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Microbial Genomics Dec 2023This study presents the assembly and comparative genomic analysis of luminous strains isolated from the light organs of 12 fish species using Oxford Nanopore...
This study presents the assembly and comparative genomic analysis of luminous strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for and its subspecies , enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the and strains. A comparison of the and lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the operon, responsible for light production, indicated congruence between the presence of and host family, challenging its role in differentiating from . Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of genome evolution, highlighting subtle differences between closely related lineages, specifically and . These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.
Topics: Animals; Photobacterium; Symbiosis; DNA, Bacterial; Genomics; Genome, Bacterial
PubMed: 38112751
DOI: 10.1099/mgen.0.001161 -
Marine Pollution Bulletin Feb 2024In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the...
In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the South China Sea. We found that the quantity and quality of root exudates varied seasonally, with higher exudation rates and more bioavailable dissolved organic matter (DOM) during the seedling and vegetative stages in spring and summer. Using Illumina NovaSeq sequencing, we analyzed bacterial and fungal communities and discovered that microbial diversity and composition were influenced by root exudate characteristics s and seagrass biomass, which were strongly dependent on seagrass growth stages. Certain bacterial groups, such as Ruegeria, Sulfurovum, Photobacterium, and Ralstonia were closely associated with root exudation and may contribute to sulfur cycling, nitrogen fixation, and carbon remineralization, which were important for plant early development. Similarly, specific fungal taxa, including Astraeus, Alternaria, Rocella, and Tomentella, were enriched in spring and summer and showed growth-promoting abilities. Overall, our study suggests that seagrass secretes different compounds in its exudates at various developmental stages, shaping the rhizosphere microbial assemblages.
Topics: Microbiota; Carbon; Rhizosphere; Biomass; Growth and Development; Plant Roots; Soil Microbiology
PubMed: 38150979
DOI: 10.1016/j.marpolbul.2023.115940 -
International Journal of Food... Apr 2024The commercialization of processed fish products is rising in restaurants and small to medium enterprises. However, there is a lack of data related to the...
The commercialization of processed fish products is rising in restaurants and small to medium enterprises. However, there is a lack of data related to the microbiological safety of such products. In this study total aerobic colony count and Enterobacteriaceae, as proxy of process hygiene criteria, and detection of Listeria monocytogenes and concentration of histamine, as food safety criteria, were investigated in Salmo salar (salmon), Xiphias gladius (swordfish) and Thunnus albacares (yellowfin tuna), before, during, and at the end of a dry-curing process, performed in a dedicated cabinet, at controlled temperature, relative humidity and ventilation, up to 240 h. The microbiological parameters were investigated in the tested fish products by culture methods and shotgun metagenomic, while the presence of histamine, and other biogenic amines, was quantified by High Performance Liquid Chromatography. In the raw material, and up to the end of the dry curing process, the concentration of Enterobacteriaceae was always lower than 10 CFU/g, while total aerobic colony counts ranged between 3.9 and 5.4 Log CFU/g in salmon; 5.5 and 5.9 Log CFU/g in swordfish; 4.4 and 4.8 Log CFU/g in tuna. The pH values were significantly different between fish species, in the raw materials and during processing except for T4, occurring 70 h after the start of the process for salmon and after 114 h for swordfish and tuna. Water activity was different at specific sampling points and at the end of processing. Overall, 79 % of the sequences identified in the tested fish samples were assigned to y bacteria. The most abundant phyla were Pseudomonadota, Bacillota and Mycoplasmatota. The microbial populations identified by shotgun metagenomic in the tested fish species clustered well separated one from the other. Moreover, the microbial richness was significantly higher in salmon and tuna in comparison to swordfish. Listeria monocytogenes was not detected in the raw material by using the reference cultural method and very few reads (relative abundance <0.007) were detected in swordfish and tuna by shotgun metagenomic. Histamine producing bacteria, belonging to the genera Vibrio, Morganella, Photobacterium and Klebsiella, were identified primarily in swordfish. However, histamine and other biogenic amines were not detected in any sample. To the best of our knowledge this is the first paper reporting time point determinations of microbiological quality and safety parameters in salmon, swordfish and tuna, before, during and at the end of a dry-curing process. The data collected in this paper can help to predict the risk profile of ready to eat dry-cured fish products during storage before consumption.
Topics: Animals; Histamine; Food Microbiology; Seafood; Biogenic Amines; Enterobacteriaceae; Fishes; Bacteria; Tuna; Colony Count, Microbial
PubMed: 38432054
DOI: 10.1016/j.ijfoodmicro.2024.110641 -
Fish & Shellfish Immunology Jul 2024Enteritis posed a significant health challenge to golden pompano (Trachinotus ovatus) populations. In this research, a comprehensive multi-omics strategy was implemented...
Enteritis posed a significant health challenge to golden pompano (Trachinotus ovatus) populations. In this research, a comprehensive multi-omics strategy was implemented to elucidate the pathogenesis of enteritis by comparing both healthy and affected golden pompano. Histologically, enteritis was characterized by villi adhesion and increased clustering after inflammation. Analysis of the intestinal microbiota revealed a significant increase (P < 0.05) in the abundance of specific bacterial strains, including Photobacterium and Salinivibrio, in diseased fish compared to the healthy group. Metabolomic analysis identified 5479 altered metabolites, with significant impacts on terpenoid and polyketide metabolism, as well as lipid metabolism (P < 0.05). Additionally, the concentrations of several compounds such as calcitetrol, vitamin D2, arachidonic acid, and linoleic acid were significantly reduced in the intestines of diseased fish post-enteritis (P < 0.05), with the detection of harmful substances such as Efonidipine. In transcriptomic profiling, enteritis induced 68 upregulated and 73 downregulated genes, predominantly affecting steroid hormone receptor activity (P < 0.05). KEGG pathway enrichment analysis highlighted upregulation of SQLE and CYP51 in steroidogenesis, while the HSV-1 associated MHC1 gene exhibited significant downregulation. Integration of multi-omics results suggested a potential pathogenic mechanism: enteritis may have resulted from concurrent infection of harmful bacteria, specifically Photobacterium and Salinivibrio, along with HSV-1. Efonidipine production within the intestinal tract may have blocked certain calcium ion channels, leading to downregulation of MHC1 gene expression and reduced extracellular immune recognition. Upregulation of SQLE and CYP51 genes stimulated steroid hormone synthesis within cells, which, upon binding to G protein-coupled receptors, influenced calcium ion transport, inhibited immune activation reactions, and further reduced intracellular synthesis of anti-inflammatory substances like arachidonic acid. Ultimately, this cascade led to inflammation progression, weakened intestinal peristalsis, and villi adhesion. This study utilized multi-level omics detection to investigate the pathological symptoms of enteritis and proposed a plausible pathogenic mechanism, providing innovative insights into enteritis verification and treatment in offshore cage culture of golden pompano.
Topics: Animals; Enteritis; Fish Diseases; Gastrointestinal Microbiome; Gene Expression Profiling; Perciformes; Transcriptome; Metabolomics; Multiomics
PubMed: 38734118
DOI: 10.1016/j.fsi.2024.109616 -
Food Additives & Contaminants. Part A,... Jun 2024Zearalenone (ZEN), a nonsteroidal estrogenic mycotoxin, causes enormous economic losses in the food and feed industries. Simple, rapid, low-cost, and quantitative...
Zearalenone (ZEN), a nonsteroidal estrogenic mycotoxin, causes enormous economic losses in the food and feed industries. Simple, rapid, low-cost, and quantitative analysis of ZEN is particularly urgent in the fields of food safety and animal husbandry. Using the bioluminescent bacterium T3, we propose a bioluminescence inhibition assay to evaluate ZEN levels quickly. The limit of detection (LOD), limit of quantification (LOQ), and quantitative working range of this bioluminescence inhibition assay were 0.1 µg/mL, 5 µg/mL, and 5-100 µg/mL, respectively. The concentration-response curve of the bioluminescence inhibition rate and ZEN concentration was plotted within the range 5 to 100 μg/mL, as follows: y = 0.0069x - 0.0190x + 7.9907 (R = 0.9943, y is luminescence inhibition rate, x is ZEN concentration). First, we used the bioluminescence inhibition assay to detect the remaining ZEN in samples treated with purified lactonohydrolase ZHD101. The bioluminescence inhibition assay results showed a strong correlation with the HPLC analysis. Furthermore, we successfully evaluated the overall toxicity of samples treated with purified peroxidase Prx and HO using the T3 bioluminescence inhibition assay. The results indicate that the degradation products of ZEN created by purified peroxidase Prx and HO showed little toxicity to T3. In this study, a simple, rapid, and low-cost assay method of zearalenone by bioluminescent T3 was developed. The bioluminescence inhibition assay could be used to estimate the efficiency of enzymatic degradation of ZEN.
PubMed: 38857317
DOI: 10.1080/19440049.2024.2363397 -
Foods (Basel, Switzerland) Jul 2023Broomcorn millet Huangjiu brewing is usually divided into primary fermentation and post-fermentation. Microbial succession is the major factor influencing the...
Broomcorn millet Huangjiu brewing is usually divided into primary fermentation and post-fermentation. Microbial succession is the major factor influencing the development of the typical Huangjiu flavor. Here, we report the changes in flavor substances and microbial community during the primary fermentation of broomcorn millet Huangjiu. Results indicated that a total of 161 volatile flavor compounds were measured during primary fermentation, and estragole was detected for the first time in broomcorn millet Huangjiu. A total of 82 bacteria genera were identified. , , and were the dominant genera. and were dominant among the 30 fungal genera. Correlation analysis showed that 102 microorganisms were involved in major flavor substance production during primary fermentation, , , , , , , , and were most associated with flavoring substances. Four bacteria, (R1), (R2), (R3), and (R4), were isolated and identified from wheat Qu, which were added to wine Qu to prepare four kinds of fortified Qu (QR1, QR2, QR3, QR4). QR1 and QR2 fermentation can enhance the quality of Huangjiu. This work reveals the correlation between microorganisms and volatile flavor compounds and is beneficial for regulating the micro-ecosystem and flavor of the broomcorn millet Huangjiu.
PubMed: 37509772
DOI: 10.3390/foods12142680 -
Fish & Shellfish Immunology Mar 2024Immunonutrition is a promising and viable strategy for the development of prophylactic measures in aquaculture. Ulvan, a sulphated marine polysaccharide from green...
Immunonutrition is a promising and viable strategy for the development of prophylactic measures in aquaculture. Ulvan, a sulphated marine polysaccharide from green seaweeds, has many biological activities including the immunomodulatory ones. The aim of this study was to assess the short and long-term effects of an ulvan-rich extract obtained from U. ohnoi as immunonutrient in Senegalese sole juveniles. In this work, an ulvan-rich extract from Ulva ohnoi has been obtained by the hot water method and isolated by ethanol precipitation. The FTIR analysis revealed that the ulvan-rich extact had very similar characteristics to previously published ulvan spectra. The total sulfate and protein content was 24.85 ± 3.98 and 0.91 ± 0.04 %, respectively. In vitro assays performed in Senegalese sole (Solea senegalensis) macrophages showed that the ulvan obtained in this study did not compromise the cell viability at concentrations up to 1 mg ml and expression levels of lyg, irf1, il6, il10, c7, tf and txn were significantly upregulated in a concentration dependent-manner. Finally, S. senegalensis juveniles were fed basal diets and diets supplemented with the ulvan-rich extract at ratios 1 and 2 % for 30 days and then, challenged with Photobacterium damselae subsp. piscicida (Phdp). Thereafter, ulvan was withdrawn from the diet and all juveniles were fed the basal diet for 30 days. At 30 days post withdrawal (dpw), juveniles were challenged with Phdp. The expression profiles of a set of genes related to the immune system in spleen were evaluated as well as the lysozyme, peroxidase and bactericidal activity in plasma. Dietary effects of 1 % ulvan resulted in a boost of the immune response and increased disease resistance at short-term whereas juveniles fed diets supplemented with 2 % ulvan showed a significant decrease in the bactericidal activity and lack of protection against Phdp. At long-term (30 days after the withdrawal of ulvan), an improved response was observed in juveniles previously fed 1 % ulvan.
Topics: Animals; Fish Diseases; Gram-Negative Bacterial Infections; Polysaccharides; Flatfishes; Photobacterium
PubMed: 38296005
DOI: 10.1016/j.fsi.2024.109399 -
Fish & Shellfish Immunology Dec 2023Galectins, as members of lectin families, exhibit a high affinity for β-galactosides and play diverse roles in biological processes. They function as pattern...
Galectins, as members of lectin families, exhibit a high affinity for β-galactosides and play diverse roles in biological processes. They function as pattern recognition receptors (PRRs) with important roles in immune defense. In this study, galectin-1, designated as SpGal-1, was identified and characterized from silver pomfret (Pampus argenteus). The SpGal-1 comprises an open reading frame (ORF) spanning 396 base pairs (bp) and encodes a deduced amino acid (aa) sequence containing a single carbohydrate recognition domain (CRD). Sublocalization analysis revealed that SpGal-1 was mainly expressed in the cytoplasm. The mRNA transcripts of SpGal-1 were ubiquitously detected in various tissues, with a higher expression level in the intestine. In addition, when exposed to Photobacterium damselae subsp. damselae (PDD) infection, both the liver and head kidney exhibited significantly increased SpGal-1 mRNA expression. The recombinant protein of SpGal-1 (named as rSpGal-1) demonstrated hemagglutination against red blood cells (RBCs) from Larimichthys crocea and P. argenteus in a Ca or β-Mercaptoethanol (β-ME)-independent manner. Notably, rSpGal-1 could bind with various pathogen-associated molecular patterns (PAMPs) including D-galactose, D-mannose, lipopolysaccharide (LPS), and peptidoglycan (PGN), with highest affinity to PGN. Moreover, rSpGal-1 effectively interacted with an array of bacterial types encompassing Gram-positive bacteria (Staphylococcus aureus and Nocardia seriolae) and Gram-negative bacteria (PDD and Escherichia coli, among others), with the most robust binding affinity towards PDD. Collectively, these findings highlight that SpGal-1 is a crucial PRR with involvement in the host immune defense of silver pomfret.
Topics: Humans; Animals; Galectin 1; Gene Expression Regulation; Immunity, Innate; Base Sequence; RNA, Messenger; Phylogeny
PubMed: 37944682
DOI: 10.1016/j.fsi.2023.109209 -
Vavilovskii Zhurnal Genetiki I Selektsii Dec 2023The light emitted by a luminescent bacterium serves as a unique native channel of information regarding the intracellular processes within the individual cell. In the...
The light emitted by a luminescent bacterium serves as a unique native channel of information regarding the intracellular processes within the individual cell. In the presence of highly sensitive equipment, it is possible to obtain the distribution of bacterial culture cells by the intensity of light emission, which correlates with the amount of luciferase in the cells. When growing on rich media, the luminescence intensity of individual cells of brightly luminous strains of the luminescent bacteria Photobacterium leiognathi and Ph. phosporeum reaches 104-105 quanta/s. The signal of such intensity can be registered using sensitive photometric equipment. All experiments were carried out with bacterial clones (genetically homogeneous populations). A typical dynamics of luminous bacterial cells distributions with respect to intensity of light emission at various stages of batch culture growth in a liquid medium was obtained. To describe experimental distributions, a phenomenological model that links the light of a bacterial cell with the history of events at the molecular level was constructed. The proposed phenomenological model with a minimum number of fitting parameters (1.5) provides a satisfactory description of the complex process of formation of cell distributions by luminescence intensity at different stages of bacterial culture growth. This may be an indication that the structure of the model describes some essential processes of the real system. Since in the process of division all cells go through the stage of release of all regulatory molecules from the DNA molecule, the resulting distributions can be attributed not only to luciferase, but also to other proteins of constitutive (and not only) synthesis.
PubMed: 38213711
DOI: 10.18699/VJGB-23-102 -
Frontiers in Microbiology 2023The mud crab, , holds great commercial significance as a marine crustacean widely cultivated in the Indo-Pacific region. Understanding the core gut microbiota of aquatic...
INTRODUCTION
The mud crab, , holds great commercial significance as a marine crustacean widely cultivated in the Indo-Pacific region. Understanding the core gut microbiota of aquatic animals is crucial for their overall health and growth, yet the core gut microbiota of mud crab remains poorly characterized.
METHODS
In this study, we gathered gut samples from mud crabs across five locations within Sanmen Bay, China. Through the utilization of high-throughput sequencing, we delved into the composition of the gut microbial community and identified the core gut microbiome of mud crab.
RESULTS
Our results demonstrate that the gut microbial diversity of mud crab did not exhibit significant variation among the five sampling sites, although there were some differences in community richness. At the phylum level, we identified 35 representative phyla, with Firmicutes, Proteobacteria, Bacteroidota, and Campilobacterota as the dominant phyla. Among the 815 representative genera, we discovered 19 core genera, which accounted for 65.45% of the total sequences. These core genera were distributed across 6 phyla, and among them, exhibited the highest average relative abundance.
DISCUSSION
has probiotic activity and may play a crucial role in enhancing the immune response of the host and maintaining the diversity of the gut microbiota. Moreover, we observed a positive correlation between the relative abundance of core genera and the stability of the gut microbial community. Furthermore, our findings revealed distinct differences in gut microbial composition and specific taxa between the sexes of mud crab. These differences subsequently influenced the functionality of the gut microbial community. Overall, our investigation sheds light on the core gut microbiota of mud crab, emphasizing the importance of core gut microbial communities in maintaining the health and growth of these commercially significant marine crustaceans.
PubMed: 37727291
DOI: 10.3389/fmicb.2023.1243334