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The ISME Journal Oct 2021Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have...
Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found in geographically widespread deep subsurface locations. In order to constrain models for subsurface microbial evolution, we compared CDA genomes from Africa, North America and Eurasia using single cell genomics. Unexpectedly, 126 partial single amplified genomes from the three continents, a complete genome from of an isolate from Eurasia, and metagenome-assembled genomes from Africa and Eurasia shared >99.2% average nucleotide identity, low frequency of SNP's, and near-perfectly conserved prophages and CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, and unusually strong purifying selection as likely explanations for these unexpected results. We therefore conclude that the analyzed CDA populations underwent only minimal evolution since their physical separation, potentially as far back as the breakup of Pangea between 165 and 55 Ma ago. High-fidelity DNA replication and repair mechanisms are the most plausible explanation for the highly conserved genome of CDA. CDA presents a stark contrast to the current model organisms in microbial evolutionary studies, which often develop adaptive traits over far shorter periods of time.
Topics: Genomics; Metagenome; Mining; Peptococcaceae; Phylogeny
PubMed: 33824425
DOI: 10.1038/s41396-021-00965-3 -
Philosophical Transactions of the Royal... Apr 2013In this report, a complete description of Desulfitobacterium hafniense strain PCP-1 is presented. The D. hafniense strain PCP-1 was isolated from a methanogenic... (Review)
Review
In this report, a complete description of Desulfitobacterium hafniense strain PCP-1 is presented. The D. hafniense strain PCP-1 was isolated from a methanogenic consortium for its capacity to dehalogenate pentachlorophenol (PCP) into 3-chlorophenol. This strain is also capable of dehalogenating several other chloroaromatic compounds and tetrachloroethene into trichloroethene. Four gene loci encoding putative chlorophenol-reductive dehalogenases (CprA2 to CprA5) were detected, and the products of two of these loci have been demonstrated to dechlorinate different chlorinated phenols. Strain PCP-1 was used in laboratory-scale bioprocesses to degrade PCP present in contaminated environments. Desulfitobacterium hafniense PCP-1 is an excellent candidate for the development of efficient bioprocesses to degrade organohalide compounds.
Topics: Biodegradation, Environmental; Chlorophenols; Desulfitobacterium; Gene Expression Regulation, Bacterial; Gene Transfer, Horizontal; Genes, Bacterial; Genetic Loci; Halogenation; Pentachlorophenol; Phylogeny; RNA, Ribosomal, 16S; Species Specificity; Transcription, Genetic
PubMed: 23479749
DOI: 10.1098/rstb.2012.0319 -
Food Science & Nutrition Jun 2023Ulcerative colitis is a chronic and recurrent gastrointestinal intestinal disease accompanied by inflammatory disorders, immunologic inadequacy, and intestinal flora...
Ulcerative colitis is a chronic and recurrent gastrointestinal intestinal disease accompanied by inflammatory disorders, immunologic inadequacy, and intestinal flora dysbiosis, and current therapeutic pharmaceuticals have limited side effects. In this study, we revealed the extraction method of , analyzed the main component, compared the effect of its extract, , and conventional drugs with different properties on DSS (dextran sodium sulfate)-induced colitis, and indicated extract regulatory properties of inestinal flora. A colitis model was established on experimental design, and BALB/c mice (male, 7 weeks old) were randomly assigned to five groups ( = 10): control, DSS model, extract (CSE), GG (LGG), and 5-aminosalicylic acid (5-ASA) groups. The three treatments could alleviate the symptoms and remit inflammation induced by DSS, in which CSE and LGG groups could both decrease the proinflammatory cytokine IL-6, IL-8, and TNF-α levels and increase anti-inflammatory cytokines IL-10 and TGF-β. The CSE intervention significantly promoted the higher production of butyric acid than LGG and 5-ASA groups ( < .05) after DSS challenge. Analysis of intestinal flora showed that CSE administration remarkably decreased the relative abundance of pathogenic bacteria and and exhibited higher abundance of and than LGG in intestinal tract of mice ( < .05). These findings indicated that extract may have been beneficial for preventing and treating colitis.
PubMed: 37324926
DOI: 10.1002/fsn3.3282 -
Philosophical Transactions of the Royal... Apr 2013Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based... (Review)
Review
Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.
Topics: Bacterial Proteins; Databases, Genetic; Desulfitobacterium; Electron Transport; Genes, Bacterial; Hydrocarbons, Halogenated; Hydrolases; Phylogeny; RNA, Ribosomal, 16S; Species Specificity; Substrate Specificity
PubMed: 23479752
DOI: 10.1098/rstb.2012.0322 -
Frontiers in Endocrinology 2021The intestinal flora of gut microbiota in obese Chinese children and adolescents with and without insulin resistance (IR) was analyzed, as well as associations between...
OBJECTIVE
The intestinal flora of gut microbiota in obese Chinese children and adolescents with and without insulin resistance (IR) was analyzed, as well as associations between the gut microbiota and two serum cytokines related to glucose metabolism, adropin and angiopoietin-like 4 (ANGPTL4).
METHODS
Clinical data, fecal bacterial composition, glucose-related hormones, and serum adipokines (adropin and ANGPTL4) were analyzed in 65 Chinese children with exogenous obesity. The composition of the gut microbiota was determined by 16S rRNA-based metagenomics and IR was calculated using the homeostasis model assessment (HOMA).
RESULTS
The 65 obese subjects were divided into two groups: insulin sensitive (IS) (n=40, 57.5% males) or IR (n=25, 60% males). Principal coordinates analysis revealed that the gut microbiota samples from the IS group clustered together and separated partly from the IR group (p=0.008). By Mann-Whitney -test, at a phylum level, a reduction of and an increase of in the IR subjects was observed. LEfSe analysis revealed that IS subject, when compared to their IR counterparts, harbored members of the order , , and family , that were significantly more abundant. In contrast, the IR subjects had members of family that were significantly more prevalent than the IS subjects (all <0.05). Spearman's correlation analysis revealed that serum ANGPTL4 was positively associated with genus , and , and adropin was positively associated with genus and , and negatively associated with genus (all p<0.05).
CONCLUSION
In obese children, the gut microbiome in IR subjects was significantly discordant from the IS subjects, and the abundance of some metabolism-related bacteria correlated with the serum concentrations of adropin and ANGPTL4. These observations infer that the gut microbiota may be involved in the regulation of glucose metabolism in obesity.
Topics: Adolescent; Angiopoietin-Like Protein 4; Bacteria; Child; China; Cross-Sectional Studies; Cytokines; Diet; Feces; Female; Gastrointestinal Microbiome; Genomics; Glucose; Humans; Insulin Resistance; Male; Metagenome; Pediatric Obesity; Principal Component Analysis; RNA, Ribosomal, 16S
PubMed: 33815293
DOI: 10.3389/fendo.2021.636272 -
Heliyon Oct 2021Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through...
Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through production of corrosive metabolites ( sulfide), which is why clay materials are highly compacted: to reduce both physical space and access to water for microorganisms to grow. However, the highly compacted nature of clays and the resulting low activity or dormancy of microorganisms complicate the extraction of biomarkers ( PLFA, DNA .) from such barriers for predictive analysis of microbial risks. In order to overcome these challenges, we have combined culture- and 16S rRNA gene amplicon sequencing-based approaches to describe the functional diversity of microorganisms in several commercial clay products, including two different samples of Wyoming type MX-80 bentonite (Batch 1 and Batch 2), the reference clay for a future Canadian DGR, and Avonlea type Canaprill, a clay sample for comparison. Microorganisms from bentonites were enriched in anoxic 10% w/v clay microcosms for three months at ambient temperature with addition of 10% hydrogen along with presumable indigenous organics and sulfate in the clay. High-throughput sequencing of 16S rRNA gene fragments indicated a high abundance of Gram-positive bacteria of the phylum Firmicutes (82%) in MX-80 Batch 1 incubations. Bacterial libraries from microcosms with MX-80 Batch 2 were enriched with Firmicutes (53%) and Chloroflexi (43%). Firmicutes also significantly contributed (<15%) to the bacterial community in Canaprill clay microcosm, which was dominated by Gram-negative Proteobacteria (>70%). Sequence analysis revealed presence of the bacterial families and in MX-80 Batch 1 incubations; along with unidentified bacteria of the phylum Chloroflexi, in MX-80 Batch 2 clay microcosms, and in Canaprill microcosms. Exploration of potential metabolic pathways in the bacterial communities from the clay microcosms suggested variable patterns of sulfur cycling in the different clays with the possible prevalence of bacterial sulfate-reduction in MX-80 bentonite, and probably successive sulfate-reduction/sulfur-oxidation reactions in Canaprill microcosms. Furthermore, analysis of potential metabolic pathways in the bentonite enrichments suggested that bacteria with acid-producing capabilities (, fermenters and acetogens) together with sulfide-producing prokaryotes might perhaps contribute to corrosion risks in clay systems. However, the low activity or dormancy of microorganisms in highly compacted bentonites as a result of severe environmental constraints ( low water activity and high swelling pressure in the confined bentonite) would be expected to largely inhibit bacterial activity in highly compacted clay-based barriers in a future DGR.
PubMed: 34703919
DOI: 10.1016/j.heliyon.2021.e08131 -
International Journal of Molecular... Oct 2017Sulfated quercetin derivatives are important authentic standards for metabolic studies. Quercetin-3'--sulfate, quercetin-4'--sulfate, and quercetin-3--sulfate as well as...
Sulfated quercetin derivatives are important authentic standards for metabolic studies. Quercetin-3'--sulfate, quercetin-4'--sulfate, and quercetin-3--sulfate as well as quercetin-di--sulfate mixture (quercetin-7,3'-di--sulfate, quercetin-7,4'-di--sulfate, and quercetin-3',4'-di--sulfate) were synthetized by arylsulfotransferase from . Purified monosulfates and disulfates were fully characterized using MS and NMR and tested for their 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS⁺) and ,dimethyl--phenylenediamine (DMPD) radical scavenging, Folin-Ciocalteau reduction (FCR), ferric reducing antioxidant power (FRAP), and anti-lipoperoxidant activities in rat liver microsomes damaged by -butylhydroperoxide. Although, as expected, the sulfated metabolites were usually less active than quercetin, they remained still effective antiradical and reducing agents. Quercetin-3'--sulfate was more efficient than quercetin-4'--sulfate in DPPH and FCR assays. In contrast, quercetin-4'--sulfate was the best ferric reductant and lipoperoxidation inhibitor. The capacity to scavenge ABTS and DMPD was comparable for all substances, except for disulfates, which were the most efficient. Quantum calculations and molecular dynamics simulations on membrane models supported rationalization of free radical scavenging and lipid peroxidation inhibition. These results clearly showed that individual metabolites of food bioactives can markedly differ in their biological activity. Therefore, a systematic and thorough investigation of all bioavailable metabolites with respect to native compounds is needed when evaluating food health benefits.
Topics: Antioxidants; Arylsulfotransferase; Desulfitobacterium; Quercetin; Structure-Activity Relationship; Sulfates
PubMed: 29068411
DOI: 10.3390/ijms18112231 -
Nutrients Dec 2022Capsaicin, a natural bioactive component, has been reported to improve cognition and ameliorate the pathology of Alzheimer's disease (AD). Studies have linked AD to...
Capsaicin, a natural bioactive component, has been reported to improve cognition and ameliorate the pathology of Alzheimer's disease (AD). Studies have linked AD to alterations in gut microbiota composition and serum metabolites. In the present study, we examined the alterations in serum metabolome and gut microbiome in APPswe/PS1dE9 (APP/PS1) mice treated with capsaicin. Capsaicin treatments resulted in a significant increase in the abundance of , , , and and a significant decrease in the abundance of , , , and . Furthermore, the species () was significantly enriched in capsaicin-treated APP/PS1 mice ( = 0.0002). Serum metabolomic analysis showed that capsaicin-treated APP/PS1 mice had a significant higher level of tryptophan (Trp) metabolism and a significantly lower level of lipid metabolism compared with vehicle-treated mice. Capsaicin altered serum metabolites, including Kynurenine (Kyn), 5-Hydroxy-L-tryptophan (5-HIT), 5-Hydroxyindoleacetic acid (5-HIAA), indoxylsulfuric acid, lysophosphatidyl cholines (LysoPCs), and lysophosphatidyl ethanolamine (LysoPE). Significant correlations were observed between the gut bacteria and serum metabolite. With regard to the increased abundance of and the ensuing rise in tryptophan metabolites, our data show that capsaicin alters both the gut microbiota and blood metabolites. By altering the gut microbiome and serum metabolome, a diet high in capsaicin may reduce the incidence and development of AD.
Topics: Mice; Animals; Gastrointestinal Microbiome; Capsaicin; Tryptophan; Metabolome; Alzheimer Disease; Cognition
PubMed: 36615777
DOI: 10.3390/nu15010118 -
Aging Cell Mar 2024The Methionine restriction (MR) diet has been shown to delay aging and extend lifespan in various model organisms. However, the long-term effects of MR diet on the gut...
The Methionine restriction (MR) diet has been shown to delay aging and extend lifespan in various model organisms. However, the long-term effects of MR diet on the gut microbiome composition remain unclear. To study this, male mice were started on MR and control diet regimens at 6 months and continued until 22 months of age. MR mice have reduced body weight, fat mass percentage, and bone mineral density while having increased lean mass percentage. MR mice also have increased insulin sensitivity along with increasing indirect calorimetry markers such as energy expenditure, oxygen consumption, carbon dioxide production, and glucose oxidation. Fecal samples were collected at 1 week, 18 weeks, and 57 weeks after the diet onset for 16S rRNA amplicon sequencing to study the gut microbiome composition. Alpha and beta diversity metrics detected changes occurring due to the timepoint variable, but no changes were detected due to the diet variable. The results from LEfSe analysis surprisingly showed that more bacterial taxa changes were linked to age rather than diet. Interestingly, we found that the long-term MR diet feeding induced smaller changes compared to short-term feeding. Specific taxa changes due to the diet were observed at the 1 or 18-week time points, including Ileibacterium, Odoribacter, Lachnoclostridium, Marinifilaceae, and Lactobacillaceae. Furthermore, there were consistent aging-associated changes across both groups, with an increase in Ileibacterium and Erysipelotrichaceae with age, while Eubacterium_coprostanoligenes_group, Ruminococcaceae, Peptococcaceae, and Peptococcus decreased with age.
Topics: Male; Mice; Animals; Methionine; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Diet; Body Weight; Racemethionine
PubMed: 38279509
DOI: 10.1111/acel.14051 -
Microorganisms Apr 2021Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long...
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
PubMed: 33925267
DOI: 10.3390/microorganisms9050931