-
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 -
Journal of Bacteriology May 2008Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation...
Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib(2) operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib(2) operon of P. leiognathi. In none of these cases of apparent HGT, however, did acquisition of the lux genes correlate with phylogenetic divergence of the recipient strain from other members of its species. The results indicate that horizontal transfer of the lux genes in nature is rare and that horizontal acquisition of the lux genes apparently has not contributed to speciation in recipient taxa.
Topics: Bacterial Proteins; DNA, Bacterial; Gene Transfer, Horizontal; Luminescent Measurements; Multigene Family; Operon; Oxidoreductases; Phylogeny; Repressor Proteins; Trans-Activators; Vibrionaceae
PubMed: 18359809
DOI: 10.1128/JB.00101-08 -
Journal of Food Protection Apr 2020The effects of high hydrostatic pressure (HHP) treatments on histamine-forming bacteria (HFB) Morganella morganii and Photobacterium phosphoreum in phosphate buffer and...
ABSTRACT
The effects of high hydrostatic pressure (HHP) treatments on histamine-forming bacteria (HFB) Morganella morganii and Photobacterium phosphoreum in phosphate buffer and tuna meat slurry were investigated using viability counting and scanning electron microscopy. The first-order model fits the destruction kinetics of high pressure on M. morganii and P. phosphoreum during the pressure hold period. The D-values of M. morganii (200 to 600 MPa) and P. phosphoreum (100 to 400 MPa) in phosphate buffer ranged from 16.4 to 0.08 min and 26.4 to 0.19 min, respectively, whereas those in tuna meat slurry ranged from 51.0 to 0.09 min and 71.6 to 0.19 min, respectively. M. morganii had higher D-values than P. phosphoreum at the same pressure, indicating it was more resistant to HHP treatment. HFB had a higher D-value in tuna meat slurry compared with that in phosphate buffer, indicating that the HFB were more resistant to pressure in tuna meat slurry. The Zp values (pressure range that results in a 10-fold change in D-value) of M. morganii and P. phosphoreum were 162 and 140 MPa in phosphate buffer and 153 and 105 MPa in tuna meat slurry, respectively. Damage to the cell wall and cell membrane by HHP treatments can be observed by scanning electron microscopy. To our knowledge, this is the first report to demonstrate that HHP can be applied to inactivate the HFB M. morganii and P. phosphoreum by inducing morphological changes in the cells.
Topics: Animals; Food Handling; Food Preservation; Histamine; Morganella morganii; Photobacterium; Pressure
PubMed: 32221566
DOI: 10.4315/0362-028X.JFP-19-267 -
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 -
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 -
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 -
Fish and Shellfish Immunology Reports Dec 2023The effects of ssp (Phdp) on immune responses and intestinal ultrastructure of following infection and their amelioration by the probiotic bacteria and were...
The effects of ssp (Phdp) on immune responses and intestinal ultrastructure of following infection and their amelioration by the probiotic bacteria and were evaluated. Pathogen growth inhibition in coculture with each probiotic and its virulence against were confirmed with an LC of 10 CFU mL. Phdp administration to at sublethal levels resulted in depletion of superoxide dismutase, glutathione reductase, glutathione transferase and phenoloxidase activities, extensive lipid peroxidation and reduced survival. Following a combined administration of each probiotic and the pathogen, enzyme activities and survival were significantly higher, while lipid peroxidation was reduced, compared to the infected group with no probiotic treatment ( < 0.05). The transmission electron microscopy study revealed that pathogen infection resulted in disarranged and fragmented microvilli, formation of empty or pathogen containing cytoplasmic vacuoles and damaged mitochondria. In the probiotic-treated and Phdp-infected series, intestinal cells showed normal appearance, except for the presence of pathogen-containing vacuoles and highly ordered but laterally stacked microvilli. The results of the present study indicate that Phdp induces cell death through an oxidative stress response and probiotics enhance immune responses to protect it against the Phdp induced damage.
PubMed: 37671319
DOI: 10.1016/j.fsirep.2023.100113 -
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