Influence of pH and temperature on the growth of and toxin production by neurotoxigenic strains of Clostridium butyricum type E

Unpacking Food Fermentation: Clinically Relevant Tools for Fermented Food Identification and Consumption

Fermented foods have been consumed for millennia, valued for their extended shelf life, distinctive sensory properties, and potential health benefits. Emerging research suggests that fermented food consumption may contribute to gut microbiome diversity, immune modulation, and metabolic regulation; however, mechanistic insights and clinical validation remain limited. This review synthesizes current scientific evidence on the microbial and metabolite composition of fermented foods, their proposed health effects, and safety considerations for vulnerable populations. Additionally, we highlight the need for standardized definitions, serving sizes, and regulatory frameworks to enhance consumer transparency and research reproducibility. By providing a structured overview of existing data and knowledge gaps, this review establishes a foundation for integrating fermented foods into dietary recommendations and guiding future research directions.

Our extended microbiome: The human-relevant metabolites and biology of fermented foods

One of the key modes of microbial metabolism occurring in the gut microbiome is fermentation. This energy-yielding process transforms common macromolecules like polysaccharides and amino acids into a wide variety of chemicals, many of which are relevant to microbe-microbe and microbe-host interactions. Analogous transformations occur during the production of fermented foods, resulting in an abundance of bioactive metabolites. In foods, the products of fermentation can influence food safety and preservation, nutrient availability, and palatability and, once consumed, may impact immune and metabolic status, disease expression, and severity. Human signaling pathways perceive and respond to many of the currently known fermented food metabolites, though expansive chemical novelty remains to be defined. Here we discuss several aspects of fermented food-associated microbes and metabolites, including a condensed history, current understanding of their interactions with hosts and host-resident microbes, connections with commercial probiotics, and opportunities for future research on human health and disease and food sustainability.

Novel Putative Transposable Element Associated with the Subtype E5 Botulinum Toxin Gene Cluster of Neurotoxigenic Clostridium butyricum Type E Strains from China

Previously, a whole-genome comparison of three Clostridium butyricum type E strains from Italy and the United States with different C. botulinum type E strains indicated that the bont/e gene might be transferred between the two clostridia species through transposition. However, transposable elements (TEs) have never been identified close to the bont/e gene. Herein, we report the whole genome sequences for four neurotoxigenic C. butyricum type E strains that originated in China. An analysis of the obtained genome sequences revealed the presence of a novel putative TE upstream of the bont/e gene in the genome of all four strains. Two strains of environmental origin possessed an additional copy of the putative TE in their megaplasmid. Similar putative TEs were found in the megaplasmids and, less frequently, in the chromosomes of several C. butyricum strains, of which two were neurotoxigenic C. butyricum type E strains, and in the chromosome of a single C. botulinum type E strain. We speculate that the putative TE might potentially transpose the bont/e gene at the intracellular and inter-cellular levels. However, the occasional TE occurrence in the clostridia genomes might reflect rare transposition events.

Microflora of processed cheese and the factors affecting it

The basic raw materials for the production of processed cheese are natural cheese which is treated by heat with the addition of emulsifying salts. From a point of view of the melting temperatures used (and the pH-value of the product), the course of processed cheese production can be considered "pasteurisation of cheese." During the melting process, the majority of vegetative forms of microorganisms, including bacteria of the family Enterobacteriaceae, are inactivated. The melting temperatures are not sufficient to kill the endospores, which survive the process but are often weakened. From a microbiological point of view, the biggest contamination problem of processed cheese is caused by gram-positive spore-forming rod-shaped bacteria of the genera Bacillus, Geobacillus, and Clostridium. Other factors affecting the shelf-life and quality of processed cheese are mainly the microbiological quality of the raw materials used, strict hygienic conditions during the manufacturing process as well as the type of packaging materials and storage conditions. The quality of processed cheese is not only dependent on the ingredients used but also on other parameters such as the value of water activity of the processed cheese, its pH-value, the presence of salts and emulsifying salts and the amount of fat in the product.

Effects of Megaplasmid Loss on Growth of Neurotoxigenic Clostridium butyricum Strains and Botulinum Neurotoxin Type E Expression

Clostridium butyricum strains that atypically produce the botulinum neurotoxin type E (BoNT/E) possess a megaplasmid of unknown functions in their genome. In this study, we cured two botulinum neurotoxigenic C. butyricum type E strains of their megaplasmids, and compared the obtained megaplasmid-cured strains to their respective wild-type parental strains. Our results showed that the megaplasmids do not confer beta-lactam resistance on the neurotoxigenic C. butyricum type E strains, although they carry several putative beta-lactamase genes. Instead, we found that the megaplasmids are essential for growth of the neurotoxigenic C. butyricum type E strains at the relatively low temperature of 15°C, and are also relevant for growth of strains under limiting pH and salinity conditions, as well as under favorable environmental conditions. Moreover, the presence of the megaplasmids was associated with increased transcript levels of the gene encoding BoNT/E in the C. butyricum type E strains, indicating that the megaplasmids likely contain transcriptional regulators. However, the levels of BoNT/E in the supernatants of the cured and uncured strains were similar after 24 and 48 h culture, suggesting that expression of BoNT/E in the C. butyricum type E strains is not ultimately controlled by the megaplasmids. Together, our results reveal that the C. butyricum type E megaplasmids exert pleiotropic effects on the growth of their microbial hosts under optimal and limiting environmental conditions, and also highlight the possibility of original regulatory mechanisms controlling the expression of BoNT/E.

Growth Limiting pH, Water Activity, and Temperature for Neurotoxigenic Strains of Clostridium butyricum

Some rare strains of Clostridium butyricum carry the gene encoding the botulinal type E neurotoxin and must be considered as possible hazards in certain types of food. The limiting growth conditions for C. butyricum were determined in peptone yeast glucose starch (PYGS) broth incubated anaerobically at 30°C for up to 42 days. The minimum pH values permitting growth depended on the acidulant and strain. Organic acids were more effective at inhibiting growth than HCl as expected. The lowest pH values at which growth of toxigenic and nontoxigenic strains of C. butyricum was observed in broth acidified with HCl were 4.1 and 4.2, respectively. In organic acids, however, the minimum pH varied between 4.4 and 5.1 depending on acid type and concentration. The minimum water activity for growth of toxigenic strains of C. butyricum was 0.96. The minimum growth temperatures of the toxigenic strains of C. butyricum (ca 10-11°C) were somewhat higher than for non-toxigenic ones (8°C). It was concluded that control of toxigenic C. butyricum in the food industry needs to allow for the greater pH tolerance of this species compared with proteolytic C. botulinum.

Structure and genetic content of the megaplasmids of neurotoxigenic clostridium butyricum type E strains from Italy

We determined the genetic maps of the megaplasmids of six neutoroxigenic Clostridium butyricum type E strains from Italy using molecular and bioinformatics techniques. The megaplasmids are circular, not linear as we had previously proposed. The differently-sized megaplasmids share a genetic region that includes structural, metabolic and regulatory genes. In addition, we found that a 168 kb genetic region is present only in the larger megaplasmids of two tested strains, whereas it is absent from the smaller megaplasmids of the four remaining strains. The genetic region unique to the larger megaplasmids contains, among other features, a locus for clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated (cas) genes, i.e. a bacterial adaptive immune system providing sequence-specific protection from invading genetic elements. Some CRISPR spacer sequences of the neurotoxigenic C. butyricum type E strains showed homology to prophage, phage and plasmid sequences from closely related clostridia species or from distant species, all sharing the intestinal habitat, suggesting that the CRISPR locus might be involved in the microorganism adaptation to the human or animal intestinal environment. Besides, we report here that each of four distinct CRISPR spacers partially matched DNA sequences of different prophages and phages, at identical nucleotide locations. This suggests that, at least in neurotoxigenic C. butyricum type E, the CRISPR locus is potentially able to recognize the same conserved DNA sequence of different invading genetic elements, besides targeting sequences unique to previously encountered invading DNA, as currently predicted for a CRISPR locus. Thus, the results of this study introduce the possibility that CRISPR loci can provide resistance to a wider range of invading DNA elements than previously appreciated. Whether it is more advantageous for the peculiar neurotoxigenic C. butyricum type E strains to maintain or to lose the CRISPR-cas system remains an open question.

The safety of pasteurised in-pack chilled meat products with respect to the foodborne botulism hazard

There has been a substantial increase in sales of pasteurised in-pack chilled products over the last decade. It is anticipated that this trend will continue. These foods address consumer demand in being of high quality and requiring little preparation time. The microbiological safety of these foods commonly depends on a combination of a minimal heat treatment, refrigerated storage and a restricted shelf-life. The principal microbiological safety hazard for pasteurised in-pack meat products is foodborne botulism, as presented by non-proteolytic Clostridium botulinum. This review provides a summary of research that has contributed to the safe development of these foods without incidence of botulism.

Food safety objective approach for controlling Clostridium botulinum growth and toxin production in commercially sterile foods

As existing technologies are refined and novel microbial inactivation technologies are developed, there is a growing need for a metric that can be used to judge equivalent levels of hazard control stringency to ensure food safety of commercially sterile foods. A food safety objective (FSO) is an output-oriented metric that designates the maximum level of a hazard (e.g., the pathogenic microorganism or toxin) tolerated in a food at the end of the food supply chain at the moment of consumption without specifying by which measures the hazard level is controlled. Using a risk-based approach, when the total outcome of controlling initial levels (H(0)), reducing levels (ΣR), and preventing an increase in levels (ΣI) is less than or equal to the target FSO, the product is considered safe. A cross-disciplinary international consortium of specialists from industry, academia, and government was organized with the objective of developing a document to illustrate the FSO approach for controlling Clostridium botulinum toxin in commercially sterile foods. This article outlines the general principles of an FSO risk management framework for controlling C. botulinum growth and toxin production in commercially sterile foods. Topics include historical approaches to establishing commercial sterility; a perspective on the establishment of an appropriate target FSO; a discussion of control of initial levels, reduction of levels, and prevention of an increase in levels of the hazard; and deterministic and stochastic examples that illustrate the impact that various control measure combinations have on the safety of well-established commercially sterile products and the ways in which variability all levels of control can heavily influence estimates in the FSO risk management framework. This risk-based framework should encourage development of innovative technologies that result in microbial safety levels equivalent to those achieved with traditional processing methods.

Identification of novel linear megaplasmids carrying a ß-lactamase gene in neurotoxigenic Clostridium butyricum type E strains

Since the first isolation of type E botulinum toxin-producing Clostridium butyricum from two infant botulism cases in Italy in 1984, this peculiar microorganism has been implicated in different forms of botulism worldwide. By applying particular pulsed-field gel electrophoresis run conditions, we were able to show for the first time that ten neurotoxigenic C. butyricum type E strains originated from Italy and China have linear megaplasmids in their genomes. At least four different megaplasmid sizes were identified among the ten neurotoxigenic C. butyricum type E strains. Each isolate displayed a single sized megaplasmid that was shown to possess a linear structure by ATP-dependent exonuclease digestion. Some of the neurotoxigenic C. butyricum type E strains possessed additional smaller circular plasmids. In order to investigate the genetic content of the newly identified megaplasmids, selected gene probes were designed and used in Southern hybridization experiments. Our results revealed that the type E botulinum neurotoxin gene was chromosome-located in all neurotoxigenic C. butyricum type E strains. Similar results were obtained with the 16S rRNA, the tetracycline tet(P) and the lincomycin resistance protein lmrB gene probes. A specific mobA gene probe only hybridized to the smaller plasmids of the Italian C. butyricum type E strains. Of note, a ß-lactamase gene probe hybridized to the megaplasmids of eight neurotoxigenic C. butyricum type E strains, of which seven from clinical sources and the remaining one from a food implicated in foodborne botulism, whereas this ß-lactam antibiotic resistance gene was absent form the megaplasmids of the two soil strains examined. The widespread occurrence among C. butyricum type E strains associated to human disease of linear megaplasmids harboring an antibiotic resistance gene strongly suggests that the megaplasmids could have played an important role in the emergence of C. butyricum type E as a human pathogen.

Multiplex PCR for detection of botulinum neurotoxin-producing clostridia in clinical, food, and environmental samples

Botulinum neurotoxin (BoNT), the most toxic substance known, is produced by the spore-forming bacterium Clostridium botulinum and, in rare cases, also by some strains of Clostridium butyricum and Clostridium baratii. The standard procedure for definitive detection of BoNT-producing clostridia is a culture method combined with neurotoxin detection using a standard mouse bioassay (SMB). The SMB is highly sensitive and specific, but it is expensive and time-consuming and there are ethical concerns due to use of laboratory animals. PCR provides a rapid alternative for initial screening for BoNT-producing clostridia. In this study, a previously described multiplex PCR assay was modified to detect all type A, B, E, and F neurotoxin genes in isolated strains and in clinical, food, environmental samples. This assay includes an internal amplification control. The effectiveness of the multiplex PCR method for detecting clostridia possessing type A, B, E, and F neurotoxin genes was evaluated by direct comparison with the SMB. This method showed 100% inclusivity and 100% exclusivity when 182 BoNT-producing clostridia and 21 other bacterial strains were used. The relative accuracy of the multiplex PCR and SMB was evaluated using 532 clinical, food, and environmental samples and was estimated to be 99.2%. The multiplex PCR was also used to investigate 110 freshly collected food and environmental samples, and 4 of the 110 samples (3.6%) were positive for BoNT-encoding genes.

Intestinal toxemia botulism in Italy, 1984–2005

Botulism in humans is caused by botulinum neurotoxins, produced in most cases by Clostridium botulinum, although other Clostridia species are implicated as well. Of the five forms of botulism in humans, three are referred to as "infective": wound botulism, infant botulism, and adult intestinal botulism; the latter two forms are also referred to as "intestinal toxemia botulism" because the organism colonizes the lumen of the intestinal tract and produces botulinum neurotoxin in vivo. Twenty-three cases of infant botulism and three cases of adult intestinal botulism occurred in Italy between 1984 and 2005. Microbiological analyses of clinical, environmental, and food samples and analysis of clinical and epidemiological data revealed two main characteristics of intestinal toxemia botulism in Italy that are not common in cases in other countries: the isolation of a strain of C. butyricum that produced botulinum neurotoxin type E in 6 of 26 cases, including two cases of adult intestinal toxemia botulism, and the onset of botulism in these cases with concomitant severe gastrointestinal symptomatology. This report summarizes the microbiological, clinical, and epidemiological data of all cases of intestinal toxemia botulism that have occurred in Italy in the period 1984-2005.

Clostridium botulinum and the safety of minimally heated, chilled foods: an emerging issue?

Foodborne botulism is caused by consumption of preformed botulinum neurotoxin, with as little as 30 ng of neurotoxin being potentially lethal. Consumption of minute quantities of neurotoxin-containing food can result in botulism. In view of the severity of foodborne botulism, it is essential that new foods be developed safely without an increase in incidence of this disease. Minimally heated, chilled foods are a relatively new type of food, sales of which are currently increasing by about 10% per annum. These products meet consumer demand for high-quality foods that require little preparation time. Their safety and quality depends on mild heat treatment, chilled storage, restricted shelf life and sometimes on intrinsic properties of the foods. The principal microbiological hazard is nonproteolytic Clostridium botulinum, and there is a concern that this may become an emerging issue. A considerable amount of research and development over the last 15 years has underpinned the safe production of commercial, minimally heated, chilled foods with respect to foodborne botulism, and it is essential that safe food continues to be developed. In particular, the desire to use lighter heat processes and a longer shelf life presents a challenge that will only be met by significant developments in quantitative microbiological food safety.

SYBR green real-time PCR method to detect Clostridium botulinum type A

Botulinum toxins (BoNTs) are classically produced by Clostridium botulinum but rarely also from neurotoxigenic strains of Clostridium baratii and Clostridium butyricum. BoNT type A (BoNT/A), BoNT/B, BoNT/E, and very rarely BoNT/F are mainly responsible for human botulism. Standard microbiological methods take into consideration only the detection of C. botulinum. The presumptive identification of the toxigenic strains together with the typing of BoNT has to be performed by mouse bioassay. The development of PCR-based methods for the detection and typing of BoNT-producing clostridia would be an ideal alternative to the mouse bioassay. The objective of this study was to develop a rapid and robust real-time PCR method for detecting C. botulinum type A. Four different techniques for the extraction and purification of DNA from cultured samples were initially compared. Of the techniques used, Chelex 100, DNeasy tissue kit, InstaGene matrix DNA, and boiling, the boiling technique was significantly less efficient than the other three. These did not give statistically different results, and Chelex 100 was chosen because it was less expensive than the others. In order to eliminate any false-negative results, an internal amplification control was synthesized and included in the amplification mixture according to ISO 22174. The specificity of the method was tested against 75 strains of C. botulinum type A, 4 strains of C. botulinum type Ab, and 101 nontarget strains. The detection limit of the reaction was less than 6 x 10(1) copies of C. botulinum type A DNA. The robustness of the method was confirmed using naturally contaminated stool specimens to evaluate the tolerance of inhibitor substances. SYBR green real-time PCR showed very high specificity for the detection of C. botulinum types A and Ab (inclusivity and exclusivity, 100%).

Identification of type A, B, E, and F botulinum neurotoxin genes and of botulinum neurotoxigenic clostridia by denaturing high-performance liquid chromatography

Denaturing high-performance liquid chromatography (DHPLC) is a recently developed technique for rapid screening of nucleotide polymorphisms in PCR products. We used this technique for the identification of type A, B, E, and F botulinum neurotoxin genes. PCR products amplified from a conserved region of the type A, B, E, and F botulinum toxin genes from Clostridium botulinum, neurotoxigenic C. butyricum type E, and C. baratii type F strains were subjected to both DHPLC analysis and sequencing. Unique DHPLC peak profiles were obtained with each different type of botulinum toxin gene fragment, consistent with nucleotide differences observed in the related sequences. We then evaluated the ability of this technique to identify botulinal neurotoxigenic organisms at the genus and species level. A specific short region of the 16S rRNA gene which contains genus-specific and in some cases species-specific heterogeneity was amplified from botulinum neurotoxigenic clostridia and from different food-borne pathogens and subjected to DHPLC analysis. Different peak profiles were obtained for each genus and species, demonstrating that the technique could be a reliable alternative to sequencing for the rapid identification of food-borne pathogens, specifically of botulinal neurotoxigenic clostridia most frequently implicated in human botulism.

Taxonomic identity of type E botulinum toxin-producing Clostridium butyricum strains by sequencing of a short 16S rDNA region

Several micro-organisms capable of producing botulinum neurotoxin type E, though phenotypically similar to Clostridium butyricum (a normally non-neurotoxigenic organism), have recently been isolated in Italy and China. Some of these micro-organisms had been implicated in food-borne botulism, a serious neuroparalytic disease. The taxonomic identity of the type E botulinum toxin-producing strains is confirmed here, through sequencing of a genus- and species-specific segment of the 16S rRNA gene. Confirmation leads to the conclusion that neurotoxigenic C. butyricum must be regarded as an emergent food-borne pathogen.