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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 -
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 -
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 -
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 -
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 -
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 -
Marine Drugs Mar 2023Astaxanthin (3,3-dihydroxy-β, β-carotene-4,4-dione) is a ketocarotenoid synthesized by , , , , , , some bacteria (), yeasts, and lobsters, among others However, it is... (Review)
Review
Astaxanthin (3,3-dihydroxy-β, β-carotene-4,4-dione) is a ketocarotenoid synthesized by , , , , , , some bacteria (), yeasts, and lobsters, among others However, it is majorly synthesized by alone (about 4%). The richness of natural astaxanthin over synthetic astaxanthin has drawn the attention of industrialists to cultivate and extract it via two stage cultivation process. However, the cultivation in photobioreactors is expensive, and converting it in soluble form so that it can be easily assimilated by our digestive system requires downstream processing techniques which are not cost-effective. This has made the cost of astaxanthin expensive, prompting pharmaceutical and nutraceutical companies to switch over to synthetic astaxanthin. This review discusses the chemical character of astaxanthin, more inexpensive cultivating techniques, and its bioavailability. Additionally, the antioxidant character of this microalgal product against many diseases is discussed, which can make this natural compound an excellent drug to minimize inflammation and its consequences.
Topics: Antioxidants; Biological Availability; Xanthophylls; Carotenoids; Chlorophyceae
PubMed: 36976225
DOI: 10.3390/md21030176 -
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 -
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 -
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