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Acta Crystallographica. Section F,... May 2024Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO to formate, with biotechnological...
Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine S interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO reduction, together with an increased sensitivity to oxygen inactivation.
Topics: Desulfovibrio vulgaris; Formate Dehydrogenases; Catalytic Domain; Crystallography, X-Ray; Oxidation-Reduction; Models, Molecular; Formates; Carbon Dioxide; Bacterial Proteins
PubMed: 38699971
DOI: 10.1107/S2053230X24003911 -
Frontiers in Cellular and Infection... 2024Polycystic ovary syndrome (PCOS) is a common systemic disorder related to endocrine disorders, affecting the fertility of women of childbearing age. It is associated...
Polycystic ovary syndrome (PCOS) is a common systemic disorder related to endocrine disorders, affecting the fertility of women of childbearing age. It is associated with glucose and lipid metabolism disorders, altered gut microbiota, and insulin resistance. Modern treatments like pioglitazone, metformin, and spironolactone target specific symptoms of PCOS, while in Chinese medicine, moxibustion is a common treatment. This study explores moxibustion's impact on PCOS by establishing a dehydroepiandrosterone (DHEA)-induced PCOS rat model. Thirty-six specific pathogen-free female Sprague-Dawley rats were divided into four groups: a normal control group (CTRL), a PCOS model group (PCOS), a moxibustion treatment group (MBT), and a metformin treatment group (MET). The MBT rats received moxibustion, and the MET rats underwent metformin gavage for two weeks. We evaluated ovarian tissue changes, serum testosterone, fasting blood glucose (FBG), and fasting insulin levels. Additionally, we calculated the insulin sensitivity index (ISI) and the homeostasis model assessment of insulin resistance index (HOMA-IR). We used 16S rDNA sequencing for assessing the gut microbiota, H NMR spectroscopy for evaluating metabolic changes, and Spearman correlation analysis for investigating the associations between metabolites and gut microbiota composition. The results indicate that moxibustion therapy significantly ameliorated ovarian dysfunction and insulin resistance in DHEA-induced PCOS rats. We observed marked differences in the composition of gut microbiota and the spectrum of fecal metabolic products between CTRL and PCOS rats. Intriguingly, following moxibustion intervention, these differences were largely diminished, demonstrating the regulatory effect of moxibustion on gut microbiota. Specifically, moxibustion altered the gut microbiota by increasing the abundance of and , as well as decreasing the abundance of . Concurrently, we also noted that moxibustion promoted an increase in levels of short-chain fatty acids (including acetate, propionate, and butyrate) associated with the gut microbiota of PCOS rats, further emphasizing its positive impact on gut microbes. Additionally, moxibustion also exhibited effects in lowering FBG, testosterone, and fasting insulin levels, which are key biochemical indicators associated with PCOS and insulin resistance. Therefore, these findings suggest that moxibustion could alleviate DHEA-induced PCOS by regulating metabolic levels, restoring balance in gut microbiota, and modulating interactions between gut microbiota and host metabolites.
Topics: Animals; Polycystic Ovary Syndrome; Female; Moxibustion; Gastrointestinal Microbiome; Rats, Sprague-Dawley; Rats; Disease Models, Animal; Insulin Resistance; Dehydroepiandrosterone; Blood Glucose; Insulin; Metformin; Testosterone; Ovary
PubMed: 38665877
DOI: 10.3389/fcimb.2024.1328741 -
FEMS Microbiology Ecology May 2024The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage...
The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is, therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for underground geological storage, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2-selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio, and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.
Topics: Methane; Groundwater; Natural Gas; Hydrogen; Sulfates; Methanobacteriaceae; Carbon Dioxide; Bacteria; Hydrogen-Ion Concentration; Water Microbiology
PubMed: 38658197
DOI: 10.1093/femsec/fiae066 -
Food Science & Nutrition Apr 2024This study aimed to investigate the beneficial effects of probiotic yogurt on lipid metabolism and gut microbiota in metabolic-related fatty liver disease (MAFLD) golden...
This study aimed to investigate the beneficial effects of probiotic yogurt on lipid metabolism and gut microbiota in metabolic-related fatty liver disease (MAFLD) golden hamsters fed on a high-fat diet (HFD). The results demonstrated that probiotic yogurt significantly reversed the adverse effects caused by HFD, such as body and liver weight gain, liver steatosis and damage, sterol deposition, and oxidative stress after 8 weeks of intervention. qRT-PCR analysis showed that golden hamsters fed HFD had upregulated genes related to adipogenesis, increased free fatty acid infiltration, and downregulated genes related to lipolysis and very low-density lipoprotein secretion. Probiotic yogurt supplements significantly inhibited HFD-induced changes in the expression of lipid metabolism-related genes. Furthermore, 16S rRNA gene sequencing of the intestinal content microbiota suggested that probiotic yogurt changed the diversity and composition of the gut microbiota in HFD-fed hamsters. Probiotic yogurt decreased the ratio of the , the relative abundance of the LPS-producing genus , and bacteria involved in lipid metabolism, whereas it increased the relative abundance of short-chain fatty acids producing bacteria in HFD-fed hamsters. Predictive functional analysis of the microbial community showed that probiotic yogurt-modified genes involved in LPS biosynthesis and lipid metabolism. In summary, these findings support the possibility that probiotic yogurt significantly improves HFD-induced metabolic disorders through modulating intestinal microflora and lipid metabolism and effectively regulating the occurrence and development of MAFLD. Therefore, probiotic yogurt supplementation may serve as an effective nutrition strategy for the treatment of patients with MAFLD clinically.
PubMed: 38628190
DOI: 10.1002/fsn3.3930 -
Frontiers in Microbiology 2024In view of water and soil getting polluted by Pb(II), Zn(II), and other heavy metals in tailings and acid mine drainage (AMD), we explored the removal effect of...
In view of water and soil getting polluted by Pb(II), Zn(II), and other heavy metals in tailings and acid mine drainage (AMD), we explored the removal effect of sulfate-reducing bacteria (SRB) on Pb(II), Zn(II), and other pollutants in solution and tailings based on the microbial treatment technology. We used the scanning electron microscope-energy dispersive spectroscopy (SEM-EDS), X-ray diffraction (XRD), and X-ray fluorescence (XRF), to reveal the mechanism of SRB treatment of tailings. The results showed that SRB had a strong removal capacity for Zn(II) at 0-40 mg/L; however, Zn(II) at 60-100 mg/L inhibited the growth of SRB. Similarly, SRB exhibited a very strong ability to remove Pb(II) from the solution. At a Pb(II) concentration of 10-50 mg/L, its removal percentage by SRB was 100%. SRB treatment could effectively immobilize the pollutants leached from the tailings. With an increase in the amount of tailings added to each layer, the ability of SRB to treat the pollutants diminished. When 1 cm of tailingssand was added to each layer, SRB had the best effect on tailing sand treatment. After treatment, the immobilization rates of , Fe(III), Mn(II), Pb(II), Zn(II), Cu(II), and total Cr in the leachate of #1 tailing sand were 95.44%, 100%, 90.88%, 100%, 96.20%, 86.23%, and 93.34%, respectively. After the tailings were treated by SRB, although the tailings solidified into a cohesive mass from loose granular particles, their mechanical strength was <0.2 MPa. and played the predominant roles in treating tailings by mixing SRB. The S and carbonate produced by mixing SRB during the treatment of tailings could metabolize sulfate by combining with the heavy metal ions released by the tailings to form FeS, MnS, ZnS, CuS, PbS, CrS, CaCO, MnCO, and other precipitated particles. These particles were attached to the surface of the tailings, reducing the environmental pollution of the tailings in the water and soil around the mining area.
PubMed: 38618484
DOI: 10.3389/fmicb.2024.1352430 -
Transplantation Jul 2024Despite ongoing improvements to regimens preventing allograft rejection, most cardiac and other organ grafts eventually succumb to chronic vasculopathy, interstitial...
BACKGROUND
Despite ongoing improvements to regimens preventing allograft rejection, most cardiac and other organ grafts eventually succumb to chronic vasculopathy, interstitial fibrosis, or endothelial changes, and eventually graft failure. The events leading to chronic rejection are still poorly understood and the gut microbiota is a known driving force in immune dysfunction. We previously showed that gut microbiota dysbiosis profoundly influences the outcome of vascularized cardiac allografts and subsequently identified biomarker species associated with these differential graft outcomes.
METHODS
In this study, we further detailed the multifaceted immunomodulatory properties of protolerogenic and proinflammatory bacterial species over time, using our clinically relevant model of allogenic heart transplantation.
RESULTS
In addition to tracing longitudinal changes in the recipient gut microbiome over time, we observed that Bifidobacterium pseudolongum induced an early anti-inflammatory phenotype within 7 d, whereas Desulfovibrio desulfuricans resulted in a proinflammatory phenotype, defined by alterations in leukocyte distribution and lymph node (LN) structure. Indeed, in vitro results showed that B pseudolongum and D desulfuricans acted directly on primary innate immune cells. However, by 40 d after treatment, these 2 bacterial strains were associated with mixed effects in their impact on LN architecture and immune cell composition and loss of colonization within gut microbiota, despite protection of allografts from inflammation with B pseudolongum treatment.
CONCLUSIONS
These dynamic effects suggest a critical role for early microbiota-triggered immunologic events such as innate immune cell engagement, T-cell differentiation, and LN architectural changes in the subsequent modulation of protolerant versus proinflammatory immune responses in organ transplant recipients.
Topics: Heart Transplantation; Gastrointestinal Microbiome; Bifidobacterium; Graft Rejection; Animals; Male; Time Factors; Graft Survival; Dysbiosis; Mice, Inbred C57BL; Immunity, Innate; Immunomodulation; Phenotype; Probiotics; Lymph Nodes
PubMed: 38587506
DOI: 10.1097/TP.0000000000004939 -
Environmental Microbiology Reports Apr 2024Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising...
Nitrate and oxygen significantly changed the abundance rather than structure of sulphate-reducing and sulphur-oxidising bacteria in water retrieved from petroleum reservoirs.
Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising bacteria (SOB) are stimulated when nitrate and oxygen are injected, which control the growth of SRB. This study aimed to determine the distributions of SRB and SOB communities in injection-production systems and to analyse the responses of these bacteria to different treatments involving nitrate and oxygen. Desulfovibrio, Desulfobacca, Desulfobulbus, Sulfuricurvum and Dechloromonas were commonly detected via 16S rRNA gene sequencing. Still, no significant differences were observed for either the SRB or SOB communities between injection and production wells. Three groups of water samples collected from different sampling sites were incubated. Statistical analysis of functional gene (dsrB and soxB) clone libraries and quantitative polymerase chain reaction showed that the SOB community structures were more strongly affected by the nitrate and oxygen levels than SRB clustered according to the sampling site; moreover, both the SRB and SOB community abundances significantly changed. Additionally, the highest SRB inhibitory effect and the lowest dsrB/soxB ratio were obtained under high concentrations of nitrate and oxygen in the three groups, suggesting that the synergistic effect of nitrate and oxygen level was strong on the inhibition of SRB by potential SOB.
Topics: Nitrates; Petroleum; Sulfates; Water; RNA, Ribosomal, 16S; Bacteria; Desulfovibrio; Organic Chemicals; Sulfur; Oxidation-Reduction
PubMed: 38581137
DOI: 10.1111/1758-2229.13248 -
Frontiers in Microbiology 2024Hypertrophic scars affect a significant number of individuals annually, giving rise to both cosmetic concerns and functional impairments. Prior research has established...
Hypertrophic scars affect a significant number of individuals annually, giving rise to both cosmetic concerns and functional impairments. Prior research has established that an imbalance in the composition of gut microbes, termed microbial dysbiosis, can initiate the progression of various diseases through the intricate interplay between gut microbiota and the host. However, the precise nature of the causal link between gut microbiota and hypertrophic scarring remains uncertain. In this study, after compiling summary data from genome-wide association studies (GWAS) involving 418 instances of gut microbiota and hypertrophic scarring, we conducted a bidirectional Mendelian randomization (MR) to investigate the potential existence of a causal relationship between gut microbiota and the development of hypertrophic scar and to discern the directionality of causation. By utilizing MR analysis, we identified seven causal associations between gut microbiome and hypertrophic scarring, involving one positive and six negative causal directions. Among them, , , , , , and act as protective factors against hypertrophic scarring, while suggests a potential role as a risk factor for hypertrophic scars. Additionally, sensitivity analyses of these results revealed no indications of heterogeneity or pleiotropy. The findings of our MR study suggest a potential causative link between gut microbiota and hypertrophic scarring, opening up new ways for future mechanistic research and the exploration of nanobiotechnology therapies for skin disorders.
PubMed: 38577682
DOI: 10.3389/fmicb.2024.1345717 -
Water Research May 2024Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium...
Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium contamination, carbon amendments promote reducing conditions to allow microorganisms to reduce uranium to an insoluble, less mobile state. However, the reproducibility of these amendments and underlying microbial community assembly mechanisms have rarely been investigated in the field. In this study, two injections of emulsified vegetable oil were performed in 2009 and 2017 to immobilize uranium in the groundwater at Oak Ridge, TN, USA. Our objectives were to determine whether and how the injections resulted in similar abiotic and biotic responses and their underlying community assembly mechanisms. Both injections caused similar geochemical and microbial succession. Uranium, nitrate, and sulfate concentrations in the groundwater dropped following the injection, and specific microbial taxa responded at roughly the same time points in both injections, including Geobacter, Desulfovibrio, and members of the phylum Comamonadaceae, all of which are well established in uranium, nitrate, and sulfate reduction. Both injections induced a transition from relatively stochastic to more deterministic assembly of microbial taxonomic and phylogenetic community structures based on 16S rRNA gene analysis. We conclude that geochemical and microbial successions after biostimulation are reproducible, likely owing to the selection of similar phylogenetic groups in response to EVO injection.
PubMed: 38552495
DOI: 10.1016/j.watres.2024.121460 -
Microorganisms Feb 2024larvae are farm-raised for food, are used in traditional East Asian medicine, and convert organic waste into biofertilizers. Here, the comparative analysis of the gut...
larvae are farm-raised for food, are used in traditional East Asian medicine, and convert organic waste into biofertilizers. Here, the comparative analysis of the gut microbiota of third-instar larvae obtained from five different farms was investigated using 16S rRNA microbial profiling. Species richness, evenness, and diversity results using α-diversity analysis (observed species, Chao1, Shannon, Simpson) were similar between farms, except for those between the TO and KO farms. β-diversity was significantly different in distribution and relative abundance between farms (PERMANOVA, pseudo-F = 13.20, = 0.001). At the phylum level, , , , and were the most dominant, accounting for 73-88% of the hindgut microbial community. At the genus level, , and were the most abundant. Although oak sawdust was the main feed component, there were large variations in distribution and relative abundance across farms at the phylum and genus levels. Venn diagram and linear discriminant analysis effect size analyses revealed large variations in the hindgut microbial communities of larvae between farms. These results suggest environmental factors were more important than feed ingredients or genetic predisposition for the establishment of the intestinal microbiota of larvae. These findings serve as reference data to understand the intestinal microbiota of larvae.
PubMed: 38543547
DOI: 10.3390/microorganisms12030496