Molecular cloning and antimicrobial activity of enterolysin A and helveticin J of bacteriolysins from metagenome of Chinese traditional fermented foods

Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep's Milk

Dairy products play a crucial role in human nutrition as they provide essential nutrients. However, the presence of diverse microorganisms in these products can pose challenges to food safety and quality. Here, we provide a comprehensive molecular characterization of a diverse collection of lactic acid bacteria (LAB) and staphylococci isolated from raw sheep's milk. Whole-genome sequencing, phenotypic characterization, and bioinformatics were employed to gain insight into the genetic composition and functional attributes of these bacteria. Bioinformatics analysis revealed the presence of various genetic elements. Important toxin-related genes in staphylococci that contribute to their pathogenic potential were identified and confirmed using phenotypic assays, while adherence-related genes, which are essential for attachment to host tissues, surfaces in the dairy environment, and the creation of biofilms, were also present. Interestingly, the Staphylococcus aureus isolates belonged to sequence type 5, which largely consists of methicillin-susceptible isolates that have been involved in severe nosocomial infections. Although genes encoding methicillin resistance were not identified, multiple resistance genes (RGs) conferring resistance to aminoglycosides, macrolides, and fluroquinolones were found. In contrast, LAB had few inherently present RGs and no virulence genes, suggesting their likely safe status as food additives in dairy products. LAB were also richer in bacteriocins and carbohydrate-active enzymes, indicating their potential to suppress pathogens and effectively utilize carbohydrate substrates, respectively. Additionally, mobile genetic elements, present in both LAB and staphylococci, may facilitate the acquisition and dissemination of genetic traits, including RGs, virulence genes, and metabolic factors, with implications for food quality and public health. The molecular and phenotypic characterization presented herein contributes to the effort to mitigate risks and infections (e.g., mastitis) and enhance the safety and quality of milk and products thereof.

Potential Impact of Combined Inhibition by Bacteriocins and Chemical Substances of Foodborne Pathogenic and Spoilage Bacteria: A Review

In recent years, food safety caused by foodborne pathogens and spoilage bacteria has become a major public health problem worldwide. Bacteriocins are a kind of antibacterial peptide synthesized by microbial ribosomes, and are widely used as food preservatives. However, when used individually bacteriocins may have limitations such as high cost of isolation and purification, narrow inhibitory spectrum, easy degradation by enzymes, and vulnerability to complex food environments. Numerous studies have demonstrated that co-treatment with bacteriocins and a variety of chemical substances can have synergistic antibacterial effects on spoilage microorganisms and foodborne pathogens, effectively prolonging the shelf life of food and ensuring food safety. Therefore, this paper systematically summarizes the synergistic bacteriostatic strategies of bacteriocins in combination with chemical substances such as essential oils, plant extracts, and organic acids. The impacts of bacteriocins when used individually and in combination with other chemical substances on different food substrates are clarified, and bacteriocin-chemical substance compositions that enhance antibacterial effectiveness and reduce the potential negative effects of chemical preservatives are highlighted and discussed. Combined treatments involving bacteriocins and different kinds of chemical substances are expected to be a promising new antibacterial method and to become widely used in both the food industry and biological medicine.

Whole-Genome Sequence of Lactococcus lactis Subsp. lactis LL16 Confirms Safety, Probiotic Potential, and Reveals Functional Traits

Safety is the most important criteria of any substance or microorganism applied in the food industry. The whole-genome sequencing (WGS) of an indigenous dairy isolate LL16 confirmed it to be Lactococcus lactis subsp. lactis with genome size 2,589,406 bp, 35.4% GC content, 246 subsystems, and 1 plasmid (repUS4). The Nextera XT library preparation kit was used to generate the DNA libraries, and the sequencing was carried out on an Illumina MiSeq platform. In silico analysis of L. lactis LL16 strain revealed non-pathogenicity and the absence of genes involved in transferable antimicrobial resistances, virulence, and formation of biogenic amines. One region in the L. lactis LL16 genome was identified as type III polyketide synthases (T3PKS) to produce putative bacteriocins lactococcin B, and enterolysin A. The probiotic and functional potential of L. lactis LL16 was investigated by the presence of genes involved in adhesion and colonization of the host's intestines and tolerance to acid and bile, production of enzymes, amino acids, and B-group vitamins. Genes encoding the production of neurotransmitters serotonin and gamma-aminobutyric acid (GABA) were detected; however, L. lactis LL16 was able to produce only GABA during milk fermentation. These findings demonstrate a variety of positive features that support the use of L. lactis LL16 in the dairy sector as a functional strain with probiotic and GABA-producing properties.

Comparative Genomics Analysis of Habitat Adaptation by Lactobacillus kefiranofaciens

Lactobacillus kefiranofaciens is often found in fermented dairy products. Many strains of this species have probiotic properties, contributing to the regulation of immune metabolism and intestinal flora. This species was added to the list of lactic acid bacteria that can be added to food in China, in 2020. However, research on the genomics of this species is scarce. In this study we undertook whole genome sequencing analysis of 82 strains of L. kefiranofaciens from different habitats, of which 9 strains were downloaded from the NCBI RefSeq (National Center for Biotechnology Information RefSeq). The mean genome size of the 82 strains was 2.05 ± 0.25 Mbp, and the mean DNA G + C content was 37.47 ± 0.42%. The phylogenetic evolutionary tree for the core genes showed that all strains belonged to five clades with clear aggregation in relation to the isolation habitat; this indicated that the genetic evolution of L. kefiranofaciens was correlated to the isolation habitat. Analysis of the annotation results identified differences in the functional genes, carbohydrate active enzymes (CAZy) and bacteriocins amongst different isolated strains, which were related to the environment. Isolates from kefir grains had more enzymes for cellulose metabolism and a better ability to use vegetative substrates for fermentation, which could be used in feed production. Isolates from kefir grains also had fewer kinds of bacteriocin than isolates from sour milk and koumiss; helveticin J and lanthipeptide class I were not found in the isolates from kefir grains. The genomic characteristics and evolutionary process of L. kefiranofaciens were analyzed by comparative genomics and this paper explored the differences in the functional genes amongst the strains, aiming to provide a theoretical basis for the research and development of L. kefiranofaciens.

Honey bee-associated bacteria as producers of bioactive compounds for protecting hives. A biosynthetic gene-based approach

Honey bee-associated bacteria are a source of natural compounds of interest for controlling hive decline which is threatening bee health globally. Genes involved in the biosynthesis of a series of extracellular compounds released by bacteria living on the external surface of honey bees were investigated. A biosynthetic gene-based approach was adopted by developing a battery of primers to target the genes involved in the biosynthesis of four groups of bioactive compounds (pyrrolizidine alkaloids, surfactin, 2-heptanone and helveticin J). The primers were tested on 51 bacterial isolates belonging to Bacillus thuringiensis, Acetobacteraceae bacterium, Bifidobacterium asteroides and Apilactobacillus kunkeei. The developed primers led to species-specific detection and characterization of the functional genes involved in the production of three out of four groups of compounds selected for this study. The findings suggest that microbial populations inhabiting apiaries harbor genes involved in the biosynthesis of metabolites linked to the reduction of important honey bee pathogens such as Varroa destructor, Paenibacillus larvae and Nosema ceranae. The gene-based approach adopted for evaluating the biosynthetic potential of bioactive compounds in hives is promising for investigating further compounds for low input control strategies of bee enemies.

Characterization of the key aroma compounds in Yunnan goat milk cake using a sensory-directed flavor analysis

To identify the key aroma compounds in Yunnan goat milk cake, seven varieties of milk cake samples were subjected to sensory analysis and gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O), aroma recombination, omission, and addition tests. The GC-MS results revealed 53 compounds with aroma characteristics in all the samples. A further comparison of odor activity values and aroma intensities (AI) revealed 25 of these compounds as the initial key aroma compounds. The contributions of these key aroma compounds to the sensory attributes were determined using a partial least squares regression. Of these compounds, 2-heptanone and 2-nonanone were closely related to the "milky" and "cheesy" attributes and were highly abundant in the samples from Kunming. Fatty acids, including butanoic acid, hexanoic acid, octanoic acid, and decanoic acid, were the most abundant compounds detected in the milk cakes. These fatty acids were closely related to the "rancid" and "animalic (goat)" attributes and were largely detected in the samples from Dali Dengchuan and Dali Xiaguan. Sensory-directed aroma recombination, omission, and addition tests further validated the important contributions of ethyl butyrate, benzaldehyde, 3-methyl-1-butanol, 2-heptanone, hexanoic acid, and octanoic acid to the overall sensory properties. Moreover, ethyl butyrate, benzaldehyde, and 2-heptanone, when added, had evident inhibitory or masking effects on the AI of "sour," "rancid," and "animalic (goat)" attributes. PRACTICAL APPLICATION: Goat milk cake is a popular acid-curd cheese in Yunnan, China, however, our limited knowledge to its key aroma compounds restricts its development and industrial production. In this study, a sensory-directed flavor analysis was used to characterized the key aroma compounds of Yunnan goat milk cake, which will help to enhance our understanding on the flavor profile of Yunnan goat milk cake and provide a reference for optimizing the flavor feature and organoleptic quality of this fresh goat cheese.

Class III bacteriocin Helveticin-M causes sublethal damage on target cells through impairment of cell wall and membrane

Helveticin-M, a novel Class III bacteriocin produced by Lactobacillus crispatus exhibited an antimicrobial activity against Staphylococcus aureus, S. saprophyticus, and Enterobacter cloacae. To understand how Helveticin-M injured target cells, Helveticin-M was cloned and heterologously expressed in Escherichia coli. Subsequently, the cell wall organization and cell membrane integrity of target cells were determined. The mechanism of cellular damage differed according to bacterial species. Based on morphology analysis, Helveticin-M disrupted the cell wall of Gram-positive bacteria and disorganized the outer membrane of Gram-negative bacteria, therefore, altering surface structure. Helveticin-M also disrupted the inner membrane, as confirmed by leakage of intracellular ATP from cells and depolarization of membrane potential of target bacteria. Based on cell population analysis, Helveticin-M treatment caused the increase of cell membrane permeability, but the cytosolic enzymes were not influenced, indicating that it was the sublethal injury. Therefore, the mode of Helveticin-M action is bacteriostatic rather than bactericidal.

Isolation, Identification, and Evaluation of New Lactic Acid Bacteria Strains with Both Cellular Antioxidant and Bile Salt Hydrolase Activities In Vitro

In this study, we analyzed Chinese traditional fermented food to isolate and identify new lactic acid bacteria (LAB) strains with novel functional properties and to evaluate their cellular antioxidant and bile salt hydrolase (BSH) activities in vitro. A sequential screening strategy was developed to efficiently isolate and obtain 261 LAB strains tolerant of bile salt, acid, and H₂O₂ from nine Chinese traditional fermented foods. Among these strains, 70 were identified as having 2,2-diphenyl-1-picrylhydrazyl radical scavenging and/or BSH activity. These strains belonged to eight species: Enterococcus faecium (33% of the strains), Lactobacillus plantarum (26%), Leuconostoc mesenteroides (14%), Pediococcus pentosaceus (6%), Enterococcus durans (9%), Lactobacillus brevis (9%), Pediococcus ethanolidurans (3%), and Lactobacillus casei (1%). The pulsed-field gel electrophoresis genome fingerprinting profiles of these strains revealed 38 distinct pulsotypes, indicating a high level of genomic diversity among the tested strains. Twenty strains were further evaluated for hydroxyl radical scavenging activity, reducing power, and ferrous ion chelating activity exerted by both viable intact cells and/or intracellular cell-free extracts. Some strains, such as L. plantarum D28 and E. faecium B28, had high levels of both cellular antioxidant and BSH activities in vitro. These strains are promising probiotic components for health-promoting functional foods.

Identification of bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei reveals distinct temperature-driven patterns

Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL). Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT) and at lower (WLT) temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry.

A novel carboxyl-terminal protease derived from Paenibacillus lautus CHN26 exhibiting high activities at multiple sites of substrates

Background

Carboxyl-terminal protease (CtpA) plays essential functions in posttranslational protein processing in prokaryotic and eukaryotic cells. To date, only a few bacterial ctpA genes have been characterized. Here we cloned and characterized a novel CtpA. The encoding gene, ctpAp (ctpA of Paenibacillus lautus), was derived from P. lautus CHN26, a Gram-positive bacterium isolated by functional screening. Recombinant protein was obtained from protein over-expression in Escherichia coli and the biochemical properties of the enzyme were investigated.

Results

Screening of environmental sediment samples with a skim milk-containing medium led to the isolation of a P. lautus CHN26 strain that exhibited a high proteolytic activity. A gene encoding a carboxyl-terminal protease (ctpAp) was cloned from the isolate and characterized. The deduced mature protein contains 466 aa with a calculated molecular mass of 51.94 kDa, displaying 29-38% amino acid sequence identity to characterized bacterial CtpA enzymes. CtpAp contains an unusual catalytic dyad (Ser₃₀₉-Lys₃₃₄) and a PDZ substrate-binding motif, characteristic for carboxyl-terminal proteases. CtpAp was expressed as a recombinant protein and characterized. The purified enzyme showed an endopeptidase activity, which effectively cleaved α S1- and β- casein substrates at carboxyl-terminus as well as at multiple internal sites. Furthermore, CtpAp exhibited a high activity at room temperature and strong tolerance to conventional protease inhibitors, demonstrating that CtpAp is a novel endopeptidase.

Conclusions

Our work on CtpA represents the first investigation of a member of Family II CtpA enzymes. The gene was derived from a newly isolated P. lautus CHN26 strain exhibiting a high protease activity in the skim milk assay. We have demonstrated that CtpAp is a novel endopeptidase with distinct cleavage specificities, showing a strong potential in biotechnology and industry applications.