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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 -
Ecotoxicology and Environmental Safety Dec 2021Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their...
Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their potentially negative environmental impacts. Recently, the degradability of neonicotinoid in soil has gained more attentions. However, what role soil microbes play in this degradation remains vastly underexplored. In this study, we compared the capacity of soil microbes sampled from different geographic regions and fields to degrade the neonicotinoid insecticide imidacloprid. Additionally, the composition of microbiota having low, middle, and high degradation activity was analyzed via high throughput sequencing. Correlations between microbiota composition and degradation activities were analyzed and reconfirmed. The results showed that the composition of soil microbiota and their degradation activity (ranged from zero to 96.25%) varied significantly between soil samples from different geographic locations. Correlation analysis showed that Paracoccus and Achromobacter bacteria were positively correlated with high degradation activity. Imidacloprid degradation experiments using these bacteria showed that Achromobacter sp. alone exhibited degradation activity reaching and sustaining 100% by day 20 while Paracoccus sp. did not. However, combining these bacteria resulted in increased degradation activity which reached 100% at day 15 relative to that achieved by Achromobacter sp. alone. This study demonstrated the capacity of soil microbes to degrade imidacloprid, and identified two promising bacterial candidates that could be potentially used in future to reduce imidacloprid accumulation in soils.
Topics: Achromobacter; Bacteria; Biodegradation, Environmental; Insecticides; Neonicotinoids; Nitro Compounds; Paracoccus; Soil; Soil Microbiology; Soil Pollutants
PubMed: 34544021
DOI: 10.1016/j.ecoenv.2021.112785 -
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 -
Bioscience, Biotechnology, and... Sep 2019Bacteria can communicate through diffusible signaling molecules that are perceived by cognate receptors. It is now well established that bacterial communication... (Review)
Review
Bacteria can communicate through diffusible signaling molecules that are perceived by cognate receptors. It is now well established that bacterial communication regulates hundreds of genes. Hydrophobic molecules which do not diffuse in aqueous environments alone have been identified in bacterial communication, that raised the question on how these molecules are transported between cells and trigger gene expressions. Recent studies show that these hydrophobic signaling molecules, including a long-chain -acyl homoserine lactone signal produced in , are carried by membrane vesicles (MVs). MVs were thought to be formed only through the blebbing of the cell membrane, but new findings in and revealed that different types of MVs can be formed through explosive cell lysis or bubbling cell death, which findings have certain implications on our view of bacterial interactions.
Topics: 4-Butyrolactone; Bacterial Physiological Phenomena; Cell Membrane; Hydrophobic and Hydrophilic Interactions; Quorum Sensing; Signal Transduction
PubMed: 31021698
DOI: 10.1080/09168451.2019.1608809 -
Journal of Applied Microbiology Jun 2022The genus Paracoccus represents a taxonomically diverse group comprising more than 80 novel species isolated from various pristine and polluted environments. The species... (Review)
Review
The genus Paracoccus represents a taxonomically diverse group comprising more than 80 novel species isolated from various pristine and polluted environments. The species are characterized as coccoid-shaped Gram-negative bacteria with versatile metabolic attributes and classified as autotrophs, heterotrophs and/or methylotrophs. The present study highlights the up-to-date global taxonomic diversity and critically discusses the significance of genome analysis for identifying the genomic determinants related to functional attributes mainly bioplastic synthesis and biodegradation potential that makes these isolates commercially viable. The analysis accentuates polyphasic and genomic attributes of Paracoccus spp. which could be harnessed for commercial applications and emphasizes the need of integrating genome-based computational analysis for evolutionary species and functional diversification. The work reflects on the underexplored genetic potential for bioplastic synthesis which can be harnessed using advanced genomic methods. It also underlines the degradation potential and possible use of naturally-occurring pollutant-degrading Paracoccus isolates for the development of a biodegradation system and efficient removal of contaminants. The work contemplates plausible use of such potent isolates to establish the plant-microbe interaction, contributing toward contaminated land reclamation. Overall, the work signifies the need and application of genome analysis to identify and explore the prospective potential of Paracoccus spp. for environmental application toward achieving sustainability.
Topics: Bacterial Typing Techniques; Biodegradation, Environmental; DNA, Bacterial; Fatty Acids; Genomics; Paracoccus; Phylogeny; Prospective Studies; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Xenobiotics
PubMed: 35294092
DOI: 10.1111/jam.15530 -
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 -
Applied Microbiology and Biotechnology Mar 2020Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked... (Review)
Review
Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked eye, and biofilm formation is a tightly regulated process. Paracoccus denitrificans is a non-motile, Gram-negative bacterium that forms a very thin, unique biofilm. A key factor in the biofilm formed by this bacterium is a large surface protein named biofilm-associated protein A (BapA), which was recently reported to be regulated by cyclic diguanosine monophosphate (cyclic-di-GMP or c-di-GMP). Cyclic-di-GMP is a major second messenger involved in biofilm formation in many bacteria. Though cyclic-di-GMP is generally reported as a positive regulatory factor in biofilm formation, it represses biofilm formation in P. denitrificans. Furthermore, quorum sensing (QS) represses biofilm formation in this bacterium, which is also reported as a positive regulator of biofilm formation in most bacteria. The QS signal used in P. denitrificans is hydrophobic and is delivered through membrane vesicles. Studies on QS show that P. denitrificans can potentially form a thick biofilm but maintains a thin biofilm under normal growth conditions. In this review, we discuss the peculiarities of biofilm formation by P. denitrificans with the aim of deepening the overall understanding of bacterial biofilm formation and functions.
Topics: Bacterial Proteins; Biofilms; Cyclic GMP; Gene Expression Regulation, Bacterial; Membrane Proteins; Paracoccus denitrificans; Quorum Sensing
PubMed: 32002601
DOI: 10.1007/s00253-020-10400-w -
Applied and Environmental Microbiology Aug 2021Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as...
Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, sp. 363 and sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of sp. 363 carries three synthase genes and transcribes genes along three PHA pathways (I to III), whereas sp. 392 carries only one gene and transcribes genes along one pathway (I). Thus, sp. 363 has a versatile repertoire of genes and pathways enabling production of both short- and medium-chain-length PHA products. Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, sp. 363 and sp. 392, are able to produce various types of PHA from inexpensive carbon sources. sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.
Topics: Bacterial Proteins; Cold Temperature; Genome, Bacterial; Halomonas; Ice Cover; Paracoccus; Phylogeny; Polyhydroxyalkanoates; Seawater; Temperature
PubMed: 34160268
DOI: 10.1128/AEM.00929-21 -
Frontiers in Endocrinology 2023The female reproductive tract harbours unique microbial communities (known as microbiota) which have been associated with reproductive functions in health and disease....
INTRODUCTION
The female reproductive tract harbours unique microbial communities (known as microbiota) which have been associated with reproductive functions in health and disease. While endometrial microbiome studies have shown that the uterus possesses higher bacterial diversity and richness compared to the vagina, the knowledge regarding the composition of the Fallopian tubes (FT) is lacking, especially in fertile women without any underlying conditions.
METHODS
To address this gap, our study included 19 patients who underwent abdominal hysterectomy for benign uterine pathology, and 5 women who underwent tubal ligation as a permanent contraceptive method at Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA). We analyzed the microbiome of samples collected from the FT and endometrium using 16S rRNA gene sequencing.
RESULTS
Our findings revealed distinct microbiome profiles in the endometrial and FT samples, indicating that the upper reproductive tract harbors an endogenous microbiome. However, these two sites also shared some similarities, with 69% of the detected taxa Being common to both. Interestingly, we identified seventeen bacterial taxa exclusively present in the FT samples, including the genera , and , among others. On the other hand, 10 bacterial taxa were only found in the endometrium, including the genera and (FDR <0.05). Furthermore, our study highlighted the influence of the endometrial collection method on the findings. Samples obtained transcervically showed a dominance of the genus Lactobacillus, which may indicate potential vaginal contamination. In contrast, uterine samples obtained through hysterescopy revealed higher abundance of the genera , and .
DISCUSSION
Although the upper reproductive tract appears to have a low microbial biomass, our results suggest that the endometrial and FT microbiome is unique to each individual. In fact, samples obtained from the same individual showed more microbial similarity between the endometrium and FT compared to samples from different women. Understanding the composition of the female upper reproductive microbiome provides valuable insights into the natural microenvironment where processes such as oocyte fertilization, embryo development and implantation occur. This knowledge can improve fertilization and embryo culture conditions for the treatment of infertility.
Topics: Female; Humans; RNA, Ribosomal, 16S; Uterus; Endometrium; Vagina; Infertility; Bacteria
PubMed: 37415669
DOI: 10.3389/fendo.2023.1096050