-
International Journal of Food Science 2022Fish products are highly vulnerable to microbial contamination due to their soft tissues, making them perishable and harmful to consumers. The clinical and subclinical...
Fish products are highly vulnerable to microbial contamination due to their soft tissues, making them perishable and harmful to consumers. The clinical and subclinical infections reported by fish consumers are mainly associated with pathogenic microorganisms in fish products. Therefore, this study aimed at establishing the molecular profiles and diversity of the bacterial isolates from fish and fish products obtained from Kirinyaga County markets in Kenya. A total of 660 samples were randomly sampled in six Kirinyaga County markets and transported to Kenyatta University for bacterial isolation. The fish skin surface was cut using a sterile knife and blended in buffered peptone water. The blended product was serially diluted and plated on nutrient agar. After 24 hours, the bacteria cultures were subcultured to obtain pure bacterial isolates. The pure isolates were grouped and characterized based on their morphology and biochemical characteristics. One representative of each group was selected for bacterial DNA extraction. The 16S rRNA gene was amplified using the 27F and 1492R primers, and the obtained PCR product was subjected to Sanger-based sequencing using the same primers. Morphological characterization yielded 54 morpho groups. Phylogenetic analysis revealed diverse bacterial strains, including , , , sp. and sp. was the most dominant group, as compared to other isolates in the study. The study, therefore, revealed diverse bacterial strains from the fish products. This high microbial diversity calls for heightened surveillance to prevent possible foodborne disease outbreaks.
PubMed: 35898416
DOI: 10.1155/2022/2379323 -
Applied and Environmental Microbiology Jul 2022Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis...
Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-ydroxyiicolinic cid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study, a gene cluster responsible for DPA degradation was cloned from strain JQ135. The expression of genes was induced by DPA and negatively regulated by DipR. A novel monooxygenase gene, , was crucial for the initial hydroxylation of DPA into 3HDPA and proposed to encode the key catalytic component of the multicomponent DPA monooxygenase. The heme binding protein gene , ferredoxin reductase gene , and ferredoxin genes were also involved in the DPA hydroxylation and proposed to encode other components of the multicomponent DPA monooxygenase. The O stable isotope labeling experiments confirmed that the oxygen atom in the hydroxyl group of 3HDPA came from dioxygen molecule rather than water. The protein sequence of DipD exhibits no significant sequence similarities with known oxygenases, suggesting that DipD was a new member of oxygenase family. Moreover, bioinformatic survey suggested that the gene cluster was widely distributed in many , , and , including soil bacteria, aquatic bacteria, and pathogens. This study provides new molecular insights into the catabolism of DPA in bacteria. Dipicolinic acid (DPA) is a natural pyridine derivative that serves as an essential component of the spore. DPA accounts for 5 to 15% of the dry weight of spores. Due to the huge number of spores in the environment, DPA is also considered to be an important component of the global biomass carbon pool. DPA could be decomposed by microorganisms and enter the global carbon cycling; however, the underlying molecular mechanisms are rarely studied. In this study, a DPA catabolic gene cluster () was cloned and found to be widespread in , , and . The genes responsible for the initial hydroxylation of DPA to 3-hydroxyl-dipicolinic acid were investigated in Alcaligenes faecalis strain JQ135. The present study opens a door to elucidate the mechanism of DPA degradation and its possible role in DPA-based carbon biotransformation on earth.
Topics: Alcaligenes faecalis; Bacillus; Carbon; Ferredoxins; Mixed Function Oxygenases; Multigene Family; Oxygenases; Picolinic Acids; Pyridines; Spores, Bacterial
PubMed: 35766505
DOI: 10.1128/aem.00360-22 -
Journal of Fungi (Basel, Switzerland) Jun 2022Simultaneous treatment with antagonistic bacteria (SF14), (ACBC1), and the food additive sodium bicarbonate (SBC) to control post-harvest brown rot disease caused by ,...
Simultaneous treatment with antagonistic bacteria (SF14), (ACBC1), and the food additive sodium bicarbonate (SBC) to control post-harvest brown rot disease caused by , and their effect on the post-harvest quality of nectarines were evaluated. Four concentrations of SBC (0.5, 2, 3.5, and 5%) were tested. Results showed that bacterial antagonists displayed remarkable compatibility with different concentrations of SBC and that their viability was not affected. The results obtained in vitro and in vivo bioassays showed a strong inhibitory effect of all treatments. The combination of each bacterial antagonist with SBC revealed a significant improvement in their biocontrol efficacies. The inhibition rates of mycelial growth ranged from 60.97 to 100%. These results also indicated that bacterial antagonists (SF14 or ACBC1) used at 1 × 10 CFU/ mL in combination with 2, 3.5, or 5% SBC significantly improved the control of by inhibiting the germination of spores. Interestingly, disease incidence and lesion diameter in fruits treated with SF14, ACBC1 alone, or in combination with SBC were significantly lower than those in the untreated fruits. In vivo results showed a significant reduction in disease severity ranging from 9.27 to 64.83% compared to the untreated control, while maintaining the appearance, firmness, total soluble solids (TSS), and titratable acidity (TA) of fruits. These results suggested that the improved disease control by the two antagonistic bacteria was more likely due to the additional inhibitory effects of SBC on the mycelial growth and spore germination of the pathogenic fungus. Overall, the combination of both bacteria with SBC provided better control of brown rot disease. Therefore, a mixture of different management strategies can effectively control brown rot decay on fruits.
PubMed: 35736119
DOI: 10.3390/jof8060636 -
Polymers Jun 2022Polyethylene and Polyester materials are resistant to degradation and a significant source of microplastics pollution, which is an emerging concern. In the present...
Polyethylene and Polyester materials are resistant to degradation and a significant source of microplastics pollution, which is an emerging concern. In the present study, the potential of a dumped site bacterial community was evaluated. After primary screening, it was observed that 68.5% were linear low-density polyethylene, 33.3% were high-density, and 12.9% were Polyester degraders. Five strains were chosen for secondary screening, in which they were monitored by FTIR, SEM and weight loss degradation trials. Major results were observed for (MK517568) and (MK517567), as they showed the highest degradation activity. (MK517568) degrades LLDPE by 3.5%, HDPE by 5.8% and Polyester by 17.3%. (MK517567) is better tolerated at 30 °C and degrades Polyester by 29%. Changes in infrared spectra indicated degradation pathways of different strains depending on the types of plastics targeted. Through SEM analysis, groves, piths and holes were observed on the surface. These findings suggest that soil bacteria develop an effective mechanism for degradation of microplastics and beads that enables them to utilize plastics as a source of energy without the need for pre-treatments, which highlights the importance of these soil bacteria for the future of effective plastic waste management in a soil environment.
PubMed: 35683947
DOI: 10.3390/polym14112275 -
Applied and Environmental Microbiology Jun 2022Picolinic acid (PA) is a natural toxic pyridine derivative as well as an important intermediate used in the chemical industry. In a previous study, we identified a gene...
Picolinic acid (PA) is a natural toxic pyridine derivative as well as an important intermediate used in the chemical industry. In a previous study, we identified a gene cluster, , that responsible for the catabolism of PA in Alcaligenes faecalis JQ135. However, the transcriptional regulation of the cluster remains known. This study showed that the entire cluster was composed of 17 genes and transcribed as four operons: , , , and . Deletion of , encoding a putative MarR-type regulator, greatly shortened the lag phase of PA degradation. An electrophoretic mobility shift assay and DNase I footprinting showed that PicR has one binding site in the - intergenic region and two binding sites in the - intergenic region. The DNA sequences of the three binding sites have the palindromic characteristics of TCAG-N-CTNN: the space consists of four nonspecific bases, and the four palindromic bases on the left and the first two palindromic bases on the right are strictly conserved, while the last two bases on the right vary among the three binding sites. An β-galactosidase activity reporter assay indicated that 6-hydroxypicolinic acid but not PA acted as a ligand of PicR, preventing PicR from binding to promoter regions and thus derepressing the transcription of the cluster. This study revealed the negative transcriptional regulation mechanism of PA degradation by PicR in JQ135 and provides new insights into the structure and function of the MarR-type regulator. The gene cluster was found to be responsible for PA degradation and widely distributed in , , and . Thus, it is very necessary to understand the regulation mechanism of the cluster in these strains. This study revealed that PicR binds to three sites of the promoter regions of the cluster to multiply regulate the transcription of the cluster, which enables JQ135 to efficiently utilize PA. Furthermore, the study also found a unique palindrome sequence for binding of the MarR-type regulator. This study enhanced our understanding of microbial catabolism of environmental toxic pyridine derivatives.
Topics: Alcaligenes faecalis; Bacterial Proteins; Binding Sites; DNA, Intergenic; Gene Expression Regulation, Bacterial; Multigene Family; Picolinic Acids; Protein Binding; Pyridines; Transcription Factors
PubMed: 35604228
DOI: 10.1128/aem.00172-22 -
Biology Mar 2022Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important...
Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism.
PubMed: 35453719
DOI: 10.3390/biology11040519 -
BMC Genomics Apr 2022Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment...
BACKGROUND
Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment strategies. Long-read sequencing platforms such as the Oxford Nanopore sequencer can improve genome assembly efficiency particularly when they are combined with short-read sequencing data.
RESULTS
Alcaligenes faecalis PGB1 was isolated and identified with resistance to penicillin and three other antibiotics. After being sequenced by Nanopore MinION and Illumina sequencer, its entire genome was hybrid-assembled. One chromosome and one plasmid was assembled and annotated with 4,433 genes (including 91 RNA genes). Function annotation and comparison between strains were performed. A phylogenetic analysis revealed that it was closest to A. faecalis ZD02. Resistome related sequences was explored, including ARGs, Insert sequence, phage. Two plasmid aminoglycoside genes were determined to be acquired ARGs. The main ARG category was antibiotic efflux resistance and β-lactamase (EC 3.5.2.6) of PGB1 was assigned to Class A, Subclass A1b, and Cluster LSBL3.
CONCLUSIONS
The present study identified the newly isolated bacterium A. faecalis PGB1 and systematically annotated its genome sequence and ARGs.
Topics: Alcaligenes faecalis; Anti-Bacterial Agents; High-Throughput Nucleotide Sequencing; Nanopores; Phylogeny; Prostaglandins B; Sequence Analysis, DNA
PubMed: 35443609
DOI: 10.1186/s12864-022-08507-7 -
Applied and Environmental Microbiology May 2022Pichia pastoris is widely used for the production of valuable recombinant proteins. An advantage of P. pastoris over other expression systems is that it secretes low...
Pichia pastoris is widely used for the production of valuable recombinant proteins. An advantage of P. pastoris over other expression systems is that it secretes low levels of endogenous proteins, which facilitates the purification processes if the desired recombinant proteins are efficiently secreted into the culture medium. However, not all recombinant proteins can be successfully secreted by P. pastoris, especially enzymes that are located in intracellular compartments in their native hosts. Few studies have reported strategies for releasing recombinant proteins which cannot be secreted by standard protocols. Here, we investigated whether this challenge can be addressed using novel secretion leaders. Analysis of the secretome and transcriptome of P. pastoris indicated that the four genes with the highest protein-to-transcript ratios were , , , and , suggesting that their gene products contain efficient secretion leaders. Our data revealed that the signal peptide derived from the gene product conferred secretion competence to certain industrial enzymes, e.g., a nitrilase of Alcaligenes faecalis ZJUTB10, a ribosylnicotinamide kinase of P. pastoris, and a glucose dehydrogenase of Exiguobacterium sibiricum. Therefore, the signal peptide derived from the gene product represents a novel secretion sequence for the secretory expression of recombinant enzymes in P. pastoris. Although P. pastoris is widely used for the secretory production of pharmaceutical proteins, its successful applications in the secretory production of industrial enzymes are limited. The α-mating factor pre-pro leader is the most widely used secretion signal in P. pastoris, but numerous industrial enzymes cannot be secreted using it. The importance of this study is that we identified a signal peptide derived from the gene product which conferred secretion competence to three-quarters of the enzymes tested. This signal peptide derived from the gene product may facilitate the application of P. pastoris in industrial biocatalysis.
Topics: Pichia; Protein Sorting Signals; Recombinant Proteins; Saccharomycetales
PubMed: 35435711
DOI: 10.1128/aem.00296-22 -
Vaccines Mar 2022This study involved therapeutic targets mining for the extremely drug-resistant bacterial species called , which is known to infect humans. The infections caused by this...
This study involved therapeutic targets mining for the extremely drug-resistant bacterial species called , which is known to infect humans. The infections caused by this species in different parts of the human body have been linked with a higher degree of resistance to several classes of antibiotics. Meanwhile, alternate therapeutic options are needed to treat these bacterial infections in clinical settings. In the current study, a subtractive proteomics approach was adapted to annotate the whole proteome of and prioritize target proteins for vaccine-related therapeutics design. This was followed by targeted protein-specific immune epitope prediction and prioritization. The shortlisted epitopes were further subjected to structural design and in silico validation of putative vaccines against . The final vaccine designs were also evaluated for potential interaction analysis with human TLR-2 through molecular docking. Finally, the putative vaccines were subjected to in silico cloning and immune simulation approaches to ensure the feasibility of the target-specific vaccine constructs in further experimental designs.
PubMed: 35335094
DOI: 10.3390/vaccines10030462 -
Microbiology Resource Announcements Apr 2022Alcaligenes faecalis is an opportunistic pathogen exhibiting drug resistance. Here, the 35,451-bp genome of phage Piluca is described. Piluca is not closely related to...
Alcaligenes faecalis is an opportunistic pathogen exhibiting drug resistance. Here, the 35,451-bp genome of phage Piluca is described. Piluca is not closely related to any isolated phages in the NCBI database. Piluca possesses genes encoding CI-like and Cro-like repressors and a tyrosine integrase, suggesting its temperate lifestyle.
PubMed: 35289650
DOI: 10.1128/mra.00124-22