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Marine Drugs Dec 2016Chitinolytic microorganisms secrete a range of chitin modifying enzymes, which can be exploited for production of chitin derived products or as fungal or pest control...
Chitinolytic microorganisms secrete a range of chitin modifying enzymes, which can be exploited for production of chitin derived products or as fungal or pest control agents. Here, we explored the potential of 11 marine bacteria (, ) for chitin degradation using in silico and phenotypic assays. Of 10 chitinolytic strains, three strains, S2753, S2040 and S2724, produced large clearing zones on chitin plates. All strains were antifungal, but against different fungal targets. One strain, S2040, had a pronounced antifungal activity against all seven fungal strains. There was no correlation between the number of chitin modifying enzymes as found by genome mining and the chitin degrading activity as measured by size of clearing zones on chitin agar. Based on in silico and in vitro analyses, we cloned and expressed two ChiA-like chitinases from the two most potent candidates to exemplify the industrial potential.
Topics: Antifungal Agents; Chitin; Chitinases; Marine Biology; Pseudoalteromonas; Vibrionaceae
PubMed: 27999269
DOI: 10.3390/md14120230 -
Infection, Genetics and Evolution :... Jan 2023Vibrio parahaemolyticus is a gram-negative bacterium capable of causing diseases in humans and aquatic animals. The global relationships among V. parahaemolyticus...
Vibrio parahaemolyticus is a gram-negative bacterium capable of causing diseases in humans and aquatic animals. The global relationships among V. parahaemolyticus genomes have been studied using multilocus sequence typing (MLST). Recently, the MLST gene recA has shown difficulties in amplification and/or a larger PCR fragment for some V. parahaemolyticus genomes due to genetic recombination. We aimed to investigate these recombination events of recA gene by analyzing 500 publicly available whole genomes from the NCBI database. The genomes with untypable recA genes were separated using BIGSdb and CGEMLST 2.0 servers, followed by annotation with RAST and NCBI pipelines. Moreover, the variable nature of V. parahaemolyticus was investigated by wgMLST analysis. The hypothetical proteins in recombinant regions were analyzed with VCIMPred tool. In the results, 3 genomes were detected with recA gene recombination, in which 2 were associated with phages and 1 to an AHPND causing strain. All 3 recombinant regions had a G + C content of 39%-40% with 15-30 ORFs, including a newly incorporated recA gene. These acquired recA genes were closely related to 3 different genera namely Aliivibrio, Photobacterium, and Vibrio. The wgMLST analysis indicated genetic recombination events occur independently among V. parahaemolyticus on a global scale. The in silico analysis revealed 4 hypothetical proteins associated with virulence factors in recombinant regions. The present study confirms, recombination events of V. parahaemolyticus recA gene, are diverse and may have an impact on the evolutionary process. Moreover, understanding these genetic recombination events of the recA gene is necessary to determine their STs and, therefore assessing epidemiological relationships.
Topics: Animals; Humans; Multilocus Sequence Typing; Phylogeny; Rec A Recombinases; Recombination, Genetic; Vibrio Infections; Vibrio parahaemolyticus
PubMed: 36549419
DOI: 10.1016/j.meegid.2022.105396 -
Animals : An Open Access Journal From... Nov 2022Bacteria belonging to the species are pathogens of cultured marine fish, causing diseases of high importance, such as Pasteurellosis. Thus, they are considered a major...
Bacteria belonging to the species are pathogens of cultured marine fish, causing diseases of high importance, such as Pasteurellosis. Thus, they are considered a major threat to the aquaculture sector. Despite the great importance of fish mariculture for the Greek economy, the distribution and abundance of these bacteria are not well documented in aquaculture units in Greece. Keeping this in mind, the scope of the present study was to investigate the presence, antibiotic profile, and virulence of bacteria originating from a representative sample of mariculture units throughout Greece. Samples were collected from diseased fish belonging to three different cultured fish species, namely , and from both the Aegean and the Ionian Sea. Tissue samples were cultured in agar media, and bacteria were molecularly identified using both bacterial universal and species-specific primer pairs for spp. Additionally, the identified strains were characterized for the presence of virulence genes as well as antibiotic profiles. According to the results, the aforementioned bacteria are distributed in the Greek aquaculture units and are characterized by high pathogenicity based on the abundance of virulence genes. Furthermore, the majority of the detected strains exhibit some level of antibiotic resistance. In summary, our results indicate the need for systematic surveillance and study of their antibiotic profiles in Greek aquaculture since these bacteria constitute a major threat to the sector.
PubMed: 36428362
DOI: 10.3390/ani12223133 -
Biotechnology Reports (Amsterdam,... Sep 2020Industrial enzymes are important for various biotechnological applications. Currently, the diversity of industrial enzymes-producing marine bacteria from Malaysia...
Industrial enzymes are important for various biotechnological applications. Currently, the diversity of industrial enzymes-producing marine bacteria from Malaysia remains mostly unknown. This study investigated the diversity of industrial enzyme-producing marine bacteria from culture collections at the Institute of Marine Biotechnology, Universiti Malaysia Terengganu. Out of 200 bacterial isolates revived, 163 bacteria isolate were successfully growth. Marine bacteria produced enzymes with total scoring higher than four were selected for molecular identification using 16S rDNA. About 161 bacteria isolate secreted amylase (68.7 %), lipase (88.3 %) and protease (68.7 %). The phylogenetic analysis led to the identification of three major phyla, namely Proteobacteria, Firmicutes and Bacteroidetes. These phyla were differentiated into nine genera consisted of , , , , , , , and . Genetic variation was more likely to occur within similar marine bacteria species. The microbial community was found to affect the production of industrial enzymes and the diversity of marine bacteria.
PubMed: 32514406
DOI: 10.1016/j.btre.2020.e00482 -
Foods (Basel, Switzerland) Apr 2021Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the...
Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the chicken-associated microbiome that will lead to moderation of food spoilage or safety. This study was undertaken to explore the bacterial communities of chicken breast and thigh fillets stored at refrigeration (0 °C and 5 °C) and slightly abuse (10 °C) temperatures for 5 days through conventional cultural methods along with next-generation sequencing (NGS) analysis. Total viable counts (TVC), , spp., and lactic acid bacteria (LAB) were enumerated, while the bacterial communities were mapped through 16S rRNA gene amplicon sequencing. Chicken breast and thigh fillets possessed a complex bacterial structure that incorporated a total of >200 Operational Taxonomic Units (OTUs) at the genus level. The core microbiota of fresh samples consisted of , , , , , and (family). These genera persisted until the end of storage in >80% of samples, except and , while was also identified. Hierarchical clustering showed a distinction of samples based on storage time and chicken part. Conventional plate counting with growth media commonly used in spoilage studies did not always correspond to the microbial community profiles derived from NGS analysis, especially in , , , and . Results of the present study highlight and , in general, as potent chicken meat spoilers and suggest the necessity to combine classical microbiological methods along with NGS technologies to characterize chicken meat spoilage microbiota.
PubMed: 33916748
DOI: 10.3390/foods10040765 -
International Journal of Food... Feb 2016Accumulation of volatile organic compounds was monitored in association with sensory quality, bacterial concentrations and culture-independent microbial community...
Accumulation of volatile organic compounds was monitored in association with sensory quality, bacterial concentrations and culture-independent microbial community analyses in raw pork loin and pork collar during storage under high-oxygen modified atmosphere at +4 °C. Of the 48 volatile compounds detected in the pork samples, the levels of acetoin, diacetyl and 3-methyl-1-butanol had the highest correlations with the sensory scores and bacterial concentrations. These compounds accumulated in all of the four monitored lots of non-sterile pork but not in the sterilized pork during chilled storage. According to the culture-dependent and culture-independent characterization of bacterial communities, Brochothrix thermosphacta, lactic acid bacteria (Carnobacterium, Lactobacillus, Lactococcus, Leuconostoc, Weissella) and Photobacterium spp. predominated in pork samples. Photobacterium spp., typically not associated with spoilage of meat, were detected also in 8 of the 11 retail packages of pork investigated subsequently. Eleven isolates from the pork samples were shown to belong to Photobacterium phosphoreum by phenotypic tests and sequencing of the 16S rRNA and gyrB gene fragments. Off-odors in pork samples with high proportion of Photobacterium spp. were associated with accumulation of acetoin, diacetyl and 3-methyl-1-butanol in meat, but these compounds did not explain all the off-odors reported in sensory analyses.
Topics: Acetoin; Animals; Carnobacterium; DNA Gyrase; Diacetyl; Food Microbiology; Food Packaging; Gas Chromatography-Mass Spectrometry; Lactococcus; Leuconostoc; Odorants; Pentanols; Photobacterium; RNA, Ribosomal, 16S; Red Meat; Swine; Volatile Organic Compounds
PubMed: 26623935
DOI: 10.1016/j.ijfoodmicro.2015.11.003 -
Applied and Environmental Microbiology Apr 2018Symbiotic microorganisms have been found in the hemolymph (blood) of many aquatic invertebrates, such as crabs, shrimp, and oysters. Hemolymph is a critical site in the...
Symbiotic microorganisms have been found in the hemolymph (blood) of many aquatic invertebrates, such as crabs, shrimp, and oysters. Hemolymph is a critical site in the host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies using selective media (e.g., thiosulfate-citrate-bile salts-sucrose [TCBS], 2216E, and LB) for enumerating and isolating microbial cells. However, doubts remain about the "true" representation of the microbial abundance and diversity of symbiotic microorganisms in hemolymph, particularly for uncultivable microorganisms, which are believed to be more abundant than the cultured microorganisms. To explore this, we developed a culture-independent cell extraction method for separating microbial cells from the hemolymph of three aquatic invertebrates ( [mud crab], [whiteleg shrimp], and [Portuguese oysters]) involving filtration through a 5-μm-pore-size mesh filter membrane (the filtration method). A combination of the filtration method with fluorescence microscopy and high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. More than 2.6 × 10 cells/ml of microbial cells dominated by and , and , and and were detected in the hemolymph of , , and , respectively. A parallel study for investigating the hemolymph microbiomes by comparing the filtration method and a culture-dependent method (the plate count method) showed significantly higher microbial abundances (between 26- and 369-fold difference; < 0.05) and less biased community structures of the filtration method than those of the plate count method. Furthermore, hemolymph of the three invertebrates harbored many potential pathogens, including , , and species. Finally, the filtration method provides a solution that improves the understanding of the metabolic functions of uncultivable hemolymph microorganisms (e.g., metagenomics) devoid of host hemocyte contamination. Microorganisms are found in the hemolymph of invertebrates, a critical site in the host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies. However, doubts remain about the "true" representation of the hemolymph microbiome. This study developed a culture-independent cell extraction method that could separate microbial cells from the hemolymph of three aquatic invertebrates (, , and ) based on filtration through a 5-μm-pore-size mesh filter membrane (the filtration method). A combination of the filtration method with fluorescence microscopy and a high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. Our results demonstrate that the hemolymph of aquatic invertebrates harbors a much higher microbial abundance and more distinct microbial community composition than previously estimated. Furthermore, this work provides a less biased solution for studying the metabolic functions of uncultivable hemolymph microbiota devoid of host hemocyte contamination.
Topics: Analytic Sample Preparation Methods; Animals; Brachyura; Crassostrea; Hemolymph; Microbiota; Penaeidae
PubMed: 29453260
DOI: 10.1128/AEM.02824-17 -
Microorganisms Feb 2023Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the...
Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the coelomic fluid or the gut microbiota. In this study, the epibiota community associated with four wild Caribbean sea urchin species, , , , and , was characterized for the first time. Using 57 sea urchin animal samples, we evaluated the influence of animal species, trophic niches, and geographical location on the composition of the epibiotic microbiota. We found significant differences in the bacterial biota among species and trophic niches, but not among geographical locations. exhibited the highest alpha diversity with high dominance of Fusobacteria, Planctomycetes, and Cyanobacteria, whereas and were dominated by Firmicutes. inhabiting the seagrass biotope dominated by meadows had mostly In contrast, samples located in the reef (dominated by corals and other reef builders) had a higher abundance of and Our findings confirm that the epibiotic microbiota is species-specific, but also niche-dependent, revealing the trophic networks emerging from the organic matter being recycled in the seagrass and reef niches. As echinoids are important grazers of benthic communities, their microbiota will likely influence ecosystem processes.
PubMed: 36838357
DOI: 10.3390/microorganisms11020391 -
Foods (Basel, Switzerland) Feb 2023"Pirot 'ironed' sausage" (Pis) is a traditional, fermented sausage, made from different types of meat (beef and chevon), without additives or starter cultures. The...
"Pirot 'ironed' sausage" (Pis) is a traditional, fermented sausage, made from different types of meat (beef and chevon), without additives or starter cultures. The physical-chemical properties (pH, water activity, fats, moisture, and protein contents) were examined in the initial meat batter stuffing and during ripening. Total bacterial diversity was examined at different time points using both culturable (traditional) and non-culturable (NGS sequencing) approaches. During the ripening, a decrease in pH value, a, and moisture content was observed, as well as an increase in protein and fat content. At least a two-fold significant decrease was noted for colorimetric values during the ripening period. The dominance of and was observed in the non-culturable approach in all studied samples. During the ripening process, an increase in (from 33.5% to 63.5%) with a decrease in (from 65.4% to 22.3%) was observed. The bacterial genera that were dominant throughout the ripening process were , , , , and , while , , and were found also, but in negligible abundance. Among the culturable bacteria, () and were present in all stages of ripening.
PubMed: 36766190
DOI: 10.3390/foods12030664 -
The Journal of General and Applied... Sep 2020Oscillation in bacterial bioluminescence from Photobacterium kishitanii liquid culture was examined regarding reproducibility and bacterial cell activities, i.e.,...
Oscillation in bacterial bioluminescence from Photobacterium kishitanii liquid culture was examined regarding reproducibility and bacterial cell activities, i.e., dissolved oxygen (DO) consumption, esterase activity, and product production rate. A frequent increase in DO was suspected to be due to a rapid decrease in luminescence, and a simple model describing not only the monotonous decrease in cell activity, but also the luminescence-DO relationship is proposed.
Topics: Biological Clocks; Biomarkers; Esterases; Fluoresceins; Luminescence; Luminescent Measurements; Microbial Viability; Oxygen; Photobacterium; Reproducibility of Results; Time Factors
PubMed: 31827021
DOI: 10.2323/jgam.2019.07.002