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Biochimica Et Biophysica Acta.... Sep 2021Studies of the lipidomes of twenty-one species of clostridia have revealed considerable diversity. Even among those species now defined as Clostridium sensu stricto,... (Review)
Review
Studies of the lipidomes of twenty-one species of clostridia have revealed considerable diversity. Even among those species now defined as Clostridium sensu stricto, which are related to Clostridium butyricum, the type species, lipid analysis has shown that a number of distinct clades have characteristic polar lipids. All species of Clostridium sensu stricto have phosphatidylethanolamine, phosphatidylglycerol and cardiolipin which are present as all acyl or alk-1'-enyl acyl (plasmalogen) species. In addition, almost every clade has specialized polar lipids. For example, the group closely related to Clostridium beijerinckii and several other solventogenic species has glycerol acetals of plasmenylethanolamine, which protects the membrane bilayer arrangement when the lipids are highly unsaturated or in the presence of solvents. The group related to Clostridium novyi has aminoacyl-phosphatidylglycerol, which protects these pathogens from cationic antimicrobial peptides (CAMPs) of innate immunity. Clostridium botulinum species, which fall into several groups, align with these clades, and have the same specific lipids. This review will present the current state of knowledge on clostridial lipids.
Topics: Clostridium; Lipidomics
PubMed: 33974975
DOI: 10.1016/j.bbalip.2021.158966 -
BMJ Open Diabetes Research & Care Jul 2020A growing body of evidence suggests that specific, naturally occurring gut bacteria are under-represented in the intestinal tracts of subjects with type 2 diabetes (T2D)... (Randomized Controlled Trial)
Randomized Controlled Trial
Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation.
INTRODUCTION
A growing body of evidence suggests that specific, naturally occurring gut bacteria are under-represented in the intestinal tracts of subjects with type 2 diabetes (T2D) and that their functions, like gut barrier stability and butyrate production, are important to glucose and insulin homeostasis. The objective of this study was to test the hypothesis that enteral exposure to microbes with these proposed functions can safely improve clinical measures of glycemic control and thereby play a role in the overall dietary management of diabetes.
RESEARCH DESIGN AND METHODS
We evaluated whether a probiotic comprised of these anaerobic bacteria would enhance dietary management by (1) manufacturing two novel probiotic formulations containing three (WBF-010) or five (WBF-011) distinct strains in a Current Good Manufacturing Practice (cGMP) facility, (2) establishing consistent live-cell concentrations, (3) confirming safety at target concentrations dispensed in both animal and human studies and (4) conducting a 12-week parallel, double-blind, placebo-controlled, proof-of-concept study in which subjects previously diagnosed with T2D (n=76) were randomly assigned to a two times a day regimen of placebo, WBF-010 or WBF-011.
RESULTS
No safety or tolerability issues were observed. Compared with the placebo group, subjects administered WBF-011 (which contains inulin, and ) significantly improved in the primary outcome, glucose total area under the curve (AUC): -36.1 mg/dL/180 min, p=0.0500 and also improved in secondary outcomes, glycated hemoglobin (A1c): -0.6, glucose incremental-AUC: -28.6 mg/dL/180 min.
CONCLUSIONS
To our knowledge, this is the first randomized controlled trial to administer four of the five strains to human subjects with T2D. This proof-of-concept study (clinical trial number NCT03893422) shows that the intervention was safe and well tolerated and that supplementation with WBF-011 improves postprandial glucose control. The limited sample size and intersubject variability justifies future studies designed to confirm and expand on these observations.
Topics: Blood Glucose; Clostridiales; Diabetes Mellitus, Type 2; Humans; Hypoglycemic Agents; Probiotics
PubMed: 32675291
DOI: 10.1136/bmjdrc-2020-001319 -
Frontiers in Bioengineering and... 2022The presence of lignocellulose-derived microbial inhibitory compounds (LDMICs) in lignocellulosic biomass (LB) hydrolysates is a barrier to efficient conversion of LB...
The presence of lignocellulose-derived microbial inhibitory compounds (LDMICs) in lignocellulosic biomass (LB) hydrolysates is a barrier to efficient conversion of LB hydrolysates to fuels and chemicals by fermenting microorganisms. Results from this study provide convincing evidence regarding the effectiveness of metabolically engineered NCIMB 8052 for the fermentation of LB-derived hydrolysates to acetone-butanol-ethanol (ABE). The engineered microbial strain (_SDR) was produced by the integration of an additional copy of a short-chain dehydrogenase/reductase (SDR) gene (3904) into the chromosome of NCIMB 8052 wildtype, where it is controlled by the constitutive thiolase promoter. The _SDR and NCIMB 8052 wildtype were used for comparative fermentation of non-detoxified and detoxified hydrothermolysis-pretreated switchgrass hydrolysates (SHs) with and without (NH)CO supplementation. In the absence of (NH)CO, fermentation of non-detoxified SH with _SDR resulted in the production of 3.13- and 2.25-fold greater quantities of butanol (11.21 g/L) and total ABE (20.24 g/L), respectively, than the 3.58 g/L butanol and 8.98 g/L ABE produced by _wildtype. When the non-detoxified SH was supplemented with (NH)CO, concentrations were similar for butanol (9.5 compared with 9.2 g/L) and ABE (14.2 compared with 13.5 g/L) produced by _SDR and _wildtype, respectively. Furthermore, when _SDR and _wildtype were cultured in detoxified SH medium, _SDR produced 1.11- and 1.18-fold greater quantities of butanol and ABE, respectively, than when there was culturing with _wildtype. When the combined results of the present study are considered, conclusions are that the microbial strain and medium modifications of the fermentation milieu resulted in greater production of fuels and chemicals from non-detoxified LB hydrolysates.
PubMed: 35992339
DOI: 10.3389/fbioe.2022.942701 -
Biology Nov 2022One of the most severe soil-borne pathogens in the world is the root-knot nematode (Meloidogyne incognita). Biological control is gaining more importance as...
One of the most severe soil-borne pathogens in the world is the root-knot nematode (Meloidogyne incognita). Biological control is gaining more importance as environmental awareness increases. Thus, keeping this in mind, a total of 712 bacterial strains were isolated from 117 rhizosphere soil samples and investigated for potential biological control activity against M. incognita. Strain Sneb518 (Clostridium beijerinckii) was identified as having solid biocontrol activity against M. incognita. Sneb518 demonstrated significant inhibition against M. incognita, with J2 mortality reaching 90.73% at 12 h and with eggs hatching at a rate of 6.00% at 24 h, compared to a hatchability level of 29.07% for the control. Additionally, Sneb518 was excellent for enhancing seed germination. The seeds coated with a fermentation broth containing Sneb518 efficiently boosted the germination rate to 88.49%. The effectiveness and stability of C. beijerinckii Sneb518 against M. incognita were then further evaluated in a greenhouse. According to the pot experiment data, Sneb518 considerably (p < 0.05) reduced the number of root galls and egg masses on roots and also significantly (p < 0.05) increased tomato plant growth. C. beijerinckii Sneb518-treated tomato seedlings exhibited 50.26% biocontrol effectiveness compared to the control group. Our results demonstrate that C. beijerinckii Sneb518 can be a potential biological control agent against root-knot nematode disease and a biomass enhancer. This research will give new options for the sustainable control of root-knot nematode disease in tomatoes and other host plants.
PubMed: 36552234
DOI: 10.3390/biology11121724 -
AMB Express May 2022Acetone-butanol-ethanol (ABE) fermentation is a traditional way for solvents production through bioconversion by Clostridium species. It is still a challenge to obtain...
Acetone-butanol-ethanol (ABE) fermentation is a traditional way for solvents production through bioconversion by Clostridium species. It is still a challenge to obtain metabolic engineering strains with high ABE yield. Screening strains with remarkable characteristics from nature and improving ABE yield by mutation are viable approaches. Clostridium beijerinckii XH 0906, a newly isolated strain, produces butanol and isopropanol (BI) as the main end-products (9.1 g/L BI) during fermentation with glucose as the sole carbon source. The screening process for this strain was performed under aerobic conditions rather than anaerobic environment. Thus, it is a robust stain capable of oxygen-tolerant BI fermentation. Furthermore, C. beijerinckii XH 0906 fermented xylose and glucose simultaneously to produce BI. A mutant strain obtained by ultraviolet (UV) mutagenesis, C. beijerinckii XH 29, had improved BI production capacity and could produce 17.0 g/L BI and 18.4 g/L BI using glucose or corn stover hydrolysate, respectively as the carbon source. Interestingly, C. beijerinckii XH 29 also produced up to 19.3 g/L isopropanol through fermentation of a glucose-acetone mix. These results indicate that C. beijerinckii XH 29 is an excellent BI producer with great potential for industrial applications.
PubMed: 35567691
DOI: 10.1186/s13568-022-01399-6 -
BMC Genomics Apr 2018There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of...
BACKGROUND
There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C. beijerinckii DSM 6423 (NRRL B-593). This strain metabolizes sugars into a mix of IBE with only low concentrations of ethanol produced (< 1 g/L). However, despite its relative ancient discovery, few genomic details have been described for this strain. Research efforts including omics and genetic engineering approaches are therefore needed to enable the use of C. beijerinckii as a microbial cell factory for production of isopropanol.
RESULTS
The complete genome sequence and a first transcriptome analysis of C. beijerinckii DSM 6423 are described in this manuscript. The combination of MiSeq and de novo PacBio sequencing revealed a 6.38 Mbp chromosome containing 6254 genomic objects. Three Mobile Genetic Elements (MGE) were also detected: a linear double stranded DNA bacteriophage (ϕ6423) and two plasmids (pNF1 and pNF2) highlighting the genomic complexity of this strain. A first RNA-seq transcriptomic study was then performed on 3 independent glucose fermentations. Clustering analysis allowed us to detect some key gene clusters involved in the main life cycle steps (acidogenesis, solvantogenesis and sporulation) and differentially regulated among the fermentation. These putative clusters included some putative metabolic operons comparable to those found in other reference strains such as C. beijerinckii NCIMB 8052 or C. acetobutylicum ATCC 824. Interestingly, only one gene was encoding for an alcohol dehydrogenase converting acetone into isopropanol, suggesting a single genomic event occurred on this strain to produce isopropanol.
CONCLUSIONS
We present the full genome sequence of Clostridium beijerinckii DSM 6423, providing a complete genetic background of this strain. This offer a great opportunity for the development of dedicated genetic tools currently lacking for this strain. Moreover, a first RNA-seq analysis allow us to better understand the global metabolism of this natural isopropanol producer, opening the door to future targeted engineering approaches.
Topics: 2-Propanol; Bioreactors; Clostridium beijerinckii; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genome, Bacterial; Sequence Analysis, RNA; Spores, Bacterial; Transcriptome
PubMed: 29636009
DOI: 10.1186/s12864-018-4636-7 -
Biotechnology For Biofuels 2018One of the main challenges of acetone-butanol-ethanol fermentation is to reduce acetone production with high butanol yield. Converting acetone into isopropanol is an...
BACKGROUND
One of the main challenges of acetone-butanol-ethanol fermentation is to reduce acetone production with high butanol yield. Converting acetone into isopropanol is an alternative pathway to reduce fermentation by-products in the fermentation broth. Here, we aimed to cultivate a wild-type strain with high isopropanol and butanol production and reveal its genome information.
RESULTS
strain BGS1 was found to be capable of producing 10.21 g/L butanol and 3.41 g/L isopropanol, higher than previously known wild-type isopropanol-butanol-producing species. Moreover, culture BGS1 exhibited a broad carbon spectrum utilizing diverse sugars such as arabinose, xylose, galactose, cellobiose, and sucrose, with 9.61 g/L butanol and 2.57 g/L isopropanol generated from 60 g/L sucrose and less amount from other sugars. Based on genome analysis, protein-based sequence of strain BGS1 was closer to NCIMB 8052, reaching 90.82% similarity, while compared to DSM 6423, the similarity was 89.53%. In addition, a unique secondary alcohol dehydrogenase (sAdhE) was revealed in the genome of strain BGS1, which distinguished it from other species. Average nucleotide identity analysis identified strain BGS1 belonging to . The transcription profile and enzymatic activity of sAdhE proved its function of converting acetone into isopropanol.
CONCLUSIONS
strain BGS1 is a potential candidate for industrial isopropanol and butanol production. Its genome provides unique information for genetic engineering of isopropanol-butanol-producing microorganisms.
PubMed: 30337959
DOI: 10.1186/s13068-018-1274-x -
Frontiers in Microbiology 2020SpoIIE is a phosphatase involved in the activation of the first sigma factor of the forespore, σ , during sporulation. A Δ mutant of NCIMB 8052, previously generated...
SpoIIE is a phosphatase involved in the activation of the first sigma factor of the forespore, σ , during sporulation. A Δ mutant of NCIMB 8052, previously generated by CRISPR-Cas9, did not sporulate but still produced granulose and solvents. Microscopy analysis also showed that the cells of the Δ mutant are elongated with the presence of multiple septa. This observation suggests that in , SpoIIE is necessary for the completion of the sporulation process, as seen in and . Moreover, when grown in reactors, the mutant produced higher levels of solvents than the wild type strain. The impact of the inactivation on gene transcription was assessed by comparative transcriptome analysis at three time points (4 h, 11 h and 23 h). Approximately 5% of the genes were differentially expressed in the mutant compared to the wild type strain at all time points. Out of those only 12% were known sporulation genes. As expected, the genes belonging to the regulon of the sporulation specific transcription factors (σ , σ , σ , σ ) were strongly down-regulated in the mutant. Inactivation of also caused differential expression of genes involved in various cell processes at each time point. Moreover, at 23 h, genes involved in butanol formation and tolerance, as well as in cell motility, were up-regulated in the mutant. In contrast, several genes involved in cell wall composition, oxidative stress and amino acid transport were down-regulated. These results indicate an intricate interdependence of sporulation and stationary phase cellular events in .
PubMed: 33042064
DOI: 10.3389/fmicb.2020.556064 -
Toxins Aug 2019The aim of this study was to assess occurrence of and in honey samples from Kazakhstan. Analyses were carried out using a set of PCR methods for identification of...
The aim of this study was to assess occurrence of and in honey samples from Kazakhstan. Analyses were carried out using a set of PCR methods for identification of anaerobic bacteria, and detection of toxin genes of and . Among 197 samples, was noticed in only one (0.5%). The isolated strain of this pathogen showed the presence of the and genes. strains were isolated from 18 (9%) samples, and mPCR (multiplex PCR) analysis led to them all being classified as toxin type A with the ability to produce α toxin. Sequence analysis of 16S rDNA genes showed occurrence in 4 samples of other anaerobes related to , which were and strains. prevalence in honey samples from Kazakhstan in comparison to the prevalence in samples collected from the other regions seems to be less. The highest prevalence of sp. was noticed in the East Kazakhstan province. Our study is the first survey on BoNT-producing clostridia and prevalence in Kazakh honey.
Topics: Clostridium botulinum; Clostridium perfringens; DNA, Ribosomal; Honey; Kazakhstan; RNA, Ribosomal, 16S; Real-Time Polymerase Chain Reaction
PubMed: 31412583
DOI: 10.3390/toxins11080472 -
Biotechnology For Biofuels 2019Inefficient utilization of glycerol by () is a major impediment to adopting glycerol metabolism as a strategy for increasing NAD(P)H regeneration, which would in turn,...
BACKGROUND
Inefficient utilization of glycerol by () is a major impediment to adopting glycerol metabolism as a strategy for increasing NAD(P)H regeneration, which would in turn, alleviate the toxicity of lignocellulose-derived microbial inhibitory compounds (LDMICs, e.g., furfural), and improve the fermentation of lignocellulosic biomass hydrolysates (LBH) to butanol. To address this problem, we employed a metabolic engineering strategy to enhance glycerol utilization by .
RESULTS
By overexpressing two glycerol dehydrogenase (Gldh) genes ( and ) from the glycerol hyper-utilizing () as a fused protein in , we achieved approximately 43% increase in glycerol consumption, when compared to the plasmid control. Further, _+ achieved a 59% increase in growth, while butanol and acetone-butanol-ethanol (ABE) concentrations and productivities increased 14.0%, 17.3%, and 55.6%, respectively, relative to the control. Co-expression of + and + dihydroxyacetone kinase () resulted in significant payoffs in cell growth and ABE production compared to expression of one Gldh. In the presence of 4-6 g/L furfural, increased glycerol consumption by the + strain increased cell growth (> 50%), the rate of furfural detoxification (up to 68%), and ABE production (up to 40%), relative to the plasmid control. Likewise, over-expression of [(+ ) ] improved butanol and ABE production by 70% and 50%, respectively, in the presence of 5 and 6 g/L furfural relative to the plasmid control.
CONCLUSIONS
Overexpression of and in significantly enhanced glycerol utilization, ABE production, and furfural tolerance by . Future research will address the inability of recombinant to metabolize glycerol as a sole substrate.
PubMed: 30899330
DOI: 10.1186/s13068-019-1388-9