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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 -
Protein Science : a Publication of the... Dec 2015Nitrate reductases (NR) belong to the DMSO reductase family of Mo-containing enzymes and perform key roles in the metabolism of the nitrogen cycle, reducing nitrate to... (Review)
Review
Nitrate reductases (NR) belong to the DMSO reductase family of Mo-containing enzymes and perform key roles in the metabolism of the nitrogen cycle, reducing nitrate to nitrite. Due to variable cell location, structure and function, they have been divided into periplasmic (Nap), cytoplasmic, and membrane-bound (Nar) nitrate reductases. The first crystal structure obtained for a NR was that of the monomeric NapA from Desulfovibrio desulfuricans in 1999. Since then several new crystal structures were solved providing novel insights that led to the revision of the commonly accepted reaction mechanism for periplasmic nitrate reductases. The two crystal structures available for the NarGHI protein are from the same organism (Escherichia coli) and the combination with electrochemical and spectroscopic studies also lead to the proposal of a reaction mechanism for this group of enzymes. Here we present an overview on the current advances in structural and functional aspects of bacterial nitrate reductases, focusing on the mechanistic implications drawn from the crystallographic data.
Topics: Bacteria; Bacterial Proteins; Catalytic Domain; Cell Membrane; Crystallography, X-Ray; Cytoplasm; Models, Molecular; Nitrate Reductase; Periplasm
PubMed: 26362109
DOI: 10.1002/pro.2801 -
Frontiers in Microbiology 2023The association between gut microbiota and leukemia has been established, but the causal relationship between the two remains unclear.
BACKGROUND
The association between gut microbiota and leukemia has been established, but the causal relationship between the two remains unclear.
METHODS
A bidirectional two-sample Mendelian randomization (MR) was used to analyze the causal relationship between gut microbiota and leukemia. Microbiome data ( = 14,306) and leukemia ( = 1,145) data were both sourced from European populations. Single nucleotide polymorphisms (SNPs) were selected as instrumental variables based on several criteria. We employed various MR methods, such as the inverse variance weighted (IVW) method, to evaluate the causal effect between exposure and outcomes and conducted sensitivity analyses to validate the heterogeneity and pleiotropy of the instrumental variables.
RESULTS
5,742 qualified instrumental variables were included. In the primary MR results, a total of 10 gut microbial taxa were associated with leukemia risk. Genus Blautia and genus Lactococcus are risk factors for acute lymphoblastic leukemia [genus Blautia odds ratio (OR): 1.643, 95% confidence interval (CI): 1.592 ~ 1.695, Adjusted < 0.001; genus Lactococcus OR: 2.152, 95% CI: 1.447 ~ 3.199, Adjusted = 0.011]. Genus Rikenellaceae RC9 gut group, genus Anaerostipes, genus Slackia, and genus Lachnospiraceae ND3007 group are risk factors for acute myeloid leukemia [genus Rikenellaceae RC9 gut group OR: 1.964, 95% CI: 1.573 ~ 2.453, Adjusted < 0.001; genus Anaerostipes OR: 2.515, 95% CI: 1.503 ~ 4.209, Adjusted = 0.017; genus Slackia OR: 2.553, 95% CI: 1.481 ~ 4.401, Adjusted = 0.022; genus Lachnospiraceae ND3007 group OR: 3.417, 95% CI: 1.960 ~ 5.959, Adjusted = 0.001]. Genus Ruminococcaceae UCG011 and genus Ruminococcaceae UCG014 were risk factors for chronic myeloid leukemia (genus Ruminococcaceae UCG011 OR: 2.010, 95% CI: 1.363 ~ 2.963, Adjusted = 0.044; genus Ruminococcaceae UCG014 OR: 3.101, 95% CI: 1.626 ~ 5.915, Adjusted = 0.044). Genus Slackia was a protective factor for acute lymphoblastic leukemia (genus Slackia OR: 0.166, 95% CI: 0.062 ~ 0.443, Adjusted = 0.017). Family Acidaminococcaceae was a protective factor for acute myeloid leukemia (family Acidaminococcaceae OR: 0.208, 95% CI: 0.120 ~ 0.361, Adjusted 0.001). Genus Desulfovibrio was a protective factor for chronic lymphoblastic leukemia (genus Desulfovibrio OR: 0.581, 95% CI: 0.440 ~ 0.768, Adjusted = 0.020). Sensitivity analysis revealed no heterogeneity or pleiotropy between SNPs.
CONCLUSION
This study revealed the causal relationship between the gut microbiota and leukemia, and identified potential pathogenic bacteria and probiotic taxa associated with the onset of leukemia. This research may aid in the early detection of various types of leukemia and offer a new direction for the prevention and treatment of leukemia.
PubMed: 38075916
DOI: 10.3389/fmicb.2023.1293333 -
Animal Nutrition (Zhongguo Xu Mu Shou... Jun 2022Methane (CH) production from ruminants accounts for 16% of the global greenhouse gas emissions and represents 2% to 12% of feed energy. Mitigating CH production from... (Review)
Review
Methane (CH) production from ruminants accounts for 16% of the global greenhouse gas emissions and represents 2% to 12% of feed energy. Mitigating CH production from ruminants is of great importance for sustainable development of the ruminant industry. H is the primary substrate for CH production in the processes of ruminal methanogenesis. Sulfate reducing bacteria are able to compete with methanogens for H in the rumen, and consequently inhibit the methanogenesis. Enhancing the ruminal sulfate reducing pathway is an important approach to mitigate CH emissions in ruminants. The review summarized the effects of sulfate and elemental S on ruminal methanogenesis, and clarified the related mechanisms through the impacts of sulfate and elemental S on major ruminal sulfate reducing bacteria. Enhancing the activities of the major ruminal sulfate reducing bacteria including , and through dietary sulfate addition, elemental S and dried distillers grains with solubles can effectively decrease the ruminal CH emissions. Suitable levels of dietary addition with different S sources for reducing the ruminal CH production, as well as maintaining the performance and health of ruminants, need to be investigated in the future.
PubMed: 35600554
DOI: 10.1016/j.aninu.2022.01.006 -
Frontiers in Cellular and Infection... 2021Parkinson's disease (PD) is the most prevalent movement disorder known and predominantly affects the elderly. It is a progressive neurodegenerative disease wherein...
Parkinson's disease (PD) is the most prevalent movement disorder known and predominantly affects the elderly. It is a progressive neurodegenerative disease wherein α-synuclein, a neuronal protein, aggregates to form toxic structures in nerve cells. The cause of Parkinson's disease (PD) remains unknown. Intestinal dysfunction and changes in the gut microbiota, common symptoms of PD, are evidently linked to the pathogenesis of PD. Although a multitude of studies have investigated microbial etiologies of PD, the microbial role in disease progression remains unclear. Here, we show that Gram-negative sulfate-reducing bacteria of the genus may play a potential role in the development of PD. Conventional and quantitative real-time PCR analysis of feces from twenty PD patients and twenty healthy controls revealed that all PD patients harbored bacteria in their gut microbiota and these bacteria were present at higher levels in PD patients than in healthy controls. Additionally, the concentration of species correlated with the severity of PD. bacteria produce hydrogen sulfide and lipopolysaccharide, and several strains synthesize magnetite, all of which likely induce the oligomerization and aggregation of α-synuclein protein. The substances originating from bacteria likely take part in pathogenesis of PD. These findings may open new avenues for the treatment of PD and the identification of people at risk for developing PD.
Topics: Aged; Bacteria; Desulfovibrio; Humans; Neurodegenerative Diseases; Parkinson Disease; alpha-Synuclein
PubMed: 34012926
DOI: 10.3389/fcimb.2021.652617 -
International Journal of Molecular... May 2023The gut-liver axis may provide a new perspective for treating anti-tuberculosis drug-induced liver injury (ATDILI). Herein, the protective effect of (Lc) was...
The gut-liver axis may provide a new perspective for treating anti-tuberculosis drug-induced liver injury (ATDILI). Herein, the protective effect of (Lc) was investigated by modulating gut microflora (GM) and the toll like receptor 4 (TLR4)-nuclear factor (NF)-κB-myeloiddifferentiationfactor 88 (MyD88) pathway. C57BL/6J mice were given three levels of Lc intragastrically for 2 h before administering isoniazid and rifampicin for 8 weeks. Blood, liver, and colon tissues, as well as cecal contents, were collected for biochemical and histological examination, as well as Western blot, quantitative real time polymerase chain reaction (qRT-PCR), and 16S rRNA analyses. Lc intervention decreased alkaline phosphatase (ALP), superoxide dismutase (SOD), glutathione (GSH), malondialdehyde (MDA), and tumor necrosis factor (TNF)-α levels ( < 0.05), recovered hepatic lobules, and reduced hepatocyte necrosis to alleviate liver injury induced by anti-tuberculosis drugs. Moreover, Lc also increased the abundance of and and decreased abundance, while enhancing zona occludens (ZO)-1 and claudin-1 protein expression compared with the model group ( < 0.05). Furthermore, Lc pretreatment reduced the lipopolysaccharide (LPS) level and downregulated NF-κB and MyD88 protein expression ( < 0.05), thus restraining pathway activation. Spearman correlation analysis indicated that and were positively correlated with ZO-1 or occludin protein expression and negatively correlated with pathway protein expression. had significant negative relationships with alanine aminotransferase (ALT) and LPS levels. In contrast, had negative associations with ZO-1, occludin, and claudin-1 protein expressions and positive correlations with LPS and pathway proteins. The results prove that can enhance the intestinal barrier and change the composition of the gut microflora. Moreover, may also inhibit TLR4-NF-κB-MyD88 pathway activation and alleviate ATDILI.
Topics: Mice; Animals; NF-kappa B; Lipopolysaccharides; Lacticaseibacillus casei; Toll-Like Receptor 4; Signal Transduction; Antitubercular Agents; Gastrointestinal Microbiome; Myeloid Differentiation Factor 88; Occludin; Claudin-1; RNA, Ribosomal, 16S; Mice, Inbred C57BL; Tumor Necrosis Factor-alpha; Chemical and Drug Induced Liver Injury; Glutathione
PubMed: 37298396
DOI: 10.3390/ijms24119444 -
Microbiome Jan 2024The overgrowth of Desulfovibrio, an inflammation promoting flagellated bacteria, has been found in ulcerative colitis (UC) patients. However, the molecular mechanism in...
BACKGROUND
The overgrowth of Desulfovibrio, an inflammation promoting flagellated bacteria, has been found in ulcerative colitis (UC) patients. However, the molecular mechanism in promoting colitis remains unestablished.
METHODS
The relative abundance Desulfovibrio vulgaris (D. vulgaris) in stool samples of UC patients was detected. Mice were treated with dextran sulfate sodium to induce colitis with or without administration of D. vulgaris or D. vulgaris flagellin (DVF), and the severity of colitis and the leucine-rich repeat containing 19 (LRRC19) signaling were assessed. The interaction between DVF and LRRC19 was identified by surface plasmon resonance and intestinal organoid culture. Lrrc19 and Tlr5 mice were used to investigate the indispensable role of LRRC19. Finally, the blockade of DVF-LRRC19 interaction was selected through virtual screening and the efficacy in colitis was assessed.
RESULTS
D. vulgaris was enriched in fecal samples of UC patients and was correlated with the disease severity. D. vulgaris or DVF treatment significantly exacerbated colitis in germ-free mice and conventional mice. Mechanistically, DVF could interact with LRRC19 (rather than TLR5) in colitis mice and organoids, and then induce the production of pro-inflammatory cytokines. Lrrc19 knockdown blunted the severity of colitis. Furthermore, typhaneoside, a blockade of binding interfaces, blocked DVF-LRRC19 interaction and dramatically ameliorated DVF-induced colitis.
CONCLUSIONS
D. vulgaris could promote colitis through DVF-LRRC19 interaction. Targeting DVF-LRRC19 interaction might be a new therapeutic strategy for UC therapy. Video Abstract.
Topics: Humans; Mice; Animals; Toll-Like Receptor 5; Desulfovibrio vulgaris; Colitis; Colitis, Ulcerative; Inflammation; Dextran Sulfate; Disease Models, Animal; Mice, Inbred C57BL; Colon; Receptors, Cell Surface
PubMed: 38172943
DOI: 10.1186/s40168-023-01722-8 -
EBioMedicine Apr 2024Chemoresistance is a critical factor contributing to poor prognosis in clinical patients with cancer undergoing postoperative adjuvant chemotherapy. The role of gut...
BACKGROUND
Chemoresistance is a critical factor contributing to poor prognosis in clinical patients with cancer undergoing postoperative adjuvant chemotherapy. The role of gut microbiota in mediating resistance to tumour chemotherapy remains to be investigated.
METHODS
Patients with CRC were categorised into clinical benefit responders (CBR) and no clinical benefit responders (NCB) based on chemotherapy efficacy. Differential bacterial analysis using 16S rRNA sequencing revealed Desulfovibrio as a distinct microbe between the two groups. Employing a syngeneic transplantation model, we assessed the effect of Desulfovibrio on chemotherapy by measuring tumour burden, weight, and Ki-67 expression. We further explored the mechanisms underlying the compromised chemotherapeutic efficacy of Desulfovibrio using metabolomics, western blotting, colony formation, and cell apoptosis assays.
FINDINGS
In comparison, Desulfovibrio was more abundant in the NCB group. In vivo experiments revealed that Desulfovibrio colonisation in the gut weakened the efficacy of FOLFOX. Treatment with Desulfovibrio desulfuricans elevates serum S-adenosylmethionine (SAM) levels. Interestingly, SAM reduced the sensitivity of CRC cells to FOLFOX, thereby promoting the growth of CRC tumours. These experiments suggest that SAM promotes the growth and metastasis of CRC by driving the expression of methyltransferase-like 3 (METTL3).
INTERPRETATION
A high abundance of Desulfovibrio in the intestines indicates poor therapeutic outcomes for postoperative neoadjuvant FOLFOX chemotherapy in CRC. Desulfovibrio drives the manifestation of METTL3 in CRC, promoting resistance to FOLFOX chemotherapy by increasing the concentration of SAM.
FUNDING
This study is supported by Wuxi City Social Development Science and Technology Demonstration Project (N20201005).
Topics: Humans; Apoptosis; Colorectal Neoplasms; Desulfovibrio desulfuricans; Fluorouracil; Methyltransferases; RNA, Ribosomal, 16S; Leucovorin; Organoplatinum Compounds; Antineoplastic Combined Chemotherapy Protocols
PubMed: 38484555
DOI: 10.1016/j.ebiom.2024.105041 -
Aging Mar 2021To investigate the changes of intestinal microbiota and metabolites in sepsis mice with acute gastrointestinal injury before and after the use of antibiotics, and to...
BACKGROUND
To investigate the changes of intestinal microbiota and metabolites in sepsis mice with acute gastrointestinal injury before and after the use of antibiotics, and to explore the possible effects of these changes on the body.
METHODS
Twenty-four 6-8-w-old SPF-grade C57BL/6J male mice were selected, and the mice were randomly divided into three groups. The mice were treated by tail vein injection for 3 days. The intestinal motility of mice after administration was detected. The mice feces were collected for 16S rRNA and Untargeted metabonomics detection.
RESULTS
The use of antibiotics in sepsis mice can change the composition of intestinal microbiota and metabolites. LD3, AD3 and LAD3 samples had significant differences in bacterial species. was the species with a significant difference in LAD3. In addition, we found that the composition of those intestinal microbiota were correlated with changes in intestinal motility. The untargeted metabolomics analysis showed that the fecal metabolites of LD3 and LAD3 samples were significantly different. In addition to the basic metabolites, Benzoic acid and 4-Hydroxybenzoic acid were also found, and was associated with them.
CONCLUSIONS
The use of antibiotics in sepsis mice can lead to changes in the intestinal microbiota and metabolite levels, which may be related to the severity of acute gastrointestinal injury in sepsis mice. Inhibiting in the intestine and using Benzoic acid and 4-Hydroxybenzoic acid as a marker for the production of may reduce the inflammatory degree of acute gastrointestinal injury in sepsis.
Topics: Animals; Anti-Bacterial Agents; Cilastatin; Feces; Gastrointestinal Microbiome; Gastrointestinal Motility; Imipenem; Male; Mice; RNA, Ribosomal, 16S; Sepsis
PubMed: 33818419
DOI: 10.18632/aging.202768 -
Scientific Reports Aug 2017Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial cells to capture electrons from a cathode and fix carbon. Yet...
Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial cells to capture electrons from a cathode and fix carbon. Yet despite the promise of this technology, the metabolic capacity of the microbes that inhabit the electrode surface and catalyze electron transfer in these systems remains largely unknown. We assembled thirteen draft genomes from a microbial electrosynthesis system producing primarily acetate from carbon dioxide, and their transcriptional activity was mapped to genomes from cells on the electrode surface and in the supernatant. This allowed us to create a metabolic model of the predominant community members belonging to Acetobacterium, Sulfurospirillum, and Desulfovibrio. According to the model, the Acetobacterium was the primary carbon fixer, and a keystone member of the community. Transcripts of soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were found in high abundance near the electrode surface. Cytochrome c oxidases of facultative members of the community were highly expressed in the supernatant despite completely sealed reactors and constant flushing with anaerobic gases. These molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.
Topics: Acetates; Acetobacterium; Bioelectric Energy Sources; Campylobacteraceae; Carbon Dioxide; Desulfovibrio; Electricity; Electrodes; Electron Transport; Gene Expression Profiling; Genome, Bacterial; Metabolic Networks and Pathways
PubMed: 28827682
DOI: 10.1038/s41598-017-08877-z