Physiology and Sporulation in Clostridium

Application of bacteria-mediated gene therapy in tumor treatment

INTRODUCTION

Gene therapy refers to the use of vectors to introduce target genes into target cells to exert a therapeutic effect on tumors. As a new type of tumor therapy, gene therapy has the advantage of precision and specificity. Excellent delivery vehicles have a major impact on the efficiency, precision and safety of gene therapy. Unlike traditional vectors, bacteria based on prokaryotes have the advantages of good targeting, large load, and simplicity. In addition, different types of bacteria also have characteristics that can be used in various scenarios.

AREAS COVERED

In this review, we searched the gene therapy-related literature in PubMed, mainly in the last five years, and compared the characteristics of different gene vectors, focusing on the bacterial gene therapy and aiming to explore excellent bacterial gene therapy programs.

EXPERT OPINION

Compared with traditional tumor gene therapy vectors, bacteria have many advantages, such as good targeting, large carrying capacity, and simple production. Meanwhile, the combination of artificial intelligence technology, bacterial imaging probe technology and suicide genes will be expected to control the bacterial therapy process, improve the safety of treatment, and promote the translational application of bacterial gene therapy.

Recovery of Clostridium from soil using Heat Shock enrichment technique and Agar Deeps

Some members of the genus Clostridium can produce butanol and hydrogen from renewable substrates contributing to biofuel production. In recent years, there has been a growing social demand for its utilization to realize a sustainable society. Clostridium is also attracting attention in the medical field, and research is being conducted to use it as a prodrug treatment and an intestinal bacterium to reduce cancer. Clostridium is a very attractive research subject. However, because Clostridium is an obligatory anaerobe, it requires expensive equipment not used to culture aerobic bacteria, making it difficult to start research on it. In this study, we developed an inexpensive and highly selective method for isolating Clostridium that does not require special equipment. This method combines two methods to increase the selectivity of Clostridium: the heat shock enrichment method, which selects non-spore-forming bacteria, and the agar deep method, which selects anaerobic bacteria based on their oxygen requirement. Using the isolation method developed in this study, we succeeded in isolating 11 new species of Clostridium. In total, 17 species of 3 genera were obtained from soil samples (0.2 g each) from only eight locations. Surprisingly, this represents 7.5 % of Clostridium reported to date.

The Probiotic Strain Clostridium butyricum TO-A Produces Butyrate by Utilizing Lactate and Acetate

Lactate-utilizing bacteria (LUB) are intestinal bacteria that produce butyrate from lactate and acetate, key metabolites in the gut. As LUB help maintain lactate and butyrate concentrations in the intestinal tract, they are promising probiotic candidates. Clostridium butyricum TO-A (CBTOA) has reportedly been effective in treating various gastrointestinal issues in humans and animals. Although CBTOA is known to increase intestinal butyrate levels, it is unclear how it utilizes lactate and acetate, similar to LUB, to produce butyrate. We investigated lactate utilization-related genes in CBTOA and examined the relationship between lactate and acetate utilization and butyrate production using peptone-yeast medium supplemented with D-lactate, L-lactate, and/or acetate. This study demonstrates for the first time that the probiotic strain CBTOA harbors lactate utilization-related genes and efficiently produces butyrate only in the presence of exogenous lactate and acetate instead of sugars. Furthermore, CBTOA expresses a lactate racemase that enables the bacterium to utilize both lactate enantiomers while regulating the ratio of D-lactate to L-lactate in the intestinal microenvironment via racemization. In conclusion, CBTOA efficiently produces butyrate utilizing lactate and acetate, similar to LUB; therefore, CBTOA could be an efficient butyrate supplier as a probiotic strain in the intestinal tract.

The "brain-gut" mechanism of postherpetic neuralgia: a mini-review

Postherpetic neuralgia (PHN), a representative type of neuropathic pain, has attracted much research on its diagnosis and therapy at the molecular level. Interestingly, this study based on the brain-gut axis provided a novel point of view to interpret the mechanism of PHN. Past neuroanatomical and neuroimaging studies of pain suggest that the prefrontal cortex, anterior cingulate cortex, amygdala, and other regions of the brain may play crucial roles in the descending inhibition of PHN. Dominant bacterial species in patients with PHN, such as Lactobacillus, generate short-chain fatty acids, including butyrate. Evidence indicates that disturbance of some metabolites (such as butyrate) is closely related to the development of hyperalgesia. In addition, tryptophan and 5-HT in the intestinal tract act as neurotransmitters that regulate the descending transmission of neuropathic pain signals. Concurrently, the enteric nervous system establishes close connections with the central nervous system through the vagus nerve and other pathways. This review aims to investigate and elucidate the molecular mechanisms associated with PHN, focusing on the interplay among PHN, the gut microbiota, and relevant metabolites while scrutinizing its pathogenesis.

From pre-culture to solvent: current trends in Clostridium acetobutylicum cultivation

The biological production of butanol via ABE (acetone-butanol-ethanol) fermentation using Clostridium acetobutylicum has a storied history of over 100 years, initially driven by the demand for synthetic rubber during World War I and later for industrial applications. Despite its decline due to the rise of petrochemical alternatives, renewed interest has emerged due to the global shift towards sustainable energy sources and rising oil prices. This review highlights the challenges in the cultivation process of C. acetobutylicum, such as strain degeneration, solvent toxicity, and substrate costs, and presents recent advancements aimed at overcoming these issues. Detailed documentation of the entire cultivation process including cell conservation, pre-culture, and main culture is seen as a fundamental step to facilitate further progress in research. Key strategies to improve production efficiency were identified as controlling pH to facilitate the metabolic shift from acidogenesis to solventogenesis, employing in situ product removal techniques, and advancing metabolic engineering for improved solvent tolerance of C. acetobutylicum. Furthermore, the use of renewable resources, particularly lignocellulosic biomass, positions ABE fermentation as a viable solution for sustainable solvent production. By focusing on innovative research avenues, including co-cultivation and bioelectrochemical systems, the potential for C. acetobutylicum to contribute significantly to a bio-based economy can be realized. KEY POINTS: • Historical significance and revival of ABE fermentation with Clostridium acetobutylicum • Current challenges and innovative solutions in cultivating C. acetobutylicum • New avenues for enhancing productivity and sustainability.

Gut microbiota and their metabolites in the immune response of rheumatoid arthritis: Therapeutic potential and future directions

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by persistent joint inflammation, damage, and loss of function. In recent years, the role of gut microbiota and its metabolites in immune regulation has attracted increasing attention. The gut microbiota influences the host immune system's homeostasis through various mechanisms, regulating the differentiation, function, and immune tolerance of immune cells. Dysbiosis of the gut microbiota in RA patients is closely associated with abnormal activation of immune cells and excessive secretion of inflammatory cytokines. Metabolites produced by the gut microbiota, such as short-chain fatty acids (SCFAs), tryptophan metabolites, bile acids, and amino acid metabolites, play a critical role in immune responses, regulating the functions of immune cells like T cells, B cells, and macrophages, and inhibiting the release of pro-inflammatory cytokines. Restoring the balance of the gut microbiota and optimizing the production of metabolic products may become a new strategy for RA treatment. This review discusses the role of gut microbiota and its metabolites in the immune response of RA, exploring how they influence the immunopathological process of RA through the regulation of immune cells and key immune factors. It also provides a theoretical basis for future therapeutic strategies based on gut microbiota modulation.

Isolation of Acanthamoeba Species and Bacterial Symbiont Variability in Puna Salt Plains, Argentina

Acanthamoeba spp. are widespread protists that feed on bacteria via phagocytosis. This predation pressure has led many bacteria to evolve strategies to resist and survive inside these protists. The impact of this is not well understood, but it may limit detection and allow survival in extreme environments. Three sites in the Puna salt plains, Catamarca province, Argentina, were sampled for Acanthamoeba spp., verified using PCR and Sanger sequencing. The intracellular microbiome was analysed with 16S rRNA gene sequencing and compared to the overall site microbiome. Acanthamoeba were found at all locations, and their intracellular microbiome was similar across samples but differed from the overall site microbiome. Pseudomonas spp., a clinically relevant genus, was most abundant in all isolates. This study suggests Acanthamoeba can protect bacteria, aiding their detection avoidance and survival in harsh conditions.

Effects of combined Bacillus coagulans and yeast fermentation culture on growth performance, plasma biochemical indices, intestinal morphology, and microbial of broilers

The favorable impacts of Bacillus coagulans or yeast culture on broiler production performance and immune function have been acknowledged. However, the effects of the combined them (BcYc) on the broilers remained unknown. Thus, the current research aimed to assess the effects of BcYc (at dosages of 0, 200, 300, and 400 mg/kg) on growth performance, plasma biochemical indices, antioxidant capacity, and intestinal morphology and microbial composition in broilers. The results revealed that 1) broilers receiving 300 and 400 mg/kg of BcYc showed significantly higher body weights than the control group at 4 d and 21 d (P < 0.05). Additionally, when contrasted with the control group, the feed conversion ratio was significantly decreased in 300 mg/kg group during 4 to 21 d and in 400 mg/kg group during 4 to 42 d (P < 0.05). 2) At 21 d, the broilers supplemented with 300 and 400 mg/kg of BcYc demonstrated significantly elevated levels of albumin (ALB), glutathione peroxidase activity (GSH-Px), total antioxidant capacity, and catalase activity than the group that not supplemented with BcYc (P < 0.05). At 42 d, 400 mg/kg group showed significantly higher ALB and total protein and lower glutamic-pyruvic transaminase activity and malondialdehyde content in contrast to the control group (P < 0.05). Furthermore, at 42 d, GSH-Px activity in all experimental groups showed significantly higher compared to the control group (P < 0.05). 3) Nevertheless, no significant variation was observed neither in the jejunum or duodenum morphology among all groups (P > 0.05). 4) Adding 400 mg/kg of BcYc led to a significantly higher Sobs index and a lower Simpson index (P < 0.05), and an extremely significantly raised in Shannon index (P < 0.01), while adding 300 mg/kg of BcYc led to a significantly enhanced in Shannon index (P < 0.05). Additionally, supplementary BcYc significantly elevated the abundance of Firmicutes at the phylum level and Clostridia, Ruminococcus, Rikenella, Butyricicoccus, and Eubacterium in the genus level (P < 0.05). To sum up, supplementing BcYc at dosages of 400 mg/kg to yellow-feathered broilers diet can help improve growth performance, regulate plasma biochemical indicators, increase antioxidant capacity, and improve gut community composition.

Multi-omics Analysis Reveals Key Gut Microbiota and Metabolites Closely Associated with Huntington's Disease

Dysbiosis of the gut microbiota is closely associated with neurodegenerative diseases, including Huntington's disease (HD). Gut microbiome-derived metabolites are key factors in host-microbiome interactions. This study aimed to investigate the crucial gut microbiome and metabolites in HD and their correlations. Fecal and serum samples from 11 to 26 patients with HD, respectively, and 16 and 23 healthy controls, respectively, were collected. The fecal samples were used for shotgun metagenomics while the serum samples for metabolomics analysis. Integrated analysis of the metagenomics and metabolomics data was also conducted. Firmicutes, Bacteroidota, Proteobacteria, Uroviricota, Actinobacteria, and Verrucomicrobia were the dominant phyla. At the genus level, the presence of Bacteroides, Faecalibacterium, Parabacteroides, Alistipes, Dialister, and Christensenella was higher in HD patients, while the abundance of Lachnospira, Roseburia, Clostridium, Ruminococcus, Blautia, Butyricicoccus, Agathobaculum, Phocaeicola, Coprococcus, and Fusicatenibacter decreased. A total of 244 differential metabolites were identified and found to be enriched in the glycerophospholipid, nucleotide, biotin, galactose, and alpha-linolenic acid metabolic pathways. The AUC value from the integrated analysis (1) was higher than that from the analysis of the gut microbiota (0.8632). No significant differences were found in the ACE, Simpson, Shannon, Sobs, and Chao indexes between HD patients and controls. Our study determined crucial functional gut microbiota and potential biomarkers associated with HD pathogenesis, providing new insights into the role of the gut microbiota-brain axis in HD occurrence and development.

Clostridium butyricum attenuates LPS-induced myocardial injury in septic mice by modulating CD4 + CD25 + FOXP3 + Treg

Sepsis-induced myocardial injury has become a major threat to patient health and safety. Intestinal microbiota imbalance plays a crucial role in sepsis regulation. Using 16srRNA technology, we explored how intestinal colonization of Clostridium butyricum over 28 days impacted mice with LPS-induced sepsis. Significant changes were noted in the gut microbiota of the mice, highlighting that C. butyricum can positively influence the immune state in septic myocardial injury models. The bacterium's ability to prevent intestinal mucosal damage and alleviate the immunosuppressive state during the later stages of sepsis by regulating CD4 + CD25 + FOXP3 + Treg cells is particularly noteworthy. This suggests a therapeutic role for C. butyricum in sepsis management by protecting against myocardial injury and improving immune regulation.

Resveratrol and β-hydroxy-β-methylbutyric acid supplementation promotes ileal development and digestive function by altering microbial community abundance and metabolites in Tibetan sheep

Introduction

The effects of resveratrol (RES) and β-hydroxy-β-methylbutyric acid (HMB) on phenotype, immunity, digestive enzyme activity and short-chain fatty acids (SCFAs) contents in ileum of Tibetan sheep were investigated.

Methods

A total of 120 two-month-old Tibetan sheep (15.5 ± 0.14 kg) were randomly allocated to 4 treatments: control group (basal diet), RES group (basal diet +1.5 g RES/d), HMB group (basal diet +1.25 g HMB/d), RES-HMB group (basal diet +1.5 g RES/d + 1.25 g HMB/d).

Results

Results indicated that dietary RES and (or) HMB supplementation significantly improved the phenotype (mucosal thickness and villus width), SCFAs concentrations, and digestive enzymes (lipase, cellulase, and α-amylase) (p < 0.05). The relative abundance of Brevibacillus, Clostridium sensu stricto 3, and Eubacterium hallii group were increased, while the abundance of Ruminococcus and Mogibacterium were decreased (p < 0.05) in the RES-HMB group. The metabolic profiling indicated an increase in the differential metabolites (DMs) including L-arginine, butanoic acid, D-mannose, and retinol were increased in the RES-HMB group (p < 0.05).

Discussion

In summary, our results suggested that RES and (or) HMB supplementation improved SCFAs concentration by up-regulating the microbial community abundance (Brevibacillus, Clostridium sensu stricto 3, and Eubacterium hallii group) and metabolism (L-arginine, butanoic acid, D-mannose, and retinol), thus contributing to ileal morphology and digestive enzyme activity. These findings may provides a novel reference for the nutritional regulation to improve the production of Tibetan sheep.

Bacterial microbiota associated with raw plant-based meat analogue products and their influences on selective enrichment for Escherichia coli O157:H7

Towards fostering a more sustainable food production system in face of the climate change challenge, alternative protein meat-substitute products that are plant-based and free of animal by-products have been gaining attractions from both food manufacturers and consumers. With these so-called plant-based meat analogues (PBMAs) becoming increasingly available at supermarkets, there is very little known about their microbial properties. In this short report, we characterized the bacterial composition of raw plant-based ground meat imitation retail products using 16S rRNA gene amplicon sequencing. Despite the observed bacterial community dissimilarity between sample brands, a total of 18 shared genera (dominated by Bacilli and Gammaproteobacteria classes) were identified as the core constituents of the bacterial microbiota of these PBMA products. Within the scope of food safety testing, to gain insights on the dynamics of the enrichment process for E. coli O157:H7 in accordance with the Health Canada reference method MFHPB-10, bacterial taxonomic analyses were conducted at different stages of the prescribed cultural procedures. Using both control and E. coli O157:H7-inoculated PBMA samples it was revealed that, independent of the presence of E. coli O157:H7, off-target bacteria of the Clostridium sensu stricto 1 genus were significantly enriched from the uncultured samples. Additionally, the abundance of Hafnia-Obesumbacterium bacteria in the PBMA samples was also increased in the enrichment products, but only when E. coli O157:H7 was absent. Consistent with the spread-plating results indicating that the inoculated E. coli O157:H7 cells were capable of reaching a high density (>108 CFU/ml) in the resultant enrichment cultures, the significant enrichment of bacterial 16S rRNA gene sequences belonging to the targeted genus of Escherichia, but not Hafnia-Obesumbacterium. This further highlights the competitive nature of the selective enrichment for E. coli O157:H7 against specific background bacteria associated with the PBMA products.

Gallic acid as biofilm inhibitor can improve transformation efficiency of Ruminiclostridium papyrosolvens

Ruminiclostridium papyrosolvens is an anaerobic, mesophilic, and cellulolytic clostridia, promising consolidated bioprocessing (CBP) candidate for producing renewable green chemicals from cellulose, but its genetic transformation has been severely impeded by extracellular biofilm. Here, we analyzed the effects of five different inhibitors with gradient concentrations on R. papyrosolvens growth and biofilm formation. Gallic acid was proved to be a potent inhibitor of biofilm synthesis of R. papyrosolvens. Furthermore, the transformation efficiency of R. papyrosolvens was significantly increased when the cells were treated by the gallic acid, and the mutant strain was successfully obtained by the improved transformation method. Thus, inhibition of biofilm formation of R. papyrosolvens by using gallic acid will contribute to its genetic transformation and efficient metabolic engineering.

Harnessing native-cryptic plasmids for stable overexpression of heterologous genes in Clostridium butyricum DSM 10702 for industrial and medical applications

Clostridium butyricum has emerged as a promising candidate for both industrial and medical biotechnologies, underscoring the key pursuit of stable gene overexpression in engineering C. butyricum. Unlike antibiotic-selective vectors, native-cryptic plasmids can be utilized for antibiotic-free expression systems in bacteria but have not been effectively exploited in C. butyricum to date. This study focuses on leveraging these plasmids, pCB101 and pCB102, in C. butyricum DSM10702 for stable gene overexpression without antibiotic selection via efficient gene integration using the SacB-based allelic exchange method. Integration of reporter IFP2.0 and glucuronidase generated sustained near-infrared fluorescence and robust enzyme activity across successive subcultures. Furthermore, successful secretion of a cellulase, Cel9M, and the human interleukin 10 from pCB102 highlights native-cryptic plasmids' potential in conferring stable gene products for industrial and medical applications in C. butyricum. This work appears to be the first study to harness the Clostridium native-cryptic plasmid for stable gene overexpression without antibiotics, thereby advancing the biotechnological prospects of C. butyricum.

Gut microbiota causally impacts adrenal function: a two-sample mendelian randomization study

Some studies have reported that the gut microbiota can influence adrenal-related hormone levels. However, the causal effects of the gut microbiota on adrenal function remain unknown. Therefore, we employed a two-sample Mendelian randomization (MR) study to systematically investigate the impact of gut microbiota on the function of different regions of the adrenal gland. The summary statistics for gut microbiota and adrenal-related hormones used in the two-sample MR analysis were derived from publicly available genome-wide association studies (GWAS). In the MR analysis, inverse variance weighting (IVW) was used as the primary method, with MR-Egger, weighted median, and cML-MA serving as supplementary methods for causal inference. Sensitivity analyses such as the MR-Egger intercept test, Cochran's Q test, and leave-one-out analysis were used to assess pleiotropy and heterogeneity. We identified 27 causal relationships between 23 gut microbiota and adrenal function using the IVW method. Among these, Sellimonas enhanced the function of the adrenal cortex reticularis zone (beta = 0.008, 95% CI: 0.002-0.013, P = 0.0057). The cML-MA method supported our estimate (beta = 0.009, 95% CI: 0.004-0.013, P = 2 × 10- 4). Parasutterella, Sutterella, and Anaerofilum affect the functioning of different regions of the adrenal gland. Notably, pleiotropy was not observed. Our findings revealed that the gut microbiota is causally associated with adrenal function. This enhances our understanding of the gut-microbiota-brain axis and provides assistance in the early diagnosis and treatment of adrenal-related diseases in clinical practice.

The causal relationship between gut microbiota and nine infectious diseases: a two-sample Mendelian randomization analysis

Background

Evidence from observational studies and clinical trials has associated gut microbiota with infectious diseases. However, the causal relationship between gut microbiota and infectious diseases remains unclear.

Methods

We identified gut microbiota based on phylum, class, order, family, and genus classifications, and obtained infectious disease datasets from the IEU OpenGWAS database. The two-sample Mendelian Randomization (MR) analysis was then performed to determine whether the gut microbiota were causally associated with different infectious diseases. In addition, we performed reverse MR analysis to test for causality.

Results

Herein, we characterized causal relationships between genetic predispositions in the gut microbiota and nine infectious diseases. Eight strong associations were found between genetic predisposition in the gut microbiota and infectious diseases. Specifically, the abundance of class Coriobacteriia, order Coriobacteriales, and family Coriobacteriaceae was found to be positively associated with the risk of lower respiratory tract infections (LRTIs). On the other hand, family Acidaminococcaceae, genus Clostridiumsensustricto1, and class Bacilli were positively associated with the risk of endocarditis, cellulitis, and osteomyelitis, respectively. We also discovered that the abundance of class Lentisphaeria and order Victivallales lowered the risk of sepsis.

Conclusion

Through MR analysis, we found that gut microbiota were causally associated with infectious diseases. This finding offers new insights into the microbe-mediated infection mechanisms for further clinical research.

Pathogenic avian mycoplasmas show phenotypic differences in their biofilm forming ability compared to non-pathogenic species in vitro

Mycoplasmas are known as the minimalist microorganisms in the microbes' world. Their minimalist nature makes them highly sensitive to the environmental conditions and limits their ability to survive for extended periods outside their animal host. Nevertheless, there are documented instances of mycoplasma transmission over significant distances and this phenomenon may be linked to relatively unexplored abilities of mycoplasmas, such as their capacity to synthesize biofilm-the predominant mode of bacterial growth in nature. The authors decided to establish a method aimed at inducing the clustering of mycoplasma planktonic cells within a biofilm in vitro and subsequently assess the capacity of certain avian mycoplasmas to synthesize a biofilm. A total of 299 avian mycoplasma isolates were included in the study, encompassing both pathogenic (Mycoplasma gallisepticum, M. synoviae, M. meleagridis, M. iowae) and non-pathogenic species (M. gallinaceum, M. gallinarum, M. iners and M. pullorum). The authors successfully demonstrated the feasibility of inducing avian mycoplasmas to synthetize in vitro a biofilm, which can be visually quantified. The only species that did not produce any biofilm was M. iowae. In general, the pathogenic mycoplasmas produced greater quantities of biofilm compared to the non-pathogenic ones. Furthermore, it was observed that the ability to produce biofilm appeared to vary, both qualitatively and quantitatively, not only among different species but also among isolates of a single species. Future studies will be necessary to determine whether biofilm production plays a pivotal epidemiological role for the pathogenic avian mycoplasmas.

Short-chain fatty acids: Important components of the gut-brain axis against AD

Alzheimer's disease (AD) comprises a group of neurodegenerative disorders with some changes in the brain, which could lead to the deposition of certain proteins and result in the degeneration and death of brain cells. Patients with AD manifest primarily as cognitive decline, psychiatric symptoms, and behavioural disorders. Short-chain fatty acids (SCFAs) are a class of saturated fatty acids (SFAs) produced by gut microorganisms through the fermentation of dietary fibre ingested. SCFAs, as a significant mediator of signalling, can have diverse physiological and pathological roles in the brain through the gut-brain axis, and play a positive effect on AD via multiple pathways. Firstly, differences in SCFAs and microbial changes have been stated in AD cases of humans and mice in this paper. And then, mechanisms of three main SCFAs in treating with AD have been summarized, as well as differences of gut bacteria. Finally, functions of SCFAs played in regulating intestinal flora homeostasis, modulating the immune system, and the metabolic system, which were considered to be beneficial for the treatment of AD, have been elucidated, and the key roles of gut bacteria and SCFAs were pointed out. All in all, this paper provides an overview of SCFAs and gut bacteria in AD, and can help people to understand the importance of gut-brain axis in AD.

Silk-derived sericin/fibroin mixture drink fermented with plant-derived Lactococcus lactis BM32-1 improves constipation and related microbiota: a randomized, double-blind, and placebo-controlled clinical trial

We previously showed through clinical trials that one plant-derived lactic acid bacteria (LAB) can improve constipation. We preliminarily found that the plant-derived LAB Lactococcus lactis BM32-1 can grow in a mixture of sericin and fibroin, which are extracted from silk and have been reported to help promote health. Thus, in the present study, we evaluated the favorable effect of a sericin/fibroin mixture (S/F-M), which was extracted from silk prepared from cocoons reared in an aseptic rearing system using an artificial diet, fermented with the BM32-1 strain through a clinical trial. The trial was conducted at Hiroshima University from June to October 2022 as a double-blind, placebo-controlled, randomized parallel-group comparative study with 50 eligible subjects (aged 23-71) who had an average defecation frequency of less than 5 times per week. The subjects were instructed to drink 100 mL of fermented S/F-M or placebo every day. After the 12 weeks of the clinical trial period, the average defecation frequency increased significantly-1.4 times higher than that at baseline in the test group-as compared with the placebo group. Furthermore, the fecal microbiota was also compared before and after treatment, revealing that intake of the fermented S/F-M significantly multiplied the relative abundance of the genera Enterococcus and Clostridium, which have been reported to contribute to the amelioration of constipation by improving the gut microbiota and producing butyric acid, respectively. In conclusion, the S/F-M fermented using the BM32-1 strain improves defecation frequency through alteration of the gut microbiota.

Multiplex genetic manipulations in Clostridium butyricum and Clostridium sporogenes to secrete recombinant antigen proteins for oral-spore vaccination

BACKGROUND

Clostridium spp. has demonstrated therapeutic potential in cancer treatment through intravenous or intratumoral administration. This approach has expanded to include non-pathogenic clostridia for the treatment of various diseases, underscoring the innovative concept of oral-spore vaccination using clostridia. Recent advancements in the field of synthetic biology have significantly enhanced the development of Clostridium-based bio-therapeutics. These advancements are particularly notable in the areas of efficient protein overexpression and secretion, which are crucial for the feasibility of oral vaccination strategies. Here, we present two examples of genetically engineered Clostridium candidates: one as an oral cancer vaccine and the other as an antiviral oral vaccine against SARS-CoV-2.

RESULTS

Using five validated promoters and a signal peptide derived from Clostridium sporogenes, a series of full-length NY-ESO-1/CTAG1, a promising cancer vaccine candidate, expression vectors were constructed and transformed into C. sporogenes and Clostridium butyricum. Western blotting analysis confirmed efficient expression and secretion of NY-ESO-1 in clostridia, with specific promoters leading to enhanced detection signals. Additionally, the fusion of a reported bacterial adjuvant to NY-ESO-1 for improved immune recognition led to the cloning difficulties in E. coli. The use of an AUU start codon successfully mitigated potential toxicity issues in E. coli, enabling the secretion of recombinant proteins in C. sporogenes and C. butyricum. We further demonstrate the successful replacement of PyrE loci with high-expression cassettes carrying NY-ESO-1 and adjuvant-fused NY-ESO-1, achieving plasmid-free clostridia capable of secreting the antigens. Lastly, the study successfully extends its multiplex genetic manipulations to engineer clostridia for the secretion of SARS-CoV-2-related Spike_S1 antigens.

CONCLUSIONS

This study successfully demonstrated that C. butyricum and C. sporogenes can produce the two recombinant antigen proteins (NY-ESO-1 and SARS-CoV-2-related Spike_S1 antigens) through genetic manipulations, utilizing the AUU start codon. This approach overcomes challenges in cloning difficult proteins in E. coli. These findings underscore the feasibility of harnessing commensal clostridia for antigen protein secretion, emphasizing the applicability of non-canonical translation initiation across diverse species with broad implications for medical or industrial biotechnology.

The impact of indole and mucin on sporulation, biofilm formation, and enterotoxin production in foodborne Clostridium perfringens

AIMS

Indole and mucin are compounds found in the host environment as they are produced by the host or by the host-associated microbiota. This study investigated whether indole and mucin impact Clostridium perfringens growth and sporulation, as well as enterotoxin production and biofilm formation.

METHODS AND RESULTS

There was no impact on growth of Cl. perfringens for up to 400 µM indole and 240 mg/l mucin, and neither indole nor mucin affected sporulation. Reverse-transcriptase qPCR showed that mucin strongly upregulated the expression of Cl. perfringens enterotoxin (up to 121-fold increase), whereas indole had a much more modest effect (2-fold). This was also reflected in increased Cl. perfringens enterotoxin levels in mucin-treated Cl. perfringens (as assessed by a reversed passive latex agglutination assay). Finally, mucin and indole significantly increased biofilm formation of Cl. perfringens, although the effect size was relatively small (less than 1.5 fold).

CONCLUSION

These results indicate that Cl. perfringens can sense its presence in a host environment by responding to mucin, and thereby markedly increased enterotoxin production.

Methylmalonic acid in aging and disease

Metabolic byproducts have conventionally been disregarded as waste products without functions. In this opinion article, we bring to light the multifaceted role of methylmalonic acid (MMA), a byproduct of the propionate metabolism pathway mostly commonly known as a clinical biomarker of vitamin B12 deficiency. MMA is normally present at low levels in the body, but increased levels can come from different sources, such as vitamin B12 deficiency, genetic mutations in enzymes related to the propionate pathway, the gut microbiota, and aggressive cancers. Here, we describe the diverse metabolic and signaling functions of MMA and discuss the consequences of increased MMA levels, such as during the aging process, for several age-related human pathologies.

Enhancing and monitoring spore production in Clostridium butyricum using pH-based regulation strategy and a robust soft sensor based on back-propagation neural networks

Clostridium butyricum is a probiotic that forms anaerobic spores and plays a crucial role in regulating gut microbiota. However, the total viable cell count and spore yield of C. butyricum in industrial production are comparatively low. To this end, we investigated the metabolic characteristics of the strain and proposed three distinct pH regulation strategies for enhancing spore production. In addition, precise measurement of fermentation parameters such as substrate concentration, total viable cell count, and spore concentration is crucial for successful industrial probiotics production. Nevertheless, online measurement of these intricate parameters in the fermentation of C. butyricum poses a considerable challenge owing to the complex, nonlinear, multivariate, and strongly coupled characteristics of the production process. Therefore, we analyzed the capacitance and conductivity acquired from a viable cell sensor as the core parameters for the fermentation process. Subsequently, a robust soft sensor was developed using a seven-input back-propagation neural network model with input variables of fermentation time, capacitance, conductivity, pH, initial total sugar concentration, ammonium ion concentration, and calcium ion concentration. The model enables the online monitoring of total viable biomass count, substrate concentrations, and spore yield, and can be extended to similar fermentation processes with pH changes as a characteristic feature.

Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer

Probiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.

The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force

Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.

Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis

Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.

Performance of fish sludge solubilization and phototrophic bioconversion by purple phototrophic bacteria for nutrient recovery in aquaponic system

Nutrient recovery from fish sludge in aquaponics is crucial to improve the economic output of a system sustainably and hygienically. Currently, fish sludge is treated using conventional anaerobic and aerobic mineralization, which does not allow the recovery of valuable nutrients in fish wastes. In this study, a two-stage approach (named as solubilization process and phototrophic bioconversion) is proposed to convert fish sludge into mineral nutrients and biomass nutrients using purple phototrophic bacteria (PPB), thereby promoting the growth of plants and fish simultaneously in aquaponics. Anaerobic and aerobic solubilization methods are tested to pretreat the fish sludge, generating substrates for PPB. Anaerobic solubilization yields 2.1 times more soluble chemical oxygen demand (SCOD) and 3.7 times more total volatile fatty acid (t-VFA) from fish sludge compared with aerobic solubilization. The anaerobic solubilization effluent indicates a CODt-VFA/SCOD of 60% and a VFA comprising 13.3% acetate and 49.0% propionate for PPB. The phototrophic bioconversion using anaerobic solubilization effluent under the light-anaerobic condition results in the highest biomass yield (0.94 g CODbiomass/g CODremoved) and the highest PPB dominance (Ectothiorhodospira, 58.7%). The anaerobic solubilization and light-anaerobic phototrophic bioconversion achieves 54.1% of carbon recovery efficiency (CRE) (in terms of COD), as well as 44.8% and 91.3% of nutrient recovery efficiency (NRE) for N and P. A novel multiloop aquaponic system combined with PPB-based nutrient recovery is proposed for the reuse of mineral nutrients and PPB biomass generated from fish sludge.

Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia

Carbohydrate utilization is critical to microbial survival. The phosphotransferase system (PTS) is a well-documented microbial system with a prominent role in carbohydrate metabolism, which can transport carbohydrates through forming a phosphorylation cascade and regulate metabolism by protein phosphorylation or interactions in model strains. However, those PTS-mediated regulated mechanisms have been underexplored in non-model prokaryotes. Here, we performed massive genome mining for PTS components in nearly 15,000 prokaryotic genomes from 4,293 species and revealed a high prevalence of incomplete PTSs in prokaryotes with no association to microbial phylogeny. Among these incomplete PTS carriers, a group of lignocellulose degrading clostridia was identified to have lost PTS sugar transporters and carry a substitution of the conserved histidine residue in the core PTS component, HPr (histidine-phosphorylatable phosphocarrier). Ruminiclostridium cellulolyticum was then selected as a representative to interrogate the function of incomplete PTS components in carbohydrate metabolism. Inactivation of the HPr homolog reduced rather than increased carbohydrate utilization as previously indicated. In addition to regulating distinct transcriptional profiles, PTS associated CcpA (Catabolite Control Protein A) homologs diverged from previously described CcpA with varied metabolic relevance and distinct DNA binding motifs. Furthermore, the DNA binding of CcpA homologs is independent of HPr homolog, which is determined by structural changes at the interface of CcpA homologs, rather than in HPr homolog. These data concordantly support functional and structural diversification of PTS components in metabolic regulation and bring novel understanding of regulatory mechanisms of incomplete PTSs in cellulose-degrading clostridia.

Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic

Objectives

To evaluate the population structure of environmental bacteria and fungi in three different types of medical institutions and the potential risks due to antibiotic resistance during the coronavirus disease 2019 (COVID-19) pandemic.

Methods

One hundred twenty-six environmental surface samples were collected from three medical institutions during the COVID-19 pandemic. A total of 6,093 and 13,514 representative sequences of 16S and ITS ribosomal RNA (rRNA) were obtained by amplicon sequencing analysis. The functional prediction was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States tool based on the Greengenes database and the FAPROTAX database.

Results

On environmental surfaces in three medical institutions during the COVID-19 pandemic, Firmicutes (51.6%) and Bacteroidetes (25%) were the dominant bacteria, while Ascomycota (39.4%) and Basidiomycota (14.2%) were the dominant fungi. A number of potential bacterial and fungal pathogens were successfully identified by the metagenomic approach. Furthermore, compared with the bacterial results, the fungi showed a generally closer Bray Curtis distance between samples. The overall ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7. The proportion of stress-tolerant bacteria in medical institutions A, B and C reached 88.9, 93.0 and 93.8%, respectively. Anaerobic bacteria accounted for 39.6% in outdoor environments, 77.7% in public areas, 87.9% in inpatient areas and 79.6% in restricted areas. Finally, the β-Lactam resistance pathway and polymyxin resistance pathway were revealed through functional prediction.

Conclusion

We described the microbial population structure changes in three different types of medical institutions using the metagenomic approach during the COVID-19 pandemic. We found that the disinfection measures performed by three healthcare facilities may be effective on the "ESKAPE" pathogens, but less effective on fungal pathogens. Moreover, emphasis should be given to the prevention and control of β-lactam and polymyxin antibiotics resistance bacteria during the COVID-19 pandemic.

Differences in clinical features and gut microbiota between individuals with methamphetamine casual use and methamphetamine use disorder

Background

The transition from methamphetamine (MA) casual use (MCU) to compulsive use is enigmatic as some MA users can remain in casual use, but some cannot. There is a knowledge gap if gut microbiota (GM) play a role in differing MCU from MA use disorder (MUD). We aimed to investigate the clinical features and GM differences between individuals with MCU and MUD.

Method

We recruited two groups of MA users -MCU and MUD - and matched them according to age and body mass index (n=21 in each group). Participants were accessed using the Semi-Structured Assessment for Drug Dependence and Alcoholism, and their fecal samples were undergone 16S ribosomal DNA sequencing. We compared the hosts' clinical features and GM diversity, composition, and structure (represented by enterotypes) between the two groups. We have identified differential microbes between the two groups and performed network analyses connecting GM and the clinical traits.

Result

Compared with the casual users, individuals with MUD had higher incidences of MA-induced neuropsychiatric symptoms (e.g., paranoia, depression) and withdrawal symptoms (e.g., fatigue, drowsiness, and increased appetite), as well as stronger cravings for and intentions to use MA, and increased MA tolerance. The GM diversity showed no significant differences between the two groups, but four genera (Halomonas, Clostridium, Devosia, and Dorea) were enriched in the individuals with MUD (p<0.05). Three distinct enterotypes were identified in all MA users, and Ruminococcus-driven enterotype 2 was dominant in individuals with MUD compared to the MCU (61.90% vs. 28.60%, p=0.03). Network analysis shows that Devosia is the hub genus (hub index = 0.75), which is not only related to the counts of the MUD diagnostic criteria (ρ=0.40; p=0.01) but also to the clinical features of MA users such as reduced social activities (ρ=0.54; p<0.01). Devosia is also associated with the increased intention to use MA (ρ=0.48; p<0.01), increased MA tolerance (ρ=0.38; p=0.01), craving for MA (ρ=0.37; p=0.01), and MA-induced withdrawal symptoms (p<0.05).

Conclusion

Our findings suggest that Ruminococcus-driven enterotype 2 and the genera Devosia might be two influential factors that differentiate MA casual use from MUD, but further studies are warranted.

Comparison of the Effects between Tannins Extracted from Different Natural Plants on Growth Performance, Antioxidant Capacity, Immunity, and Intestinal Flora of Broiler Chickens

In this study, four plant tannins, including AT (Acacia mearnsii tannin, 68%), CT (Castanea sativa tannin, 60%), QT (Schinopsis lorenzii tannin, 73%) and TT (Caesalpinia spinosa tannin, 50%) were added to broiler diets for 42 days to evaluate and compare their effects on growth performance, antioxidant capacity, immune performance and gut microbiota in broilers. The results showed that the supplementation of five tannins could increase the production of T-AOC, GSH-Px, SOD and CAT and reduce the production of MDA in the serum of broilers (p < 0.01), but the antioxidant effect of the AT group was lower than that of the other three groups (p < 0.01). All four tannins decreased the level of the pro-inflammatory factor IL-1β and increased the level of the anti-inflammatory factor IL-10 (p < 0.01). CT, QT and TT decreased the levels of pro-inflammatory factors IL-6 and TNF-α (p < 0.01), while AT and CT increased the level of IL-2 in serum (p < 0.01). Supplementation with four tannins also increased the levels of IgG, IgM, IgA and sIgA in serum (p < 0.01) and the levels of ZO-1, claudin-1 and occludin in the jejunum (p < 0.01). The detection results of ALT and AST showed that CT, QT and TT decreased the concentrations of ALT and AST in serum (p < 0.01). The results of the gut microbiota showed that the abundance of Clostridia and Subdoligranulum increased, and the abundance of Oscillospiraceae decreased, compared to the control group after adding the four tannins to the diets (p > 0.05). In addition, CT, QT and TT decreased the abundance of Lactobacillus and increased the abundance of Bacteroides compared to the control group, while AT showed the opposite result (p > 0.05). Overall, our study shows that tannins derived from different plants have their own unique effects on broilers. AT and CT can promote broilers' growth better than other tannins, CT has the best ability to improve immune and antioxidant properties, and QT and TT have the best effect on broilers' liver protection.

Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity

Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when grown continuously. This phenomenon sees cells lose their ability to produce solvents and spores, posing a significant problem for industrial applications. To investigate the mechanistic and evolutionary basis of degeneration we combined comparative genomics, ultra-deep sequencing, and concepts of sociomicrobiology using Clostridium beijerinckii NCIMB 8052 as our model organism. These approaches revealed spo0A, the master regulator gene involved in spore and solvent formation, to be key to the degeneration process in this strain. Comparative genomics of 71 degenerate variants revealed four distinct hotspot regions that contained considerably more mutations than the rest of the genome. These included spo0A as well as genes suspected to regulate its expression and activity. Ultra-deep sequencing of populations during the subculturing process showed transient increases in mutations we believe linked to the spo0A network, however, these were ultimately dominated by mutations in the master regulator itself. Through frequency-dependent fitness assays, we found that spo0A mutants gained a fitness advantage, relative to the wild type, presumably allowing for propagation throughout the culture. Combined, our data provides new insights into the phenomenon of clostridial strain degeneration and the C. beijerinckii NCIMB 8052 solvent and spore regulation network.

Protective Effect of Clostridium butyricum on Escherichia coli-Induced Endometritis in Mice via Ameliorating Endometrial Barrier and Inhibiting Inflammatory Response

Endometritis is a common reproductive disease occurs both in human and animals. Clostridium butyricum is a Gram-positive anaerobic bacterium that can ferment various carbohydrates into butyric acid. In this study, we investigated the effects of C. butyricum on Escherichia coli-induced endometritis and clarified the underlying mechanism. We first verified the protective effect of C. butyricum in vivo by establishing a mouse model of E. coli-induced endometritis. It was determined that C. butyricum pretreatment significantly reversed E. coli-induced uterine histopathological changes. Meanwhile, C. butyricum pretreatment significantly decreased the production of pro-inflammatory mediators and the levels of myeloperoxidase (MPO) and malondialdehyde (MDA). We found that C. butyricum could inhibit TLR4-mediated phosphorylation of NF-κB and the activity of histone deacetylase (HDAC). Furthermore, C. butyricum significantly increased the expression of the tight junction proteins (TJPs) ZO-1, claudin-3, and occludin. Additionally, treatment with C. butyricum culture supernatant dramatically suppressed the degree of inflammation in the uterus, and inactivated C. butyricum did not exert a protective effect. We subsequently investigated butyrate levels in both the uterus and blood and observed a marked augment in the C. butyricum treatment group. Collectively, our data suggest that C. butyricum maintains epithelial barrier function and suppresses inflammatory response during E. coli-induced endometritis and that the protective effect of C. butyricum may be related to the production of butyrate. IMPORTANCE Endometritis is a common reproductive disease both in human and animals. It impairs female fertility by disrupting endometrial function. Antibiotics are widely used to treat endometritis in clinical practice, but the misuse of antibiotics often leads to antibiotic resistance. Therefore, there is an urgent need for new therapeutic agents to treat bacterial endometritis and overcome bacterial resistance. In this study, we found that C. butyricum could protect from E. coli-induced endometritis.

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species

Soil-transmitted intestinal worms known as helminths colonize over 1.5 billion people worldwide. Although helminth colonization has been associated with altered composition of the gut microbiota, such as increases in Clostridia, individual species have not been isolated and characterized. Here, we isolate and sequence the genome of 13 Clostridia from the Orang Asli, an indigenous population in Malaysia with a high prevalence of helminth infections. Metagenomic analysis of 650 fecal samples from urban and rural Malaysians confirm the prevalence of species corresponding to these isolates and reveal a specific association between Peptostreptococcaceae family members and helminth colonization. Remarkably, Peptostreptococcaceae isolated from the Orang Asli display superior capacity to promote the life cycle of whipworm species, including hatching of eggs from Trichuris muris and Trichuris trichiura. These findings support a model in which helminths select for gut colonization of microbes that support their life cycle.

Recent advances in bacteria-mediated cancer therapy

Cancer is among the leading cause of deaths worldwide. Although conventional therapies have been applied in the fight against the cancer, the poor oxygen, low extracellular pH, and high interstitial fluid pressure of the tumor microenvironment mean that these treatments fail to completely eradicate cancer cells. Recently, bacteria have increasingly been considered to be a promising platform for cancer therapy thanks to their many unique properties, such as specific tumor-targeting ability, high motility, immunogenicity, and their use as gene or drug carriers. Several types of bacteria have already been used for solid and metastatic tumor therapies, with promising results. With the development of synthetic biology, engineered bacteria have been endowed with the controllable expression of therapeutic proteins. Meanwhile, nanomaterials have been widely used to modify bacteria for targeted drug delivery, photothermal therapy, magnetothermal therapy, and photodynamic therapy, while promoting the antitumor efficiency of synergistic cancer therapies. This review will provide a brief introduction to the foundation of bacterial biotherapy. We begin by summarizing the recent advances in the use of many different types of bacteria in multiple targeted tumor therapies. We will then discuss the future prospects of bacteria-mediated cancer therapies.

Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation

Solvents such as butanol are important platform chemicals and are often produced from petrochemical sources. Production of butanol and other compounds from renewable and sustainable resources can be achieved by solventogenic bacteria, such as the hyper-butanol producer Clostridium saccharoperbutylacetonicum. Its sol operon consists of the genes encoding butyraldehyde dehydrogenase, CoA transferase, and acetoacetate decarboxylase (bld, ctfA, ctfB, adc) and the gene products are involved in butanol and acetone formation. It is important to understand its regulation to further optimize the solvent production. In this study, a new long non-coding antisense transcript complementary to the complete sol operon, now called Assolrna, was identified by transcriptomic analysis and the regulatory mechanism of Assolrna was investigated. For this purpose, the promoter-exchange strain C. saccharoperbutylacetonicum ΔP_asr::P_asr^** was constructed. Additionally, Assolrna was expressed plasmid-based under control of the native P_asr promoter and the lactose-inducible P_bgaL promoter in both the wild type and the promoter-exchange strain. Solvent formation was strongly decreased for all strains based on C. saccharoperbutylacetonicum ΔP_asr::P_asr^** and growth could not be restored by plasmid-based complementation of the exchanged promoter. Interestingly, very little sol mRNA expression was detected in the strain C. saccharoperbutylacetonicum ΔP_asr::P_asr^** lacking Assolrna expression. Butanol titers were further increased for the overexpression strain C. saccharoperbutylacetonicum [pMTL83151_asr_P_bgaL] compared to the wild type. These results suggest that Assolrna has a positive effect on sol operon expression. Therefore, a possible stabilization mechanism of the sol mRNA by Assolrna under physiological concentrations is proposed.

Characterization of Putative Sporulation and Germination Genes in Clostridium perfringens Food-Poisoning Strain SM101

Bacterial sporulation and spore germination are two intriguing processes that involve the expression of many genes coherently. Phylogenetic analyses revealed gene conservation among spore-forming Firmicutes, especially in Bacilli and Clostridia. In this study, by homology search, we found Bacillus subtilis sporulation gene homologs of bkdR, ylmC, ylxY, ylzA, ytaF, ytxC, yyaC1, and yyaC2 in Clostridium perfringenes food-poisoning Type F strain SM101. The β-glucuronidase reporter assay revealed that promoters of six out of eight tested genes (i.e., bkdR, ylmC, ytaF, ytxC, yyaC1, and yyaC2) were expressed only during sporulation, but not vegetative growth, suggesting that these genes are sporulation-specific. Gene knock-out studies demonstrated that C. perfringens ΔbkdR, ΔylmC, ΔytxC, and ΔyyaC1 mutant strains produced a significantly lower number of spores compared to the wild-type strain. When the spores of these six mutant strains were examined for their germination abilities in presence of known germinants, an almost wild-type level germination was observed with spores of ΔytaF or ΔyyaC1 mutants; and a slightly lower level with spores of ΔbkdR or ΔylmC mutants. In contrast, almost no germination was observed with spores of ΔytxC or ΔyyaC2 mutants. Consistent with germination defects, ΔytxC or ΔyyaC2 spores were also defective in spore outgrowth and colony formation. The germination, outgrowth, and colony formation defects of ΔytxC or ΔyyaC2 spores were restored when ΔytxC or ΔyyaC2 mutant was complemented with wild-type ytxC or yyaC2, respectively. Collectively, our current study identified new sporulation and germination genes in C. perfringens.

The Many Ages of Microbiome–Gut–Brain Axis

Frailty during aging is an increasing problem associated with locomotor and cognitive decline, implicated in poor quality of life and adverse health consequences. Considering the microbiome–gut–brain axis, we investigated, in a longitudinal study, whether and how physiological aging affects gut microbiome composition in wild-type male mice, and if and how cognitive frailty is related to gut microbiome composition. To assess these points, we monitored mice during aging at five selected experimental time points, from adulthood to senescence. At all selected experimental times, we monitored cognitive performance using novel object recognition and emergence tests and measured the corresponding Cognitive Frailty Index. Parallelly, murine fecal samples were collected and analyzed to determine the respective alpha and beta diversities, as well as the relative abundance of different bacterial taxa. We demonstrated that physiological aging significantly affected the overall gut microbiome composition, as well as the relative abundance of specific bacterial taxa, including Deferribacterota, Akkermansia, Muribaculaceae, Alistipes, and Clostridia VadinBB60. We also revealed that 218 amplicon sequence variants were significantly associated to the Cognitive Frailty Index. We speculated that some of them may guide the microbiome toward maladaptive and dysbiotic conditions, while others may compensate with changes toward adaptive and eubiotic conditions.

Regulatory Networks Controlling Neurotoxin Synthesis in Clostridium botulinum and Clostridium tetani

Clostridium botulinum and Clostridium tetani are Gram-positive, spore-forming, and anaerobic bacteria that produce the most potent neurotoxins, botulinum toxin (BoNT) and tetanus toxin (TeNT), responsible for flaccid and spastic paralysis, respectively. The main habitat of these toxigenic bacteria is the environment (soil, sediments, cadavers, decayed plants, intestinal content of healthy carrier animals). C. botulinum can grow and produce BoNT in food, leading to food-borne botulism, and in some circumstances, C. botulinum can colonize the intestinal tract and induce infant botulism or adult intestinal toxemia botulism. More rarely, C. botulinum colonizes wounds, whereas tetanus is always a result of wound contamination by C. tetani. The synthesis of neurotoxins is strictly regulated by complex regulatory networks. The highest levels of neurotoxins are produced at the end of the exponential growth and in the early stationary growth phase. Both microorganisms, except C. botulinum E, share an alternative sigma factor, BotR and TetR, respectively, the genes of which are located upstream of the neurotoxin genes. These factors are essential for neurotoxin gene expression. C. botulinum and C. tetani share also a two-component system (TCS) that negatively regulates neurotoxin synthesis, but each microorganism uses additional distinct sets of TCSs. Neurotoxin synthesis is interlocked with the general metabolism, and CodY, a master regulator of metabolism in Gram-positive bacteria, is involved in both clostridial species. The environmental and nutritional factors controlling neurotoxin synthesis are still poorly understood. The transition from amino acid to peptide metabolism seems to be an important factor. Moreover, a small non-coding RNA in C. tetani, and quorum-sensing systems in C. botulinum and possibly in C. tetani, also control toxin synthesis. However, both species use also distinct regulatory pathways; this reflects the adaptation of C. botulinum and C. tetani to different ecological niches.

Comparison of Microbial Community and Metabolites in Four Stomach Compartments of Myostatin-Gene-Edited and Non-edited Cattle

Myostatin (MSTN), a major negative regulator of skeletal muscle mass and an endocrine factor, can regulate the metabolism of various organisms. Inhibition of the MSTN gene can improve meat production from livestock. Rumen microorganisms are associated with production and health traits of cattle, but changes in the microbial composition and metabolome in the four stomach compartments of MSTN gene-edited cattle have not previously been studied. Our results indicated that microbial diversity and dominant bacteria in the four stomach compartments were very similar between MSTN gene-edited and wild-type (WT) cattle. The microbiota composition was significantly different between MSTN gene-edited and WT cattle. Our results show that the relative abundance of the phylum Proteobacteria in the reticulum of MSTN gene-edited cattle was lower than that of WT cattle, whereas the relative abundance of the genus Prevotella in the omasum of MSTN gene-edited cattle was significantly higher than that of WT cattle. Metabolomics analysis revealed that the intensity of L-proline and acetic acid was significantly different in the rumen, reticulum, and abomasum between the two types of cattle. Meanwhile, pathway topology analysis indicated that the differential metabolites were predominantly involved in arginine biosynthesis and glutamate metabolism in the rumen, reticulum, and omasum but were mainly involved in pyruvate metabolism and glycolysis/gluconeogenesis in the abomasum. Spearman correlation network analysis further demonstrated that there was a significant correlation between microflora composition and metabolic pathways. These findings provide clues for studying nutrient digestion and absorption ability of MSTN gene-edited cattle.

Xylanase production by Thermobacillus xylanilyticus is impaired by population diversification but can be mitigated based on the management of cheating behavior

Background

The microbial production of hemicellulasic cocktails is still a challenge for the biorefineries sector and agro-waste valorization. In this work, the production of hemicellulolytic enzymes by Thermobacillus xylanilyticus has been considered. This microorganism is of interest since it is able to produce an original set of thermostable hemicellulolytic enzymes, notably a xylanase GH11, Tx-xyn11. However, cell-to-cell heterogeneity impairs the production capability of the whole microbial population.

Results

Sequential cultivations of the strain on xylan as a carbon source has been considered in order to highlight and better understand this cell-to-cell heterogeneity. Successive cultivations pointed out a fast decrease of xylanase activity (loss of ~ 75%) and Tx-xyn11 gene expression after 23.5 generations. During serial cultivations on xylan, flow cytometry analyses pointed out that two subpopulations, differing at their light-scattering properties, were present. An increase of the recurrence of the subpopulation exhibiting low forward scatter (FSC) signal was correlated with a progressive loss of xylanase activity over several generations. Cell sorting and direct observation of the sorted subpopulations revealed that the low-FSC subpopulation was not sporulating, whereas the high-FSC subpopulation contained cells at the onset of the sporulation stage. The subpopulation differences (growth and xylanase activity) were assessed during independent growth. The low-FSC subpopulation exhibited a lag phase of 10 h of cultivation (and xylanase activities from 0.15 ± 0.21 to 3.89 ± 0.14 IU/mL along the cultivation) and the high-FSC subpopulation exhibited a lag phase of 5 h (and xylanase activities from 0.52 ± 0.00 to 4.43 ± 0.61 over subcultivations). Serial cultivations on glucose, followed by a switch to xylan led to a ~ 1.5-fold to ~ 15-fold improvement of xylanase activity, suggesting that alternating cultivation conditions could lead to an efficient population management strategy for the production of xylanase.

Conclusions

Taken altogether, the data from this study point out that a cheating behavior is responsible for the progressive reduction in xylanase activity during serial cultivations of T. xylanilyticus. Alternating cultivation conditions between glucose and xylan could be used as an efficient strategy for promoting population stability and higher enzymatic productivity from this bacterium.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01762-z.

Deep sequencing reveals changes in prokaryotic taxonomy and functional diversity of pit muds in different distilleries of China

Purpose

The microbial community in the pit mud correlated closely with the quality of the final product of Chinese strong-flavored Baijiu (CSFB). However, environmental conditions and brewing processes can vary by region and distilleries. This may lead to differences in microbial composition and function in pit mud. Therefore, revealing the features of the pit mud microbial community structure and functions of different distilleries will provide key information for understanding the diversity and difference of microbes in the brewing of CSFB, which will be beneficial for the improvement of the quality of pit mud and CSFB in the future.

Methods and results

Illumina MiSeq sequencing of 16S rRNA gene amplicons was used to analyze the similarities and differences in microbial community structure and function in pit muds of different distilleries located in Shihezi (Xinjiang), Xiangyang (Hubei), and Yibin (Sichuan). At the genus level, Clostridium, Lactobacillus, Aminobacterium, Petrimonas, Syntrophomonas, Methanoculleus, Syntrophaceticus, Sedimentibacter, Caloramator, Ruminococcus, Bacillus, Methanosarcina, and Garciella were the dominated genera of pit muds. There were great differences in the composition of microorganisms in pit muds used by different distilleries. The significantly enriched prokaryotic microbiotas of pit muds collected in the distilleries of Xiangyang were mainly affiliated with Bacillus, Lactobacillus, and Croceifilum, and the relative abundance of methanogens, such as Methanomicrobia and Methanobacteria, were only significantly enriched in the pit mud collected from the distilleries of Yibin (P < 0.05). Functional analysis indicated that the difference of microbial composition in pit mud will further lead to significant differences in various metabolic functions.

Conclusion

The compositions and functions of dominant microorganisms in pit mud used for the production of CSFB by different enterprises across regions in China were greatly different, and there was a close relationship between the compositions and functions of microorganisms in pit mud. Therefore, it may be an effective method to improve CSFB fermentation processes by directionally regulating the microbial community functions of pit mud using specific strains.

Role of Microbiota-Gut-Brain Axis in Regulating Dopaminergic Signaling

Dopamine is a neurotransmitter that plays a critical role both peripherally and centrally in vital functions such as cognition, reward, satiety, voluntary motor movements, pleasure, and motivation. Optimal dopamine bioavailability is essential for normal brain functioning and protection against the development of neurological diseases. Emerging evidence shows that gut microbiota have significant roles in maintaining adequate concentrations of dopamine via intricate, bidirectional communication known as the microbiota-gut-brain axis. The vagus nerve, immune system, hypothalamus–pituitary–adrenal axis, and microbial metabolites serve as important mediators of the reciprocal microbiota-gut-brain signaling. Furthermore, gut microbiota contain intrinsic enzymatic activity that is highly involved in dopamine metabolism, facilitating dopamine synthesis as well as its metabolite breakdown. This review examines the relationship between key genera of gut microbiota such as Prevotella, Bacteroides, Lactobacillus, Bifidobacterium, Clostridium, Enterococcus, and Ruminococcus and their effects on dopamine. The effects of gut dysbiosis on dopamine bioavailability and the subsequent impact on dopamine-related pathological conditions such as Parkinson’s disease are also discussed. Understanding the role of gut microbiota in modulating dopamine activity and bioavailability both in the periphery and in the central nervous system can help identify new therapeutic targets as well as optimize available methods to prevent, delay, or restore dopaminergic deficits in neurologic and metabolic disorders.

A high-efficient strategy for combinatorial engineering paralogous gene family: A case study on histidine kinases in Clostridium

Microorganisms harbor bulks of functionally similar or undefined genes, which belong to paralogous gene family. There is a necessity of exploring combinatorial or interactive functions of these genes, but conventional loss-of-function strategy with one-by-one rounds suffers extremely low efficiency for generating mutant libraries with all gene permutations. Here, taking histidine kinases (HKs) in Clostridium acetobutylicum as a proof-of-concept, we developed a multi-plasmid cotransformation strategy for generating all theoretical HKs combinations in one round. For five HKs with 31 theoretical combinations, the library containing 22 mutants within all the possible HKs-inactivated combinations was constructed with 11 days compared to 242 days by conventional strategy, while the other 9 combinations cannot survive. Six mutants with the enhanced butanol production and tolerance were obtained with changes of cell development during fermentation, one of which could produce 54.2% more butanol (56.4% more solvents), while the butanol production of other mutants was unchanged or decreased. The cotransformation strategy demonstrated potentials for fast exploring pleiotropic function of paralogous family genes in cell survival, cell development, and target product metabolism.

Sporulation in solventogenic and acetogenic clostridia

The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.

Draft Genome Sequence of Clostridium beijerinckii Strain mbf-VZ-132, Isolated from an Environmental Soil Sample

Clostridium beijerinckii strain mbf-VZ-132 was isolated from soil in Freising-Weihenstephan (Bavaria, Germany). The 16S rRNA gene sequence showed a 99.9% sequence identity to Clostridium diolis DSM 15410, which was recently reclassified as C. beijerinckii. In this study, we present the draft genome sequence of C. beijerinckii mbf-VZ-132, based on PacBio sequencing.

Clostridium beijerinckii strain mbf-VZ-132 was isolated from soil in Freising-Weihenstephan (Bavaria, Germany). The 16S rRNA gene sequence showed a 99.9% sequence identity to that of Clostridium diolis DSM 15410, which was recently reclassified as C. beijerinckii. In this study, we present the draft genome sequence of C. beijerinckii mbf-VZ-132 based on PacBio sequencing.

The selective advantage of facultative anaerobes relies on their unique ability to cope with changing oxygen levels during infection

Bacteria, including those that are pathogenic, have been generally classified according to their ability to survive and grow in the presence or absence of oxygen: aerobic and anaerobic bacteria, respectively. Strict aerobes require oxygen to grow (e.g., Neisseria), and strict anaerobes grow exclusively without, and do not survive oxygen exposure (e.g., Clostridia); aerotolerant bacteria (e.g., Lactobacilli) are insensitive to oxygen exposure. Facultative anaerobes (e.g., E. coli) have the unique ability to grow in the presence or in the absence of oxygen and are thus well-adapted to these changing conditions, which may constitute an underestimated selective advantage for infection. In the WHO antibiotic-resistant 'priority pathogens' list, facultative anaerobes are overrepresented (8 among 12 listed pathogens), consistent with clinical studies performed in populations particularly susceptible to infectious diseases. Bacteria aerobic respiratory chain plays a central role in oxygen consumption, leading to the formation of hypoxic infectious sites (infectious hypoxia). Facultative anaerobes have developed a wide diversity of aerotolerance and anaerotolerance strategies in vivo. However, at a single cell level, the modulation of the intracellular oxygen level in host infected cells remains elusive and will be discussed in this review. In conclusion, the ability of facultative bacteria to evolve in the presence or the absence of oxygen is essential for their virulence strategy and constitute a selective advantage. TAKE AWAY: Most life-threatening pathogenic bacteria are facultative anaerobes. Only facultative anaerobes are aerotolerant, anaerotolerant and capable of consuming O₂ . Facultative anaerobes induce and are well adapted to cellular hypoxia.

Bacterial community structure in acidic gruel from different regions and its influence on quality

Acidic gruel is a popular and nutritious fermented cereal food in China. However, the relationship between microbial function and quality of traditionally-fermented acidic gruel has not been evaluated. In this study, the microbiome, sensory quality and nutritional components of 98 samples of naturally fermented acidic gruel collected from Guangxi, Shanxi and Inner Mongolia were analyzed by high-throughput sequencing combined with various determination methods. High-throughput sequencing showed bacteria in acidic gruel belonged mainly to the genera Lactobacillus, Acetobacter, Bacillus, Clostridium and Weissella. Bacterial community composition and sensory quality of samples from Shanxi and Inner Mongolia were similar, but significantly different from Guangxi samples (p < 0.05). PICRUSt showed that gene functions were mostly related to carbohydrate and amino acid metabolism; all dominant bacterial genera, except Lactobacillus, were related to taste and volatile flavour indices. Acidic gruel was rich in amino acids, organic acids and soluble solids, which were in significantly higher concentrations in samples from Guangxi than in samples from Shanxi and Inner Mongolia; pH values of samples from Guangxi were also the highest. These differences may be caused by geographical, environmental or manufacturing differences.

Spo0A Suppresses sin Locus Expression in Clostridioides difficile

Clostridioides difficile is the leading cause of nosocomial infection and is the causative agent of antibiotic-associated diarrhea. The severity of the disease is directly associated with toxin production, and spores are responsible for the transmission and persistence of the organism. Previously, we characterized sin locus regulators SinR and SinR' (we renamed it SinI), where SinR is the regulator of toxin production and sporulation. The SinI regulator acts as its antagonist. In Bacillus subtilis, Spo0A, the master regulator of sporulation, controls SinR by regulating the expression of its antagonist, sinI However, the role of Spo0A in the expression of sinR and sinI in C. difficile had not yet been reported. In this study, we tested spo0A mutants in three different C. difficile strains, R20291, UK1, and JIR8094, to understand the role of Spo0A in sin locus expression. Western blot analysis revealed that spo0A mutants had increased SinR levels. Quantitative reverse transcription-PCR (qRT-PCR) analysis of its expression further supported these data. By carrying out genetic and biochemical assays, we show that Spo0A can bind to the upstream region of this locus to regulates its expression. This study provides vital information that Spo0A regulates the sin locus, which controls critical pathogenic traits such as sporulation, toxin production, and motility in C. difficile IMPORTANCE Clostridioides difficile is the leading cause of antibiotic-associated diarrheal disease in the United States. During infection, C. difficile spores germinate, and the vegetative bacterial cells produce toxins that damage host tissue. In C. difficile, the sin locus is known to regulate both sporulation and toxin production. In this study, we show that Spo0A, the master regulator of sporulation, controls sin locus expression. Results from our study suggest that Spo0A directly regulates the expression of this locus by binding to its upstream DNA region. This observation adds new detail to the gene regulatory network that connects sporulation and toxin production in this pathogen.