Microbiome analyses of pacific white shrimp (Litopenaeus vannamei) collected from disparate geographical locations.
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ABSTRACT:
SUBMITTER: Seetharam AS
PROVIDER: S-EPMC4664682 | biostudies-literature | 2015 Dec
REPOSITORIES: biostudies-literature
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Project description:Bacteria capable of producing different extracellular enzymes of potential relevance in digestive processes were isolated from the stomach, hepatopancreas and intestine of Pacific white shrimp Litopenaeus vannamei. A total of 64 strains with proteolytic activity were isolated and grouped into 16 clusters based on morphological characteristics: 4 groups were isolated from the intestine; 5 from the hepatopancreas; and 7 from the stomach. Molecular methods (16S rRNA gene amplification and sequencing) and phenotypic criteria (Gram stain, catalase and oxidase tests, cell and colony morphology) were used to identify strains, which corresponded to Pseudoalteromonas and Vibrio genera. These genera are reported to form part of the digestive tract microbial community in shrimp. Both genera were isolated from all three tested tissues. One member of each morphologic group was selected for analysis of the presence of amylases, lipases/esterases and chitinases. Most of the strains had all the tested enzymes, indicating that the L. vannamei digestive tract microbiotic flora includes groups which have the potential to contribute to the degradation of dietary components.
| S-EPMC4062704 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-06-18 | GSE107698 | GEO
Project description:BACKGROUND: In recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involving arthropods. As a member of the phylum Arthropoda, the Pacific white shrimp Litopenaeus vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms, which provide a platform for horizontal gene transfer (HGT). RESULTS: In this study, we analyzed the genome-wide HGT events in L. vannamei. Through homology search and phylogenetic analysis, followed by experimental PCR confirmation, 14 genes with HGT event were identified: 12 of them were transferred from bacteria and two from fungi. Structure analysis of these genes showed that the introns of the two fungi-originated genes were substituted by shrimp DNA fragment, two genes transferred from bacteria had shrimp specific introns inserted in them. Furthermore, around other three bacteria-originated genes, there were three large DNA segments inserted into the shrimp genome. One segment was a transposon that fully transferred, and the other two segments contained only coding regions of bacteria. Functional prediction of these 14 genes showed that 6 of them might be related to energy metabolism, and 4 others related to defense of the organism. CONCLUSIONS: HGT events from bacteria or fungi were happened in the genome of L. vannamei, and these horizontally transferred genes can be transcribed in shrimp. This is the first time to report the existence of horizontally transferred genes in shrimp. Importantly, most of these genes are exposed to a negative selection pressure and appeared to be functional.
| S-EPMC3750580 | biostudies-literature
Project description:A simple bioassay that quantifies feed intake as an estimation of relative attractability of feeds containing different ingredients in the Pacific white shrimp Litopenaeus vannamei is described. Fish meal (FM), fish protein hydrolysate (FPH), squid meal (SqM) and casein (CN) were assessed at the same dietary level for their relative influence on feed intake rates of Litopenaeus vannamei. A bland diet containing 92% whole wheat grain meal, 6% diatomaceous earth and 2% alginate with a known low attractability was used as the standard control or base diet. Ingredients were added to the bland base control diet at a level of 3% as fed. Shrimp were stocked into 80 L glass tanks (n= 20 per tank) in a recirculating aquaculture system. Tanks were randomly assigned to one of five diet treatments (3tanks/treatment). Experiments measuring the attractability of each feed were conducted twice daily at 0900 hours and 1330 hours over a five day period. For each experiment, 40 feed pellets (ca. 1 g) corresponding to the assigned treatment were provided to each tank. To calculate the rate of feed intake, pellets remaining in each tank were counted at six minute intervals for a seventy-two minute period. Differences in rate of feed intake among diets were evaluated using Cox Regression Analysis. This attractability assay required only small amounts of ingredients and incorporated ingredients into a bland feed, which significantly reduces the influence from other ingredients or compound in the pellets. All of the test protein ingredients, especially SqM, in the feeds significantly increased the feed consumption rate. The diet containing SqM was consumed at a significantly higher rate than those containing casein and FM but not FPH. FPH and CN containing diets were not significantly different but consumed at a higher rate than the diet containing FM. Results of these trials indicate that the presence of certain ingredients can increase feed intake, thereby increasing nutrient availability of the diets. This reported method to determine consumption of diets containing certain ingredients can be considered as a valid method to estimate attractability.
| S-EPMC8730358 | biostudies-literature
Project description:BackgroundEugenol is the most commonly used plant anesthetic to relieve the stressors during various aquaculture procedures. This study aims to investigate the pharmacokinetics of eugenol in Pacific white shrimp by immersion baths in a simulated transportation.ResultsThe pharmacokinetics of eugenol were firstly investigated in Pacific white shrimp by immersion baths of 300 mg L- 1 eugenol over 5 min (Treatment 1), 10 mg L- 1 eugenol during 24 h (Treatment 2) and a sequential immersion administration (Treatment 3). Concentrations of eugenol in hemolymph, hepatopancreas, and muscle were determined using Gas chromatography-tandem mass spectrometry (GC-MS/MS). After immersion bath of Treatment 1, the elimination half-life (t1/2z) values are 1.3 h and 11 h for hepatopancreas and muscles, indicating the rapid absorption and elimination of eugenol in shrimp. Under the Treatment 2 administration, the eugenol peak concentration is 6527.9 μg/kg in muscle, followed by 402.8 μg/kg in hepatopancreas, with the lowest concentration of 37.9 μg/L in hemolymph. Area under the curve (AUC0-∞) values lie in the order of muscle > hepatopancreas > hemolymph, suggesting that eugenol tends to accumulate in muscle by the immersion administration. Moreover, the average residence time (MRT0-∞) values of 38.6, 23.0 and 115.3 h for hemolymph, hepatopancreas and muscle are achieved, which may indicate that hepatopancreas is the main organ for elimination of eugenol. After combining the conditions in a sequential bath immersion of eugenol (Treatment 3), the maximum concentration (Cmax) values of eugenol are higher than those achieved in Treatment 2, indicating that accumulation of eugenol happened in haemolymph, hepatopancreas and muscle. In addition, the corresponding t1/2z values are 4.7, 14.9 and 47.6 h, respectively, suggesting the faster elimination from the tissues following sequential administration. After the immersion bath, eugenol concentrations in muscle of Pacific white shrimp are lower than 2.5 mg/kg at 2 h, 48 h and 24.5 h in Treatment 1 ~ 3.ConclusionsA withdrawal period of 2 h, 48 h and 24.5 h following a 300 mg L- 1 of eugenol over a 5-min, 10 mg L- 1 eugenol concentration during a 24-h and combined conditions in a sequential immersion bath were suggested.
| S-EPMC8969250 | biostudies-literature
Project description:Penaeid shrimp has a distinctive metamorphosis stage during early development. Although morphological and biochemical studies about this ontogeny have been developed for decades, researches on gene expression level are still scarce. In this study, we have investigated the transcriptomes of five continuous developmental stages in Pacific white shrimp (Litopenaeus vannamei) with high throughput Illumina sequencing technology. The reads were assembled and clustered into 66,815 unigenes, of which 32,398 have putative homologues in nr database, 14,981 have been classified into diverse functional categories by Gene Ontology (GO) annotation and 26,257 have been associated with 255 pathways by KEGG pathway mapping. Meanwhile, the differentially expressed genes (DEGs) between adjacent developmental stages were identified and gene expression patterns were clustered. By GO term enrichment analysis, KEGG pathway enrichment analysis and functional gene profiling, the physiological changes during shrimp metamorphosis could be better understood, especially histogenesis, diet transition, muscle development and exoskeleton reconstruction. In conclusion, this is the first study that characterized the integrated transcriptomic profiles during early development of penaeid shrimp, and these findings will serve as significant references for shrimp developmental biology and aquaculture research.
| S-EPMC4157780 | biostudies-literature
Project description:In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a transcriptome analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.
2020-06-18 | GSE107697 | GEO
Project description:The Pacific white shrimp (Litopenaeus vannamei), a euryhaline penaeid species, can tolerate a wide range of salinities, but little is known on its strategies to cope with low salinity fluctuations from the aspect of lipidomics. Thus, in this study, L. vannamei were grown in two different salinities [3 and 30‰ (control)] for 8 weeks, and then an liquid chromatography (LC)-mass spectrometry (MS)-based lipidomics analysis was performed to reveal the lipid profile differences in gill and muscle. L. vannamei under low salinity had lower weight gain and condition factor than the control shrimp at 30‰, but no differences were found in survival and hepatopancreas index. A higher number of differential lipid metabolites were identified in gill than in muscle in L. vannamei at salinity 3‰ relative to the control shrimp at salinity of 30‰ (159 versus 37), which belonged to 11 and 6 lipids classes, respectively. Of these lipids, phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidic acid (PA), phosphatidylethanolamine (PE), and triglyceride (TG) were the main lipids in both shrimp gill and muscle, regardless of salinities. Compared with the control shrimp at salinity 30‰, the percentage of PC significantly reduced, but TG and PA significantly increased in gill of shrimp at salinity 3‰. Moreover, the relative fatty acid abundances showed significant changes in L. vannamei between the two salinity groups, but the patterns of the changes were complex and were fatty acid dependent. Neither lipid nor fatty acid composition in muscle was affected by salinity. Further pathway analysis showed that these metabolites were closely related to lipid and fatty acid metabolic pathways. All the findings in this study reveal that the lipid variations are closely related to bio-membrane structure, mitochondrial function, energy supply, or organic osmolyte contents in hemolymph for improving osmoregulatory capacity of L. vannamei under low salinity.
| S-EPMC6716509 | biostudies-literature
Project description:Temperature is a significant environmental factor in aquaculture. To investigate the physiological responses during temperature fluctuation (28~13°C), experimental shrimps (Litopenaeus vannamei) were treated with gradual cooling from acclimation temperature (AT, 28°C) to 13°C with a cooling rate of 7.5°C/day and rose back to 28°C at the same rate after 13°C for 24 h. Hepatopancreas histological changes, plasma metabolites concentrations, relative mRNA expression of unfolded protein response (UPR) pathway and apoptosis in hepatopancreas and hemocyte were investigated. The results showed that with the decline of temperature, the number and volume of the secretory cells in hepatopancreas increased significantly, the tubule lumen appeared dilatated, and the epithelial cell layer became thinner. The contents of glucose (Glu) significantly decreased to the minimum value of 13°C for 24 h. The contents of triglyceride (TG), total cholesterol (TC), and total protein (TP) increased and reached the peak of 13°C for 24 h. Alkaline phosphatase (ALP) and alanine aminotransferase (ALT) activities in plasma reached the lowest and highest value in 13°C, respectively. The expressions of all genes related to UPR and apoptosis in the hepatopancreas and hemocytes were significantly changed during the cooling process and reached the highest level of 13 and 13°C for 24 h, respectively. During re-warming stage, the histopathological symptoms got remission and each of the plasma metabolite concentrations and gene expressions returned to AT levels. These results revealed that pacific white shrimp can adapt to a certain level of temperature fluctuation by self-regulation.
| S-EPMC6700251 | biostudies-literature
Project description:White Spot Syndrome Virus (WSSV) is regarded as a virus with the strongest pathogenicity to shrimp. For the threshold trait such as disease resistance, marker assisted selection (MAS) was considered to be a more effective approach. In the present study, association analyses of single nucleotide polymorphisms (SNPs) located in a set of immune related genes were conducted to identify markers associated with WSSV resistance. SNPs were detected by bioinformatics analysis on RNA sequencing data generated by Illimina sequencing platform and Roche 454 sequencing technology. A total of 681 SNPs located in the exons of immune related genes were selected as candidate SNPs. Among these SNPs, 77 loci were genotyped in WSSV susceptible group and resistant group. Association analysis was performed based on logistic regression method under an additive and dominance model in GenABEL package. As a result, five SNPs showed associations with WSSV resistance at a significant level of 0.05. Besides, SNP-SNP interaction analysis was conducted. The combination of SNP loci in TRAF6, Cu/Zn SOD and nLvALF2 exhibited a significant effect on the WSSV resistance of shrimp. Gene expression analysis revealed that these SNPs might influence the expression of these immune-related genes. This study provides a useful method for performing MAS in shrimp.
| S-EPMC5240139 | biostudies-literature