquatic animals. Predominant intestinal bacteria included; Gammaproteobacteria, Fusobacteria, Mollicutes, Spirochaetia, Cyanobacteria, Bacteroidia and Bacilli. Similarly, anaerobic bacteria were highly diverse in animal intestines and included; Vibrio, Photobacterium, Cetobacterium, Propionigenium, Candidatus Hepatoplasma, Paraclostridium, and Lactobacillus. Principal co–ordinate analysis indicated that the distribution characteristics of intestinal microbes varied with animal species; in particular, we observed a high variability among shrimp intestinal samples. This variability indicated these genera had suitability for the different intestinal environment. Function prediction analysis indicated significant differences amongst different animals in the major functional groups, and that microbial functional profiles were strongly shaped by the intestinal environment. Thus, this study provides an important reference for future studies investigating crosstalk between aquatic animal hosts and their intestinal microbiota.