-
The Journal of International Medical... Oct 2022Although uncommon, infection caused by may be life threatening particularly in immunocompromised patients. We report here a rare presentation of a patient with diffuse... (Review)
Review
Although uncommon, infection caused by may be life threatening particularly in immunocompromised patients. We report here a rare presentation of a patient with diffuse large B-cell lymphoma and haemophagocytic syndrome associated with bacteraemia. The management of the patient is described as well as a review of medical literature. Infection by species, including should be considered in a febrile patient with a haematologic malignancy. The case highlights the importance of using gene sequencing for identification of this anaerobic organism.
Topics: Clostridium; Clostridium Infections; Humans; Lymphohistiocytosis, Hemophagocytic; Lymphoma, Large B-Cell, Diffuse; RNA, Ribosomal, 16S
PubMed: 36217260
DOI: 10.1177/03000605221129558 -
IDCases 2022is an anaerobic spore-forming bacterium rarely isolated in human infections. This case study presents a necrotizing infection stemming from a dental abscess that...
is an anaerobic spore-forming bacterium rarely isolated in human infections. This case study presents a necrotizing infection stemming from a dental abscess that progressed into sepsis, a small pericardial effusion, moderate bilateral pulmonary effusions, and multiple organ dysfunction syndrome. The management of the infection, along with other relevant cases is discussed.
PubMed: 35127448
DOI: 10.1016/j.idcr.2022.e01416 -
Nature Chemical Biology Feb 2022Substrate efflux by ATP-binding cassette (ABC) transporters, which play a major role in multidrug resistance, entails the ATP-powered interconversion between transporter...
Substrate efflux by ATP-binding cassette (ABC) transporters, which play a major role in multidrug resistance, entails the ATP-powered interconversion between transporter intermediates. Despite recent progress in structure elucidation, a number of intermediates have yet to be visualized and mechanistically interpreted. Here, we combine cryogenic-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy and molecular dynamics simulations to profile a previously unobserved intermediate of BmrCD, a heterodimeric multidrug ABC exporter from Bacillus subtilis. In our cryo-EM structure, ATP-bound BmrCD adopts an inward-facing architecture featuring two molecules of the substrate Hoechst-33342 in a striking asymmetric head-to-tail arrangement. Deletion of the extracellular domain capping the substrate-binding chamber or mutation of Hoechst-coordinating residues abrogates cooperative stimulation of ATP hydrolysis. Together, our findings support a mechanistic role for symmetry mismatch between the nucleotide binding and the transmembrane domains in the conformational cycle of ABC transporters and is of notable importance for rational design of molecules for targeted ABC transporter inhibition.
Topics: ATP-Binding Cassette Transporters; Adenosine Triphosphate; Bacterial Proteins; Benzimidazoles; Binding Sites; Clostridium; Cryoelectron Microscopy; Models, Molecular; Molecular Dynamics Simulation; Protein Conformation
PubMed: 34931066
DOI: 10.1038/s41589-021-00936-x -
Applied Microbiology and Biotechnology Oct 2020Gluten is a cereal protein that is incompletely digested by human proteolytic enzymes that create immunogenic peptides that accumulate in the gastrointestinal tract...
Gluten is a cereal protein that is incompletely digested by human proteolytic enzymes that create immunogenic peptides that accumulate in the gastrointestinal tract (GIT). Although both environmental and human bacteria have been shown to expedite gluten hydrolysis, gluten intolerance is a growing concern. Here we hypothesize that together with food, we acquire environmental bacteria that could impact our GIT with gluten-degrading bacteria. Using in vitro gastrointestinal simulation conditions, we evaluated the capacity of endophytic bacteria that inhabit root vegetables, potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), and topinambur (Jerusalem artichoke) (Helianthus tuberosus), to resist these conditions and degrade gluten. By 16S rDNA sequencing, we discovered that bacteria from the families Enterobacteriaceae, Bacillaceae, and Clostridiaceae most effectively multiply in conditions similar to the human GIT (microoxic conditions, 37 °C) while utilizing vegetable material and gluten as nutrients. Additionally, we used stomach simulation (1 h, pH 3) and intestinal simulation (1 h, bile salts 0.4%) treatments. The bacteria that survived this treatment retained the ability to degrade gluten epitopes but at lower levels. Four bacterial strains belonging to species Bacillus pumilus, Clostridium subterminale, and Clostridium sporogenes isolated from vegetable roots produced proteases with postproline cleaving activity that successfully neutralized the toxic immunogenic epitopes. KEY POINTS: • Bacteria from root vegetables can degrade gluten. • Some of these bacteria can resist conditions mimicking gastrointestinal tract.
Topics: Bacteria; Celiac Disease; Clostridium; Gliadin; Glutens; Helianthus; Humans; Microbiota; Vegetables
PubMed: 32875365
DOI: 10.1007/s00253-020-10852-0 -
Scientific Reports May 2020Uncontrolled oxidative stress, reported in Salmonella and HIV infections, colorectal cancer or severe acute malnutrition, has been associated with anaerobic gut...
Uncontrolled oxidative stress, reported in Salmonella and HIV infections, colorectal cancer or severe acute malnutrition, has been associated with anaerobic gut microbiome alteration, impaired butyrate production, mucosal immunity dysregulation and disruption of host-bacterial mutualism. However, the role of major antioxidant molecules in the human body, such as glutathione, ascorbic acid and uric acid, has been neglected in this context. Here, we performed an in vitro metabolomics study of the 3 most odorous anaerobic microbes isolated from the human gut in our laboratory (Clostridium sporogenes, Clostridium subterminale and Romboutsia lituseburensis) when grown in anaerobiosis or in aerobiosis with these 3 antioxidant molecules via gas and liquid chromatography-mass spectrometry (GC/MS and LC/MS). There was no growth or volatile organic compound production in aerobic cultures without the 3 antioxidant molecules. In anaerobiosis, the major metabolic products of the bacteria were thiols, alcohols and short-chain fatty acid esters. The production of alkanes, cycloheptatriene and, paradoxically, increased butyrate production, was observed in the cultures grown in aerobiosis with the 3 antioxidant molecules. The qualitative shift suggests specific molecular mechanisms that remain to be elucidated. The increased production of butyrate, but also isobutyrate and isovalerate in vitro suggests that these 3 antioxidant molecules contributed to the maintenance and active resilience of host-bacterial mutualism against mucosal oxygen and uncontrolled oxidative stress in vivo.
Topics: Aerobiosis; Anaerobiosis; Antioxidants; Ascorbic Acid; Butyrates; Chromatography, Liquid; Clostridiales; Clostridium; Gas Chromatography-Mass Spectrometry; Gastrointestinal Microbiome; Glutathione; Humans; Metabolomics; Oxidative Stress; Oxygen; Uric Acid
PubMed: 32382092
DOI: 10.1038/s41598-020-64834-3 -
The Journal of Biological Chemistry May 2020There are a number of riboswitches that utilize the same ligand-binding domain to regulate transcription or translation. S-box (SAM-I) riboswitches, including the...
There are a number of riboswitches that utilize the same ligand-binding domain to regulate transcription or translation. S-box (SAM-I) riboswitches, including the riboswitch present in the gene, which encodes cystathionine γ-synthase, regulate the expression of genes involved in methionine metabolism in response to SAM, primarily at the level of transcriptional attenuation. A rarer class of S-box riboswitches is predicted to regulate translation initiation. Here we identified and characterized a translational S-box riboswitch in the gene from The regulatory mechanisms of riboswitches are influenced by the kinetics of ligand interaction. The half-life of the translational RNA-SAM complex is significantly shorter than that of the transcriptional RNA. This finding suggests that, unlike the transcriptional RNA, the translational riboswitch can make multiple reversible regulatory decisions. Comparison of both RNAs revealed that the second internal loop of helix P3 in the transcriptional RNA usually contains an A residue, whereas the translational RNA contains a C residue that is conserved in other S-box RNAs that are predicted to regulate translation. Mutational analysis indicated that the presence of an A or C residue correlates with RNA-SAM complex stability. Biochemical analyses indicate that the internal loop sequence critically determines the stability of the RNA-SAM complex by influencing the flexibility of residues involved in SAM binding and thereby affects the molecular mechanism of riboswitch function.
Topics: Bacteria; Clostridium; Gene Expression Regulation, Bacterial; Ligands; Protein Biosynthesis; RNA, Bacterial; Riboswitch; Transcription, Genetic
PubMed: 32209653
DOI: 10.1074/jbc.RA120.012853 -
Ultrasonics Sonochemistry Jun 2020Anticoagulants are the main drugs for the prevention and treatment of thromboembolism. However, most of the present anticoagulants have shortcomings and novel...
Anticoagulants are the main drugs for the prevention and treatment of thromboembolism. However, most of the present anticoagulants have shortcomings and novel anticoagulants are in great demand. Marine microorganisms are an important source of new drugs. Therefore, in this study, ultrasound was applied to enhance anticoagulant accumulation by marine Bacillus subtilis ZHX. Ultrasound parameters were optimized by single-factor experiments exploring the effects of ultrasound power, duration, duty cycle and the cell growth phases. The optimum conditions were exponential prophase (5 h) with 25 kHz frequency, 140 W power, and a 40% duty cycle for 5 min. The maximum anticoagulant activity (55.36 U/mL) was 1.73 times that of the control group, and the fermentation time was shortened by 3 h. Under optimal conditions, ultrasound increased the carbon utilization by Bacillus subtilis ZHX without significant changes in morphology, favoring cell growth and anticoagulant production. However, excessive ultrasound caused intracellular damage, which inhibited biomass accumulation, decreasing anticoagulant activity and even leading to cell rupture. This is the first report on the use of ultrasound to enhance anticoagulant production by Bacillus, and it provides useful information for scaling-up the process.
Topics: Anticoagulants; Biotechnology; Clostridium; Fermentation; Time Factors; Ultrasonic Waves
PubMed: 32044681
DOI: 10.1016/j.ultsonch.2020.104994 -
PloS One 2019It is extremely important to identify transcription factor binding sites (TFBSs). Some TFBSs are proposed to be bipartite motifs known as two-block motifs separated by...
It is extremely important to identify transcription factor binding sites (TFBSs). Some TFBSs are proposed to be bipartite motifs known as two-block motifs separated by gap sequences with variable lengths. While position weight matrix (PWM) is commonly used for the representation and prediction of TFBSs, dinucleotide weight matrix (DWM) enables expression of the interdependencies of neighboring bases. By incorporating DWM into the detection of bipartite motifs, we have developed a novel tool for ab initio motif detection, DIpartite (bipartite motif detection tool based on dinucleotide weight matrix) using a Gibbs sampling strategy and the minimization of Shannon's entropy. DIpartite predicts the bipartite motifs by considering the interdependencies of neighboring positions, that is, DWM. We compared DIpartite with other available alternatives by using test datasets, namely, of CRP in E. coli, sigma factors in B. subtilis, and promoter sequences in humans. We have developed DIpartite for the detection of TFBSs, particularly bipartite motifs. DIpartite enables ab initio prediction of conserved motifs based on not only PWM, but also DWM. We evaluated the performance of DIpartite by comparing it with freely available tools, such as MEME, BioProspector, BiPad, and AMD. Taken the obtained findings together, DIpartite performs equivalently to or better than these other tools, especially for detecting bipartite motifs with variable gaps. DIpartite requires users to specify the motif lengths, gap length, and PWM or DWM. DIpartite is available for use at https://github.com/Mohammad-Vahed/DIpartite.
Topics: Base Pairing; Clostridium; Computational Biology; Cyclic AMP Receptor Protein; Escherichia coli; Escherichia coli Proteins; Humans; Nucleotide Motifs; Position-Specific Scoring Matrices; Promoter Regions, Genetic; Sigma Factor
PubMed: 31469855
DOI: 10.1371/journal.pone.0220207 -
Infectious Disease Reports Sep 2018Botulism is caused by toxin production from many species of , most commonly as well as and . Development of wound botulism is associated with injection drug users but...
Botulism is caused by toxin production from many species of , most commonly as well as and . Development of wound botulism is associated with injection drug users but has also been described in traumatic injuries with exposure to soil. A patient presented to the emergency department with a complaint of descending, progressive weakness. He recently reported skin popping with heroin injections. Heptavalent botulinum antitoxin was obtained from the [Center for Disease Control and Prevention (CDC)]. On hospital day seven, the anaerobic wound cultures resulted with growth of .
PubMed: 30344967
DOI: 10.4081/idr.2018.7654 -
Case Reports in Infectious Diseases 2018is a rare member of the family that is rarely cultured. This report examines a case of cultured from the blood of a 72-year-old man who was ultimately diagnosed with...
is a rare member of the family that is rarely cultured. This report examines a case of cultured from the blood of a 72-year-old man who was ultimately diagnosed with metastatic gastrointestinal (GI) adenocarcinoma. The patient was receiving treatment for nosocomial pneumonia prior to culture of the , which led to suspicion for malignancy. Extensive GI and oncologic workup demonstrated multiple comorbidities and a primary GI cancer, which likely caused a breach in the GI mucosa and entrance into the bloodstream. After a prolonged intensive care unit (ICU) stay, the patient died on hospital day 23. Though rarely reported, septicemia has been demonstrated in patients with malignancy, specifically of the GI tract. Therefore, this case represents a typical septicemia patient. Given the prevalence of and the contemporary emergence of multidrug resistant (MDR) microorganisms, both typical and atypical cases regarding rare members of the species have a significant role in the clinical management and public health planning.
PubMed: 29951328
DOI: 10.1155/2018/6031510