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Scientific Reports May 2022The aim of this study was to evaluate an effect of short and medium chain carboxylic acids (CAs) rich stream derived from acidogenic mixed culture fermentation of acid...
The aim of this study was to evaluate an effect of short and medium chain carboxylic acids (CAs) rich stream derived from acidogenic mixed culture fermentation of acid whey on polyhydroxyalkanoates (PHAs) synthesis by Paracoccus homiensis and compare it with the impact of individual synthetic CAs. The obtained results confirmed that the analyzed bacterium is able to metabolize synthetic CAs as the only carbon sources in the growth medium with maximum PHAs production yields of 26% of cell dry mass (CDM). The replacement of the individual CAs by a CAs-rich residual stream was found to be beneficial for the Paracoccus homiensis growth. The highest biomass concentration reached about 2.5 g/L with PHAs content of 17% of CDM. The purified PHAs were identified as poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by applying gas chromatography coupled with mass spectrometry, Fourier transform infrared spectroscopic spectra and UV-Vis spectra. Furthermore, a differential scanning calorimetric, thermogravimetric and water contact angle analysis proved that the extracted copolymers have useful properties. The obtained data are promising in the perspective of developing a microbial PHAs production as a part of an integrated valorization process of high CAs content waste-derived streams.
Topics: Acids; Carboxylic Acids; Culture Media; Gas Chromatography-Mass Spectrometry; Paracoccus; Polyhydroxyalkanoates
PubMed: 35508573
DOI: 10.1038/s41598-022-11114-x -
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 -
BMC Cardiovascular Disorders Jul 2022Little is known about the association between bacterial DNA in human blood and the risk of cardiovascular disease (CVD) mortality.
BACKGROUND
Little is known about the association between bacterial DNA in human blood and the risk of cardiovascular disease (CVD) mortality.
METHODS
A case-cohort study was performed based on a 9 ½ year follow-up of the Oslo II study from 2000. Eligible for this analysis were men born in 1923 and from 1926 to 1932. The cases were men (n = 227) who had died from CVD, and the controls were randomly selected participants from the same cohort (n = 178). Analysis of the bacterial microbiome was performed on stored frozen blood samples for both cases and controls. Association analyses for CVD mortality were performed by Cox proportional hazard regression adapted to the case-cohort design. We used the Bonferroni correction due to the many bacterial genera that were identified.
RESULTS
Bacterial DNA was identified in 372 (82%) of the blood samples and included 78 bacterial genera from six phyla. Three genera were significantly associated with CVD mortality. The genera Kocuria (adjusted hazard ratio (HR) 8.50, 95% confidence interval (CI) (4.05, 17.84)) and Enhydrobacter (HR 3.30 (2.01, 5.57)) indicate an association with CVD mortality with increasing levels. The genera Paracoccus (HR 0.29 (0.15, 0.57)) was inversely related. Significant predictors of CVD mortality were: the feeling of bad health; and the consumption of more than three cups of coffee per day. The following registered factors were borderline significant, namely: a history of heart failure; increased systolic blood pressure; and currently taking antihypertensive drugs now, versus previously.
CONCLUSIONS
The increasing levels of two bacterial genera Kocuria (skin and oral) and Enhydrobacter (skin) and low levels of Paracoccus (soil) were associated with CVD mortality independent of known risk factors for CVD.
Topics: Aged, 80 and over; Cardiovascular Diseases; Cohort Studies; DNA, Bacterial; Female; Humans; Male; Microbiota; Proportional Hazards Models; Risk Factors
PubMed: 35909117
DOI: 10.1186/s12872-022-02791-7 -
The Journal of Biological Chemistry 2021Heme oxygenases (HOs) play a critical role in recouping iron from the labile heme pool. The acquisition and liberation of heme iron are especially important for the...
Heme oxygenases (HOs) play a critical role in recouping iron from the labile heme pool. The acquisition and liberation of heme iron are especially important for the survival of pathogenic bacteria. All characterized HOs, including those belonging to the HugZ superfamily, preferentially cleave free b-type heme. Another common form of heme found in nature is c-type heme, which is covalently linked to proteinaceous cysteine residues. However, mechanisms for direct iron acquisition from the c-type heme pool are unknown. Here we identify a HugZ homolog from the oligopeptide permease (opp) gene cluster of Paracoccus denitrificans that lacks any observable reactivity with heme b and show that it instead rapidly degrades c-type hemopeptides. This c-type heme oxygenase catalyzes the oxidative cleavage of the model substrate microperoxidase-11 at the β- and/or δ-meso position(s), yielding the corresponding peptide-linked biliverdin, CO, and free iron. X-ray crystallographic analysis suggests that the switch in substrate specificity from b-to c-type heme involves loss of the N-terminal α/β domain and C-terminal loop containing the coordinating histidine residue characteristic of HugZ homologs, thereby accommodating a larger substrate that provides its own iron ligand. These structural features are also absent in certain heme utilization/storage proteins from human pathogens that exhibit low or no HO activity with free heme. This study thus expands the scope of known iron acquisition strategies to include direct oxidative cleavage of heme-containing proteolytic fragments of c-type cytochromes and helps to explain why certain oligopeptide permeases show specificity for the import of heme in addition to peptides.
Topics: Bacterial Proteins; Biliverdine; Catalysis; Crystallography, X-Ray; Heme; Heme Oxygenase (Decyclizing); Iron; Membrane Transport Proteins; Paracoccus denitrificans; Substrate Specificity
PubMed: 33862082
DOI: 10.1016/j.jbc.2021.100666 -
Life (Basel, Switzerland) Mar 2023The beneficial effects of balneotherapy have been proven by numerous clinical studies on locomotor disorders. To date, there is only scant data on changes in the...
The beneficial effects of balneotherapy have been proven by numerous clinical studies on locomotor disorders. To date, there is only scant data on changes in the microbiome system of the skin during balneotherapy. The aim of this study was to compare the effects of thermal water and tap water on the skin's microbiome in healthy volunteers. 30 healthy female volunteers participated in the study. The experimental group (of 15 women) spent 30-min 10 times, in Gabriella Spring's thermal baths (i.e., mineral water containing sodium hydrogen carbonate).The controlled group (15 women) had the same, but in tap water. The results of this study have proven that there is a difference in the influencing effects of tap water and medicinal water on the microbiome of the skin. After bathing in the thermal water of Lakitelek, increased significantly at the genus level, and the tendency for bacteria also increased. At the species level, increased significantly, while and the tendency for decreased. When the values of the two trial groups after bathing at the genus level were compared, increased significantly, while tended to increase, tended to decrease, tended to increase significantly, and tended to decrease. At the species level, decreased significantly, and the tendency for decreased. The growth of and the decrease in the tendency of , and confirm the beneficial effect of balneotherapy. In this study, trends are represented by the uncorrected value. The main result was that the thermal water changed certain bacteria of the skin, both on the genus and species levels, but there were no significant changes in the tap water used, either at the genus or species level. We first compared the worlds of thermal water and tap water's microbiome systems. The thermal water decreased the number of certain inflammatory infectious agents and could enhance some of their positive effects, which have been proven at the molecular level. Our results can provide an important clue in the treatment of certain skin diseases. The research of the skin microbiome during balneotherapy can be one of the most intriguing and exciting topics of the future and can bring us closer to understanding the mechanism of action of balneotherapy.
PubMed: 36983902
DOI: 10.3390/life13030746 -
Applied and Environmental Microbiology Apr 2022Partitioning systems ensure the stable inheritance of bacterial low-copy-number replicons, such as chromosomes, chromids, and megaplasmids. These loci consist of two...
Partitioning systems ensure the stable inheritance of bacterial low-copy-number replicons, such as chromosomes, chromids, and megaplasmids. These loci consist of two genes encoding partition proteins A and B, and at least one centromere-like sequence. In chromids and megaplasmids, partitioning systems are often located in the vicinity of replication systems. An extreme example of this co-localization are alphaproteobacterial replicons, where the partition () and replication () genes form a single operon, with sequences usually positioned in close proximity to these genes. In this study, we characterized a more complex system found in Paracoccus aminophilus () megaplasmid pAMI4 (438 kb). Besides the operon with a single site, this replicon has a 2-kb non-coding locus positioned 11.5 kb downstream of , which contains three additional repeats (). We demonstrated that is bound by partition protein B and is essential for proper pAMI4 partitioning . In search of similar loci, we conducted a comparative analysis of distribution in other replicons. This revealed different patterns of localization in and . However, in both these taxonomic orders, sites are almost always located inside or close to the operon. No other -like loci were found in the closest relatives of pAMI4. Another evolutionarily-independent example of such a locus was identified as a conserved feature in chromosome 2 of Allorhizobium vitis and related replicons. The replication/partitioning loci are widespread in extrachromosomal replicons of . They are evolutionarily diverse, subject to multi-layer self-regulation, and are responsible for the maintenance of different types of replicons, such as plasmids (e.g., pTi and pRi tumorigenic and rhizogenic plasmids), megaplasmids (e.g., pSymA and pSymB) and essential chromids (e.g., secondary chromosomes of , Brucella and ). In this study, we functionally analyzed an atypical partition-related component of systems, the locus, found in the megaplasmid pAMI4. We also identified centromere-like site distribution patterns in different groups of replicons and found other unrelated -like loci, which had been overlooked. Our findings raise questions concerning the biological reasons for differential distribution, which may reflect variations in operon regulation as well as different replication and partition modes of replicons belonging to the family.
Topics: Alphaproteobacteria; Bacterial Proteins; Centromere; Plasmids; Replicon
PubMed: 35389251
DOI: 10.1128/aem.00207-22 -
Microbiology Spectrum Sep 2023Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the...
Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the environment and human health. Although microbial degradation methods have been widely applied, some issues remain, including low degradation efficiency and poor environmental adaptability. In this regard, constructing efficient degrading bacteria by metabolic engineering is an ideal solution to these challenges. In this study, we used DYTN-1, a superior nitrogen removal environment strain, as chassis to construct an SMX degradation pathway, obtaining a new bacteria for simultaneous degradation of SMX and removal of ammonia nitrogen. In doing this, we first identified and characterized four native promoters of DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. After degradation pathway expression level optimization and FMN reductase optimization, SMX degradation efficiency was significantly improved. The constructed pIAB-P strain exhibited superior co-degradation of SMX and ammonia nitrogen contaminants with degradation rates of 44% and 71%, respectively. This study could pave the way for SMX degradation engineered strain design and evolution of environmental bioremediation. IMPORTANCE The abuse of sulfamethoxazole (SMX) had led to an increased accumulation in the environment, resulting in the disruption of the structure of microbial communities, further disrupting the bio-degradation process of other pollutants, such as ammonia nitrogen. To solve this challenge, we first identified and characterized four native promoters of DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. Then SMX degradation efficiency was significantly improved with degradation pathway expression level optimization and FMN reductase optimization. Finally, the superior nitrogen removal environment strain, DYTN-1, obtained an SMX degradation function. This pioneering study of metabolic engineering to enhance the SMX degradation in microorganisms could pave the way for designing the engineered strains of SMX and nitrogen co-degradation and the environmental bioremediation.
PubMed: 37732744
DOI: 10.1128/spectrum.00146-23 -
Microbiological Research Jan 2021The endophytic bacteria were isolated from coffee roots and seeds in Vietnam and identified with 16S rDNA sequencing as belonging to the Actinobacteria, Firmicutes and...
The endophytic bacteria were isolated from coffee roots and seeds in Vietnam and identified with 16S rDNA sequencing as belonging to the Actinobacteria, Firmicutes and Proteobacteria phyla with the Nocardia, Bacillus and Burkholderia as dominant genera, respectively. Out of the thirty genera recovered from Coffea canephora and Coffea liberica, twelve were reported for the first time in endophytic association with coffee including members of the genera Brachybacterium, Caballeronia, Kitasatospora, Lechevalieria, Leifsonia, Luteibacter, Lysinibacillus, Mycolicibacterium, Nakamurella, Paracoccus, Sinomonas and Sphingobium. A total of eighty bacterial endophytes were characterized in vitro for several plant growth promoting and biocontrol traits including: the phosphate solubilization, the indolic compounds, siderophores, HCN, esterase, lipase, gelatinase and chitinase production. A subset of fifty selected bacteria were tested for their potential as biocontrol agents with in vitro confrontations with the fungal pathogen Fusarium oxysporum as well as the coffee parasitic nematodes Radopholus duriophilus and Pratylenchus coffeae. The three most efficient isolates on F. oxysporum belonging to the Bacillus, Burkholderia, and Streptomyces genera displayed a growth inhibition rate higher than 40%. Finally, five isolates from the Bacillus genus were able to lead to 100% of mortality in 24 h on both R. duriophilus and P. coffeae.
Topics: Antifungal Agents; Antinematodal Agents; Bacteria; Biological Control Agents; Coffea; Coffee; DNA, Ribosomal; Endophytes; Fungi; Fusarium; Phylogeny; Plant Development; Plant Diseases; Plant Roots; RNA, Ribosomal, 16S
PubMed: 33070050
DOI: 10.1016/j.micres.2020.126613 -
Journal of Microbiology and... Apr 2021The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in...
The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in Chengdu, China. , a ubiquitously distributed and extensively applied Chinese herb, was also chosen for experiment. Total genome DNA was extracted from leaf samples, and for metagenome sequencing, an Illumina HiSeq 2500 platform was applied. The results showed that the gene numbers of phyllosphere microbiota derived from haze leaves were lower than those of the clean control. The phyllosphere microbiota derived from both haze and clean groups shared the same top ten phyla; the abundances of Proteobacteria, Actinomycetes and Anorthococcuso of the haze group were substantially increased, while Ascomycetes and Basidiomycetes decreased. At the genus level, the abundances of , , and from haze leaves were markedly increased, while the yeasts were statistically decreased. KEGG retrieval demonstrated that the functional genes were most annotated to metabolism. An interesting find of this work is that the phyllosphere microbiota responsible for the synthesis of primary and secondary metabolites in were significantly increased under a haze environment. Relatively enriched genes annotated by eggNOG belong to replication, recombination and repair, and genes classified into the glycoside hydrolase and glycosyltransferase enzymes were significantly increased. In summary, we found that both structure and function of phyllosphere microbiota are globally impacted by haze, while primary and secondary metabolites responsible for haze tolerance were considerably increased. These results suggest an adaptive strategy of plants for tolerating and confronting haze damage.
Topics: Air Pollution; Artemisia; Bacteria; China; Fungi; Metagenome; Microbiota; Plant Leaves; Secondary Metabolism
PubMed: 33746186
DOI: 10.4014/jmb.2009.09024 -
Frontiers in Microbiology 2021Harmful algal blooms caused by frequently occur worldwide and severely threaten the marine environment. In this study, the biochemical and physiological responses of...
Harmful algal blooms caused by frequently occur worldwide and severely threaten the marine environment. In this study, the biochemical and physiological responses of to the algicidal bacterium O-4 were investigated, and the effects on the levels of reactive oxygen species (ROS), malondialdehyde content, multiple antioxidant systems and metabolites, photosynthetic pigments, and photosynthetic index were examined. The cell-free supernatant in strain O-4 significantly inhibited cell growth. The bacterium caused the cells to activate their antioxidant defenses to mitigate ROS, and this effect was accompanied by the upregulation of intracellular antioxidant enzymes and non-enzyme systems. However, the overproduction of ROS induced lipid peroxidation and oxidative damage within cells, ultimately leading to algal death. In addition, the photosynthetic efficiency of the algal cells was significantly inhibited by O-4 and was accompanied by a reduction in photosynthetic pigments. This study indicates that O-4 inhibits through excessive oxidative stress and impaired photosynthesis. This research into the biochemical and physiological responses of to algicidal bacteria provides insights into the prophylaxis and control of harmful algal blooms interactions between harmful algae and algicidal bacteria.
PubMed: 34917053
DOI: 10.3389/fmicb.2021.771381