Development of a specific fluorescent phage endolysin for in situ detection of Clostridium species associated with cheese spoilage

Microbiome-based classification models for fresh produce safety and quality evaluation

Small sample sizes and loss of sequencing reads during the microbiome data preprocessing can limit the statistical power of differentiating fresh produce phenotypes and prevent the detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored a machine learning-based k-mer hash analysis strategy to identify DNA signatures predictive of produce safety (PS) and produce quality (PQ) and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step and ASV-based taxonomy strategy. Random forest-based classifiers for PS and PQ using 7-mer hash data sets had significantly higher classification accuracy than those using the ASV data sets. We also demonstrated that the proposed combination of integrating multiple data sets and leveraging a 7-mer hash strategy leads to better classification performance for PS and PQ compared to the ASV method but presents lower PS classification accuracy compared to the feature-selected ASV-based taxonomy strategy. Due to the current limitation of generating taxonomy using the 7-mer hash strategy, the ASV-based taxonomy strategy with remarkably less computing time and memory usage is more efficient for PS and PQ classification and applicable for important taxa identification. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing data sets for the application of machine learning in the area of microbial safety and quality of food.

IMPORTANCE

Identification of generalizable indicators for produce safety (PS) and produce quality (PQ) improves the detection of produce contamination and quality decline. However, effective sequencing read loss during microbiome data preprocessing and the limited sample size of individual studies restrain statistical power to identify important features contributing to differentiating PS and PQ phenotypes. We applied machine learning-based models using individual and integrated k-mer hash and amplicon sequence variant (ASV) data sets for PS and PQ classification and evaluated their classification performance and found that random forest (RF)-based models using integrated 7-mer hash data sets achieved significantly higher PS and PQ classification accuracy. Due to the limitation of taxonomic analysis for the 7-mer hash, we also developed RF-based models using feature-selected ASV-based taxonomic data sets, which performed better PS classification than those using the integrated 7-mer hash data set. The RF feature selection method identified 480 PS indicators and 263 PQ indicators with a positive contribution to the PS and PQ classification.

Unraveling Physical Interactions of Clostridioides difficile with Phage and Phage-Derived Proteins Using In Vitro and Whole-Cell Assays

Physical interactions between bacteria and phages provide valuable insights into the mechanisms of phage infection and may provide information on the use of phages as a therapeutic approach. In this study, we employed a combination of in vitro and whole-cell assays to examine the interactions between Clostridioides difficile and phages and phage-derived proteins. These techniques can also be adapted for studying the physical interactions between other bacterial species and their associated phages.

Characterization of Lactobacilli Phage Endolysins and Their Functional Domains-Potential Live Biotherapeutic Testing Reagents

Phage endolysin-specific binding characteristics and killing activity support their potential use in biotechnological applications, including potency and purity testing of live biotherapeutic products (LBPs). LBPs contain live organisms, such as lactic acid bacteria (LAB), and are intended for use as drugs. Our approach uses the endolysin cell wall binding domains (CBD) for LBP potency assays and the endolysin killing activity for purity assays. CBDs of the following five lactobacilli phage lysins were characterized: CL1, Jlb1, Lj965, LL-H, and ΦJB. They exhibited different bindings to 27 LAB strains and were found to bind peptidoglycan or surface polymers. Flow cytometry based on CBD binding was used to enumerate viable counts of two strains in the mixture. CL1-lys, jlb1-lys, and ΦJB-lys and their enzymatic domains (EADs) exhibited cell wall digestive activity and lytic activity against LAB. Jlb1-EAD and ΦJB-EAD were more sensitive than their respective hololysins to buffer pH and NaCl changes. The ΦJB-EAD exhibited stronger lytic activity than ΦJB-lys, possibly due to ΦJB-CBD-mediated sequestration of ΦJB-lys by cell debris. CBD multiplex assays indicate that these proteins may be useful LBP potency reagents, and the lytic activity suggests that CL1-lys, jlb1-lys, and ΦJB-lys and their EADs are good candidates for LBP purity reagent development.

Wild-type Lactococcus lactis producing bacteriocin-like prophage lysins

Introduction

Lactococcus is a genus of lactic acid bacteria used in the dairy industry as a starter. Lactococci have been found to produce altogether more than 40 different bacteriocins, ribosomally synthesized antimicrobial proteins. All known Lactococcus spp. bacteriocins belong to classes I and II, which are mainly heat-resistant peptides. No class III bacteriocins, bigger heat-sensitive proteins, including phage tail-like bacteriocins, have been found from the Lactococcus spp. Unlike phage tail-like bacteriocins, prophage lysins have not been regarded as bacteriocins, possibly because phage lysins contribute to autolysis, degrading the host's own cell wall.

Methods

Wild-type Lactococcus lactis strain LAC460, isolated from spontaneously fermented idli batter, was examined for its antimicrobial activity. We sequenced the genome, searched phage lysins from the culture supernatant, and created knock-out mutants to find out the source of the antimicrobial activity.

Results and discussion

The strain LAC460 was shown to kill other Lactococcus strains with protease- and heat-sensitive lytic activity. Three phage lysins were identified in the culture supernatant. The genes encoding the three lysins were localized in different prophage regions in the chromosome. By knock-out mutants, two of the lysins, namely LysL and LysP, were demonstrated to be responsible for the antimicrobial activity. The strain LAC460 was found to be resistant to the lytic action of its own culture supernatant, and as a consequence, the phage lysins could behave like bacteriocins targeting and killing other closely related bacteria. Hence, similar to phage tail-like bacteriocins, phage lysin-like bacteriocins could be regarded as a novel type of class III bacteriocins.

Potential of bacteriophage proteins as recognition molecules for pathogen detection

Bacterial pathogens are leading causes of infections with high mortality worldwide having a great impact on healthcare systems and the food industry. Gold standard methods for bacterial detection mainly rely on culture-based technologies and biochemical tests which are laborious and time-consuming. Regardless of several developments in existing methods, the goal of achieving high sensitivity and specificity, as well as a low detection limit, remains unaccomplished. In past years, various biorecognition elements, such as antibodies, enzymes, aptamers, or nucleic acids, have been widely used, being crucial for the pathogens detection in different complex matrices. However, these molecules are usually associated with high detection limits, demand laborious and costly production, and usually present cross-reactivity. (Bacterio)phage-encoded proteins, especially the receptor binding proteins (RBPs) and cell-wall binding domains (CBDs) of endolysins, are responsible for the phage binding to the bacterial surface receptors in different stages of the phage lytic cycle. Due to their remarkable properties, such as high specificity, sensitivity, stability, and ability to be easily engineered, they are appointed as excellent candidates to replace conventional recognition molecules, thereby contributing to the improvement of the detection methods. Moreover, they offer several possibilities of application in a variety of detection systems, such as magnetic, optical, and electrochemical. Herein we provide a review of phage-derived bacterial binding proteins, namely the RBPs and CBDs, with the prospect to be employed as recognition elements for bacteria. Moreover, we summarize and discuss the various existing methods based on these proteins for the detection of nosocomial and foodborne pathogens.

Bacteriophage Tail Proteins as a Tool for Bacterial Pathogen Recognition—A Literature Review

In recent years, a number of bacterial detection methods have been developed to replace time-consuming culture methods. One interesting approach is to mobilize the ability of phage tail proteins to recognize and bind to bacterial hosts. In this paper, the authors provide an overview of the current methodologies in which phage proteins play major roles in detecting pathogenic bacteria. Authors focus on proteins capable of recognizing highly pathogenic strains, such as Acinetobacter baumannii, Campylobacter spp., Yersinia pestis, Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus, Enterococcus spp., Salmonella spp., and Shigella. These pathogens may be diagnosed by capture-based detection methods involving the use of phage protein-coated nanoparticles, ELISA (enzyme-linked immunosorbent assay)-based methods, or biosensors. The reviewed studies show that phage proteins are becoming an important diagnostic tool due to the discovery of new phages and the increasing knowledge of understanding the specificity and functions of phage tail proteins.

Phage lysin that specifically eliminates Clostridium botulinum Group I cells

Clostridium botulinum poses a serious threat to food safety and public health by producing potent neurotoxin during its vegetative growth and causing life-threatening neuroparalysis, botulism. While high temperature can be utilized to eliminate C. botulinum spores and the neurotoxin, non-thermal elimination of newly germinated C. botulinum cells before onset of toxin production could provide an alternative or additional factor controlling the risk of botulism in some applications. Here we introduce a putative phage lysin that specifically lyses vegetative C. botulinum Group I cells. This lysin, called CBO1751, efficiently kills cells of C. botulinum Group I strains at the concentration of 5 µM, but shows little or no lytic activity against C. botulinum Group II or III or other Firmicutes strains. CBO1751 is active at pH from 6.5 to 10.5. The lytic activity of CBO1751 is tolerant to NaCl (200 mM), but highly susceptible to divalent cations Ca2+ and Mg2+ (50 mM). CBO1751 readily and effectively eliminates C. botulinum during spore germination, an early stage preceding vegetative growth and neurotoxin production. This is the first report of an antimicrobial lysin against C. botulinum, presenting high potential for developing a novel antibotulinal agent for non-thermal applications in food and agricultural industries.

Engineered Bacteriophages for Practical Applications

The diversity of advanced genetic engineering techniques that have become available in recent years has enabled a more precise manipulation of genes and genomes. Among these, bacteriophage genomes stand out as an interesting target due to their dependence on a host for replication, which previously complicated their manipulation, and due as well to the many possible fields in which they can be used. In this review, we highlight recent applications for which genetically modified bacteriophages are being employed: as phage therapy in medicine, animal industries and agricultural settings; as a source of new antimicrobials; as biosensors for research, health and environmental purposes; and as genetic engineering tools themselves.

Reporter Phage-Based Detection of Bacterial Pathogens: Design Guidelines and Recent Developments

Fast and reliable detection of bacterial pathogens in clinical samples, contaminated food products, and water supplies can drastically improve clinical outcomes and reduce the socio-economic impact of disease. As natural predators of bacteria, bacteriophages (phages) have evolved to bind their hosts with unparalleled specificity and to rapidly deliver and replicate their viral genome. Not surprisingly, phages and phage-encoded proteins have been used to develop a vast repertoire of diagnostic assays, many of which outperform conventional culture-based and molecular detection methods. While intact phages or phage-encoded affinity proteins can be used to capture bacteria, most phage-inspired detection systems harness viral genome delivery and amplification: to this end, suitable phages are genetically reprogrammed to deliver heterologous reporter genes, whose activity is typically detected through enzymatic substrate conversion to indicate the presence of a viable host cell. Infection with such engineered reporter phages typically leads to a rapid burst of reporter protein production that enables highly sensitive detection. In this review, we highlight recent advances in infection-based detection methods, present guidelines for reporter phage construction, outline technical aspects of reporter phage engineering, and discuss some of the advantages and pitfalls of phage-based pathogen detection. Recent improvements in reporter phage construction and engineering further substantiate the potential of these highly evolved nanomachines as rapid and inexpensive detection systems to replace or complement traditional diagnostic approaches.

Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review

Bacteria will likely become our most significant enemies of the 21st century, as we are approaching a post-antibiotic era. Bacteriophages, viruses that infect bacteria, allow us to fight infections caused by drug-resistant bacteria and create specific, cheap, and stable sensors for bacteria detection. Here, we summarize the recent developments in the field of phage-based methods for bacteria detection. We focus on works published after mid-2017. We underline the need for further advancements, especially related to lowering the detection (below 1 CFU/mL; CFU stands for colony forming units) and shortening the time of analysis (below one hour). From the application point of view, portable, cheap, and fast devices are needed, even at the expense of sensitivity.

Use of fluorescent CTP1L endolysin cell wall-binding domain to study the evolution of Clostridium tyrobutyricum during cheese ripening

Clostridium tyrobutyricum is a bacteria of concern in the cheese industry, capable of surviving the manufacturing process and causing butyric acid fermentation and late blowing defect of cheese. In this work, we implement a method based on the cell wall-binding domain (CBD) of endolysin CTP1L, which detects C. tyrobutyricum, to monitor its evolution in cheeses challenged with clostridial spores and in the presence or absence of reuterin, an anti-clostridial agent. For this purpose, total bacteria were extracted from cheese samples and C. tyrobutyricum cells were specifically labelled with the CBD of CTP1L attached to green fluorescent protein (GFP), and detected by fluorescence microscopy. By using this GFP-CBD, germinated spores were visualized on day 1 in all cheeses inoculated with clostridial spores. Vegetative cells of C. tyrobutyricum, responsible for butyric acid fermentation, were detected in cheeses without reuterin from 30 d onwards, when LBD symptoms also became evident. The number of fluorescent Clostridium cells increased during ripening in the blowing cheeses. However, vegetative cells of C. tyrobutyricum were not detected in cheese containing the antimicrobial reuterin, which also did not show LBD throughout ripening. This simple and fast method provides a helpful tool to study the evolution of C. tyrobutyricum during cheese ripening.

LysPBC2, a Novel Endolysin Harboring a Bacillus cereus Spore Binding Domain

To control the spore-forming human pathogen Bacillus cereus, we isolated and characterized a novel endolysin, LysPBC2, from a newly isolated B. cereus phage, PBC2. Compared to the narrow host range of phage PBC2, LysPBC2 showed very broad lytic activity against all Bacillus, Listeria, and Clostridium species tested. In addition to a catalytic domain and a cell wall binding domain, LysPBC2 has a spore binding domain (SBD) partially overlapping its catalytic domain, which specifically binds to B. cereus spores but not to vegetative cells of B. cereus Both immunogold electron microscopy and a binding assay indicated that the SBD binds the external region of the spore cortex layer. Several amino acid residues required for catalytic or spore binding activity of LysPBC2 were determined by mutagenesis studies. Interestingly, LysPBC2 derivatives with impaired spore binding activity showed an increased lytic activity against vegetative cells of B. cereus compared with that of wild-type LysPBC2. Further biochemical studies revealed that these LysPBC2 derivatives have lower thermal stability, suggesting a stabilizing role of SBD in LysPBC2 structure.IMPORTANCE Bacteriophages produce highly evolved lytic enzymes, called endolysins, to lyse peptidoglycan and release their progeny from bacterial cells. Due to their potent lytic activity and specificity, the use of endolysins has gained increasing attention as a natural alternative to antibiotics. Since most endolysins from Gram-positive-bacterium-infecting phages have a modular structure, understanding the function of each domain is crucial to make effective endolysin-based therapeutics. Here, we report the functional and biochemical characterization of a Bacillus cereus phage endolysin, LysPBC2, which has an unusual spore binding domain and a cell wall binding domain. A single point mutation in the spore binding domain greatly enhanced the lytic activity of endolysin at the cost of reduced thermostability. This work contributes to the understanding of the role of each domain in LysPBC2 and will provide insight for the rational design of efficient antimicrobials or diagnostic tools for controlling B. cereus.

Bacteriophages in Food Applications: From Foe to Friend

Bacteriophages (phages) have traditionally been considered troublesome in food fermentations, as they are an important cause of starter-culture failure and trigger significant financial losses. In addition, from an evolutionary perspective, phages have contributed to the pathogenicity of many bacteria through transduction of virulence genes. In contrast, phages have played an important positive role in molecular biology. Moreover, these agents are increasingly being recognized as a potential solution to the detection and biocontrol of various undesirable bacteria, which cause either spoilage of food materials, decreased microbiological safety of foods, or infectious diseases in food animals and crops. The documented successful applications of phages and various phage-derived molecules are discussed in this review, as are many promising new uses that are currently under development.

Swapping the roles of bacteriocins and bacteriophages in food biotechnology

To move towards a safer and more sustainable food production chain, natural antimicrobials have been traditionally applied to enhance safety. This is well exemplified by the use of bacteriocins, antimicrobial peptides synthesized by bacteria, as food biopreservatives. However, as knowledge on bacteriocin biology develops, novel functions beyond food preservation emerge and a shift towards health applications is positioning bacteriocins as anti-infectives and modulators of gut microbiota. On the other hand, bacteriophages, viruses infecting bacteria, have been long regarded as a threat for dairy fermentations. However, they may also become allies when specific phages infecting pathogenic or spoilage bacteria are intentionally used. This review summarizes the `dark side' and rather unexplored roles of bacteriocins and phages that, certainly, have much to learn from each other.

Molecular Basis of Bacterial Host Interactions by Gram-Positive Targeting Bacteriophages

The inherent ability of bacteriophages (phages) to infect specific bacterial hosts makes them ideal candidates to develop into antimicrobial agents for pathogen-specific remediation in food processing, biotechnology, and medicine (e.g., phage therapy). Conversely, phage contaminations of fermentation processes are a major concern to dairy and bioprocessing industries. The first stage of any successful phage infection is adsorption to a bacterial host cell, mediated by receptor-binding proteins (RBPs). As the first point of contact, the binding specificity of phage RBPs is the primary determinant of bacterial host range, and thus defines the remediative potential of a phage for a given bacterium. Co-evolution of RBPs and their bacterial receptors has forced endless adaptation cycles of phage-host interactions, which in turn has created a diverse array of phage adsorption mechanisms utilizing an assortment of RBPs. Over the last decade, these intricate mechanisms have been studied intensely using electron microscopy and X-ray crystallography, providing atomic-level details of this fundamental stage in the phage infection cycle. This review summarizes current knowledge surrounding the molecular basis of host interaction for various socioeconomically important Gram-positive targeting phage RBPs to their protein- and saccharide-based receptors. Special attention is paid to the abundant and best-characterized Siphoviridae family of tailed phages. Unravelling these complex phage-host dynamics is essential to harness the full potential of phage-based technologies, or for generating novel strategies to combat industrial phage contaminations.

Phage-Based Applications in Synthetic Biology

Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their host, and our growing ability to engineer them further enhances this potential. Phages have also been used as scaffolds for genetically programmable biomaterials that have highly tunable properties. Furthermore, phages are central to powerful directed evolution platforms, which are being leveraged to enhance existing biological functions and even produce new ones. In this review, we discuss recent examples of how phage research is influencing these next-generation biotechnologies.