-
Biophysical Reviews Oct 2023The processes of microbiological destruction of toxic and large-tonnage waste are the most attractive processes for protecting the environment. The review considers the... (Review)
Review
The processes of microbiological destruction of toxic and large-tonnage waste are the most attractive processes for protecting the environment. The review considers the results of studies of microbial decomposition of nitrate esters, including hardly decomposable nitrocellulose. The published data show that specific microorganisms are able to degrade nitrated cellulose compounds under both anaerobic and aerobic conditions. The most promising microorganisms in terms of the efficiency of the nitrocellulose degradation process are bacteria belonging to genera, fungi and , as well as their co-cultivation. Recently, the first information about the enzymes involved in the process of nitrocellulose degradation, possible mechanisms of reactions carried out by these enzymes, and the effect of electron donors and acceptors adding to the process have been obtained. Contamination of industrial wastewater with nitrocellulose leads to treatment necessity by using cost-effective, harmless methods. A combined aerobic-anaerobic system, including both bacteria and fungi, has shown hopeful results.
PubMed: 37974989
DOI: 10.1007/s12551-023-01159-1 -
Molecules (Basel, Switzerland) May 2023A story going back almost 40 years is presented in this manuscript. This is a different and more challenging way of reporting my research and I hope it will be useful to... (Review)
Review
A story going back almost 40 years is presented in this manuscript. This is a different and more challenging way of reporting my research and I hope it will be useful to and target a wide-ranging audience. When preparing the manuscript and collecting references on the subject of this paper-aldehyde oxidoreductase from -I felt like I was travelling back in time (and space), bringing together the people that have contributed most to this area of research. I sincerely hope that I can give my collaborators the credit they deserve. This study is not presented as a chronologic narrative but as a grouping of topics, the development of which occurred over many years.
Topics: Humans; Aldehyde Oxidoreductases; Desulfovibrio gigas; Desulfovibrio; Molybdenum; Aldehyde Dehydrogenase
PubMed: 37241969
DOI: 10.3390/molecules28104229 -
Frontiers in Cellular and Infection... 2023The aggregation of the neuronal protein alpha-synuclein (alpha-syn) is a key feature in the pathology of Parkinson's disease (PD). Alpha-syn aggregation has been...
INTRODUCTION
The aggregation of the neuronal protein alpha-synuclein (alpha-syn) is a key feature in the pathology of Parkinson's disease (PD). Alpha-syn aggregation has been suggested to be induced in the gut cells by pathogenic gut microbes such as bacteria, which has been shown to be associated with PD. This study aimed to investigate whether bacteria induce alpha-syn aggregation.
METHODS
Fecal samples of ten PD patients and their healthy spouses were collected for molecular detection of species, followed by bacterial isolation. Isolated strains were used as diets to feed nematodes which overexpress human alpha-syn fused with yellow fluorescence protein. Curli-producing MC4100, which has been shown to facilitate alpha-syn aggregation in animal models, was used as a control bacterial strain, and LSR11, incapable of producing curli, was used as another control strain. The head sections of the worms were imaged using confocal microscopy. We also performed survival assay to determine the effect of bacteria on the survival of the nematodes.
RESULTS AND DISCUSSION
Statistical analysis revealed that worms fed bacteria from PD patients harbored significantly more (<0.001, Kruskal-Wallis and Mann-Whitney U test) and larger alpha-syn aggregates (<0.001) than worms fed bacteria from healthy individuals or worms fed strains. In addition, during similar follow-up time, worms fed strains from PD patients died in significantly higher quantities than worms fed LSR11 bacteria (<0.01). These results suggest that bacteria contribute to PD development by inducing alpha-syn aggregation.
Topics: Animals; Humans; Parkinson Disease; alpha-Synuclein; Caenorhabditis elegans; Escherichia coli; Desulfovibrio
PubMed: 37197200
DOI: 10.3389/fcimb.2023.1181315 -
International Journal of Molecular... Apr 2021This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and... (Review)
Review
This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications was described. This method enables visual identification of SRB, determining their abundance and spatial distribution in environmental biofilms and gut samples.
Topics: Animals; Bacteria; Ecosystem; Humans; Metagenomics; Microscopy; Oxidation-Reduction; Sulfates
PubMed: 33924516
DOI: 10.3390/ijms22084007 -
PLoS Genetics Feb 2020Many species of bacteria can manufacture materials on a finer scale than those that are synthetically made. These products are often produced within intracellular... (Review)
Review
Many species of bacteria can manufacture materials on a finer scale than those that are synthetically made. These products are often produced within intracellular compartments that bear many hallmarks of eukaryotic organelles. One unique and elegant group of organisms is at the forefront of studies into the mechanisms of organelle formation and biomineralization. Magnetotactic bacteria (MTB) produce organelles called magnetosomes that contain nanocrystals of magnetic material, and understanding the molecular mechanisms behind magnetosome formation and biomineralization is a rich area of study. In this Review, we focus on the genetics behind the formation of magnetosomes and biomineralization. We cover the history of genetic discoveries in MTB and key insights that have been found in recent years and provide a perspective on the future of genetic studies in MTB.
Topics: Bacterial Proteins; Biomineralization; DNA Transposable Elements; Desulfovibrio; Ferrosoferric Oxide; Genes, Bacterial; Magnetosomes; Magnetospirillum; Metal Nanoparticles; Mutagenesis; Mutation
PubMed: 32053597
DOI: 10.1371/journal.pgen.1008499 -
Frontiers in Cellular and Infection... 2023There are several clinical and molecular predictors of responses to antidepressant therapy. However, these markers are either too subjective or complex for clinical use....
BACKGROUND
There are several clinical and molecular predictors of responses to antidepressant therapy. However, these markers are either too subjective or complex for clinical use. The gut microbiota could provide an easily accessible set of biomarkers to predict therapeutic efficacy, but its value in predicting therapy responses to acupuncture in patients with depression is unknown. Here we analyzed the predictive value of the gut microbiota in patients with postpartum depressive disorder (PPD) treated with acupuncture.
METHODS
Seventy-nine PPD patients were enrolled: 55 were treated with acupuncture and 24 did not received any treatment. The 17-item Hamilton depression rating scale (HAMD-17) was used to assess patients at baseline and after eight weeks. Patients receiving acupuncture treatment were divided into an acupuncture-responsive group or non-responsive group according to HAMD-17 scores changes. Baseline fecal samples were obtained from the patients receiving acupuncture and were analyzed by high-throughput 16S ribosomal RNA sequencing to characterize the gut microbiome.
RESULTS
47.27% patients responded to acupuncture treatment and 12.5% patients with no treatment recovered after 8-week follow-up. There was no significant difference in α-diversity between responders and non-responders. The β-diversity of non-responders was significantly higher than responders. and spp. were significantly enriched in acupuncture responders, and these organisms had an area under the curve of 0.76 and 0.66 for predicting responder patients, respectively.
CONCLUSIONS
and are may be useful predictive biomarkers to predict PPD patients likely to respond to acupuncture. Larger studies and validation in independent cohorts are now needed to validate our findings.
Topics: Female; Humans; Treatment Outcome; Acupuncture Therapy; Microbiota; Depressive Disorder; Biomarkers; Postpartum Period
PubMed: 38053532
DOI: 10.3389/fcimb.2023.1228940 -
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 -
Cells Dec 2022Sulfate-reducing bacteria is an opportunistic pathogen that widely exists in the human intestine and can cause severe infectious diseases. However, the mechanisms...
Sulfate-reducing bacteria is an opportunistic pathogen that widely exists in the human intestine and can cause severe infectious diseases. However, the mechanisms contributing to its pathogenesis remain of great interest. In this study, we aim to investigate the outer membrane vesicles (OMVs) secreted by and their pathogenic effect. The OMVs separated by ultracentrifugation were spherical and displayed a characteristic bilayer lipid structure observed by transmission electron microscopy, with an average hydrodynamic diameter of 75 nm measurement using the particle size analyzer. We identified 1496 and 916 proteins from and its OMVs using label-free non-target quantitative proteomics, respectively. The 560 co-expressed proteins could participate in bacterial life activities by function prediction. The translocation protein TolB, which participates in OMVs biogenesis and transporting toxins was highly expressed in OMVs. The OMVs inhibited the expression of tight junction proteins OCCLUDIN and ZO-1 in human colonic epithelial cells (Caco-2). The OMVs decreased the cell viability of monocyte macrophages (THP-1-Mφ) and activated various inflammatory factors secretion, including interferon-γ (IFN-γ), tumor necrosis factor (TNF-α), and many interleukins. Further, we found the OMVs induced the expression of cleaved-gasdermin D, caspase-1, and c-IL-1β and caused pyroptosis in THP-1-Mφ cells. Taken together, these data reveal that the OMVs can damage the intestinal epithelial barrier and activate intrinsic inflammation.
Topics: Humans; Caco-2 Cells; Pyroptosis; Inflammation; Tumor Necrosis Factor-alpha; Macrophages
PubMed: 36611884
DOI: 10.3390/cells12010089 -
Nutrients Apr 2023Shifts in the maternal gut microbiome and vitamin D deficiency during pregnancy have been associated, separately, with health problems for both the mother and the child.... (Randomized Controlled Trial)
Randomized Controlled Trial
Shifts in the maternal gut microbiome and vitamin D deficiency during pregnancy have been associated, separately, with health problems for both the mother and the child. Yet, they have rarely been studied simultaneously. Here, we analyzed the gut microbiome (from stool samples obtained in late pregnancy) and vitamin D level (from blood samples obtained both in early and late pregnancy) data of pregnant women in the Vitamin D Antenatal Asthma Reduction Trial (VDAART), a randomized controlled trial of vitamin D supplementation during pregnancy, to investigate the association of vitamin D status on the pregnant women's microbiome. To find associations, we ran linear regressions on alpha diversity measures, PERMANOVA tests on beta diversity distances, and used the ANCOM-BC and Maaslin2 algorithms to find differentially abundant taxa. Analyses were deemed significant using a cut-off -value of 0.05. We found that gut microbiome composition is associated with the vitamin D level in early pregnancy (baseline), the maternal gut microbiome does not show a shift in response to vitamin D supplementation during pregnancy, and that the genus is enriched in women without a substantial increase in vitamin D level between the first and the third trimesters of pregnancy. We conclude that increasing the vitamin D level during pregnancy could be protective against the growth of sulfate-reducing bacteria such as , which has been associated with chronic intestinal inflammatory disorders. More in-depth investigations are needed to confirm this hypothesis.
Topics: Child; Female; Humans; Pregnancy; Vitamin D; Gastrointestinal Microbiome; Vitamins; Mothers; Dietary Supplements
PubMed: 37432235
DOI: 10.3390/nu15092059 -
BMC Biology Dec 2022The rumen is the hallmark organ of ruminants, playing a vital role in their nutrition and providing products for humans. In newborn suckling ruminants milk bypasses the...
BACKGROUND
The rumen is the hallmark organ of ruminants, playing a vital role in their nutrition and providing products for humans. In newborn suckling ruminants milk bypasses the rumen, while in adults this first chamber of the forestomach has developed to become the principal site of microbial fermentation of plant fibers. With the advent of single-cell transcriptomics, it is now possible to study the underlying cell composition of rumen tissues and investigate how this relates the development of mutualistic symbiosis between the rumen and its epithelium-attached microbes.
RESULTS
We constructed a comprehensive cell landscape of the rumen epithelium, based on single-cell RNA sequencing of 49,689 high-quality single cells from newborn and adult rumen tissues. Our single-cell analysis identified six immune cell subtypes and seventeen non-immune cell subtypes of the rumen. On performing cross-species analysis of orthologous genes expressed in epithelial cells of cattle rumen and the human stomach and skin, we observed that the species difference overrides any cross-species cell-type similarity. Comparing adult with newborn cattle samples, we found fewer epithelial cell subtypes and more abundant immune cells, dominated by T helper type 17 cells in the rumen tissue of adult cattle. In newborns, there were more fibroblasts and myofibroblasts, an IGFBP3 epithelial cell subtype not seen in adults, while dendritic cells were the most prevalent immune cell subtype. Metabolism-related functions and the oxidation-reduction process were significantly upregulated in adult rumen epithelial cells. Using 16S rDNA sequencing, fluorescence in situ hybridization, and absolute quantitative real-time PCR, we found that epithelial Desulfovibrio was significantly enriched in the adult cattle. Integrating the microbiome and metabolome analysis of rumen tissues revealed a high co-occurrence probability of Desulfovibrio with pyridoxal in the adult cattle compared with newborn ones while the scRNA-seq data indicated a stronger ability of pyroxidal binding in the adult rumen epithelial cell subtypes. These findings indicate that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in the adult rumen.
CONCLUSIONS
Our integrated multi-omics analysis provides novel insights into rumen development and function and may facilitate the future precision improvement of rumen function and milk/meat production in cattle.
Topics: Infant, Newborn; Humans; Cattle; Animals; Rumen; In Situ Hybridization, Fluorescence; Microbiota; Ruminants; Pyridoxal; Animal Feed
PubMed: 36514051
DOI: 10.1186/s12915-022-01490-1