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Journal of Clinical Periodontology Jul 2023To characterize the subgingival microbiome in subjects with different periodontal health statuses. (Observational Study)
Observational Study
AIM
To characterize the subgingival microbiome in subjects with different periodontal health statuses.
MATERIALS AND METHODS
In this cross-sectional observational study, subgingival samples were harvested from Spanish subjects with different periodontal health statuses, based on the 2018 Classification of Periodontal and Peri-Implant Diseases and Conditions. Samples were processed using high-throughput sequencing technologies (Illumina MiSeq). Taxa differentially abundant were identified using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). α- and β-diversity metrics were calculated using q2-diversity in QIIME2. The analyses were adjusted for age, gender and smoking status.
RESULTS
The identified subgingival microbiome showed statistically significant differences among subjects, categorized into periodontal health, gingivitis and stages I-II and III-IV periodontitis (p < .05). In patients with severe (stages III-IV) periodontitis, the genera Filifactor and Fretibacterium were detected 24 times more frequently than in periodontally healthy subjects. Similarly, the genera Porphyromonas, Prevotella and Tannerella were detected four times more frequently (p < .05). The genera Granulicatella, Streptococcus, Paracoccus, Pseudomonas, Haemophilus, Actinobacteria, Bergeyella and Capnocytophaga were significantly associated with healthier periodontal status (p < .05).
CONCLUSIONS
Significant differences were detected in the subgingival microbiome among periodontal health, gingivitis and stages I-II or III-IV periodontitis, suggesting overlapping, yet distinguishable microbial profiles.
Topics: Humans; Cross-Sectional Studies; Periodontitis; Gingivitis; Bacteria; Microbiota; RNA, Ribosomal, 16S
PubMed: 36792073
DOI: 10.1111/jcpe.13793 -
Applied Microbiology and Biotechnology Jun 2024Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene... (Review)
Review
Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene terephthalate) (PET). Recently, the use of EG as a starting material for the production of bio-fuels or bio-chemicals is gaining attention as a sustainable process since EG can be derived from materials not competing with human food stocks including CO, syngas, lignocellulolytic biomass, and PET waste. In order to design and construct microbial process for the conversion of EG to value-added chemicals, microbes capable of catabolizing EG such as Escherichia coli, Pseudomonas putida, Rhodococcus jostii, Ideonella sakaiensis, Paracoccus denitrificans, and Acetobacterium woodii are candidates of chassis for the construction of synthetic pathways. In this mini-review, we describe EG catabolic pathways and catabolic enzymes in these microbes, and further review recent advances in microbial conversion of EG to value-added chemicals by means of metabolic engineering. KEY POINTS: • Ethylene glycol is a potential next-generation feedstock for sustainable industry. • Microbial conversion of ethylene glycol to value-added chemicals is gaining attention. • Ethylene glycol-utilizing microbes are useful as chassis for synthetic pathways.
Topics: Ethylene Glycol; Metabolic Engineering; Metabolic Networks and Pathways; Bacteria; Pseudomonas putida; Biofuels; Escherichia coli
PubMed: 38861200
DOI: 10.1007/s00253-024-13179-2 -
Scientific Reports Sep 2023Gut microbiota is an emerging editable cardiovascular risk factor. We aim to investigate gut and coronary plaque microbiota, using fecal samples and angioplasty balloons...
Gut microbiota is an emerging editable cardiovascular risk factor. We aim to investigate gut and coronary plaque microbiota, using fecal samples and angioplasty balloons from patients with acute coronary syndrome (ACS), chronic coronary syndrome (CCS) and control subjects. We examined bacterial communities in gut and coronary plaques by 16S rRNA sequencing and we performed droplet digital PCR analysis to investigate the gut relative abundance of the bacterial genes CutC/CntA involved in trimethylamine N-oxide synthesis. Linear discriminant analysis effect size (LEfSe) at the genus and species levels displayed gut enrichment in Streptococcus, Granulicatella and P. distasonis in ACS compared with CCS and controls; Roseburia, C. aerofaciens and F. prausnitzii were more abundant in controls than in patients. Principal component analysis (PCA) of 41 differentially abundant gut taxa showed a clustering of the three groups. In coronary plaque, LEfSe at the genus level revealed an enrichment of Staphylococcus and Streptococcus in ACS, and Paracoccus in CCS, whereas PCA of 15 differentially abundant plaque taxa exhibited clustering of ACS and CCS patients. CutC and CntA genes were more abundant in ACS and CCS than in controls while no significant difference emerged between ACS and CCS. Our results indicate that ACS and CCS exhibit a different gut and plaque microbial signature, suggesting a possible role of these microbiotas in coronary plaque instability.
Topics: Humans; Acute Coronary Syndrome; RNA, Ribosomal, 16S; Heart; Angioplasty, Balloon; Carnobacteriaceae
PubMed: 37679428
DOI: 10.1038/s41598-023-41867-y -
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 -
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 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 -
Archives of Biochemistry and Biophysics Jun 2024Paracoccus denitrificans has a classical cytochrome-dependent electron transport chain and two alternative oxidases. The classical transport chain is very similar to...
Paracoccus denitrificans has a classical cytochrome-dependent electron transport chain and two alternative oxidases. The classical transport chain is very similar to that in eukaryotic mitochondria. Thus, P. denitrificans can serve as a model of the mammalian mitochondrion that may be more tractable in elucidating mechanisms of regulation of energy production than are mitochondria. In a previous publication we reported detailed studies on respiration in P. denitrificans grown aerobically on glucose or malate. We noted that P. denitrificans has large stores of lactate under various growth conditions. This is surprising because P. denitrificans lacks an NAD-dependent lactate dehydrogenase. The aim of this study was to investigate the mechanisms of lactate oxidation in P. denitrificans. We found that the bacterium grows well on either d-lactate or l-lactate. Growth on lactate supported a rate of maximum respiration that was equal to that of cells grown on glucose or malate. We report proteomic, metabolomic, and biochemical studies that establish that the metabolism of lactate by P. denitrificans is mediated by two non-NAD-dependent lactate dehydrogenases. One prefers d-lactate over l-lactate (D-iLDH) and the other prefers l-lactate (L-iLDH). We cloned and produced the D-iLDH and characterized it. The K for d-lactate was 34 μM, and for l-lactate it was 3.7 mM. Pyruvate was not a substrate, rendering the reaction unidirectional with lactate being converted to pyruvate for entry into the TCA cycle. The intracellular lactate was ∼14 mM such that both isomers could be metabolized by the enzyme. The enzyme has 1 FAD per molecule and utilizes a quinone rather than NAD as an electron acceptor. D-iLDH provides a direct entry of lactate reducing equivalents into the cytochrome chain, potentially explaining the high respiratory capacity of P. denitrificans in the presence of lactate.
Topics: Paracoccus denitrificans; Oxidation-Reduction; Lactic Acid; Glucose
PubMed: 38631502
DOI: 10.1016/j.abb.2024.109988 -
Environmental Research Nov 2023The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for...
The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.
Topics: Petroleum; Ecosystem; Sewage; Soil Pollutants; Soil Microbiology; RNA, Ribosomal, 16S; Bacteria; Biodegradation, Environmental; Soil; Genetic Variation
PubMed: 37517495
DOI: 10.1016/j.envres.2023.116779 -
Current Microbiology Apr 2024A novel Paracoccus-related strain, designated YLB-12, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The...
A novel Paracoccus-related strain, designated YLB-12, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The novel strain is a Gram-stain-negative, short, rod-shaped, nonmotile, catalase- and oxidase-positive strain that grows at 10-37 °C and pH 5.0-9.0 in the presence of 0-12.0% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain belongs to the genus Paracoccus and that its highest sequence similarity was to Paracoccus homiensis DD-R11 (98.5%), followed by Paracoccus zeaxanthinifaciens ATCC 21588 (97.4%), Paracoccus rhizosphaerae LMG 26205 (97.2%), Paracoccus beibuensis CGMCC 1.7295 (97.1%) and Paracoccus halotolerans CFH 90064 (97.0%). The DNA‒DNA hybridization values between strain YLB-12 and the five closely related type strains ranged from 20.4 to 22.4%. The genomic G+C content of strain YLB-12 was 63.7%. In addition to diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol, the polar lipids of the strain YLB-12 also consisted of an unidentified glycolipid and four unidentified polar lipids. The cells contained summed feature 8 (Cω6c /Cω7c, 62.7%) as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. On the basis of its phenotypic and genotypic characteristics, strain YLB-12 represents a novel species within the genus Paracoccus, for which the name Paracoccus maritimus sp. nov. is proposed. The type strain was YLB-12 (= MCCC 1A17213 = KCTC 82197).
Topics: Phylogeny; RNA, Ribosomal, 16S; Fatty Acids; Paracoccus; DNA
PubMed: 38592513
DOI: 10.1007/s00284-024-03637-5 -
International Journal of Systematic and... Aug 2023Strain designated TK19116 was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China. The bacterium was Gram-stain-negative, aerobic,...
Strain designated TK19116 was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China. The bacterium was Gram-stain-negative, aerobic, oxidase-positive and catalase-positive. Cells of the strain TK19116 were short-rod-shaped and non-motile. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain TK19116 belonged to the genus , with the highest sequence similarity to 4-2 (97.1 %). The average nucleotide identity values between the strain TK19116 with 4-2, J6, M26 and BM15 were 75.3, 76.7, 76.7 and 75.8%, respectively. The digital DNA-DNA hybridization value between the strain TK19116 with 4-2, J6, M26 and BM15 were 19.7, 20.3, 20.5 and 20.0%, respectively. The main respiratory quinone of strain TK19116 was ubiquinone 10. The polar lipids include aminolipid, phosphatidylcholine, diphosphatidylglycerol, glycolipid, phosphatidylglycerol and phospholipid. The principal fatty acid of strain TK19116 was summed feature 8 (C 6 and/or C 7). The G+C content of the chromosomal DNA was 64.2 %. The combination of the results of the phylogenetic, phenotypic and chemotaxonomic analysis, strain TK19116 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TK19116 (= MCCC 1K08025=JCM 35527).
Topics: Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Base Composition; Bacterial Typing Techniques; Sequence Analysis, DNA; Phospholipids; Paracoccus
PubMed: 37535057
DOI: 10.1099/ijsem.0.005998