Anisakidae parasitism activated immune response and induced liver fibrosis in wild anadromous Coilia nasus.

Anisakidae nematode larvae is one of the most common parasites in wild anadromous Coilia nasus. This study aims to explore the mechanism of the C. nasus immune response to the parasitism of Anisakid nematode larvae. Results found that Anisakid nematode larvae parasitism caused liver injury as evidenced by histomorphology results as well as high levels of aminotransferase and aspertate aminotransferase. Furthermore, Anisakid nematode larvae parasitism induced an immune response in the host, which was characterized by the elevated populations of macrophages and neutrophils in the liver and head-kidney in the Anisakidae-infected group compared to the noninfected group. The expression of immunoglobulin IgM and IgD in the liver and head-kidney was also increased in the Anisakidae-infected group. The Anisakidae-infected group showed higher activity of antioxidant enzymes catalase and superoxide dismutase, which indicates severe oxidative stress, and increased production of pro-inflammatory cytokines, TNF-α, IL-6 as well as MCP-1 in the liver compared with the noninfected group. As a result of inflammation, livers of hosts in the Anisakidae-infected group showed fibrosis, and elevated expression of associated proteins including α-smooth muscle actin, fibronectin, collagen type I and type III compared with the noninfected group. We demonstrated that Anisakid nematode larvae parasitism results in injury and fibrosis in the liver, and triggers immune cell infiltration and inflammation in the liver and head-kidney of C. nasus. Altogether, the results provide a foundation for building an interaction between parasite and host, and will contribute to C. nasus population and fishery resource protection.

Metabolic mechanisms of Coilia nasus in the natural food intake state during migration.

As a prominent member of freshwater and coastal fish faunas, Coilia nasus migrates annually from the sea up the Yangtze River in China to spawn. It is traditionally believed that C. nasus generally do not feed during their spawning migration. However, we recently documented the occurrence of food intake phenomenon in C. nasus following voluntary fasting. The purpose of the current study is to explore the metabolic mechanisms on C. nasus in response to food intake during migration. A total of 23,159 differentially expressed mRNA molecules and 204 metabolites were identified in transcriptome and metabolome analyses. Our results provide insights into the activation of energy consumption and reinforcement of energy storage during migration, and also identify key genes involved in food intake regulation. Our findings will be useful for future research on population recruitment and energy utilization in wild C. nasus.

Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus.

Coilia nasus is influenced by various external pressures during spawning migration and these anadromous transitions can lead to specific gut microbiome characteristics that affecting the host biological process. Therefore, the purpose of this study was to determine the variations of components and functions in the gut prokaryotic microbiome during spawning migration as well as the key factors that triggered the changes. The gut microbiome in C. nasus was mainly consisted of Proteobacteria, Bacteroidetes, Firmicutes, Deinococcus-Thermus and Fusobacteria via 16S rRNA Gene Amplicon Sequencing. The relative abundance of Acinetobacter and Clostridium increased, while Corynebacterium, Actinomyces, Bacillus, Klebsiella and Ochrobactrum decreased after entering freshwater, indicated the preference of C. nasus gut microbial members transferred from seawater to freshwater. Additionally, the proportion of Firmicutes significantly decreased and then increased, as well as the arise of some soil bacteria in gut, corresponding to the phenomenon that C. nasus are fasting during the upstream process and refeeding after entering the spawning grounds. The function prediction of gut microbiome was also consistent with the above results. The present study generally demonstrated the gut microbiome dynamics and the significant correlation between the gut microbiome and salinity and feeding behavior in the spawning migration of C. nasus.

Hepatic immune response of Coilia nasus infected with Anisakidae during ovarian development.

Anisakidae parasitism is a prevalent disease in wild populations of Coilia nasus, and can result in a significant loss of germplasm resources. To elucidate the immune response mechanism of C. nasus livers to Anisakidae infection, we collected and analysed 18 parasitic and 18 non-parasitic livers at gonadal developmental stages II, III, and V using histopathology, molecular biology and transcriptome methods. The hepatic portal area of the parasitic group exhibited an increase in the fibrous stroma and thickened hepatic arteries with positive Ly-6G staining, indicating inflammation and immune responses in the liver. Hepatocyte cytokine levels and the expression of liver function-related genes indicated that fish livers responded similarly to Anisakidae parasitism across different gonadal developmental stages. Oxidative stress indices showed more intense changes in stage II samples, whereas gene expression levels of Nrf2 and C3 were significantly increased in parasitised livers during stage III and V. Liver transcriptome sequencing identified 2575 differentially expressed genes between the parasitic and non-parasitic groups at the three gonadal developmental stages. KEGG pathway analysis showed that natural killer cell-mediated cytotoxicity, the NOD-like receptor signaling pathway, neutrophil extracellular trap formation, and other immune pathways were significantly enriched. Expression patterns varied across developmental stages, suggesting that innate immunity was primarily responsible for the liver immune response to Anisakidae infection during C. nasus migration, possibly related to water temperature changes or shifts in the gonadal developmental stage. In summary, this study investigated the immune response of C. nasus to Anisakidae parasitism under natural conditions, focusing on reproductive aspects and environmental changes, thereby establishing a foundation for elucidating the molecular mechanisms underlying the immune response of Anisakidae in C. nasus.

Comparative Blood Transcriptome Analysis of Semi-Natural and Controlled Environment Populations of Yangtze Finless Porpoise.

The Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis) living in different environments display significant differences in behavior and physiology. To compare and analyze gene expression differences between an ex situ population and a controlled environment population of the Yangtze finless porpoise, we sequenced the transcriptome of blood tissues living in a semi-natural reserve and an artificial facility, respectively. We identified 6860 differentially expressed genes (DEGs), of which 6603 were up-regulated and 257 were down-regulated in the controlled environment vs ex situ comparison. GO and KEGG enrichment analysis showed that the up-regulated genes in the controlled environment population were significantly associated with glucose metabolism, amino acid metabolism, and the nervous system, while those up-regulated in the ex situ population were significantly associated with energy supply and biosynthesis. Further analysis showed that metabolic and hearing-related genes were significantly affected by changes in the environment, and key metabolic genes such as HK, PFK, IDH, and GLS and key hearing-related genes such as OTOA, OTOF, SLC38A1, and GABBR2 were identified. These results suggest that the controlled environment population may have enhanced glucose metabolic ability via activation of glycolysis/gluconeogenesis, the TCA cycle, and inositol phosphate metabolism, while the ex situ population may meet higher energy requirements via enhancement of the amino acid metabolism of the liver and muscle and oxidative phosphorylation. Additionally, the acoustic behavior and auditory-related genes of Yangtze finless porpoise may show responsive changes and differential expression under different environment conditions, and thus the auditory sensitivity may also show corresponding adaptive characteristics. This study provides a new perspective for further exploration of the responsive changes of the two populations to various environments and provides a theoretical reference for further improvements in conservation practices for the Yangtze finless porpoise.

The bacteria of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment.

Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.

Gapless genome assembly of East Asian finless porpoise.

In recent years, conservation efforts have increased for rare and endangered aquatic wildlife, especially cetaceans. However, the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri), which has a wide distribution in China, has received far less attention and protection. As an endangered small cetacean, the lack of a chromosomal-level reference for the East Asian finless porpoise limits our understanding of its population genetics and conservation biology. To address this issue, we combined PacBio HiFi long reads and Hi-C sequencing data to generate a gapless genome of the East Asian finless porpoise that is approximately 2.5 Gb in size over its 21 autosomes and two sex chromosomes (X and Y). A total of 22,814 protein-coding genes were predicted where ~97.31% were functionally annotated. This high-quality genome assembly of East Asian finless porpoise will not only provide new resources for the comparative genomics of cetaceans and conservation biology of threatened species, but also lay a foundation for more speciation, ecology, and evolutionary studies. Measurement(s) Neophocaena asiaeorientalis sunameri • Gapless genome assembly • sequence annotation Technology Type(s) MGISEQ. 2000 • PacBio HiFi Sequencing • Hi-C Sample Characteristic - Organism Neophocaena asiaeorientalis sunameri Sample Characteristic - Environment seawater Sample Characteristic - Location Yellow Sea near Lianyungang City, Jiangsu Province, China.

Integrated analysis of blood mRNAs and microRNAs reveals immune changes with age in the Yangtze finless porpoise (Neophocaena asiaeorientalis).

Populations of Yangtze finless porpoises (YFPs) have rapidly declined in recent decades, raising the specter of extinction. In order to protect YFPs, a greater understanding of their biology is needed, including studying how their immune functioning changes with age. Here, we systematically studied the hematologic and biochemical parameters, as well as mRNAs and miRNAs profiles of old, adult, and young YFPs. The lymphocyte (LYMPH), neutrophils (NEUT) and eosinophils (EOS) counts in old YFPs were lower than those in young or adult YFPs. When comparing old to adult YFPs, the latter showed higher expression of genes associated with the innate and adaptive immune systems, including complement components, major histocompatibility complex, interleukins, TNF receptors, and chemokines/cytokines. When comparing old to young YFPs, the most striking difference was in higher toll-like receptor signaling in the latter. When comparing adult to young YFPs, the former exhibited higher expression of genes related to adaptive immunity and the FoxO signaling pathway, but lower expression of genes associated with the PI3K-Akt signaling pathway. Negative miRNA-mRNA interactions were predicted in comparisons of the old and adult (326), old and young (316), adult and young (211) groups. Overall, these results delineate a progression from early innate immune function dominance to adaptive immune function enhancement (young to adult) and deterioration (adult to old), and the changes in miRNAs profile correlate with the effects of age on immune functions. This study is the first to observe the changes of immune function of Yangtze finless porpoise with age using transcriptome method, and the study's findings are of great significance for protecting this endangered species.

Changes in the fecal microbiome of the Yangtze finless porpoise during a short-term therapeutic treatment.

The fecal microbiome is an integral part of aquatic mammals, like an inner organ. But we know very little about this inner organ of the threatened aquatic species, Yangtze finless porpoise (YFP). Four YFPs were placed into a purse seine for skin ulceration treatment, and this opportunity was taken to nurse the animals closer. In particular, we collected the feces of the YFPs before and after the paired healing and therapeutic treatment, along with samples of their fish diet and water habitat, to explore the changes in their fecal microbiome. Firmicutes (20.9-96.1%), Proteobacteria (3.8-78.7%), Actinobacteria (0.1-35.0%) and Tenericutes (0.8-17.1%) were the most dominant phyla present in the feces. The proportion of Proteobacteria and Actinobacteria increased after the treatment. Firmicutes showed a significant decrease, and most potential pathogens were absent, which reflected the administration of ciprofloxacin hydrochloride. Moreover, environmental shifts can also contribute to changes in the fecal microbiome. These results indicate that certain microbial interactions can be affected by environmental shifts, dietary changes and health-care treatments, which can also help maintain the internal environment of YFPs. These findings will inform the future enhanced protection and management of endangered YFPs and other vulnerable aquatic animals.

The intestinal microbiota of lake anchovy varies according to sex, body size, and local habitat in Taihu Lake, China.

Lake anchovy (Coilia ectenes taihuensis) is a sedentary, dominant fish species that forms an unmanaged fishery in Taihu Lake, eastern China. The environment and developmental stage of lake anchovy are likely important drivers of their gut microbiome, which is linked to host health and development. To investigate the relationship between the gut microbiome and three defined factors (fish sex, fish body size, and the local habitat), high-throughput sequencing of the 16S ribosomal RNA gene was used to study the microorganisms of 184 fish samples and four water samples collected in Taihu Lake. Four dominant bacterial phyla (Proteobacteria, Firmicutes, Planctomycetes, and Cyanobacteria) were present in all fish samples. We compared the microbial communities of males and females and found that the relative abundance of Corynebacteriaceae was significantly higher in males than in females, while the opposite trend was detected for Sphingomonadaceae. We also discovered that the relative abundance of Firmicutes was positively correlated with fish body size and that the proportions of Proteobacteria and Tenericutes were lower in larger fish than in fish of other sizes. Finally, we found that the difference in microbial richness between eastern and northern Taihu Lake was the most marked. Lake anchovy was rich in Lactobacillus and Clostridium in the eastern site, while those in the northern site had the highest abundance of Sphingomonas and Methylobacterium, suggesting that the local habitat may also influence the intestinal microbiome. These findings will not only help researchers understand the community composition of the intestinal microflora of lake anchovy but also contribute to the protection of fish resources in Lake Taihu and the sustainable use of lake anchovy.