Characterization of an operon required for growth on cellobiose in Clostridioides difficile

Regulatory networks: Linking toxin production and sporulation in Clostridioides difficile

Clostridioides difficile has been recognized as an important nosocomial pathogen that causes diarrheal disease as a consequence of antibiotic exposure and costs the healthcare system billions of dollars every year. C. difficile enters the host gut as dormant spores, germinates into vegetative cells, colonizes the gut, and produces toxins TcdA and/or TcdB, leading to diarrhea and inflammation. Spores are the primary transmission vehicle, while the toxins A and B directly contribute to the disease. Thus, toxin production and sporulation are the key traits that determine the success of C. difficile as a pathogen. Both toxins and spores are produced during the late stationary phase in response to various stimuli. This review provides a comprehensive analysis of the current knowledge on the molecular mechanisms, highlighting the regulatory pathways that interconnect toxin gene expression and sporulation in C. difficile. The roles of carbohydrates, amino acids and other nutrients and signals, in modulating these virulence traits through global regulatory networks are discussed. Understanding the links within the gene regulatory network is crucial for developing effective therapeutic strategies against C. difficile infections, potentially leading to targeted interventions that disrupt the co-regulation of toxin production and sporulation.

Influence of microbiota on the growth and gene expression of Clostridioides difficile in an in vitro coculture model

Clostridioides difficile is an anaerobic, spore-forming, Gram-positive pathogenic bacterium. This study aimed to analyze the effect of two samples of healthy fecal microbiota on C. difficile gene expression and growth using an in vitro coculture model. The inner compartment was cocultured with spores of the C. difficile polymerase chain reaction (PCR)-ribotype 078, while the outer compartment contained fecal samples from donors to mimic the microbiota (FD1 and FD2). A fecal-free plate served as a control (CT). RNA-Seq and quantitative PCR confirmation were performed on the inner compartment sample. Similarities in gene expression were observed in the presence of the microbiota. After 12 h, the expression of genes associated with germination, sporulation, toxin production, and growth was downregulated in the presence of the microbiota. At 24 h, in an iron-deficient environment, C. difficile activated several genes to counteract iron deficiency. The expression of genes associated with germination and sporulation was upregulated at 24 h compared with 12 h in the presence of microbiota from donor 1 (FD1). This study confirmed previous findings that C. difficile can use ethanolamine as a primary nutrient source. To further investigate this interaction, future studies will use a simplified coculture model with an artificial bacterial consortium instead of fecal samples.

Role of glycogen metabolism in Clostridioides difficile virulence

Glycogen plays a vital role as an energy reserve in various bacterial and fungal species. Clostridioides difficile possesses a glycogen metabolism operon that contains genes for both glycogen synthesis and utilization. In our investigation, we focused on understanding the significance of glycogen metabolism in the physiology and pathogenesis of C. difficile. To explore this, we engineered a C. difficile JIR8094 strain lacking glycogen synthesis capability by introducing a group II intron into the glgC gene, the operon's first component. Quantification of intracellular glycogen levels validated the impact of this modification. Interestingly, the mutant strain exhibited a 1.5-fold increase in toxin production compared with the parental strain, without significant changes in the sporulation rate. Our analysis also revealed that wild-type C. difficile spores contained glycogen, whereas spores from the mutant strain lacking stored glycogen showed increased sensitivity to physical and chemical treatments and had a shorter storage life. By suppressing glgP expression, the gene coding for glycogen-phosphorylase, via CRISPRi, we demonstrated that glycogen accumulation but not the utilization is needed for spore resilience in C. difficile. Transmission electron microscopy analysis revealed a significantly lower core/cortex ratio in glgC mutant strain spores. In hamster challenge experiments, both the parental and glgC mutant strains colonized hosts similarly; however, the mutant strain failed to induce infection relapse after antibiotic treatment cessation. These findings highlight the importance of glycogen metabolism in C. difficile spore resilience and suggest its role in disease relapse.IMPORTANCEThis study on the role of glycogen metabolism in Clostridioides difficile highlights its critical involvement in the pathogen's energy management, its pathogenicity, and its resilience. Our results also revealed that glycogen presence in spores is pivotal for their structural integrity and resistance to adverse conditions, which is essential for their longevity and infectivity. Importantly, the inability of the mutant strain to cause infection relapse in hamsters post-antibiotic treatment pinpoints a potential target for therapeutic interventions, highlighting the importance of glycogen in disease dynamics. This research thus significantly advances our understanding of C. difficile physiology and pathogenesis, offering new avenues for combating its persistence and recurrence.

Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability

BACKGROUND

Paenibacillus polymyxa is a bacterial species of high interest, as suggested by the increased number of publications on its functions in the past years. Accordingly, the number of described strains and sequenced genomes is also on the rise. While functional diversity of P. polymyxa has been suggested before, the available genomic data is now sufficient for robust comparative genomics analyses.

RESULTS

Using 157 genomes, we found significant disparities among strains currently affiliated to P. polymyxa. Multiple taxonomic groups were identified with conserved predicted functions putatively impacting their respective ecology. As strains of this species have been reported to exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic organization to facilitate reliable and durable approval as active ingredients.

CONCLUSIONS

Strains currently affiliated to P. polymyxa can be separated into two major species groups with differential potential in nitrogen fixation, plant interaction, secondary metabolism, and antimicrobial resistance, as inferred from genomic data.

The state of play of rodent models for the study of Clostridioides difficile infection

Clostridioides difficile is the most common cause of nosocomial antibiotic-associated diarrhoea and is responsible for a spectrum of diseases characterized by high levels of recurrence and morbidity. In some cases, complications can lead to death. Currently, several types of animal models have been developed to study various aspects of C. difficile infection (CDI), such as colonization, virulence, transmission and recurrence. These models have also been used to test the role of environmental conditions, such as diet, age and microbiome that modulate infection outcome, and to evaluate several therapeutic strategies. Different rodent models have been used successfully, such as the hamster model and the gnotobiotic and conventional mouse models. These models can be applied to study either the initial CDI infectious process or recurrences. The applications of existing rodent models and their advantages and disadvantages are discussed here.

Transcriptional regulation of cellobiose utilization by PRD-domain containing Sigma54-dependent transcriptional activator (CelR) and catabolite control protein A (CcpA) in Bacillus thuringiensis

Cellobiose, a β-1,4-linked glucose dimer, is a major cellodextrin resulting from the enzymatic hydrolysis of cellulose. It is a major source of carbon for soil bacteria. In bacteria, the phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS), encoded by the cel operon, is responsible for the transport and utilization of cellobiose. In this study, we analyzed the transcription and regulation of the cel operon in Bacillus thuringiensis (Bt). The cel operon is composed of five genes forming one transcription unit. β-Galactosidase assays revealed that cel operon transcription is induced by cellobiose, controlled by Sigma54, and positively regulated by CelR. The HTH-AAA+ domain of CelR recognized and specifically bound to three possible binding sites in the celA promoter region. CelR contains two PTS regulation domains (PRD1 and PRD2), which are separated by two PTS-like domains-the mannose transporter enzyme IIA component domain (EIIAMan) and the galactitol transporter enzyme IIB component domain (EIIBGat). Mutations of His-546 on the EIIAMan domain and Cys-682 on the EIIBGat domain resulted in decreased transcription of the cel operon, and mutations of His-839 on PRD2 increased transcription of the cel operon. Glucose repressed the transcription of the cel operon and catabolite control protein A (CcpA) positively regulated this process by binding the cel promoter. In the celABCDE and celR mutants, PTS activities were decreased, and cellobiose utilization was abolished, suggesting that the cel operon is essential for cellobiose utilization. Bt has been widely used as a biological pesticide. The metabolic properties of Bt are critical for fermentation. Nutrient utilization is also essential for the environmental adaptation of Bt. Glucose is the preferred energy source for many bacteria, and the presence of the phosphotransferase system allows bacteria to utilize other sugars in addition to glucose. Cellobiose utilization pathways have been of particular interest owing to their potential for developing alternative energy sources for bacteria. The data presented in this study improve our understanding of the transcription patterns of cel gene clusters. This will further help us to better understand how cellobiose is utilized for bacterial growth.

Extracellular succinate induces spatially organized biofilm formation in Clostridioides difficile

Clostridioides difficile infection associated to gut microbiome dysbiosis is the leading cause for nosocomial diarrhea. The ability of C. difficile to form biofilms has been progressively linked to its pathogenesis as well as its persistence in the gut. Although C. difficile has been reported to form biofilms in an increasing number of conditions, little is known about how these biofilms are formed in the gut and what factors may trigger their formation. Here we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, induces in vitro biofilm formation of C. difficile strains. We characterized the morphology and spatial composition of succinate-induced biofilms, and compared to non-induced or deoxycholate (DCA) induced biofilms. Biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS). We then applied transcriptomics and genetics to characterize the early stages of succinate-induced biofilm formation and we showed that succinate-induced biofilm results from major metabolic shifts and cell-wall composition changes. Similar to DCA-induced biofilms, biofilms induced by succinate depend on the presence of a rapidly metabolized sugar. Finally, although succinate can be consumed by the bacteria, we found that the extracellular succinate is in fact responsible for the induction of biofilm formation through complex regulation involving global metabolic regulators and the osmotic stress response. Thus, our work suggests that as a gut signal, succinate may drive biofilm formation and help persistence of C. difficile in the gut, increasing the risk of relapse.

A comprehensive review on the properties, production, and applications of functional glucobioses

Glucobiose is a range of disaccharides consisting of two glucose molecules, generally including trehalose, kojibiose, sophorose, nigerose, laminaribiose, maltose, cellobiose, isomaltose, and gentiobiose. The difference glycosidic bonds of two glucose molecules result in the diverse molecular structures, physiochemical properties and physiological functions of these glucobioses. Some glucobioses are abundant in nature but have unconspicuous roles on health like maltose, whereas some rare glucobioses display remarkable biological effects. It is unpractical process to extract these rare glucobioses from natural resources, while biological synthesis is a feasible approach. Recently, the production and application of glucobiose have attracted considerable attention. This review provides a comprehensive overview of glucobioses, including their natural sources and physicochemical properties like structure, sweetness, digestive performance, toxicology, and cariogenicity. Specific enzymes used for the production of various glucobioses and fermentation production processes are summarized. Additionally, their versatile functions and broad applications are also introduced.

One size does not fit all - Trehalose metabolism by Clostridioides difficile is variable across the five phylogenetic lineages

Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. Here, growth in trehalose as the sole carbon source was shown to be non-uniform across representative C. difficile strains, even though the genes for its metabolism were induced. Growth in trehalose reduced the expression of genes associated with toxin production and sporulation in the C. difficile R20291 (RT027) and M120 (RT078) strains in vitro, suggesting an inhibitory effect on virulence factors. Interestingly, the R20291 TreR transcriptional regulatory protein appeared to possess an activator function as its DNA-binding ability was increased in the presence of its effector, trehalose-6-phosphate. Using RNA-sequencing analysis, we report the identification of a putative trehalose metabolism pathway which is induced during growth in trehalose: this has not been previously described within the C. difficile species. These data demonstrate the metabolic diversity exhibited by C. difficile which warrants further investigation to elucidate the molecular basis of trehalose metabolism within this important gut pathogen.

Food for thought-The link between Clostridioides difficile metabolism and pathogenesis

Clostridioides difficile (C. difficile) is an opportunistic pathogen that leads to antibiotic-associated diarrhoea and is a leading cause of morbidity and mortality worldwide. Antibiotic usage is the main risk factor leading to C. difficile infection (CDI), as a dysbiotic gut environment allows colonisation and eventual pathology manifested by toxin production. Although colonisation resistance is mediated by the action of secondary bile acids inhibiting vegetative outgrowth, nutrient competition also plays a role in preventing CDI as the gut microbiota compete for nutrient niches inhibiting C. difficile growth. C. difficile is able to metabolise carbon dioxide, the amino acids proline, hydroxyproline, and ornithine, the cell membrane constituent ethanolamine, and the carbohydrates trehalose, cellobiose, sorbitol, and mucin degradation products as carbon and energy sources through multiple pathways. Zinc sequestration by the host response mediates metabolic adaptation of C. difficile by perhaps signalling an inflamed gut allowing it to acquire abundant nutrients. Persistence within the gut environment is also mediated by the by-products of metabolism through the production of p-cresol, which inhibit gut commensal species growth promoting dysbiosis. This review aims to explore and describe the various metabolic pathways of C. difficile, which facilitate its survival and pathogenesis within the colonised host gut.

Development and evaluation of temperature-sensitive Mycoplasma anserisalpingitidis clones as vaccine candidates

Mycoplasma anserisalpingitidis is economically the most important pathogenic Mycoplasma species of waterfowl in Europe and Asia. The lack of commercially available vaccines against M. anserisalpingitidis had prompted this study with the aim to produce temperature-sensitive (ts⁺) clones as candidates for an attenuated live vaccine. The production of ts⁺ clones was performed by N-methyl-N'-nitro-N-nitrosoguanidine (NTG)-evoked mutagenesis of Hungarian M. anserisalpingitidis field isolates. The clones were administered via eye drop and intracloacally to 33-day-old geese. Colonisation ability was examined by PCR and isolation from the trachea and cloaca, while the serological response of the birds was tested by ELISA. Pathological and histopathological examinations were performed at the eighth week after inoculation. Whole-genome sequence (WGS) analysis of the selected clone and its parent strain was also performed. NTG-treatment provided three ts⁺ mutants (MA177/1/11, MA177/1/12, MA271). MA271 was detected at the highest rate from cloacal (86.25%) and tracheal (30%) samples, while MA177/1/12 and MA271 elicited remarkable serological responses with 90% of the animals showing seroconversion. Re-isolates of MA271 remained ts⁺ throughout the experiment. Based on these properties, clone MA271 was found to be the most promising vaccine candidate. WGS analysis revealed 59 mutations in the genome of MA271 when compared to its parent strain, affecting both polypeptides involved in different cellular processes and proteins previously linked to bacterial fitness and virulence. Although further studies are needed to prove that MA271 is in all aspects a suitable vaccine strain, it is expected that this ts⁺ clone will contribute to the control of M. anserisalpingitidis infection.