-
Microorganisms Apr 2022Cytochrome oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form... (Review)
Review
Cytochrome oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form water in a reaction coupled to energy conservation. The three-subunit core of the enzyme is conserved, whereas several proteins identified to function in the biosynthesis of the common family A1 cytochrome oxidase show diversity in bacteria. Using the model organisms , , , and , the present review focuses on proteins for assembly of the heme , heme , Cu, and Cu metal centers. The known biosynthesis proteins are, in most cases, discovered through the analysis of mutants. All proteins directly involved in cytochrome oxidase assembly have likely not been identified in any organism. Limitations in the use of mutants to identify and functionally analyze biosynthesis proteins are discussed in the review. Comparative biochemistry helps to determine the role of assembly factors. This information can, for example, explain the cause of some human mitochondrion-based diseases and be used to find targets for new antimicrobial drugs. It also provides information regarding the evolution of aerobic bacteria.
PubMed: 35630371
DOI: 10.3390/microorganisms10050926 -
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 -
Microbes and Environments 2022Bacteria communicate through signaling molecules that coordinate group behavior. Hydrophobic signals that do not diffuse in aqueous environments are used as signaling...
Bacteria communicate through signaling molecules that coordinate group behavior. Hydrophobic signals that do not diffuse in aqueous environments are used as signaling molecules by several bacteria. However, limited information is currently available on the mechanisms by which these molecules are transported between cells. Membrane vesicles (MVs) with diverse functions play important roles in the release and delivery of hydrophobic signaling molecules, leading to differences in the dynamics of signal transportation from those of free diffusion. Studies on Paracoccus denitrificans, which produces a hydrophobic long-chain N-acyl homoserine lactone (AHL), showed that signals were loaded into MVs at a concentration with the potential to trigger the quorum sensing (QS) response with a "single shot" to the cell. Furthermore, stimulating the formation of MVs increased the release of signals from the cell; therefore, a basic understanding of MV formation is important. Novel findings revealed the formation of MVs through different routes, resulting in the production of different types of MVs. Methods such as high-speed atomic force microscopy (AFM) phase imaging allow the physical properties of MVs to be analyzed at a nanometer resolution, revealing their heterogeneity. In this special minireview, we introduce the role of MVs in bacterial communication and highlight recent findings on MV formation and their physical heterogeneity by referring to our research. We hope that this minireview will provide basic information for understanding the functionality of MVs in ecological systems.
Topics: Acyl-Butyrolactones; Biological Transport; Quorum Sensing; Ecosystem
PubMed: 36504177
DOI: 10.1264/jsme2.ME22083 -
Frontiers in Public Health 2021Disinfection is a key element in controlling infections. Fogging, also known as fumigation, is one of the most effective chemical disinfection methods. Peracetic acid...
Disinfection is a key element in controlling infections. Fogging, also known as fumigation, is one of the most effective chemical disinfection methods. Peracetic acid (PAA) is a powerful oxidant with bactericidal and fungicidal properties. The aim of this study is to determine the type of bacteria and fungi present in educational institutions and whether disinfection by PAA fumigation in these institutions is also effective and useful, as demonstrated previously in healthcare centers. This study was carried out in five kindergartens and five primary schools in Bialystok, Poland. Three rooms have been selected in each of these educational institutions, and the disinfection was carried out in 30 rooms in total. Fogging with PAA was performed in selected rooms. Before and after disinfection, samples were collected from four surfaces: walls, tables, doors, and chair backs. Most frequently detected microorganisms in schools and kindergartens were ssp. . In addition, ssp. were the most prevalent in kindergartens, whereas was the most prevalent in schools. Comparison of the bacterial flora of schools and kindergartens showed statistically significant differences in the prevalence of bacteria on different surfaces. A significant decrease in the number of colonies after disinfection was observed on all surfaces ( < 0.05). In addition, the calculated effectiveness of disinfection was 99.7% in kindergartens and 99.3% in schools. The results indicate that fogging of PAA is a highly effective method of surface disinfection in kindergartens and schools.
Topics: Acinetobacter; Actinobacteria; Micrococcaceae; Paracoccus; Peracetic Acid; Schools; Staphylococcus
PubMed: 34604154
DOI: 10.3389/fpubh.2021.697917 -
Bioresource Technology Jun 2022This study demonstrates effects of sulfamethoxazole (SMX) on carbon-nitrogen transformation pathways and microbial community and metabolic function response mechanisms...
This study demonstrates effects of sulfamethoxazole (SMX) on carbon-nitrogen transformation pathways and microbial community and metabolic function response mechanisms in constructed wetlands. Findings showed co-metabolism of SMX with organic pollutants resulted in high removal of 98.92 ± 0.25% at influent concentrations of 103.08 ± 13.70 μg/L (SMX) and 601.92 ± 22.69 mg/L (COD), and 2 d hydraulic retention. Microbial community, co-occurrence networks, and metabolic pathways analyses showed SMX promoted enrichment of COD and SMX co-metabolizing bacteria like Mycobacterium, Chryseobacterium and Comamonas. Relative abundances of co-metabolic pathways like Amino acid, carbohydrate, and Xenobiotics biodegradation and metabolism were elevated. SMX also increased relative abundances of the resistant heterotrophic nitrification-aerobic denitrification bacteria Paracoccus and Comamonas and functional genes nxrA, narI, norC and nosZ involved in simultaneous heterotrophic nitrification-aerobic denitrification. Consequently, denitrification rate increased by 1.30 mg/(L∙d). However, insufficient reaction substrate and accumulation of 15.29 ± 2.30 mg/L NO-N exacerbate inhibitory effects of SMX on expression of some denitrification genes.
Topics: Anti-Bacterial Agents; Bacteria; Carbon; Denitrification; Microbiota; Nitrification; Nitrogen; Sulfamethoxazole; Wastewater; Wetlands
PubMed: 35470002
DOI: 10.1016/j.biortech.2022.127217 -
Antonie Van Leeuwenhoek May 2024A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6, was isolated from a natural wetland reserve in Hebei...
A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25-37 °C (optimum, 30 °C), pH 5-9 (optimum, pH 7), and in the presence of 1.0-4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6 belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2 with 98.1% similarity, Paracoccus fontiphilus MVW-1 (97.9%), Paracoccus everestensis S8-55 (97.7%), Paracoccus subflavus GY0581 (97.6%), Paracoccus sediminis CMB17 (97.3%), Paracoccus caeni MJ17 (97.0%), and Paracoccus angustae E6 (97.0%). The genome size of strain EF6 was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6 and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C ω6c and/or C ω7c) and C (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6 displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6 possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6 a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6 is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6 (= GDMCC 1.3400 = JCM 35642 = MCCC 1K08702).
Topics: Wetlands; Phylogeny; Paracoccus; RNA, Ribosomal, 16S; Fatty Acids; Base Composition; DNA, Bacterial; China; Sodium Selenite; Bacterial Typing Techniques; Phospholipids; Sequence Analysis, DNA; Nucleic Acid Hybridization; Oxidation-Reduction; Drug Resistance, Bacterial
PubMed: 38777900
DOI: 10.1007/s10482-024-01969-7 -
PloS One 2021Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage...
Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage between biofilms and bacteremia in patients with ECMO, an improved understanding of the microbial community within catheter biofilms is necessary. Hence, we aimed to evaluate the biofilm microbiome of ECMO catheters from adults with (n = 6) and without (n = 15) bacteremia. The microbiomes of the catheter biofilms were evaluated by profiling the V3 and V4 regions of bacterial 16s rRNA genes using the Illumina MiSeq sequencing platform. In total, 2,548,172 reads, with an average of 121,341 reads per sample, were generated. Although alpha diversity was slightly higher in the non-bacteremic group, the difference was not statistically significant. In addition, there was no difference in beta diversity between the two groups. We found 367 different genera, of which 8 were present in all samples regardless of group; Limnohabitans, Flavobacterium, Delftia, Massilia, Bacillus, Candidatus, Xiphinematobacter, and CL0-1 showed an abundance of more than 1% in the sample. In particular, Arthrobacter, SMB53, Neisseria, Ortrobactrum, Candidatus Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were highly abundant in the bacteremic group. Network analysis indicated that the microbiome of the bacteremic group was more complex than that of the non-bacteremic group. Flavobacterium and CL0.1, which were abundant in the bacteremic group, were considered important genera because they connected different subnetworks. Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia. There were no significant differences in diversity between the two groups, but there were significant differences in the community composition of the biofilms. The biofilm-associated community was dynamic, with the bacteremic group showing very complex network connections within the microbiome.
Topics: Arthrobacter; Bacteremia; Bacteria; Biofilms; Catheter-Related Infections; Extracorporeal Membrane Oxygenation; Female; Humans; Male; Microbiota; Middle Aged; Neisseria; RNA, Ribosomal, 16S; Retrospective Studies
PubMed: 34529734
DOI: 10.1371/journal.pone.0257449 -
Current Microbiology Dec 2021A novel strain, wg2, was isolated from activated sludge obtained from wastewater treatment plant in Shandong province, China. The bacterium was Gram-strain-negative,...
A novel strain, wg2, was isolated from activated sludge obtained from wastewater treatment plant in Shandong province, China. The bacterium was Gram-strain-negative, aerobic, rod-shaped, non-flagellated and non-gliding. This bacterium was characterized to determine its taxonomic position using the polyphasic approach. Strain wg2 grew at 25-45 °C (optimum, 30 °C), at salinities of 0-7.0% (w/v) NaCl (optimum, 0-2.0%) and at pH 7-9 (optimum, pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain wg2 clustered with species of genus Paracoccus and shares high similarities with Paracoccus sediminis DSM 26170 (98.1%) and Paracoccus fontiphilus MVW-1 (97.7%), respectively. The genome size of strain wg2 was 3.93 Mbp and the DNA G + C content was 66.05%. The dDDH values and ANI between strain wg2 and each of reference strains P. sediminis DSM 26170, P. fontiphilus MVW-1 and P. denitrificans DSM 413 were 18.3, 12.5, 24.5% and 85.3, 87.0, 78.4%, respectively. The major respiratory quinone was found to be Q-10 and the major fatty acid was C ω7c. The polar lipids consisted of aminoglycolipid (AGL), phosphatidylcholine (PC), glycolipid (GL), phosphatidylserine (PS), phosphatidylglycerol phosphate (PGP), aminophospholipids (APL). Combining above descriptions, strain wg2 should represent a novel species of genus Paracoccus, for which the name Paracoccus shandongensis sp. nov., is proposed. The type strain is wg2 (= KCTC 72862 = CCTCC AB 2019401).
Topics: Bacterial Typing Techniques; China; DNA, Bacterial; Fatty Acids; Paracoccus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage
PubMed: 34905098
DOI: 10.1007/s00284-021-02705-4 -
Current Microbiology Feb 2021Strain YIM 132242, isolated from lichen collected from Pu'er, Yunnan Province, China, was short-rod-shaped, Gram-reaction-negative, aerobic, catalase- and...
Strain YIM 132242, isolated from lichen collected from Pu'er, Yunnan Province, China, was short-rod-shaped, Gram-reaction-negative, aerobic, catalase- and oxidase-positive. Growth of the strain was occurred at 10-39 °C (optimum, 28-35 °C), at pH 4.0-10.0 (optimum, pH 7.0-8.0) and at salinities of 0-8% (w/v) NaCl (optimum, 0-2%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM 132242 belonged to the genus Paracoccus and had the highest levels of sequence similarity to Paracoccus aerius KCTC 42845 (97.0% similarity), Paracoccus sediminis CMB17 (96.8% similarity), and Paracoccus fontiphilus MVW-1 (96.4% similarity). The major fatty acid was identified as C ω7c (77.6%). The predominant respiratory quinone was ubiquinone-10 (Q-10). Polar lipid analysis indicated the presence of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), an unidentified lipid (L), and three unidentified phospholipids (PL1-PL3). Based on the draft genome sequence, the DNA G + C content of the strain was 67.1 mol%, and the values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of strain YIM 132242 with Paracoccus aerius KCTC 42845 were 85.4% and 29.1%, respectively. On the basis of the data from this polyphasic characterization, strain YIM 132242 represents a novel species of the genus Paracoccus, for which the name Paracoccus lichenicola sp. nov. is proposed. The type strain is YIM 132242 (= KCTC 72463 = CGMCC1.17191).
Topics: Bacterial Typing Techniques; China; DNA, Bacterial; Fatty Acids; Lichens; Paracoccus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33388938
DOI: 10.1007/s00284-020-02321-8 -
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