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Microbial Cell Factories Feb 2024To contribute to the discovery of new microbial strains with metabolic and physiological robustness and develop them into successful chasses, Paracoccus pantotrophus DSM...
BACKGROUND
To contribute to the discovery of new microbial strains with metabolic and physiological robustness and develop them into successful chasses, Paracoccus pantotrophus DSM 2944, a Gram-negative bacterium from the phylum Alphaproteobacteria and the family Rhodobacteraceae, was chosen. The strain possesses an innate ability to tolerate high salt concentrations. It utilizes diverse substrates, including cheap and renewable feedstocks, such as C1 and C2 compounds. Also, it can consume short-chain alkanes, predominately found in hydrocarbon-rich environments, making it a potential bioremediation agent. The demonstrated metabolic versatility, coupled with the synthesis of the biodegradable polymer polyhydroxyalkanoate, positions this microbial strain as a noteworthy candidate for advancing the principles of a circular bioeconomy.
RESULTS
The study aims to follow the chassis roadmap, as depicted by Calero and Nikel, and de Lorenzo, to transform wild-type P. pantotrophus DSM 2944 into a proficient SynBio (Synthetic Biology) chassis. The initial findings highlight the antibiotic resistance profile of this prospective SynBio chassis. Subsequently, the best origin of replication (ori) was identified as RK2. In contrast, the non-replicative ori R6K was selected for the development of a suicide plasmid necessary for genome integration or gene deletion. Moreover, when assessing the most effective method for gene transfer, it was observed that conjugation had superior efficiency compared to electroporation, while transformation by heat shock was ineffective. Robust host fitness was demonstrated by stable plasmid maintenance, while standardized gene expression using an array of synthetic promoters could be shown. pEMG-based scarless gene deletion was successfully adapted, allowing gene deletion and integration. The successful integration of a gene cassette for terephthalic acid degradation is showcased. The resulting strain can grow on both monomers of polyethylene terephthalate (PET), with an increased growth rate achieved through adaptive laboratory evolution.
CONCLUSION
The chassis roadmap for the development of P. pantotrophus DSM 2944 into a proficient SynBio chassis was implemented. The presented genetic toolkit allows genome editing and therewith the possibility to exploit Paracoccus for a myriad of applications.
Topics: Humans; Paracoccus pantotrophus; Prospective Studies; Plasmids; Paracoccus; Biodegradation, Environmental
PubMed: 38360576
DOI: 10.1186/s12934-024-02325-0 -
Dermatology (Basel, Switzerland) 2024Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection...
INTRODUCTION
Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection of skin lesions is common, and Staphylococcus aureus commonly colonizes these lesions. The aim of the study was to characterize the bacterial microbiome of cutaneous Darier lesions compared to normal-looking skin and disease severity.
METHODS
All patients with a history of Darier followed up at Emek Medical Center were invited to participate in the study. Patients that did not use antibiotics in the past month and signed informed consent had four skin sites sampled with swabs: scalp, chest, axilla, and palm. All samples were analyzed for bacterial microbiome using 16S rDNA sequencing.
RESULTS
Two hundred and eighty microbiome samples obtained from lesional and non-lesional skin of the scalp, chest, axilla, and palm of 42 Darier patients were included in the analysis. The most abundant bacterial genera across all skin sites were Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, and Anaerococcus. Scalp and chest lesions featured a distinct microbiome configuration that was mainly driven by an overabundance of Staphylococci species. Patients with more severe disease exhibited microbiome alterations in the chest, axilla, and palm compared with patients with only mild disease, driven by Peptoniphilus and Moryella genera in scalp and palmar lesions, respectively.
CONCLUSION
Staphylococci were significantly associated with Darier lesions and drove Darier-associated dysbiosis. Severity of the disease was associated with two other bacterial genera. Whether these associations also hold a causative role and may serve as a therapeutic target remains to be determined and requires further investigation.
Topics: Humans; Darier Disease; Male; Female; Dysbiosis; Adult; Middle Aged; Microbiota; Axilla; Skin; Corynebacterium; Young Adult; Propionibacterium; Micrococcus; Severity of Illness Index; Hand; Thorax; Scalp; Aged; Adolescent
PubMed: 38330926
DOI: 10.1159/000537714 -
MSystems Mar 2024Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for...
Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence. species, especially , were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL. co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example sp., sp., , , sp., sp., , , , and , in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.
Topics: Adult; Humans; Dermatitis, Atopic; Staphylococcus aureus; RNA, Ribosomal, 16S; Microbiota; Metabolome; Bacteria; Dipeptides
PubMed: 38319107
DOI: 10.1128/msystems.01119-23 -
Journal of Oleo Science 2024The effects of microwave drying conditions of a Paracoccus carotinifaciens culture solution on astaxanthin Z-isomerization and degradation were investigated. The...
The effects of microwave drying conditions of a Paracoccus carotinifaciens culture solution on astaxanthin Z-isomerization and degradation were investigated. The microwave drying significantly increase the ratio of astaxanthin Z-isomers, and the higher the microwave power and the longer the drying time, the higher the total Z-isomer ratio of astaxanthin, but such conditions also accelerated astaxanthin degradation. We found that the addition of powdered oils enhanced the Z-isomerization reaction. For example, when the P. carotinifaciens culture solution was dried at 1000 W power for 5 min without and with powdered rapeseed oil, total Z-isomer ratios of astaxanthin in resulting dried powder were 14.9 and 47.4%, respectively. Furthermore, the storage test of the dried P. carotinifaciens powder showed that astaxanthin Z- isomers were stable at 4℃ in a low-oxygen atmosphere. As astaxanthin Z-isomers have greater bioavailability and potentially exhibit superior biological activities than the all-E-isomer, the dried P. carotinifaciens powder obtained by the method of this study is expected to be used as a value-added astaxanthin source.
Topics: Isomerism; Microwaves; Powders; Paracoccus; Xanthophylls
PubMed: 38311406
DOI: 10.5650/jos.ess23093 -
Heliyon Jan 2024The cotton mealybug, Tinsley and papaya mealybug, Williams and Granara de Willink (Hemiptera: Pseudococcidae) are becoming major threats to the production of R. Br....
The cotton mealybug, Tinsley and papaya mealybug, Williams and Granara de Willink (Hemiptera: Pseudococcidae) are becoming major threats to the production of R. Br. (Asclepiadaceae) in India. Management mainly depends on chemical insecticides which cause a serious problem of pesticide residue and insecticide resistance. The use of biorational insecticides such as biopesticides, botanicals, insect growth regulators, and microbial insecticides is important components of an Integrated Pest Management (IPM) program for successful management. We evaluated the bio-efficacy of twelve biorational insecticides, including entomopathogenic fungi (EPF), using the leaf spray method in laboratory conditions at 25 ± 1 °C, 70 % ± 5 % RH. The results revealed that the highest percent mortality was recorded by acetamiprid 20 % SP (100.00 %), followed by azadirachtin (98.27 %), (2 × 10 spores/mL) (85.70 %) and leaf extract (76.87 %) at 120 h after treatment (HAT) in . In , 100.00 %, 96.39 % and 85.67 % and 74.90 % mortalities were achieved by acetamiprid 20 % SP, azadirachtin, (2 × 10 spores/mL) and leaf extract, respectively, at 120 HAT during the first spray. Various biorational insecticides showed a more or less similar trend of percent mortality in both species during the second spray. In both species, the lowest percent mortality was recorded by leaf extract (46.29, 44.54) and (41.03, 46.39) at 120 Hours after treatment in the first and second spray, respectively. It was concluded that all the prescribed treatments are more effective than the control. Overall, azadirachtin recorded the highest percent mortality after acetamiprid and had the shortest LT (12.52 h) and (13.87 h) values in and , respectively. Our study emphasizes that biopesticides like Azadirachtin 1 % EC (10000 ppm), (2 × 10 spores/mL) (5 mL/L) and leaf extract (5 %) may be recommended as alternatives to synthetic insecticides. Botanicals and EPF would be the most effective approach for sustainable integrated management of and in the ecosystem.
PubMed: 38187271
DOI: 10.1016/j.heliyon.2023.e23648 -
MSystems Feb 2024A genome scale metabolic model of the bacterium has been constructed. The model containing 972 metabolic genes, 1,371 reactions, and 1,388 unique metabolites has been...
A genome scale metabolic model of the bacterium has been constructed. The model containing 972 metabolic genes, 1,371 reactions, and 1,388 unique metabolites has been reconstructed. The model was used to carry out quantitative predictions of biomass yields on 10 different carbon sources under aerobic conditions. Yields on C1 compounds suggest that formate is oxidized by a formate dehydrogenase O, which uses ubiquinone as redox co-factor. The model also predicted the threshold methanol/mannitol uptake ratio, above which ribulose biphosphate carboxylase has to be expressed in order to optimize biomass yields. Biomass yields on acetate, formate, and succinate, when NO is used as electron acceptor, were also predicted correctly. The model reconstruction revealed the capability of to grow on several non-conventional substrates such as adipic acid, 1,4-butanediol, 1,3-butanediol, and ethylene glycol. The capacity to grow on these substrates was tested experimentally, and the experimental biomass yields on these substrates were accurately predicted by the model.IMPORTANCE has been broadly used as a model denitrifying organism. It grows on a large portfolio of carbon sources, under aerobic and anoxic conditions. These characteristics, together with its amenability to genetic manipulations, make a promising cell factory for industrial biotechnology. This paper presents and validates the first functional genome-scale metabolic model for , which is a key tool to enable as a platform for metabolic engineering and industrial biotechnology. Optimization of the biomass yield led to accurate predictions in a broad scope of substrates.
Topics: Paracoccus denitrificans; Bacteria; Oxidation-Reduction; Carbon; Formates
PubMed: 38180324
DOI: 10.1128/msystems.01077-23 -
PloS One 2023The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is...
The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
Topics: Paracoccus; DNA Transposable Elements; Genomics; Genomic Islands; Phylogeny; Genome, Bacterial
PubMed: 38117845
DOI: 10.1371/journal.pone.0287947 -
Environmental Microbiology Reports Feb 2024Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this...
Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this phenomenon is well-established, its consequences on ecological and evolutionary processes remain poorly understood. We hypothesize here that denitrification in oxic environments can modify the accumulation profiles of nitrogen oxide intermediates with cascading effects on the evolutionary potentials of denitrifying microorganisms. To test this, we performed laboratory experiments with Paracoccus denitrificans and complemented them with individual-based computational modelling. We found that denitrification in low oxic environments significantly increases the accumulation of nitrite and nitric oxide. We further found that the increased accumulation of these intermediates has a negative effect on growth at low pH. Finally, we found that the increased negative effect at low pH increases the number of individuals that contribute to surface-associated growth. This increases the amount of genetic diversity that is preserved from the initial population, thus increasing the number of genetic targets for natural selection to act upon and resulting in higher evolutionary potentials. Together, our data highlight that denitrification in low oxic environments can affect the ecological processes and evolutionary potentials of denitrifying microorganisms by modifying the accumulation of nitrogen oxide intermediates.
Topics: Humans; Nitric Oxide; Denitrification; Nitrites; Nitrous Oxide; Nitrogen
PubMed: 38037543
DOI: 10.1111/1758-2229.13221 -
Journal of Microbiology and... Jan 2024The study objective was to evaluate the potential production of polyhydroxyalkanoates (PHAs), a biodegradable plastic material, by for which PHA production has never...
The study objective was to evaluate the potential production of polyhydroxyalkanoates (PHAs), a biodegradable plastic material, by for which PHA production has never been reported. To identify the most effective nitrogen-limited culture conditions for PHAs production from this bacterium, batch fermentation using glucose concentrations ranging from 4 g l to 20 g l with a fixed ammonium concentration of 0.5 g l was carried out at 30°C and pH 8.0. A glucose supplement of 12 g l produced the highest PHA concentration (1.6 g l) and PHA content (0.63 g g) thereby identifying the optimal condition for PHA production from this bacterium. Gas chromatography-mass spectrometry analysis suggests that mostly produced copolymer types of poly(3-hydroxybutyrate--3-hydroxyvalerate) [P(3HB--3HV)] from glucose concentrations at 12 g l or higher under the nitrogen-limited conditions. When several other single carbon sources were evaluated for the most efficient PHA production, fructose provided the highest biomass (2.8 g l), and PHAs (1.29 g l) concentrations. Results indicated that this bacterium mostly produced the copolymers P(3HB--3HV) from single carbon sources composing a range of 93-98% of 3-hydroxybutyrate and 2-7% of 3-hydroxyvalerate, whereas mannose-supplemented conditions produced the only homopolymer type of P(3HB). However, when propionic acid as a secondary carbon source were supplemented into the media, produced the copolymer P(3HB--3HV), composed of a 50% maximum monomeric unit of 3-hydroxyvaleric acid (3HV). However, as the concentration of propionic acid increased, cell biomass and PHAs concentrations substantially decreased due to cell toxicity.
Topics: Polyesters; Carbon; Hydroxybutyrates; Polyhydroxyalkanoates; Glucose; Nitrogen; Polyhydroxybutyrates; Paracoccus; Pentanoic Acids; Propionates
PubMed: 37997264
DOI: 10.4014/jmb.2305.05025 -
Frontiers in Microbiology 2023The microorganisms associated with a plant influence its growth and fitness. These microorganisms accumulate on the aerial and root surfaces of plants, as well as within...
The microorganisms associated with a plant influence its growth and fitness. These microorganisms accumulate on the aerial and root surfaces of plants, as well as within the plants, as endophytes, although how the interaction between microorganisms protects the plant from pathogens is still little understood. In the current study, the impact of assembled the bacterial communities against the pathogenic fungus to promote L. growths was investigated. We established a model of bacterium-fungus-plant system. Eight bacterial strains and a fungal pathogen (Glo) were isolated from wild roots and leaves, respectively. We assembled the six-bacteria community (C6: , sp., sp., sp., sp., and sp.) with inhibition, and eight-bacteria community (C8) composing of C6 plus another two bacteria ( and sp.) without inhibition against Glo in individually dual culture assays. Inoculation of seedlings with C8 significantly reduced impact of Glo. The growth and disease suppression of seedlings inoculated with C8 + Glo were significantly better than those of seedlings inoculated with only Glo. C8 had more inhibitory effects on Glo, and also enhanced the contents of four metabolites in seedling roots compared to Glo treatment only. Additionally, the inhibitory effects of root extracts from seedlings showed that Glo was most sensitive, the degree of eight bacteria sensitivity were various with different concentrations. Our findings suggested that the non-inhibitory bacteria played a vital role in the bacterial community composition and that some bacterial taxa were associated with disease suppression. The construction of a defined assembled bacterial community could be used as a biological fungicide, promoting biological disease control of plants.
PubMed: 37876787
DOI: 10.3389/fmicb.2023.1218474