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Nature Reviews. Microbiology Dec 2020Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by... (Review)
Review
Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by a lipid bilayer (such as thylakoids, magnetosomes and anammoxosomes), whereas others are defined by a lipid monolayer (such as lipid bodies), a proteinaceous coat (such as carboxysomes) or have a phase-defined boundary (such as nucleolus-like compartments). These diverse organelles have various metabolic and physiological functions, facilitating adaptation to different environments and driving the evolution of cellular complexity. This Review highlights that, despite the diversity of reported organelles, some unifying concepts underlie their formation, structure and function. Bacteria have fundamental mechanisms of organelle formation, through which conserved processes can form distinct organelles in different species depending on the proteins recruited to the luminal space and the boundary of the organelle. These complex subcellular compartments provide evolutionary advantages as well as enabling metabolic specialization, biogeochemical processes and biotechnological advances. Growing evidence suggests that the presence of organelles is the rule, rather than the exception, in bacterial cells.
Topics: Bacterial Proteins; Caulobacter crescentus; Cell Compartmentation; Cell Engineering; Desulfovibrio; Escherichia coli; Macromolecular Substances; Magnetosomes; Magnetospirillum; Organelle Biogenesis; Organelles; Shewanella putrefaciens; Species Specificity
PubMed: 32710089
DOI: 10.1038/s41579-020-0413-0 -
Cells Jun 2023Multiple sclerosis (MS) is a chronic, progressive neuroinflammatory disease with a complex pathophysiological background. A variety of diverse factors have been... (Review)
Review
Multiple sclerosis (MS) is a chronic, progressive neuroinflammatory disease with a complex pathophysiological background. A variety of diverse factors have been attributed to the propagation of inflammation and neurodegeneration in MS, mainly genetic, immunological, and environmental factors such as vitamin D deficiency, infections, or hormonal disbalance. Recently, the importance of the gut-brain axis for the development of many neurological conditions, including stroke, movement disorders, and neuroinflammatory disorders, has been postulated. The purpose of our paper was to summarize current evidence confirming the role of the gut microbiome in the pathophysiology of MS and related disorders, such as neuromyelitis optica spectrum disorder (NMO-SD). For this aim, we conducted a systematic review of the literature listed in the following databases: Medline, Pubmed, and Scopus, and were able to identify several studies demonstrating the involvement of the gut microbiome in the pathophysiology of MS and NMO-SD. It seems that the most relevant bacteria for the pathophysiology of MS are those belonging to , , , , , , , and , while and have been demonstrated to play a role in the pathophysiology of NMO-SD. Following this line of evidence, there is also some preliminary data supporting the use of probiotics or other agents affecting the microbiome that could potentially have a beneficial effect on MS/NMO-SD symptoms and prognosis. The topic of the gut microbiome in the pathophysiology of MS is therefore relevant since it could be used as a biomarker of disease development and progression as well as a potential disease-modifying therapy.
Topics: Humans; Multiple Sclerosis; Gastrointestinal Microbiome; Neuromyelitis Optica; Vitamin D Deficiency; Inflammation
PubMed: 37443793
DOI: 10.3390/cells12131760 -
Nature Reviews. Microbiology Dec 2021The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these... (Review)
Review
The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.
Topics: Anaerobiosis; Bacteria, Anaerobic; Bacteroides; Clostridium; Desulfovibrio; Hydrogen Peroxide; Oxygen; Pyrococcus; Reactive Oxygen Species; Superoxides
PubMed: 34183820
DOI: 10.1038/s41579-021-00583-y -
Cells Mar 2022Several bacterial species can generate hydrogen sulfide (HS). Study evidence favors the view that the microbiome of the colon harbors increased amounts of HS producing... (Review)
Review
Several bacterial species can generate hydrogen sulfide (HS). Study evidence favors the view that the microbiome of the colon harbors increased amounts of HS producing bacteria in Parkinson's disease. Additionally, HS can easily penetrate cell membranes and enter the cell interior. In the cells, excessive amounts of HS can potentially release cytochrome c protein from the mitochondria, increase the iron content of the cytosolic iron pool, and increase the amount of reactive oxygen species. These events can lead to the formation of alpha-synuclein oligomers and fibrils in cells containing the alpha-synuclein protein. In addition, bacterially produced HS can interfere with the body urate metabolism and affect the blood erythrocytes and lymphocytes. Gut bacteria responsible for increased HS production, especially the mucus-associated species of the bacterial genera belonging to the Desulfovibrionaceae and Enterobacteriaceae families, are likely play a role in the pathogenesis of Parkinson's disease. Special attention should be devoted to changes not only in the colonic but also in the duodenal microbiome composition with regard to the pathogenesis of Parkinson's disease. Influenza infections may increase the risk of Parkinson's disease by causing the overgrowth of HS-producing bacteria both in the colon and duodenum.
Topics: Bacteria; Humans; Hydrogen Sulfide; Iron; Parkinson Disease; alpha-Synuclein
PubMed: 35326429
DOI: 10.3390/cells11060978 -
Clinical and Experimental Rheumatology Jan 2024To assess whether there is a bidirectional causal relationship between the composition of gut microbiota and rheumatoid arthritis (RA), and to identify specific...
OBJECTIVES
To assess whether there is a bidirectional causal relationship between the composition of gut microbiota and rheumatoid arthritis (RA), and to identify specific pathogenic bacterial taxa via the Mendelian randomisation (MR) analysis.
METHODS
We acquired single nucleotide polymorphisms (SNPs) associated with the composition of gut microbiota (n=18,340) and with RA (n=331,313) from publicly available genome-wide association studies (GWAS). The genome-wide threshold was 1 × 10-5 in the forward MR analysis and was 5 × 10-8 in the reverse MR analysis. Inverse variance weighted (IVW) was the main method to analyse causality, and MR results were verified by several sensitivity analyses including weighted median, MR Egger, and MR Pleiotropy Residual Sum and Outlier (PRESSO).
RESULTS
The IVW method suggested that eight taxa were positively correlated with RA, including: MollicutesRF9 (pIVW <0.01), Alphaproteobacteria (pIVW <0.01), Betaproteobacteria (p IVW =0.04), Bacteroidaceae (pIVW <0.01), Adlercreutzia (pIVW <0.01), Bacteroides (pIVW <0.01), Butyricimonas (p IVW =0.03) and Holdemanella (pIVW =0.03). Six bacterial taxa were negatively correlated with RA, including Desulfovibrionales (pIVW = 0.01), Methanobacteriales (pIVW <0.01), Methanobacteria (PIVW <0.01), Desulfovibrionaceae (pIVW <0.01), Methanobacteriaceae (pIVW <0.01) and Butyrivibrio (pIVW =0.02). Heterogeneity (p>0.05) and pleiotropy (p>0.05) analysis confirmed the robustness of the MR results.
CONCLUSIONS
We identified some specific bacterial taxa that were causally associated with the risk of RA, providing new insights into prevention and diagnosis of RA.
Topics: Humans; Gastrointestinal Microbiome; Genome-Wide Association Study; Arthritis, Rheumatoid; Polymorphism, Single Nucleotide
PubMed: 37812479
DOI: 10.55563/clinexprheumatol/p9ig7c -
Age and Ageing Jul 2023observational studies have indicated that gut microbiome dysbiosis was associated with Alzheimer's disease (ad). However, the results are largely inconsistent and it... (Observational Study)
Observational Study
BACKGROUND
observational studies have indicated that gut microbiome dysbiosis was associated with Alzheimer's disease (ad). However, the results are largely inconsistent and it remains unknown whether the association is causal in nature.
METHODS
leveraging observational studies and genome-wide association studies (GWAS) on the gut microbiome in ad patients, we pooled the microbiome data (N = 1,109) to screen the microbiota significantly altered in ad patients and then conducted Mendelian randomisation (MR) study to determine the causal associations between altered microbiota (N = 18,340) and ad using two different ad GWAS datasets (N = 63,926 and N = 472,868) using the inverse variance-weighted (IVW) method.
RESULTS
the combined effect sizes from observational studies showed that 8 phyla, 18 classes, 22 orders, 37 families, 78 genera and 109 species significantly changed in ad patients. Using the MR analysis, we found that two classes, one order, one family and one genus were suggestively associated with ad consistently in two different GWAS datasets. Both observational studies and MR analysis simultaneously showed that Desulfovibrionales (order) and Desulfovibrionaceae (family), which were mainly implicated in dissimilatory sulfate reduction, were significantly associated with an elevated risk of ad.
CONCLUSIONS
our findings demonstrated that the abundance of sulfate-reducing bacteria was increased in ad patients, which was causally linked to an increased risk of ad. Further efforts are warranted to clarify the underlying mechanisms, which will provide new insight into the prevention and treatment of ad.
Topics: Humans; Alzheimer Disease; Bacteria; Genome-Wide Association Study; Microbiota; Polymorphism, Single Nucleotide; Sulfates; Mendelian Randomization Analysis
PubMed: 37466641
DOI: 10.1093/ageing/afad112 -
FEMS Microbiology Ecology Feb 2022Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some...
Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8, or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Increasing formate concentrations delayed the onsets of growth and sulfate reduction of D. multivorans, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.
Topics: Desulfovibrio; Formates; Microbiota; Oxidation-Reduction; Sulfates
PubMed: 35040992
DOI: 10.1093/femsec/fiac003 -
Journal of Alzheimer's Disease : JAD 2022Epidemiological studies that investigate alterations in gut microbial composition associated with cognitive dysfunction are limited.
BACKGROUND
Epidemiological studies that investigate alterations in gut microbial composition associated with cognitive dysfunction are limited.
OBJECTIVE
To examine the association between the gut microbiota and subjective memory complaints (SMCs), a self-reported, validated indicator of cognitive dysfunction.
METHODS
In this cross-sectional study of 95 older women selected from the New York University Women's Health Study (NYUWHS), we characterized the gut microbial composition using 16S rRNA gene sequencing. We estimated odds ratio (OR) from beta regression which approximates the ratio of mean relative abundances of individual bacterial taxon from phylum to genus levels by binary (2+ versus < 2) and continuous SMCs.
RESULTS
Women reporting 2 or more SMCs had higher relative abundances of genus Holdemania and family Desulfovibrionaceae compared with those reporting one or no complaint. Compared with women with < 2 SMCs, the relative abundances of Holdemania and family Desulfovibrionaceae were 2.09 times (OR: 2.09, 95% confidence interval [CI]: 1.38-3.17) and 2.10 times (OR: 2.10, 95% CI: 1.43-3.09) higher in women with 2+ SMCs, respectively (false discovery rate (FDR)-adjusted p = 0.038 and 0.010, respectively). A dose-response association was observed for genus Sutterella and family Desulfovibrionaceae. Every one-unit increase in SMCs was associated with 25% and 27% higher relative abundances of Sutterella (OR: 1.25; 95% CI: 1.11-1.40) and Desulfovibrionaceae (OR: 1.27; 95% CI: 1.13-1.42), respectively (FDR-adjusted p = 0.018 and 0.006, respectively).
CONCLUSION
Our findings support an association between alterations in the gut bacterial composition and cognitive dysfunction.
Topics: Aged; Cognitive Dysfunction; Cross-Sectional Studies; Female; Gastrointestinal Microbiome; Humans; Odds Ratio; RNA, Ribosomal, 16S
PubMed: 35570486
DOI: 10.3233/JAD-220011 -
The Journal of Contemporary Dental... Jun 2022Even with the exponential popularity of the contemporary clear aligners, the main stream of orthodontic practice still remains to be metal braces especially in...
Even with the exponential popularity of the contemporary clear aligners, the main stream of orthodontic practice still remains to be metal braces especially in adolescent age-group. Along with the advantages of metal braces such as lower cost, reduced friction, etc., there goes the disadvantages such as corrosion possibility, reduced esthetics, etc. Corrosion of orthodontic appliances is a widely researched topic. It is surprising to learn that microbially induced corrosion (MIC) has not been addressed in orthodontic literature till date. Microbial corrosion is an interesting arena which requires knowledge of both corrosion science and microbiology. The microorganisms capable of corrosion include various bacteria, fungi, and algae. The most common among them which has been widely indicated in MIC are the bacteria belonging to the sulfur cycle especially the sulfate-reducing bacteria (SRB). The connecting knot with orthodontics is the reported prevalence of these SRB in the oral cavity. SRB is prevalent in healthy individuals, patients associated with periodontitis and patients with gastrointestinal issues. The prevalence of SRB in the oral cavity has a greater clinical implication since the SRB have been proven to cause corrosion of stainless steel. There is literature attributing SRB as a potential cause in periodontal diseases as well as gastrointestinal diseases such as ulcerative colitis, inflammatory bowel diseases, and Crohn's disease. With its presence in the healthy oral environment already reported in the previous studies, it further emphasizes the absolute need to be researching on its corrosion possibility in the intra oral environment. The genus generally found intraorally was and which is commonly regarded as the most "opportunistic" and ubiquitous group of sulfate reducers. There is an interesting literature on the inhibition of spp. by human saliva, the reason being quoted as salivary nitrate and nitrite. The mechanism behind the antimicrobial action of nitrate and nitrite is that they increase the oxidative stress on the bacteria. However, concentrations of salivary nitrate vary depending on the food intake, endogenous production, and salivary flow rate. Despite there exist natural inhibitors, the prevalence in oral cavity is high, 22% in healthy and 86% in patients associated with periodontitis. There is a predilection for the bacteria to grow when favorable conditions exist. Biofilms is one such favorable medium for the growth of SRB. Paster et al. identified SRB in biofilms of patients associated with refractory periodontitis, periodontitis, acute necrotizing ulcerative gingivitis (ANUG), and also in healthy subjects. Biofilm is a surface film composed of organic and inorganic saliva components that are colonized with microorganisms in extracellular polymeric substances adsorbed on all surfaces in the oral cavity. The oral biofilm formation is a complex process involving interspecies aggregation, which is surrounded by a cohesive matrix, forms a complex structure which in turn facilitates anaerobic growth. It is the intrinsic nature of oral biofilms which make the survival of facultative anaerobes such as SRB in the oral cavity possible. Literatures report that there are increased biofilm formations in orthodontic patients due to increased retentive areas caused by the brackets, ligatures, wires, mini implants, force components, and archwires. Bacteria in dental plaque function as a metabolically, functionally, and physically integrated community. The study by Mystkowska et al. mentioned that biofilm play a critical role in corrosion process by forming corrosive microcells. With time-dependent association, the microbes in the biofilm, along with saliva acting as an electrolyte and components from food, causes a decreased pH in the areas immediately under the biofilms. The decreased pH along with a change of oxygenation releases metal oxides and hydroxides from the metal surface ultimately leading to the corrosion of metallic structures. The initial roughness also acts in a vicious form promoting more biofilm adherence and the process repeats causing more corrosion. With the biofilm itself serving to initiate and propagate corrosion, the increased prevalence of SRB in patients associated with orthodontics treatment all the more increases the possibility of MIC of orthodontic materials.
Topics: Humans; Adolescent; Corrosion; Stainless Steel; Steel; Nitrates; Nitrites; Caustics; Desulfovibrio; Biofilms; Sulfates; Bacteria; Sulfur; Oxides; Anti-Infective Agents
PubMed: 36259293
DOI: No ID Found -
Frontiers in Cellular and Infection... 2023Previous research has posited a potential correlation between the gut microbiota and the onset of appendicitis; however, the precise causal connection between...
BACKGROUND
Previous research has posited a potential correlation between the gut microbiota and the onset of appendicitis; however, the precise causal connection between appendicitis and the gut microbiota remains an unresolved and contentious issue.
METHODS
In this investigation, we performed a Mendelian randomization (MR) analysis employing publicly accessible summary data extracted from genome-wide association studies (GWAS) to elucidate the potential causal nexus between the gut microbiota and the development of appendicitis. We initially identified instrumental variables (IVs) through a comprehensive array of screening methodologies, subsequently executing MR analyses using the Inverse Variance Weighted (IVW) technique as our primary approach, supplemented by several alternative methods such as MR Egger, weighted median, simple mode, and weighted mode. Additionally, we implemented a series of sensitivity analysis procedures, encompassing Cochran's Q test, MR-Egger intercept test, Mendelian Randomized Polymorphism Residual and Outlier (MR-PRESSO) test, and a leave-one-out test, to affirm the robustness and validity of our findings.
RESULTS
Our investigation indicates that an elevated prevalence of Deltaproteobacteria, Christensenellaceae, Desulfovibrionaceae, Eubacterium ruminantium group, Lachnospiraceae NK4A136 group, Methanobrevibacter, Desulfovibrionales, and Euryarchaeota is inversely associated with the risk of appendicitis. Conversely, we observed a positive correlation between an increased abundance of Family XIII, Howardella, and Veillonella and the susceptibility to appendicitis. Sensitivity analyses have corroborated the robustness of these findings, and Mendelian randomization analyses provided no indications of reverse causality.
CONCLUSION
Our Mendelian randomization (MR) analysis has unveiled potential advantageous or detrimental causal associations between the gut microbiota and the occurrence of appendicitis. This study offers novel theoretical and empirical insights into the understanding of appendicitis pathogenesis, along with its implications for preventive and therapeutic strategies.
Topics: Humans; Gastrointestinal Microbiome; Appendicitis; Genome-Wide Association Study; Mendelian Randomization Analysis; Causality; Clostridiales
PubMed: 38162578
DOI: 10.3389/fcimb.2023.1320992