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Foods (Basel, Switzerland) Oct 2021Lightly preserved seafood products, such as cold-smoked fish and fish gravlax, are traditionally consumed in Europe and are of considerable economic importance. This...
Lightly preserved seafood products, such as cold-smoked fish and fish gravlax, are traditionally consumed in Europe and are of considerable economic importance. This work aimed to compare three products that were obtained from the same batch of fish: cold-smoked salmon (CSS) stored under vacuum packaging (VP) or a modified atmosphere packaging (MAP) and VP salmon dill gravlax (SG). Classical microbiological analyses and 16S rRNA metabarcoding, biochemical analyses (trimethylamine, total volatile basic nitrogen (TVBN), biogenic amines, pH, volatile organic compounds (VOCs)) and sensory analyses (quantitative descriptive analysis) were performed on each product throughout their storage at a chilled temperature. The three products shared the same initial microbiota, which were mainly dominated by , and genera. On day 28, the VP CSS ecosystem was mainly composed of and, to a lesser extent, and genera, while was dominant in the MAP CSS. The diversity was higher in the SG, which was mainly dominated by , and . Although the sensory spoilage was generally weak, gravlax was the most perishable product (slight increase in amine and acidic off-odors and flavors, fatty appearance, slight discoloration and drop in firmness), followed by the VP CSS, while the MAP CSS did not spoil. Spoilage was associated with an increase in the TVBN, biogenic amines and spoilage associated VOCs, such as decanal, nonanal, hexadecanal, benzaldehyde, benzeneacetaldehyde, ethanol, 3-methyl-1-butanol, 2,3-butanediol, 1-octen-3-ol, 2-butanone and 1-octen-3-one. This study showed that the processing and packaging conditions both had an effect on the microbial composition and the quality of the final product.
PubMed: 34828798
DOI: 10.3390/foods10112517 -
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 -
Microbes and Environments 2021Bacterial extracellular aminopeptidases are key enzymes in protein processing in oligotrophic seawater. To the best of our knowledge, the regulation of aminopeptidase...
Bacterial extracellular aminopeptidases are key enzymes in protein processing in oligotrophic seawater. To the best of our knowledge, the regulation of aminopeptidase production in microbes inhabiting seawater has not yet been reported. The present study attempted to experimentally clarify which organic materials affect bacterial extracellular aminopeptidase production by nutrient-rich and starved cells growing in artificial seawater using Photobacterium, Alteromonas, Ruegeria, and Sulfitobacter. In all four species, we found that peptides induced bacterial extracellular aminopeptidase production. Amino acids led to cell growth with markedly lower aminopeptidase production by Photobacterium and Sulfitobacter, but not by Alteromonas and Ruegeria. These results suggest that the extracellular aminopeptidases of marine bacteria are primarily produced on demand in response to the presence of relevant substrates (peptides) in seawater. Peptidyl substances may be regulatory nutrients for marine bacterial growth in aquatic environments.
Topics: Aminopeptidases; Bacteria; Bacterial Proteins; Extracellular Space; Peptides; Phylogeny; Seawater
PubMed: 33716237
DOI: 10.1264/jsme2.ME20150 -
MSphere Feb 2021Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural...
Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from subsp. (), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( lpC-like rotein ) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the γ-d-glutamyl--diaminopimelic acid bond. However, PnpA does not cleave the PG of or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the type II secretion system and degrades the PG of and This suggests that PnpA is used by to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG. Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that subsp. , a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.
Topics: Animals; Bacteria; Cell Wall; Endopeptidases; Fishes; Peptidoglycan; Photobacterium
PubMed: 33536321
DOI: 10.1128/mSphere.00736-20 -
International Journal of Molecular... Nov 2022Polyhydroxyalkanoates (PHA) are promising biodegradable and biocompatible bioplastics, and extensive knowledge of the employed bacterial strain's metabolic capabilities...
Polyhydroxyalkanoates (PHA) are promising biodegradable and biocompatible bioplastics, and extensive knowledge of the employed bacterial strain's metabolic capabilities is necessary in choosing economically feasible production conditions. This study aimed to create an in-depth view of the utilization of C2.2 for PHA production by linking a wide array of characterization methods: metabolic pathway annotation from the strain's complete genome, high-throughput phenotypic tests, and biomass analyses through plate-based assays and flask and bioreactor cultivations. We confirmed, in PHA production conditions, urea catabolization, fatty acid degradation and synthesis, and high pH variation and osmotic stress tolerance. With urea as a nitrogen source, pure and rapeseed-biodiesel crude glycerol were analyzed comparatively as carbon sources for fermentation at 20 °C. Flask cultivations yielded 2.2 g/L and 2 g/L PHA at 120 h, respectively, with molecular weights of 428,629 g/mol and 81,515 g/mol. Bioreactor batch cultivation doubled biomass accumulation (10 g/L and 13.2 g/L) in 48 h, with a PHA productivity of 0.133 g/(L·h) and 0.05 g/(L·h). Thus, phenotypic and genomic analyses determined the successful use of C2.2 for PHA production using urea and crude glycerol and 20 g/L NaCl, without pH adjustment, providing the basis for a viable fermentation process.
Topics: Brassica napus; Polyhydroxyalkanoates; Glycerol; Biofuels; Brassica rapa; Genomics; Urea
PubMed: 36430242
DOI: 10.3390/ijms232213754 -
Gut Pathogens 2019The colibactin and cytotoxic necrotizing factor 1 (Cnf 1) are toxins with cell cycle modulating effects that contribute to tumorgenesis and hyperproliferation. This...
BACKGROUND
The colibactin and cytotoxic necrotizing factor 1 (Cnf 1) are toxins with cell cycle modulating effects that contribute to tumorgenesis and hyperproliferation. This study aimed to investigate the prevalence and pathologic effects of Cnf 1 and colibactin among hemolytic uropathogenic (). The bioinformatics approach incorporated in this study aimed to expand the domain of the in vitro study and explore the prevalence of both toxins among other bacterial species. A total of 125 isolates were recovered from UTIs patients. The isolates were tested for their hemolytic activity, subjected to tissue culture and PCR assays to detect the phenotypic and genotypic features of both toxins. A rat ascending UTI in vivo model was conducted using isolates expressing or non-expressing Cnf 1 and colibactin (ClbA and ClbQ). The bioinformatics analyses were inferred by Maximum likelihood method and the evolutionary relatedness was deduced by MEGA X.
RESULTS
Only 21 (16.8%) out of 125 isolates were hemolytic and 10 of these (47.62%) harbored the toxins encoding genes ( , and ). The phenotypic features of both toxins were exhibited by only 7 of the ( ) harboring isolates. The severest infections, hyperplastic and genotoxic changes in kidneys and bladders were observed in rats infected with the isolates.
CONCLUSION
Only 33.3% of the hemolytic isolates exhibited the phenotypic and genotypic features of Cnf 1 and Colibactin. The in vivo animal model results gives an evidence of active Cnf 1 and Colibactin expression and indicates the risks associated with recurrent and chronic UTIs caused by . The bioinformatics analyses confirmed the predominance of colibactin island among Enterobacteriaceae family (92.86%), with the highest occurrence among species (53.57%), followed by (28.57%), (7.14%), and species (3.57%). The Cnf 1 is predominant among (94.05%) and sporadically found among species (1.08%), (0.54%), (1.08%), (1.08%), (0.54%), and (0.54%). A close relatedness was observed between the 54-kb island of , the probiotic Nissle 1917, , and .
PubMed: 31139264
DOI: 10.1186/s13099-019-0304-y -
Journal of Microbiology & Biology... 2018Student-centered teaching allows students to be actively engaged in hands-on, minds-on activities that emphasize creativity and collaboration, enabling them to ask...
Student-centered teaching allows students to be actively engaged in hands-on, minds-on activities that emphasize creativity and collaboration, enabling them to ask questions and design their own investigations to real-world problems. One such problem is water contamination, which causes human health and environmental issues. However, chemical water quality testing for pollutants can be timely and expensive. In addition to chemical testing, researchers have developed assays using unicellular organisms to determine which pollutants are present and in what concentrations. In this three-hour laboratory activity, high school students and undergraduate biology or microbiology students work in pairs to help a fictional company develop a water quality microbioassay. Students design their own laboratory protocols to test the reaction of a bioluminescent bacterial species (i.e., or ) to exposure of common aquatic pollutants such as fertilizer, household cleaners, and motor oil. During this laboratory activity, students apply previously learned components of experimental design, including positive and negative controls, constants, and experimental groups. In addition, students gain experience writing a scientific explanation for a recommendation regarding the bioluminescent bacteria's suitability in a bioassay. Pre- and post-evaluation data revealed that students were successful in achieving the activity's objectives as well as in designing their investigations and writing their protocols using scaffolds within the lesson.
PubMed: 30100954
DOI: 10.1128/jmbe.v19i2.1373 -
MSphere May 2020Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and...
Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, , collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll , and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, , was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish. Pacific chub mackerel, , are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.
Topics: Animals; Cecum; Environment; Gastrointestinal Microbiome; Genetic Variation; Gills; Microbiota; Mucous Membrane; Oceans and Seas; Perciformes; Skin; Temperature
PubMed: 32434844
DOI: 10.1128/mSphere.00401-20 -
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 -
Frontiers in Microbiology 2019The RstB histidine kinase of the two component system RstAB positively regulates the expression of damselysin (Dly), phobalysin P (PhlyP) and phobalysin C (PhlyC)...
The RstAB System Impacts Virulence, Motility, Cell Morphology, Penicillin Tolerance and Production of Type II Secretion System-Dependent Factors in the Fish and Human Pathogen subsp. .
The RstB histidine kinase of the two component system RstAB positively regulates the expression of damselysin (Dly), phobalysin P (PhlyP) and phobalysin C (PhlyC) cytotoxins in the fish and human pathogen subsp. , a marine bacterium of the family . However, the function of the predicted cognate response regulator RstA has not been studied so far, and the role of the RstAB system in other cell functions and phenotypes remain uninvestigated. Here, we analyzed the effect of and mutations in cell fitness and in diverse virulence-related features. Both and mutants were severely impaired in virulence for sea bream and sea bass fish. Mutants in and genes were impaired in hemolysis and in Dly-dependent phospholipase activity but had intact PlpV-dependent phospholipase and ColP-dependent gelatinase activities. and mutants grown at 0.5% NaCl exhibited impaired swimming motility, enlarged cell size and impaired ability to separate after cell division, whereas at 1% NaCl the mutants exhibited normal phenotypes. Mutation of any of the two genes also impacted tolerance to benzylpenicillin. Notably, and mutants showed impaired secretion of a number of type II secretion system (T2SS)-dependent proteins, which included the three major cytotoxins Dly, PhlyP and PhlyC, as well as a putative delta-endotoxin and three additional uncharacterized proteins which might constitute novel virulence factors of this pathogenic bacterium. The analysis of the T2SS-dependent secretome of subsp. also led to the identification of RstAB-independent potential virulence factors as lipoproteins, sialidases and proteases. The RstAB regulon included plasmid, chromosome I and chromosome II-encoded genes that showed a differential distribution among isolates of this subspecies. This study establishes RstAB as a major regulator of virulence and diverse cellular functions in subsp. .
PubMed: 31105680
DOI: 10.3389/fmicb.2019.00897