Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms

Genome analysis reveals a biased distribution of virulence and antibiotic resistance genes in the genus Enterococcus and an abundance of safe species

Enterococci are lactic acid bacteria (LAB) that, as their name implies, often are found in the gastrointestinal tract of animals. Like many other gut-dwelling LAB, for example, various lactobacilli, they are frequently found in other niches as well, including plants and fermented foods from all over the world. In fermented foods, they contribute to flavor and other organoleptic properties, help extend shelf life, and some even possess probiotic properties. There are many positive attributes of enterococci; however, they have been overshadowed by the occurrence of antibiotic-resistant and virulent strains, often reported for the two species, Enterococcus faecalis and Enterococcus faecium. More than 40,000 whole-genome sequences covering 64 Enterococcus type species are currently available in the National Center for Biotechnology Information repository. Closer inspection of these sequences revealed that most represent the two gut-dwelling species E. faecalis and E. faecium. The remaining 62 species, many of which have been isolated from plants, are thus quite underrepresented. Of the latter species, we found that most carried no potential virulence and antibiotic resistance genes, an observation that is aligned with these species predominately occupying other niches. Thus, the culprits found in the Enterococcus genus mainly belong to E. faecalis, and a biased characterization has resulted in the opinion that enterococci do not belong in food. Since enterococci possess many industrially desirable traits and frequently are found in other niches besides the gut of animals, we suggest that their use as food fermentation microorganisms is reconsidered.IMPORTANCEWe have retrieved a large number of Enterococcus genome sequences from the National Center for Biotechnology Information repository and have scrutinized these for the presence of virulence and antibiotic resistance genes. Our results show that such genes are prevalently found in the two species Enterococcus faecalis and Enterococcus faecium. Most other species do not harbor any virulence and antibiotic resistance genes and display great potential for use as food fermentation microorganisms or as probiotics. The study contributes to the current debate on enterococci and goes against the mainstream perception of enterococci as potentially dangerous microorganisms that should not be associated with food and health.

Microbiota modulation and microbial metabolites produced during the in vitro colonic fermentation of Psidium guajava species

The interaction between gut microbiota and its metabolites is a growing area of research. Therefore, this study analyzed the bioactive compound profile of the indigestible fraction (IF) from Psidium species and evaluated its effects on microbiota composition during in vitro colonic fermentation. Hydroxycinnamic acids, hydroxybenzoic acids, and ellagitannins were the predominant phenolic compounds, with P. friedrichsthalianum ('Cas') exhibiting the highest concentrations. During in vitro colonic fermentation, a reduction in bacterial genera such as Enterobacteriaceae and Klebsiella was observed, while Faecalibacterium, Oscillibacter, Dialister, and Ruminococcaceae positively correlated with phenolic microbial metabolites. These findings suggest that the IF of Psidium species modulates gut microbiota composition and potentially contributes to the production of beneficial metabolites during human colonic fermentation, reinforcing the role of whole fruit consumption as a comprehensive matrix of nutrients and bioactive compounds beneficial to gut health.

Isolation and Characterization of β-Phenylethylamine-Producing Lactic Acid Bacteria from Dairy Products

β-phenylethylamine (PEA) is a neuroactive trace amine synthesized by the enzymatic decarboxylation of phenylalanine. PEA is involved in the improvement of mood and attention. Functional foods enriched in this compound could, therefore, be of interest to the food industry. PEA is produced by microbial activity in certain foods, but usually only in small amounts. The search for PEA-producing microorganisms with good technological properties is thus a pre-requisite if such functional foods are to be produced. This work reports the isolation of thirty-three PEA-producing bacterial strains from samples of different dairy products. They belong to the genus Enterococcus, and the species Levilactobacillus brevis. Identified strains of Enterococcus durans were then selected for technological characterization. Some of them showed properties of interest. In this species, PEA was determined to be produced via the action of tyrosine decarboxylase, encoded by the gene tdcA. This implies that, apart from PEA, a concomitant production of tyramine, a toxic biogenic amine, was observed.

Exploring the Frontiers of Nanopore Sequencing in Food Safety and Food Microbiology

Foodborne illnesses are a significant global public health challenge, with an estimated 600 million cases annually. Conventional food microbiology methods tend to be laborious and time consuming, pose difficulties in real-time utilization, and can display subpar accuracy or typing capabilities. With the recent advancements in third-generation sequencing and microbial omics, nanopore sequencing technology and its long-read sequencing capabilities have emerged as a promising platform. In recent years, nanopore sequencing technology has been benchmarked for its amplicon sequencing, whole-genome and transcriptome analysis, meta-analysis, and other advanced omics approaches. This review comprehensively covers nanopore sequencing technology's current advances in food safety applications, including outbreak investigation, pathogen surveillance, and antimicrobial resistance profiling. Despite significant progress, ongoing research and development are crucial to overcoming challenges in sequencing chemistry, accuracy, bioinformatics, and real-time adaptive sampling to fully realize nanopore sequencing technology's potential in food safety and food microbiology.

The mechanism of Enterococcus faecium on the virulence of Listeria monocytogenes during the storage of fermented sausages by whole genome analysis

This study investigated the safety characteristics and potential probiotic properties of Enterococcus faecium by using whole genome analysis, and then explored the effect of this strain on the virulence of Listeria monocytogenes in vitro and during the storage of fermented sausages. Results showed that E. faecium B1 presented enterocin A, B, and P, enterolysin A, and UviB, and the exotoxin related genes and exoenzyme related genes were not detected in the genome of E. faecium B1. However, the adherence genes including acm and scm were present in this strain, which also positively correlated with characteristics related to probiotic potential. In addition, E. faecium could adapt to the condition of fermented sausages, and decrease the survival of L. monocytogenes in vitro and in vivo. The expression of the virulence genes (prfA, hly, inlA, and inlB) and sigB-related genes (prli42, rsbT, rsbU, rsbV, rsbW, and sigB) were all inhibited by E. faecium B1 to different extents during the storage of fermented sausages at 4 °C. Moreover, compared with the E. faecium B1 group, the expression level of entA, entB, and entP genes of E. faecium B1 in the co-culture of fermented sausages was increased during the storage, which may be the inhibition mechanism of E. faecium B1 on L. monocytogenes. These results demonstrated that E. faecium B1 could potentially be used as bio-protection to control L. monocytogenes in meat products.

Isolation and characterization of enterococci from poultry reveals high incidence of Enterococcus thailandicus in Victoria, Australia

AIMS

Antibiotic resistance is a global health crisis. Roughly two-thirds of all antibiotics used are in production animals, which have the potential to impact the development of antibiotic resistance in bacterial pathogens of humans. There is little visibility on the extent of antibiotic resistance in the Australian food chain. This study sought to establish the incidence of antibiotic resistance among enterococci from poultry in Victoria.

METHODS AND RESULTS

In 2016, poultry from a Victorian processing facility were swabbed immediately post-slaughter and cultured for Enterococcus species. All isolates recovered were speciated and tested for antibiotic susceptibility to 12 antibiotics following the Clinical Laboratory Standards Institute guidelines. A total of 6 farms and 207 birds were sampled and from these 285 isolates of Enterococcus were recovered. Eight different enterococcal species were identified as follows: E. faecalis (n = 122; 43%), E. faecium (n = 92; 32%), E. durans (n = 35; 12%), E. thailandicus (n = 23; 8%), E. hirae (n = 10; 3%), and a single each of E. avium, E. gallinarum, and E. mundtii. Reduced susceptibility to older classes of antibiotics was common, in particular: erythromycin (73%), rifampin (49%), nitrofurantoin (40%), and ciprofloxacin (39%). Two vancomycin-intermediate isolates were recovered, but no resistance was detected to either linezolid or gentamicin.

CONCLUSIONS

The relatively high numbers of a recently described species, E. thailandicus, suggest this species might be well adapted to colonize poultry. The incidence of antibiotic resistance is lower in isolates from poultry than in human medicine in Australia. These results suggest that poultry may serve as a reservoir for older antibiotic resistance genes but is not driving the emergence of antimicrobial resistance in human bacterial pathogens. This is supported by the absence of resistance to linezolid and gentamicin.

Phenotypic characterization for bioremediation suitability of isolates from Southern Tunisian tannery effluent

Effluents from the leather tanning industry contain diverse pollutants, including hazardous heavy metals, posing threats to public health and the surrounding environment. Indigenous bacterial isolates can represent an eco-friendly approach for tannery wastewater treatment; however, phenotypic characterization is necessary to determine whether these strains are suitable for bioremediation. In the present study, we analyzed seven new Enterococcus faecium strains and two new Bacillus subtillis strains isolated from effluents from the Southern Tunisian Tannery (ESTT). We evaluated phenotypic features beneficial for bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities. Additionally, we examined characteristics naturally occurring in environmental bacteria but less desirable in strains selected for bioremediation, such as antibiotic resistances and pathogenicity indicators. The observed phenotypes were then compared with whole-genome analysis. We observed biofilm production in two slime-producing bacteria, B. licheniformis RLT6, and E. faecium RLT8. Hydrophobicity of E. faecium strains RLT1, RLT5, RLT8, and RLT9, as well as B. licheniformis RLT6 correlated positively with increasing ESTT concentration. Exoenzyme activities were detected in E. faecium strains RLT2, RLT4, and RLT7, as well as B. licheniformis RLT6. As anticipated, all strains exhibited common resistances to antibiotics and hemolysis, which are widespread in nature and do not hinder their application for bioremediation. Importantly, none of the strains exhibited the pathogenic hypermucoviscosity phenotype. To the best of our knowledge, this is the first report consolidating all these phenotypic characteristics concurrently, providing a complete overview of strains suitability for bioremediation. IMPORTANCE: The study evaluates the bioremediation potential of seven Enterococcus faecium strains and two Bacillus subtillis strains isolated from the effluents from the Southern Tunisian tannery (ESTT), which pose threats to public health and environmental integrity. The analysis primarily examines the phenotypic traits crucial to bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities, as well as characteristics naturally occurring in environmental bacteria related to heavy metal resistance, such as antibiotic resistances. Several strains were found to have high bioremediation potential and exhibit only antibiotic resistances commonly found in nature, ensuring their application for bioremediation remains uncompromised. The results of the exhaustive phenotypic analysis are contrasted with the whole genome sequences of the nine strains, underscoring the appropriateness of these bacterial strains for eco-friendly interventions in tannery wastewater treatment.