The Many Faces of Enterococcus spp.-Commensal, Probiotic and Opportunistic Pathogen

Searching for antibiotic-susceptible bioprotective lactic acid bacteria to control dangerous biological agents in artisanal cheese

Minas artisanal cheese (MAC) samples (n = 59) from 16 municipalities across five traditional MAC-producing regions in Brazil were used to prospect antibiotic-susceptible protective lactic acid bacteria (LAB) against three pathogenic bacteria found in the MAC. From 291 LAB isolates, 84 genetically diverse strains were selected via rep-PCR. MALDI-TOF identification revealed multiple species, predominantly Enterococcus faecalis (n = 37), Enterococcus faecium (n = 21), Lactiplantibacillus plantarum (n = 5) and Lacticaseibacillus rhamnosus (n = 3). The antagonistic activity of these strains was evaluated against Enterococcus faecalis ATCC 29212, Listeria monocytogenes ATCC 5779, and Escherichia coli O157:H7 using spot-on-lawn assays. Several strains showed strong inhibitory effects against E. coli and L. monocytogenes, with halo/colony ratios reaching 4.86 and 4.47, respectively. No antimicrobial peptide producing strain was observed. Antibiotic susceptibility was tested against nine antibiotics, and five strains were susceptible to all antibiotics, while 53 strains were susceptible to 5-8 antibiotics. However, five strains were resistant to all antibiotics, showing the highest resistance to gentamicin (66.7%), cotrimoxazole (58.3%), and streptomycin (57.2%). Resistance genes (aacA-aphD, ermA/B, tetM/O/K/L/S, blaZ, and vanA/B) were screened, and 40 strains harbored at least one gene. Taken together, these results revealed three antibiotic-susceptible bioprotective lactobacilli (L. rhamnosus 52, L. plantarum 177, and L. plantarum 272G) as superior strains, whose efficacy in eliminating E. coli O157 and Listeria monocytogenes in the milk matrix between 7- and 21-days post-inoculation was confirmed. These findings confirm the potential of these autochthonous lactobacilli to improve the safety of dairy, paving the way for their applications in product development in future projects.

Phenotypic and genomic analysis of Enterococcus avium MC09 pathogenicity isolated from Scylla spp. (mud crab) in a Thai market

Enterococcus avium is a Gram-positive pathogenic bacterium classified under the Enterococcaceae family. E. avium has been isolated from diverse environmental sources, raising concerns about its potential role in the spread of antibiotic resistance. E. avium MC09, isolated from a mud crab in a Thai market, was analyzed for its antibiotic resistance and pathogenic potential in this study. The isolation of E. avium from mud crab is significant as it highlights the potential role of seafood as a reservoir for antibiotic-resistant bacteria, which may pose risks to public health throughout the food chain. Antibiotic susceptibility testing using the Kirby-Bauer disk diffusion method revealed that E. avium MC09 is resistant to clindamycin, erythromycin, streptomycin, and tetracycline, and exhibits alpha hemolysis on blood agar, indicating its potential virulence. Genomic DNA was extracted and sequenced using the Oxford Nanopore Technologies (ONT) platform, revealing the presence of resistance genes for macrolides (ermB) and tetracyclines (tetL and tetM). Furthermore, several virulence-associated genes were detected, such as srtC, ecbA, efaA, dltA, cpsA/uppS, cpsB/cdsA, cylR2, icps4I, cpsY, epsE, vctC, mgtB, ndk, lisR, and lgt suggesting a pathogenic potential. Additionally, the study identified several insertion sequences (ISs), including (IS1216, IS1216E, IS1216V, IS6770, ISEfa7, ISEfa8, and ISS1W which are commonly found in pathogenic Enterococcus strains. The presence of these IS elements further emphasizes the strain's potential for virulence and genetic adaptability. This study provides comprehensive insights into both the phenotypic and genotypic characteristics of E. avium MC09, highlighting its antimicrobial resistance and pathogenic mechanisms, and underlines the importance of monitoring antibiotic resistance in seafood-associated bacteria.

Candida albicans impacts carbohydrate metabolism of Enterococcus faecalis in interkingdom biofilms

Objectives

This study investigated the transcriptional and physiological responses of Enterococcus faecalis, an opportunistic pathogen linked to endodontic infections, when cultivated in dual-species biofilms with Candida albicans, a yeast pathobiont found in the oral cavity.

Methods

Forty-eight-hour E. faecalis OG1RF biofilms were developed in BHI medium as mono- or dual-species with C. albicans SC5314. Biofilms were assessed for biomass, colony-forming units (CFUs), and architecture using confocal microscopy. RNA sequencing was performed on an Illumina platform. Mannose-PTS activity and glycerol quantification assays were conducted to investigate changes in carbohydrate metabolism.

Results

Transcriptomic analysis revealed 149 E. faecalis genes differentially expressed in dual-species biofilms. Genes linked to mannose-PTS and glycerol metabolism were notably upregulated. Mannose-PTS activity was significantly higher in dual-species biofilms. Mannose, as the sole carbohydrate source, increased E. faecalis CFUs and decreased C. albicans CFUs in co-culture, while glucose had no effect. As C. albicans is a glycerol net producer, glycerol levels were always higher when C. albicans was present, likely contributing to the upregulation of glycerol metabolism genes in E. faecalis when in co-cultures.

Conclusions

The presence of C. albicans alters E. faecalis gene expression and metabolism, suggesting metabolic crosstalk that may influence their pathogenicity and role in oral infections.

Genetic Comparison of Enterococcus Species Isolated from Osteomyelitis Lesions and the Barn Environment of Successive Broiler Chicken Flocks

Osteomyelitis caused by Enterococcus cecorum is an emerging disease in broiler chickens in Canada. Other Enterococcus species have been reported as causative agents in certain outbreaks. The epidemiology of this disease is unknown, but contaminated barns are affected by recurring episodes. A broiler chicken flock located in Quebec, Canada, exhibited osteomyelitis lesions positive for E. cecorum and Enterococcus faecalis. Surprisingly, the following lot, in the same barn, revealed the presence of E. faecalis- and Enterococcus raffinosus-positive lesions but no E. cecorum. To better understand the epidemiology of these two outbreaks, verify the persistence of pathogenic isolates in the barn, and identify the possible transfer of genetic material between the Enterococcus species isolated from both events, 16 isolates (1 E. cecorum, 13 E. faecalis, and 2 E. raffinosus isolates) were sequenced, and their genomes were compared. Interestingly, more than one Enterococcus species could be isolated from the same lesion, while other lesions also revealed several nonclonal isolates from the same species. This might suggest the opportunistic nature of Enterococcus spp. as there was no predominant isolate in the lesions. The number of virulence genes varied from 1 to 34 across three Enterococcus species with no common virulence gene. The number and nature of antimicrobial resistance genes among those isolates were worrisome because they indicate the presence of multidrug resistance on the farm. Both plasmids and phages were shared by different Enterococcus species, which suggests potential horizontal gene transfer of mobile genetic elements within this enterococci population.

Transcatheter aortic valve implantation: Association between skin flora and infective endocarditis?

BACKGROUND

Infective endocarditis is a rare but severe complication that may arise following transcatheter aortic valve implantation. Recent advances in microbiological epidemiology have highlighted staphylococci and enterococci as the primary pathogens involved.

AIM

To investigate the prevalence of these bacteria in patients' cutaneous flora before and after transcatheter aortic valve implantation procedures, and to assess the implications for antibiotic prophylaxis recommendations.

METHODS

A single-centre prospective epidemiological study was conducted, enrolling patients admitted consecutively for transcatheter aortic valve implantation procedures between June 2021 and February 2022. Cutaneous samples were obtained from each patient at the puncture site of the transcatheter aortic valve implantation procedure, before and after skin detersion, and from operator hands after skin detersion.

RESULTS

One hundred patients were included, with a mean age of 82±6.1years, a male-to-female ratio of 0.48 and a mean body mass index of 29±4.4kg/m2. Before skin detersion, cutaneous samples were positive in 58 patients; among them were coagulase-negative staphylococci (n=48, 82%, 95% confidence interval 71-91%), enterococci (n=12, 21%, 95% confidence interval: 11-33%), Staphylococcus aureus (n=2, 3%, 95% confidence interval 0-12%) and Enterobacteriaceae (n=4, 7%, 95% confidence interval: 2-17%).

CONCLUSIONS

Enterococci are frequently present in patients' cutaneous flora at the puncture site before skin detersion, suggesting a potential source for infective endocarditis after transcatheter aortic valve implantation. These findings support considering amoxicillin-clavulanate as antibiotic prophylaxis before transcatheter aortic valve implantation procedures to mitigate the risk of infective endocarditis associated with enterococcal colonization.

Synbiotic Sapota-do-Solimões (Quararibea cordata Vischer) Juice Improves Gut Microbiota and Short-Chain Fatty Acid Production in an In Vitro Model

Sapota-do-Solimões (Quararibea cordata Vischer) is Amazon South América fruit found in Brazil, Colombia, Ecuador, and Peru. The orange-yellow fruit is usually eaten out of hand or as juice. Despite being a source of carotenoids and dietary fibers (pectin) that can reach the colon and act as an energy source for intestinal microbiota, the fruit is rarely known outside of South America. The symbiotic juice was prepared by fermenting the fruit juice with Lacticaseibacillus casei B-442 and adding prebiotic fructooligosaccharides (FOS, 7% w/v). This study evaluated the functional juice immediately after L. casei fermentation (SSJ0) and after 30 days of cold storage (SSJ30) regarding its effect on human colonic microbiota composition after in vitro fermentation. Fecal samples were collected from two healthy female volunteers, and the 16s rRNA gene sequencing analyzed the fecal microbiota composition. In vitro, colonic fermentation was performed using a batch bioreactor to simulate gastrointestinal conditions. The L. casei viability did not change significantly after 30 days of the synbiotic juice cold storage (4 °C). After the colonic fermentation, the relative abundance of Firmicutes decreased while Proteobacteria and Actinobacteria increased. Regarding short-chain fatty acid (SCFA) production by fecal colonic microbiota, the butyric acid was higher after sample SSJ0 fecal fermentation. In contrast, propionic, isobutyric, and acetic acids were higher after SSJ30 sample fecal fermentation. This study contributes to understanding the interactions between specific foods and the gut microbiota, which can affect human health and well-being.

Exploring the dark side of probiotics to pursue light: Intrinsic and extrinsic risks to be opportunistic pathogens

Probiotics, live microorganisms with multiple health benefits, have gained popularity for their roles in maintaining daily health and treating a variety of diseases. However, they have the potential to be opportunistic pathogens in some conditions. This review delves into the intrinsic and extrinsic risks associated with probiotics. Intrinsic risks involve the production of harmful substances, such as toxins and invasive factors, biofilm formation, bacteria emboli, antibiotic resistance with relevant genetic materials, genetic plasticity, and metabolic issues, while extrinsic risks include problems in regulatory oversight and public awareness, host health status and appropriately administration. It emphasizes the need for a balanced view of their therapeutic benefits and potential hazards, advocating for further research to understand the complex interactions between probiotics and the human microbiome, to optimize the safety and efficacy of probiotics.

Real Way to Target Gram-Negative Pathogens: Discovery of a Novel Helicobacter pylori Antibiotic Class

In an era of escalating antibiotic resistance, there is a pressing need for innovative strategies to develop novel antibiotics. Gram-negative bacteria, characterized by their robust dual-membrane, are intrinsically resistant to a wide range of antibiotics and can readily develop new resistances. Members of this bacterial class comprise numerous pathogenic organisms, including the primary cause of gastric cancer, Helicobacter pylori. In this study, we used the Giga-sized collection of theoretical molecules inside Enamine's REAL Space to identify inhibitors for H. pylori glutamate racemase. These compounds displayed a diverse range of activity in preventing H. pylori growth, with our most potent hits capable of selective full growth inhibition for metronidazole and clarithromycin resistant H. pylori strains. Alongside the introduction of a novel antibiotic class for this carcinogenic pathogen, our unique implementation of REAL Space holds great promise for Gram-negative antibiotic development as a whole.

Identification of cross-reactive vaccine antigen candidates in Gram-positive ESKAPE pathogens through subtractive proteome analysis using opsonic sera

The Gram-positive pathogens of the ESKAPE group, Enterococcus faecium, and Staphylococcus aureus, are well-known to pose a serious risk to human health because of their high virulence and numerous drug resistances. To narrow down the list of previously identified promising protein vaccine candidates, a combination of several antigen discovery approaches was performed, in particular a "false positive analysis" of peptides generated by trypsin shaving with a subtractive proteome analysis. The final list of nine potential antigens included AdcAau, a protein performing the same function as AdcAfm, an already discovered antigen in enterococci. Bioinformatic analyses revealed that AdcAau and AdcAfm share a sequence identity of 41.2% and that the conserved regions present a high antigenicity. AdcAau was selected for further investigation and the results reported in this manuscript demonstrate the opsonic properties of AdcAau-specific antibodies against the Staphylococcus aureus strain MW2, as well as their cross-binding and cross-opsonic activity against several S. aureus, E. faecium, and E. faecalis strains. The experimental design revealed several promising vaccine candidates, including the newly identified S. aureus antigen, AdcAau. The study shows its potential as a vaccine candidate to prevent infections by dangerous Gram-positive ESKAPE pathogens.

Harnessing the human gut microbiota: an emerging frontier in combatting multidrug-resistant bacteria

Antimicrobial resistance (AMR) has become a major and escalating global health threat, undermining the effectiveness of current antibiotic and antimicrobial therapies. The rise of multidrug-resistant bacteria has led to increasingly difficult-to-treat infections, resulting in higher morbidity, mortality, and healthcare costs. Tackling this crisis requires the development of novel antimicrobial agents, optimization of current therapeutic strategies, and global initiatives in infection surveillance and control. Recent studies highlight the crucial role of the human gut microbiota in defending against AMR pathogens. A balanced microbiota protects the body through mechanisms such as colonization resistance, positioning it as a key ally in the fight against AMR. In contrast, gut dysbiosis disrupts this defense, thereby facilitating the persistence, colonization, and dissemination of resistant pathogens. This review will explore how gut microbiota influence drug-resistant bacterial infections, its involvement in various types of AMR-related infections, and the potential for novel microbiota-targeted therapies, such as fecal microbiota transplantation, prebiotics, probiotics, phage therapy. Elucidating the interactions between gut microbiota and AMR pathogens will provide critical insights for developing novel therapeutic strategies to prevent and treat AMR infections. While previous reviews have focused on the general impact of the microbiota on human health, this review will specifically look at the latest research on the interactions between the gut microbiota and the evolution and spread of AMR, highlighting potential therapeutic strategies.

The Effect of High-intensity Focused Ultrasound on Intracanal Bacterial Reduction, Chemical Structure, and Mechanical Properties of Root Dentine

OBJECTIVE

High-intensity focused ultrasound (HIFU) has demonstrated significant efficacy in eradicating bacteria from substrates emerging as a promising solution for root canal disinfection. This in-vitro study investigated the effects of HIFU on reducing intracanal bacteria and its impact on the chemical and mechanical properties of root dentine. It also aimed to demonstrate acoustic wave penetration and distribution within the root canal system (RCS) and characterize the associated temperature changes.

METHODS

Eighty-two extracted premolar teeth with single canals, infected with Enterococcus faecalis (E. faecalis) and cultured for two weeks, were randomly assigned to four groups: negative control, 4% sodium hypochlorite (NaOCl), 60 s HIFU, and 120 s HIFU (operated at 250 kHz/20W). Post-treatment, biofilm samples were collected from the root canals to assess viable bacterial cells using colony-forming unit (CFU) and 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assays. The root canal surfaces were subsequently examined using scanning electron microscopy, confocal laser scanning microscopy (CLSM), microhardness, and Raman spectroscopy. Acoustic wave penetration, distribution, and temperature changes within the RCS were examined using CLSM and thermal camera.

RESULTS

HIFU at 60 s and 120 s consistently demonstrated superior anti-bacterial efficacy against E. faecalis biofilms compared to 4% NaOCl. MTT and CFU assays revealed a significant reduction in biofilm viability, particularly at 120 s of HIFU exposure (p<0.05). CLSM and SEM analyses demonstrated enhanced penetration and detachment of biofilms, as well as improved smear layer removal and preservation of dentinal tubules, especially at 120 s of HIFU exposure. HIFU treatment did not adversely affect the amide/mineral content of root dentine or its surface microhardness. Additionally, HIFU enhanced acoustic wave propagation and resulted in a controlled increase in temperature within the root canal over time.

CONCLUSION

This minimally invasive approach shows promise for removing bacterial biofilms in the RCS, positioning HIFU as a valuable adjunctive treatment for enhancing root canal disinfection. (EEJ-2024-08-123).

Harnessing the Power of Donkey's Milk and Homemade Pickles: Unveiling Oxalate-Degrading Probiotics and Their Heat-Killed Cells as Antiadipogenic Agents in 3T3-L1 Adipocytes

Gut microbial dysbiosis is associated with the development of critical clinical conditions of metabolic syndrome (obesity, type II diabetes), and calcium oxalate kidney stones. The human gut microbial eubiosis with functional probiotics and their heat-killed cells of lactic acid bacteria (LAB) is considered the current therapy for metabolic syndrome (MS). In accordance with this, our study aimed to isolate oxalate-degrading, cholesterol-lowering, and anti-adipogenic bacterial strains from raw donkey's milk and homemade fermented pickles. Nine LAB strains with potential in vitro oxalate degrading, α-glucosidase inhibiting, and cholesterol-lowering activities were pre-screened from fourteen isolates. Further, the heat-killed cells of selected strains were evaluated for anti-adipogenic activity in murine 3T3-L1 adipocytes. This activity was examined by studying the lipid storage, gene, and protein expression of adipogenic and lipogenic transcription factors. Subsequently, four potential isolates demonstrated a significant reduction in lipid storage by limiting adipogenesis (reducing C/EBPα, PPARγ expression), lipid transportation (downregulating aP2 expression), and lipogenesis (reducing PLIN-1 expression). These effective isolates were characterized using 16S rRNA molecular sequencing, and were identified as closest relatives to the Enterococcus (RRLA5, RRLA1, and RRLD6) and Lactobacillus (RRLM2) genera. Further, they displayed good survivability under in vitro gastric conditions and non-haemolytic activity. Taken together, the live cells of effective isolates depicted significant in vitro oxalate degradation, and their heat-killed cells demonstrated anti-adipogenic activity through downregulating the adipogenesis and lipogenesis. Moreover, future preclinical animal model studies on the synergistic role of probiotics and their heat-killed cells in disease prevention through gut microbial modulation could provide evidence as a biotherapeutic agent.

Isolation and Characterization of Enterocin-Producing Enterococcus faecium Strains from Algerian Traditional Food "Dried Figs Marinated in Olive Oil": Functional and Safety Evaluations

The increasing consumer demand for natural and sustainable food preservation methods has highlighted the potential of lactic acid bacteria (LAB) and their bioactive metabolites, particularly bacteriocins, as effective antimicrobial agents. This study aimed to isolate and characterize Enterococcus faecium strains from Algerian traditional dried figs marinated in olive oil, a nutrient-dense and underexplored food matrix. Twelve isolates were identified as E. faecium using MALDI-TOF MS and 16S rRNA gene sequencing, ensuring precise taxonomic classification. Genotypic analyses (BOX-PCR, GTG-PCR, and ERIC-PCR) revealed substantial genetic diversity, with BOX-PCR demonstrating superior discriminatory power. Functional screening confirmed the presence of enterocin genes, including entA (100% of strains), entB (60%), and entL50A/B (20%), which correlated with inhibition zones against Enterococcus faecium VCY, Micrococcus luteus GPE 3001, Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa ATCC 27853, and Acinetobacter lwoffii GPE 3002. Genotype-phenotype correlation analysis identified strain HFM7 as the most potent antimicrobial strain, exhibiting the largest inhibition zone (20.0 ± 1.0 mm) and harboring three enterocin genes (entA, entL50A, and entL50B). Protease sensitivity confirmed the proteinaceous nature of the antimicrobial compounds. Importantly, no virulence factors (esp, gelE, and hyl) or antibiotic resistance genes (vanA, vanB, ermA, ermB, and aac(6')-Ie-alph(2″)) were detected, underscoring the safety of these isolates for food applications. These findings suggest that E. faecium strains from traditional foods are promising candidates as natural biopreservatives and starter cultures in clean-label food systems. By bridging traditional food ecosystems and modern biotechnological advancements, this study provides a foundation for sustainable, minimally processed food preservation strategies with potential applications in enhancing food safety and shelf life.

Evaluating the Impact of Kefir Consumption on Dental Caries and Periodontal Disease: A Narrative Review

Background/Objectives: Dental caries and periodontal diseases are the most common illnesses in the oral cavity and represent a public health concern globally. In recent decades, diverse studies showed that Kefir, a traditional beverage that can be milk- or water-based, contains a complex microbial community and has health benefits. The goal of this review was to update the current knowledge of kefir consumption and its impact on oral health. Methods: The search of a combination of keywords-kefir; dental caries; probiotics; microbiota; periodontal diseases; biofilm; and oral health-was conducted using PubMed, Google Scholar, and Web of Science databases for studies in human subjects. Discussion: The research suggests that kefir consumption may aid in decreasing counts of microorganisms typically associated with oral illness. Conclusions: Kefir has the potential to inhibit certain oral pathogens and reduce biofilm formation by promoting diversity within the oral microbiota, suggesting that kefir could be a promising adjuvant treatment for dental caries and periodontal diseases by improving oral health.

Multi-omic signatures of host response associated with presence, type, and outcome of enterococcal bacteremia

Despite the prevalence and severity of enterococcal bacteremia (EcB), the mechanisms underlying systemic host responses to the disease remain unclear. Here, we present an extensive study that profiles molecular differences in plasma from EcB patients using an unbiased multi-omics approach. We performed shotgun proteomics and metabolomics on 105 plasma samples, including those from EcB patients and healthy volunteers. Comparison between healthy volunteer and EcB-infected patient samples revealed significant disparities in proteins and metabolites involved in the acute phase response, inflammatory processes, and cholestasis. Several features distinguish these two groups with remarkable accuracy. Cross-referencing EcB signatures with those of Staphylococcus aureus bacteremia revealed shared reductions in cholesterol metabolism proteins and differing responses in platelet alpha granule and neutrophil-associated proteins. Characterization of Enterococcus isolates derived from patients facilitated a nuanced comparison between EcB caused by Enterococcus faecalis and Enterococcus faecium, uncovering reduced immunoglobulin abundances in E. faecium cases and features capable of distinguishing the underlying microbe. Leveraging extensive patient metadata, we now have identified features associated with mortality or survival, revealing significant multi-omic differences and pinpointing histidine-rich glycoprotein and fetuin-B as features capable of distinguishing survival status with excellent accuracy. Altogether, this study aims to culminate in the creation of objective risk stratification algorithms-a pivotal step toward enhancing patient management and care. To facilitate the exploration of this rich data source, we provide a user-friendly interface at https://gonzalezlab.shinyapps.io/EcB_multiomics/.

IMPORTANCE

Enterococcus infections have emerged as the second most common nosocomial infection, with enterococcal bacteremia (EcB) contributing to thousands of patient deaths annually. To address a lack of detailed understanding regarding the specific systemic response to EcB, we conducted a comprehensive multi-omic evaluation of the systemic host response observed in patient plasma. Our findings reveal significant features in the metabolome and proteome associated with the presence of infection, species differences, and survival outcome. We identified features capable of discriminating EcB infection from healthy states and survival from mortality with excellent accuracy, suggesting potential practical clinical utility. However, our study also established that systemic features to distinguish Enterococcus faecalis from Enterococcus faecium EcB show only a moderate degree of discriminatory accuracy, unlikely to significantly improve upon current diagnostic methods. Comparisons of differences in the plasma proteome relative to healthy samples between bacteremia caused by Enterococcus and Staphylococcus aureus suggest the presence of bacteria-specific responses alongside conserved inflammatory reactions.

Vitamin B6 Alleviates Aflatoxin B1-Induced Impairment of Testis Development by Activating the PI3K/Akt Signaling Pathway

Aflatoxin B1 (AFB1) is a harmful environmental contaminant known to disrupt gut microbiota and cause health problems. In recent years, the role of vitamin B6 (VB6) in maintaining intestinal and reproductive health has attracted much attention. AFB1 has been found to damage the intestinal barrier and cause inflammation by disrupting the intestinal microbiota, particularly by increasing the abundance of Enterococcus. In mice treated with AFB1, serum metabolites were disturbed, VB6 serum levels were reduced, and testicular inflammation was exacerbated. Enterococcus exposure in mice leads to a reduction in serum VB6 levels, which is accompanied by intestinal and testicular damage. However, VB6 supplementation significantly ameliorated AFB1-induced intestinal and testicular injury. Transcriptomics and Western blotting showed that after AFB1 exposure, VB6 could increase the expression of phosphoinositide 3-kinase (PI3K) and kinase B (AKT) as well as their phosphorylated forms in the testes of mice. Based on the results, AFB1 leads to intestinal and testicular damage by disturbing the gut microbiota, and VB6 represents a potential therapeutic to counteract this damage. In conclusion, supplementation with adequate VB6 can ameliorate AFB1-induced intestinal and testicular damage, emphasizing the importance of VB6 intervention and providing a new perspective for the prevention and treatment of AFB1-related health issues.

BNT162b2 mRNA vaccination affects the gut microbiome composition of patients with follicular lymphoma and chronic lymphocytic leukemia

BACKGROUND

In both chronic lymphatic leukemia (CLL) and follicular lymphoma (FL) immunotherapy determines B-depletion that leads to temporary suppression of humoral immunity, which is clinically relevant especially during the COVID-19 pandemic, when most patients in the first wave received the BNT162b2 vaccine during anti-neoplastic treatment.

METHODS

To capture changes in the immunome and microbiome composition in CLL and FL patients upon mRNA-based vaccination, we designed a prospective, longitudinal study to profile both the humoral and the cellular response after exposure to the BNT162b2 COVID-19 vaccine.

RESULTS

In both CLL patients and FL patients, the second and third administrations of the BNT162b2 vaccine increased the titer of specific antibodies against SARS-CoV-2. In FL patients, vaccination induced expansion of central memory CD8 + CD57dim CD279 + T cells and reduction of the neutrophil subset myeloid 1 (CD14-CD15+CD16dimCD64+CD33-CD38+PDL1+HLA-DR-); in both cohorts, CD45RA + CD27 + CD279 + NK cells were expanded after a full cycle of vaccination. After vaccination, the genera Collinsella, Gemmiger, Lachnospiraceae, Blautia, Ruminococcus and Lactobacillus increased in both CLL patients and FL patients, whereas Faecalibacterium, Enterobacteriacae, and Enterococcus decreased. Multivariate analysis failed to identify factors associated with changes in microbiome communities among the CLL and FL cohorts, considering age, sex, exposure to anti-CD20 therapy and disease activity. Only in FL patients, alpha diversity was negatively correlated with neutrophil subsets myeloid 1 e 5 at baseline and positively correlated with neutrophil subset 6 after vaccination. PICRUSt2 analysis showed how microbiome can also affect the host health promoting chronic inflammation. The L-lysine biosynthesis pathway was more represented in CLL patients, whereas the L-valine degradation pathway and the anaerobic degradation of purine nucleobases were overrepresented in the FL cohort.

CONCLUSIONS

Taken together, our findings reveal the effect of the BNT162b2 vaccine in shaping the microbiome composition in CLL and FL patients, despite receiving treatment for their underlying active disease, and highlight the importance of a comprehensive analysis of the immunome and microbiome profiling to understand immune function in these cohorts of patients.

Comprehensive analysis of bacteriocins produced by clinical enterococcal isolates and their antibacterial activity against Enterococci including VRE

It is well-known that Enterococcus species produce bacteriocins that have antibacterial activity. However, a comprehensive analysis of the bacteriocin distribution among Enterococcus strains has not been conducted. In this study, we identified the bacteriocin genes from 80 Enterococcus faecalis and 38 Enterococcus faecium strains and investigated their antibacterial activity. In the 80 E. faecalis strains, the cytolysin gene (61.3%), enterolysin A gene (27.5%) and BacL1 gene (45.0%) were identified. In the 38 E. faecium strains, the enterocin A gene (97.4%), enterocin B gene (2.6%), enterocin NKR-5-3B gene (21.0%), bacteriocin T8 gene (36.8%) and BacAS9 gene (23.7%) were identified. The antibacterial activity of all strains was tested against E. faecalis and E. faecium. The strains positive for the cytolysin, enterolysin A, BacL1, bacteriocin T8 or BacAS9 genes presented variable antibacterial activity. Several bacteriocin-positive strains showed antibacterial activity against other enterococcal species, but not against Staphylococcus or Escherichia coli. In addition, the enterolysin A-positive strain showed antibacterial activity against vancomycin-resistant E. faecium, and the bacteriocin T8- or BacAS9-positive strains showed activity against vancomycin-resistant E. faecalis and E. faecium. Our findings suggest that E. faecium and E. faecalis strains that carry different bacteriocin genes may affect the composition of the surrounding bacterial community.

Prediction of inhibitory peptides against E.coli with desired MIC value

In the past, several methods have been developed for predicting antibacterial and antimicrobial peptides, but only limited attempts have been made to predict their minimum inhibitory concentration (MIC) values. In this study, we developed predictive models for MIC values of antibacterial peptides against Escherichia coli (E. coli), comprised of 3143 peptides for training and 786 peptides for validation, with experimentally determined MIC values. We found that the Composition Enhanced Transition and Distribution (CeTD) attributes significantly correlate with MIC values. Initially, we attempted to estimate MIC using BLAST similarity searches but found them inadequate. Subsequently, we employed machine learning regression models that integrated various features, including peptide composition, binary profiles and embeddings from large language models. Feature selection techniques, particularly mRMR, were utilized to refine our model inputs. Our Random Forest regressor built using default parameters achieved a correlation coefficient (R) of 0.78, R2 of 0.59, and RMSE of 0.53 on the validation set. Our best model outperformed existing methods when benchmarked on an independent dataset of 498 anti-E. coli peptides. Additionally, we screened anti-E. coli proteins in the proteomes of three probiotic bacterial strains and created a web-based platform, "EIPpred", enabling users to design peptides with desired MIC values ( https://webs.iiitd.edu.in/raghava/eippred ).

Effects of Dietary Supplement of Probiotic Enterococcus faecium on Intestinal Microbiota and Barrier Structure, Immune Function, and Antioxidant Capacity of Soft-Shelled Turtle Pelodiscus sinensis

Enterococcus faecium inhabits animal gastrointestinal tracts and has been demonstrated to benefit livestock and poultry, but its effects on soft-shelled turtles remain unexplored. The present work investigates the effects of probiotic E. faecium on intestinal microbiota and barrier structure, immune function, and antioxidant capacity of the soft-shelled turtle. Twenty-four juvenile Pelodiscus sinensis were divided into two groups: control (fed a basal diet) and treatment (fed a diet supplemented with E. faecium, 3.3 × 108 CFU/g feed), over a period of 6 weeks. We found that E. faecium did not promote the growth of turtles at the present feeding level, but the treatment resulted in significant alterations in the intestinal microbial community structure, with increased abundance of Enterococcus, Romboutsia, and Clostridium_sensu_stricto_1, and a reduction in Aeromonas (p  < 0.05). E. faecium notably enhanced villus height/crypt depth, villus width, and villus density in the intestine. The treatment group exhibited a 1.50-fold increase in goblet cells count and a 1.18-fold higher in the muscular layer thickness compared to the control group. E. faecium also improved the immune function, with an increase in the ratio of plasma neutrophils and lymphocytes to the total number of leukocytes after feeding probiotics, and upregulation of the levels of toll-like receptor 4 (TLR 4), lysozyme, interleukin 1β (IL-1β), tumor necrosis factor α (TNF-α), and immunoglobulin A (IgA) in the intestine, as well as the level of hepatic immunoglobulin M (IgM). Additionally, E. faecium supplementation boosted antioxidant capabilities, including a significant increase in catalase (CAT) and glutathione peroxidase (GPx) activity and reduced glutathione (GSH) levels in the intestine and GSH levels in the spleen. Our study demonstrates the beneficial effects of supplemental E. faecium on the intestine and overall health of soft-shelled turtles, particularly in enhancing their immune function and antioxidant capacity.

Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda

BACKGROUND

Infection with the COVID-19-causing pathogen SARS-CoV-2 is associated with disruption in the human gut microbiome. The gut microbiome enables protection against diverse pathogens and exhibits dysbiosis during infectious and autoimmune disease. Studies based in the United States and China have found that severe COVID-19 cases have altered gut microbiome composition when compared to mild COVID-19 cases. We present the first study to investigate the gut microbiome composition of COVID-19 cases in a population from Sub-Saharan Africa. Given the impact of geography and cultural traditions on microbiome composition, it is important to investigate the microbiome globally and not draw broad conclusions from homogenous populations.

RESULTS

We used stool samples in a Ugandan biobank collected from COVID-19 cases during 2020-2022. We profiled the gut microbiomes of 83 symptomatic individuals who tested positive for SARS-CoV-2 along with 43 household contacts who did not present any symptoms of COVID-19. The inclusion of healthy controls enables us to generate hypotheses about bacterial strains potentially related to susceptibility to COVID-19 disease, which is highly heterogeneous. Comparison of the COVID-19 patients and their household contacts revealed decreased alpha diversity and blooms of Enterococcus and Eggerthella in COVID-19 cases.

CONCLUSIONS

Our study finds that the microbiome of COVID-19 individuals is more likely to be disrupted, as indicated by decreased diversity and increased pathobiont levels. This is either a consequence of the disease or may indicate that certain microbiome states increase susceptibility to COVID-19 disease. Our findings enable comparison with cohorts previously published in the Global North, as well as support new hypotheses about the interaction between the gut microbiome and SARS-CoV-2 infection.

Antimicrobial Activity of Probiotic Bacteria Isolated from Plants: A Review

Lactic acid bacteria (LAB) constitute a heterogeneous group of bacteria isolated from fermented foods, animals, plants, and mammalian guts, with many health-promoting properties. Probiotics with antagonistic properties against human pathogens and foodborne bacteria have garnered significant attention from the scientific fraternity. A dedicated review focusing on plant-derived probiotic bacteria and their antagonistic properties has not been comprehensively reviewed. Thus, this review aimed at providing an overview of LAB isolates derived from several unconventional sources such as fruits, seeds, fruit pulp, leaves, roots, vegetables, grasses, and flowers and with their antibacterial, antifungal, and antiviral properties. This paper reviewed the antimicrobial properties of different genera, Lactobacillus, Leuconostoc, Weissella, Enterococcus, Pediococcus, Bacillus, and Fructobacillus, their postbiotics, and paraprobiotics. Several important mechanisms, including the secretion of bacteriocins, bacteriocin-like substances, reuterin, organic acids (lactic and acetic), peptides, exopolysaccharides, and hydrogen peroxide, have been attributed to their antimicrobial actions against pathogens. However, their precise mode of action is poorly understood; hence, further research should be conducted to reveal detailed mechanisms. Finally, the review discusses the summary and future implications. Given the significance, LAB and derived antimicrobial compounds can potentially be exploited in food preservation and safety or for medicinal applications after evaluating their safety.

Fluvial flooding and plastic pollution - The delivery of potential human pathogenic bacteria into agricultural fields

The frequency of plastic debris entering agricultural land is likely going to increase due to increased discharge into surface waters and more frequent flood events. Microbial biofilm on the surfaces of plastic pollution (known as the 'plastisphere') in freshwater environments often includes human pathogenic bacteria capable of causing disease. Pathogens have been detected on the surface of plastics in freshwater environments, but it is yet to be determined whether plastic debris can also transport pathogens into agricultural fields during flooding. Therefore, this study quantified the presence of viable pathogenic bacteria on the surface of plastic pollution at five agricultural fields along two rivers. All visible plastic debris, including sewage-associated plastic waste, were collected along a perpendicular 100 m transect from the riparian zone into each field. All plastic pieces were screened for five target bacteria (Escherichia coli, intestinal enterococci, Salmonella spp., Campylobacter spp., and Klebsiella spp.) using selective media, and positively identified colonies subsequently tested for antimicrobial resistance. In all five fields, there were higher volumes of plastic in the areas closer to the river, with 75% ± 24% of plastic collected within 30 m from the riverbank. Overall, 49% of all plastic collected in agricultural fields was colonised by phenotypically positive colonies for at least one or more target bacteria, with resistance to commonly prescribed antibiotics detected among several of these target bacteria. Therefore, the transport of contaminated plastic debris from fluvial floodwater into agricultural fields could pose an as yet unquantified risk of introducing potentially harmful bacteria into agricultural systems and the ultimately into the food chain.

Advanced Age Worsens Respiratory Function and Pulmonary Inflammation After Burn Injury and This Correlates With Changes in the Fecal Microbiome in Mice

Cutaneous burn injury in the elderly is associated with poor clinical outcomes and increased pulmonary-related complications. We and others have shown that burn injury triggers a cascade of inflammatory mediators which increase gut permeability and dysbiosis of the fecal microbiota and this is more dramatic in the aged. Since crosstalk between intestinal microbes and the lung, termed the "gut-lung axis," impacts immunity and homeostasis in the airway, we hypothesized that the increased intestinal dysbiosis in age and burn injury may contribute to excessive pulmonary inflammation and poor prognosis after injury. To explore this hypothesis, we used a clinically relevant murine model of burn injury in which young and aged mice are subjected to a 12% TBSA dorsal scald burn or sham injury. About 24 h after injury, lung function was assessed and lungs and feces were collected for analysis of inflammatory mediators and fecal microbial species. The results show that, when compared to younger mice, burn injury in aged mice triggers a decline in respiratory function and exacerbates pulmonary inflammation. In addition to heightened levels of the neutrophil recruiting chemokine CXCL1, aged mice displayed a profound increase in the pro-inflammatory protein, calprotectin, in the lung after burn injury. Comparison of the fecal microbiome and inflammatory markers in the lung revealed unique, age-dependent, correlation patterns between individual taxa and pulmonary inflammation. Taken together, these findings suggest that the postburn dysbiosis of the gut flora in aged mice may contribute to the changes in pulmonary inflammatory profiles.

Cockroaches as Reservoirs, Vectors, and Potential Sentinels of Multidrug-Resistant Bacteria in Ugandan Communities: A Retrospective Analysis

Background: Cockroaches could play a role in the transmission dynamics of antimicrobial-resistant bacteria (ARB) at variable interfaces in Ugandan communities, acting as both reservoirs and vectors. This study investigated the burden and diversity of ARB carried by cockroaches in human settlements in Uganda, so as to understand their role in the spread of these pathogens and their potential as sentinels in antimicrobial resistance (AMR) surveillance programs. Materials and Methods: A retrospective analysis was conducted on two unpublished studies by Makerere University students. Study one and study two sampled 58 and 110 cockroaches, respectively, from secondary schools in Kampala. Cockroach species identification was determined based on physical characteristics. Bacterial isolation and characterization were performed through microbiological analyses including standard culture methods, biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), disc diffusion method, and polymerase chain reaction (PCR). Results: Majority of the cockroaches (over 80%) were Periplaneta americana. Multidrug resistance (MDR) was prevalent among the isolates, with over 30% of the isolates being resistant to three or more antibiotic classes. Specifically, MDR (over 90%) was rampant in the extended spectrum beta-lactamase (ESBL)- or AmpC-producing Escherichia coli and enterococci isolates. Critical World Health Organization (WHO) priority pathogens, such as ESBL-/AmpC-producing Enterobacteriaceae, and carbapenem-resistant E. coli, were also identified. The most abundant resistance determinants (tetracycline and sulphonamide) were tetA, sul1, and sul2 for E. coli, and tetM and tetL for enterococci. Conclusion: The findings accentuate the potential role of cockroaches: (1) in transmitting multidrug-resistant bacteria at the human-animal-environment interface and (2) as sentinels in the surveillance of community-generated AMR.

First Detection and Genomic Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolates in Bulgaria

Linezolid is an oxazolidinone antibiotic and is considered a last-resort treatment option for serious infections caused by problematic Gram-positive pathogens, including vancomycin-resistant enterococci. The present study aimed to explore the linezolid resistance mechanisms and genomic characteristics of two vancomycin-susceptible Enterococcus faecalis isolates from Bulgaria. The strains designated Efs2503-bg (inpatient from Pleven) and Efs966-bg (outpatient from Varna) were recovered from wounds in 2018 and 2023, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, multilocus sequence typing, and phylogenomic analysis based on 332 linezolid-resistant E. faecalis genomes were performed. Efs2503-bg was high-level resistant to linezolid (MIC > 256 mg/L) and displayed the G2576T mutation affecting three of the four 23S rDNA loci. Efs966-bg (MIC = 8 mg/L) carried a plasmid-located optrA determinant surrounded by fexA and ermA. No mutations in the genes encoding for ribosomal proteins L3, L4, and L22 were detected. The isolates belonged to the sequence types ST6 (Efs2503-bg) and ST1102 (Efs966-bg). Phylogenomic analysis revealed that Efs2503-bg and Efs966-bg are genetically distinct, with a difference of 12,051 single-nucleotide polymorphisms. To our knowledge, this is the first report of linezolid-resistant enterococci in Bulgaria. Although the global incidence of linezolid-resistant enterococci is still low, their emergence is alarming and poses a growing clinical threat to public health.

Study on the Effect of Radish Sprouts on Short-Chain Fatty Acids and Gut Microbial Diversity in Healthy Individuals

This study aimed to assess the impact of radish sprouts on the gut microbiota of healthy individuals. Radish sprout additives, subjected to short-term storage and steam treatment, were used to intervene in an in vitro culture of human gut microbiota. The influence of radish sprouts on the gut microbiota was evaluated by monitoring short-chain fatty acid (SCFA) content and proportion in the fermentation broth, and microbial diversity was assessed using 16S rDNA amplicon sequencing. The results indicated that the gut microbiota produced a substantial amount of SCFA within 48 h of fermentation, with a right-skewed distribution across all groups. The addition of both digestates enhanced Firmicutes diversity, while Bacteroidetes and Proteobacteria diversity remained stable between the control and fresh sprout groups. The 30 s steam treatment group showed an increase in Bacteroidetes and a decrease in Proteobacteria diversity. The abundance of Bacilli, Bacillaceae, and Bacillus was significantly higher in both the fresh and steam-treated groups compared to the control. Both fresh and steam-treated radish sprout digestates enriched gut microbiota diversity, with steam treatment showing superior effects. These findings suggest that radish sprout consumption may positively influence gut microbiota, with steam treatment potentially enhancing these benefits.

Antimicrobial Peptides: A Promising Alternative to Conventional Antimicrobials for Combating Polymicrobial Biofilms

Polymicrobial biofilms adhere to surfaces and enhance pathogen resistance to conventional treatments, significantly contributing to chronic infections in the respiratory tract, oral cavity, chronic wounds, and on medical devices. This review examines antimicrobial peptides (AMPs) as a promising alternative to traditional antibiotics for treating biofilm-associated infections. AMPs, which can be produced as part of the innate immune response or synthesized therapeutically, have broad-spectrum antimicrobial activity, often disrupting microbial cell membranes and causing cell death. Many specifically target negatively charged bacterial membranes, unlike host cell membranes. Research shows AMPs effectively inhibit and disrupt polymicrobial biofilms and can enhance conventional antibiotics' efficacy. Preclinical and clinical research is advancing, with animal studies and clinical trials showing promise against multidrug-resistant bacteria and fungi. Numerous patents indicate increasing interest in AMPs. However, challenges such as peptide stability, potential cytotoxicity, and high production costs must be addressed. Ongoing research focuses on optimizing AMP structures, enhancing stability, and developing cost-effective production methods. In summary, AMPs offer a novel approach to combating biofilm-associated infections, with their unique mechanisms and synergistic potential with existing antibiotics positioning them as promising candidates for future treatments.

Changes in Human Colonic Microbiota Promoted by Synbiotic Açai Juice Composed of Gluco-Oligosaccharides, Dextran, and Bifidobacterium breve NRRL B-41408

The present study evaluates the effects of açai juice containing gluco-oligosaccharides and dextran, fermented by Bifidobacterium breve NRRL B-41408 (synbiotic juice), on the human fecal microbiota. The juice is subjected to simulated digestion and fecal fermentation after production and 42 days of refrigerated storage. High throughput 16S rRNA sequencing and HPLC are used to identify the bacterial cells and metabolites. The results show that the viability of B. breve is stable during the refrigerated storage, indicating that the metabolism is maintained even under low temperatures and pH. Furthermore, gluco-oligosaccharides and dextran prove to be resistant to gastrointestinal conditions and are quickly consumed during fecal fermentation. The synbiotic açai juice enhances the microbial diversity and stimulates the production of short-chain fatty acids (SCFA), including acetate, propionate, and isobutyrate. Elevated propionate levels are directly associated with an increased abundance of Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides xylanisolvens, Bacteroides dorei, Bacteroides stercoris, and Bacteroides massiliensis after 48 h of fermentation. This highlights the potential of synbiotic açai juice as a functional beverage, supported by the significant increase in microbial diversity reflected in the Shannon and Simpson's diversity indexes (Shannon = 116.6%, 117.2%, 125.15%, and 116.02%; Simpson's = 151.86%, 177.22%, 152.5%, and 163.73%).

Genetic diversity and distinction of Enterococcus faecium and Enterococcus lactis in traditional Montenegrin brine cheeses and salamis

Introduction

Enterococcus faecium is a widespread acid-lactic bacterium found in the environment, humans, and animal microbiota, and it also plays a role in the production of traditional food. However, the worldwide emergence of multidrug-resistant E. faecium strains represents a major public health threat and is the primary reason that the genus Enterococcus is not recommended for the Qualified Presumption of Safety (QPS) list of the European Food Safety Authority (EFSA), raising concerns about its presence in food products.

Methods

In this study, 39 E. faecium and 5 E. lactis isolates were obtained from artisanal brine cheeses and dry sausages, sourced from 21 different Montenegrin producers. The isolates were collected following the ISO 15214:1998 international method and processed for whole-genome sequencing (WGS).

Results

Genome analysis based on core genome multilocus sequence type (cgMLST) revealed a high diversity among isolates. Furthermore, the isolates carried antimicrobial resistance genes; the virulence genes acm, sgrA, and ecbA; the bacteriocin genes Enterolysin A, Enterocin A, Enterocin P, Duracin Q, Enterocin B, Bacteriocin 31, Enterocin EJ97, Sactipeptides, and Enterocin SEK4; the secondary metabolite genes T3PKS, cyclic lactone autoinducer, RiPP-like, and NRPS and a maximum of eight plasmids.

Conclusion

This study highlights the need for careful monitoring of E. faecium and E. lactis strains in food to ensure they do not pose any potential risks to consumer safety.

Comparative analysis of the gut microbiota composition and diversity in Erinaceus amurensis from the Wandashan Mountain range area based on metagenomics

This study aimed to preliminarily explore the composition and diversity of intestinal bacteria in Erinaceus amurensis during breeding period, aiding in the field rescue and population conservation efforts of Erinaceus amurensis. This also provides foundational data for further research on the prevention and screening of Emerging Zoonotic Infectious Diseases and the experimental animalization of wild Erinaceus amurensis. Between April and July 2023, we collected 13 fresh fecal samples from Erinaceus amurensis at the Sishan Forest Farm in Jidong County, Heilongjiang Province, situated within the Wandashan Mountain range. Utilizing metagenomic sequencing technology, we conducted a comparative analysis of the gut microbiota composition and diversity in wild Erinaceus amurensis across different genders and between adult and fetal individuals within the same habitat. Our results revealed significant differences (P < 0.01) in the classification and diversity of gut microbiota between genders and between adult and fetal Erinaceus amurensis. Specifically, the dominant bacterial groups in the gut of Erinaceus amurensis were Pseudomonas, Proteobacteria, and Enterobacteriaceae. In male and female Erinaceus amurensis, the dominant bacterial groups were Pseudomonas, Bacteroides, and Firmicutes, with variations in bacterial abundance and diversity. While male and female Erinaceus amurensis exhibited similar microbial compositions, they displayed significant differences in specific bacterial classifications. The dominant bacterial group in fetal Erinaceus amurensis was Proteobacteria, which demonstrated lower diversity and abundance compared to the adult group. Furthermore, the types and abundance of pathogenic or opportunistic pathogens in the gut of fetal Erinaceus amurensis and male Erinaceus amurensis were higher than those in female Erinaceus amurensis. The analysis of experimental results indicates that Erinaceus amurensis in this region either have or are at risk of developing inflammation related to the intestinal and urinary tracts, as well as skin-related issues. Consequently, it is advised that forestry and wildlife conservation personnel in this area prioritize treatment against these specific pathogens when conducting rescue operations for Erinaceus amurensis in the wild.

A first study of meat-borne enterococci from butcher shops: prevalence, virulence characteristics, antibiotic resistance and clonal relationship

IntroductionEnterococcus, which used to be thought of as a harmless commensal living in the digestive tract, has now become a highly resistant and highly contagious pathogen that makes nosocomial infections much more common. This study examined enterococci species and their antibiotic resistance phenotypes and genotypes and virulence gene content in Turkish ground beef samples. Methodology A total of 100 ground beef samples were analyzed between May 2020 and May 2021. The isolated strains were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and confirmed using polymerase chain reaction (PCR) after which they were divided into several species using PCR and tested for antibiotic resistance against 19 antimicrobial agents using the disc diffusion method. The genetic similarity analysis, pulsed-field gel electrophoresis (PFGE) was performed. Results A total of 93 isolates in ground beef were identified, comprised of E. faecalis 72.04%; E. hirae- 11.82%; E. casseliflavous- 7.52%; E. faecium- 5.3%; E. gallinarium- 3.23%. The virulence genes observed in Enterococcus species were distributed as follows: gelE 88.1%, ace 53.7%, efaA 40.8%, asaI 19.3%, esp 6.4%, and cylA 1.07%. A high antibiotic resistance was recorded for tetracycline (43.01%), followed by ampicilin (17.2%), and chloramphenicol (13.9%). 17.2% of Enterococcus isolates were multidrug-resistant. The study determined the high prevalence of antibiotic resistance genes, specifically for tet(L) 10 (10.7%), aac(6')Ie-aph(2")-la 3 (3.2%), and ermB 3 (3.2%). The presence of efflux pump genes were identified in 74.1% of Enterococcus isolates. Genetic characterization of 67 E. faecalis isolates by PFGE revealed 41 pulsed-field gel electrophoresis (PFGE) patterns that were grouped into 15 clusters, which presented more than one strain with 100% similarity. Conclusion Isolates obtained from several areas and butchers had comparable patterns of PFGE, suggesting that the presence of circulating E. faecalis poses a potential public health concern in diverse districts. To mitigate the health hazards associated with the contamination of enterococci from raw to cooked meats, it is necessary to enhance the disinfection of butcheries, promote excellent hand hygiene among butchers, and implement appropriate meat storage and handling methods to prevent bacterial development.

Age-related features of the intestinal microbiota changes in Wistar rat pups after application of antibiotics and prebiotic 2′-fucosyllactose

The gut microbiota plays an important role in the formation of the body’s regulatory systems (nervous, endocrine, immune), which is especially important at an early age. Hence, gut dysbiosis can lead to an impaired development of both the intestinal microbiota and these regulatory systems. Prebiotics can have a positive effect on the development of the intestinal microbiome, which can correct negative changes.

The aim of this study is to investigate the features of development of antibiotic-associated dysbiosis in the early postnatal period in rats and to evaluate the effect of 2′-fucosyllactose in health and during dysbiosis.

The study was conducted on Wistar rats aged 12–26 days. To develop dysbiosis at an early age, the following mixtures were used: a mixture of ampicillin trihydrate 75 mg/kg and metronidazole 50 mg/kg and a mixture of amoxicillin 30 mg/kg and cephalexin 20 mg/kg for three days, starting on the 12th day of life. As a prebiotic 2′-fucosyllactose at a dose of 1 g/kg was used, starting on the 12th day and to the last experiment day.

In healthy animals, there is a decrease in the gut content of Bifidobacterium spp. and Enterococcus spp. at the age  of 26 days. A mixture of ampicillin trihydrate 75 mg/kg and metronidazole 50 mg/kg leads to gut dysbiosis – growth suppression of bifidobacteria, lactobacilli and enterococci. After the end of antibiotics application and continued lactation,  the titer of the described bacteria is restored. 2′-fucosyllactose has an effect on the preservation of the titer of Bifidobacterium spp. and Enterococcus spp., both in healthy animals and after early dysbiosis.

Our results indicate that antibiotic-associated dysbiosis at an early age is characterized by a temporary but powerful effect. At the same time, the use of 2′-fucosyllactose leads to preserving important probiotic groups of intestinal bacteria, both in health and after dysbiosis.

Control of Starch Molecular Weight by Enzyme Treatment Facilitates the Formation of V-Type Starch-Resveratrol Complexes in a High-Pressure Homogenization Environment and Their Modulation Effects on the Gut Microbiota

As the concept of precision nutrition has been gradually popularized in recent years, the relationship between the structure of starch-polyphenol complexes with significant health effects and their nutritional functions has been progressively investigated. In this study, G50 high-amylose maize starch with different molecular weights was first prepared by pullulanase and α-amylase, and their effects on the structural formation, digestion properties, and release behaviors of the starch-resveratrol (RA) complex were discussed. The results confirmed that enzyme-treated starch could enhance intermolecular hydrogen bonding and hydrophobic interactions between starch and RA in a high-pressure homogeneous (HPH) environment, forming stable single-helix and V-type crystalline structures while reducing the B-type crystalline structures. Meanwhile, the in vitro experiment showed that when the RA addition was 3%, the resistant starch content of the starch-RA complex could reach 60.3%, and its RA colonic transport rate could reach more than 97%. Interestingly, the starch-RA complex with a relatively higher V-type crystalline structure content contributed to the production of short-chain fatty acids (SCFAs), especially butyrate, and it might be effective in carbohydrate metabolism and immunometabolism by promoting the functions of Phascolarctobacteriu and Alistipes. These findings provide new ideas for the design of the nutritional functions of RS.

Bacteriophage Therapy as a Promising Alternative for Antibiotic-Resistant Enterococcus faecium: Advances and Challenges

Enterococcus faecium is a Gram-positive bacterium increasingly identified as a critical nosocomial pathogen that poses significant treatment challenges due to its resistance to multiple antibiotics, particularly vancomycin-resistant E. faecium (VRE) strains. The urgent need for alternative therapeutic strategies has renewed interest in bacteriophage (phage) therapy, given phages specificity and bactericidal potential. This review explores the advancements in phage therapy against antibiotic-resistant E. faecium, including phage morphological diversity, genomic characteristics, and infection mechanisms. The efficacy of phage therapy in in vitro, ex vivo, and in vivo models and the compassionate use in clinical settings are evaluated, highlighting the promising outcomes of phage-antibiotic synergies and biofilm disruption. Key challenges and future research directions are discussed, with a focus on improving therapeutic efficacy and overcoming bacterial resistance. This review emphasizes the potential of phage therapy as a viable solution for managing multidrug-resistant E. faecium infections and underscores the importance of future investigations to enhance clinical applications.

Comparative analysis of the postadmission and antemortem oropharyngeal and rectal swab microbiota of ICU patients

Shotgun metabarcoding was conducted to examine the microbiota in a total of 48 samples from 12 critically ill patients, analyzing samples from both the oropharynx and rectum. We aimed to compare their postadmission microbiota, characterized as moderately dysbiotic, with the severely dysbiotic antemortem microbiota associated with patients' deaths. We found that, compared with postadmission samples, patient antemortem swab samples presented moderate but not significantly decreased diversity indices. The antemortem oropharyngeal samples presented an increase in biofilm-forming bacteria, including Streptococcus oralis, methicillin-resistant Staphylococcus aureus (MRSA), and Enterococcus faecalis. Although the septic shock rate was 67%, no significant differences were detected in the potential pathogen ratios when the microbiota was analyzed. A notable strain-sharing rate between the oropharynx and intestine was noted. By comparing postadmission and antemortem samples, microbial biomarkers of severe dysbiosis were pinpointed through the analysis of differentially abundant and uniquely emerging species in both oropharyngeal and rectal swabs. Demonstrating strong interconnectivity along the oral-intestinal axis, these biomarkers could serve as indicators of the progression of dysbiosis. Furthermore, the microbial networks of the oropharyngeal microbiota in deceased patients presented the lowest modularity, suggesting a vulnerable community structure. Our data also highlight the critical importance of introducing treatments aimed at enhancing the resilience of the oral cavity microbiome, thereby contributing to better patient outcomes.

Vancomycin-Resistant Enterococci: Current Understandings of Resistance in Relation to Transmission and Preventive Strategies

Due to the limited treatment options and increased mortality rates, infection prevention and control strategies have been implemented for many years to mitigate dissemination of vancomycin-resistant enterococci (VRE) within healthcare settings. The overview provides an insight into the most recent research, particularly the pathogen's resilience in the healthcare environment, and the critical need for infection control strategies, which are currently being scrutinized by some researchers. The notable resilience of enterococci to various environmental conditions highlights the necessity for investigations into innovative technologies capable of effectively targeting the biofilm produced by enterococci on hospital surfaces. A critical approach to traditional infection control strategies is becoming more accepted worldwide, taking into account the epidemiological situation in the given healthcare setting as well as specific characteristics of a patient. For certain high-risk patient populations, traditional infection control strategies including CP and screening should not be omitted. Additionally, further investigation into the resistance mechanisms of available antimicrobial agents is essential, as is research into their potential association with specific successful clones through WGS genotyping, to pre-emptively mitigate their spread before it escalates.

Fecal bacterial communities of the platypus (Ornithorhynchus anatinus) reflect captivity status-Implications for conservation and management

The duck-billed platypus (Ornithorhynchus anatinus) is currently listed as near-threatened. A key part of the conservation strategy for this species is its captive maintenance; however, captive animals often have dysbiotic gut bacterial microbiomes. Here, for the first time, we characterize the gut microbiome of wild platypus via fecal samples using high-throughput sequencing of the bacterial 16S rRNA gene and identify microbial biomarkers of captivity in this species. At the phylum level, Firmicutes (50.4%) predominated among all platypuses, followed by Proteobacteria (28.7%), Fusobacteria (13.4%), and Bacteroidota (6.9%), with 21 "core" bacteria identified. Captive individuals did not differ in their microbial α-diversity compared to wild platypus but had significantly different community composition (β-diversity) and exhibited higher abundances of Enterococcus, which are potential pathogenic bacteria. Four taxa were identified as biomarkers of wild platypus, including Rickettsiella, Epulopiscium, Clostridium, and Cetobacterium. This contrast in gut microbiome composition between wild and captive platypus is an essential insight for guiding conservation management, as the rewilding of captive animal microbiomes is a new and emerging tool to improve captive animal health, maximize captive breeding efforts, and give reintroduced or translocated animals the best chance of survival.

Optimization, structural characterization, and biological applications of exopolysaccharide produced by Enterococcus faecium KT990028

The aim of this study was to select the best exopolysaccharide (EPS) producer among the Enterococcus strains to optimize, characterize, and evaluate its biological properties. Among the eleven strains, Enterococcus faecium KT990028 was selected, and the production conditions were optimized: 16.3 % (w/v) sucrose, 0.70 % (w/v) yeast extract, 8.3 % (w/v) reconstituted skimmed milk, at 38 °C in 15 h of incubation, producing 2.880 g/L of EPS. High performance anion exchange chromatography (HPAEC) analysis revealed that the molecular weight was 166.98 kDa. HPAEC, spectroscopy (FTIR), and nuclear magnetic resonance (1H NMR) analyses revealed that the EPS was a heteropolysaccharide composed of galactose (37.74 %), rhamnose (19.79 %), arabinose (17.71 %), glucose (9.50 %), fucose (7.93 %), and mannose (7.33 %). Scanning electron microscopy showed a three-dimensional microstructure in the form of decompressed plates, with wrinkles, and pores. By means of dynamic light scattering (DLS), the EPS showed an average size varying from 135.25 ± 10.56 nm and 410.60 ± 45.20 nm, as the concentration was increased from 0.5 mg/mL to 2.0 mg/mL, respectively. X-ray diffraction revealed that the EPS has an amorphous and crystalline nature, while thermogravimetric analysis indicated stability up to 400 °C. The antioxidant effect (5 mg/mL) against DPPH, ABTS, OH, and O2 was 64.50 ± 0.71 %, 47.50 ± 0.10 %, 68.36 ± 0.59 %, and 44.83 ± 0.86 %, respectively. It was also able to inhibit and biofilm disruption of Escherichia coli ATCC 25922 and Enterococcus faecalis ATCC 6057 and had an antimicrobial effect from 50 mg/mL for the strains of against Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Listeria monocytogenes ATCC 19117, Staphylococcus aureus ATCC 6538, and Enterococcus faecalis ATCC 6057. Cell cytotoxicity carried out using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay revealed that the EPS was safe and promoted the proliferation of Vero cells. Thus, the results indicated that the EPS from E. faecium KT990028 is a promising functional biopolymer for possible applications in the food and pharmaceutical fields.

Characterizing the gut microbiome of diarrheal mink under farmed conditions: A metagenomic analysis

This study aimed to comprehensively characterize the gut microbiota in diarrheal mink. We conducted Shotgun metagenomic sequencing on samples from five groups of diarrheal mink and five groups of healthy mink. The microbiota α-diversity and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology did not show significant differences between the groups. However, significant differences were observed in microbiota β-diversity and the function of carbohydrate-active enzymes (CAZymes) between diarrheal and healthy mink. Specifically, The relative abundance of Firmicutes was lower, whereas that of Bacteroidetes was higher in diarrheal mink. Fusobacteria were enriched as invasive bacteria in the gut of diarrheal mink compared with healthy mink. In addition, Escherichia albertii was identified as a new bacterium in diarrheal mink. Regarding functions, nicotinate and nicotinamide metabolism and glycoside hydrolases 2 (GH2) family were the enhanced KEGG orthology and CAZymes in diarrheal mink. Furthermore, the diversity and number of antibiotic-resistant genes were significantly higher in the diarrheal mink group than in the healthy group. These findings enhance our understanding of the gut microbiota of adult mink and may lead to new approaches to the diagnosis and treatment of mink diarrhea.

Genomic evaluation of the probiotic and pathogenic features of Enterococcus faecalis from human breast milk and comparison with the isolates from animal milk and clinical specimens

Enterococcus faecalis is considered a probiotic, commensal lactic acid bacterium in human breast milk (HBM), but there are circulating antibiotic resistant and virulence determinants that could pose a risk in some strains. The study aimed to conduct genomic analysis of E. faecalis isolates recovered from HBM and animal milk and to evaluate their probiotic and pathogenic features through comparative genomics with isolates from clinical specimens (e.g., urine, wound, and blood). Genomic analysis of 61 isolates was performed, including E. faecalis isolates recovered from HBM in Saudi Arabia. Genome sequencing was conducted using the MiSeq system. The fewest antibiotic resistance genes (lsaA, tetM, ermB) were identified in isolates from HBM and animal milk compared to clinical isolates. Several known and unknown mutations in the gyrA and parC genes were observed in clinical isolates. However, 11 virulence genes were commonly found in more than 95% of isolates, and 13 virulence genes were consistently present in the HBM isolates. Phylogenetically, the HBM isolates from China clustered with the probiotic reference strain Symbioflor 1, but all isolates from HBM and animal milk clustered separately from the clinical reference strain V583. Subsystem functions 188 of 263 were common in all analyzed genome assemblies. Regardless of the source of isolation, genes associated with carbohydrate metabolism, fatty acid, and vitamin biosynthesis were commonly found in E. faecalis isolates. In conclusion, comparative genomic analysis can help distinguish the probiotic or pathogenic potential of E. faecalis based on genomic features.

Probiotic and Postbiotic Potentials of Enterococcus faecalis EF-2001: A Safety Assessment

BACKGROUND

Probiotics, which are live microorganisms that, when given in sufficient quantities, promote the host's health, have drawn a lot of interest for their ability to enhance gut health. Enterococcus faecalis, a member of the human gut microbiota, has shown promise as a probiotic candidate due to its functional attributes. However, safety concerns associated with certain strains warrant comprehensive evaluation before therapeutic application.

MATERIALS AND METHODS

In this study, E. faecalis EF-2001, originally isolated from fecal samples of a healthy human infant, was subjected to a multi-faceted assessment for its safety and probiotic potential. In silico analysis, CAZyme, biosynthetic, and stress-responsive proteins were identified.

RESULTS

The genome lacked biogenic amine genes but contained some essential amino acid and vitamin synthetic genes, and carbohydrate-related enzymes essential for probiotic properties. The negligible difference of 0.03% between the 1st and 25th generations indicates that the genetic information of the E. faecalis EF-2001 genome remained stable. The live E. faecalis EF-2001 (E. faecalis EF-2001L) demonstrated low or no virulence potential, minimal D-Lactate production, and susceptibility to most antibiotics except some aminoglycosides. No bile salt deconjugation or biogenic amine production was observed in an in vitro assay. Hemolytic activity assessment showed a β-hemolytic pattern, indicating no red blood cell lysis. Furthermore, the EF-2001L did not produce gelatinase and tolerated simulated gastric and intestinal fluids in an in vitro study. Similarly, heat-killed E. faecalis EF-2001 (E. faecalis EF-2001HK) exhibits tolerance in both acid and base conditions in vitro. Further, no cytotoxicity of postbiotic EF-2001HK was observed in human colorectal adenocarcinoma HT-29 cells.

CONCLUSIONS

These potential properties suggest that probiotic and postbiotic E. faecalis EF-2001 could be considered safe and retain metabolic activity suitable for human consumption.

Antimicrobial starch-based cryogels and hydrogels for dual-active food packaging applications

The present study reports on the valorisation of starch waste biomass to produce dual-active cryogels and hydrogels able to adsorb water and deliver antimicrobial substances for fresh food packaging applications. Starch hydrogels were prepared by oxidation with sodium metaperiodate in water and mild conditions, while cryogels were obtained by freeze-drying process. To explore the role of starch composition on the final properties of materials, two starches differing in amylose/amylopectin ratio, were evaluated. The prepared materials were microstructurally and morphologically characterized by FTIR and NMR spectroscopy (1D, 2D, and DOSY experiments), and SEM microscopy. To provide the materials with active properties, they were loaded with antimicrobial molecules by absorption, or by crosslinking via Schiff-base reaction. All materials demonstrated high water absorption capacity and ability to deliver volatile molecules, including diacetyl and complex mixtures like mint essential oil. The release profiles of the adsorbed molecules were determined through quantitative NMR spectroscopy over time. The antibacterial activity was successfully demonstrated against Gram-positive bacterial strains for unloaded cryogels and hydrogels, and after loading with diacetyl and essential oil. The developed materials can be regarded as part of active pads for food packaging applications capable to control moisture inside the package and inhibit microbial contamination.

Cellulose from bacteria as a delivery system for improved treatment of infectious diseases: A review of updates and prospects

Cellulose from bacteria is a high-purity biomaterial naturally produced by bacteria as part of their metabolic process. Although it inherently lacks antimicrobial activity, its modification with bioactive substances can significantly enhance its efficacy beyond that of the original compounds. This biomaterial features a unique ability to retain substantial quantities of liquids within its three-dimensional network, making it a prime candidate for biomedical applications. Versatile in its properties, it can be utilized across various industries. Previous research has highlighted its capacity to exhibit antimicrobial properties and to encapsulate nanostructured materials, thereby augmenting its antibacterial effectiveness. This review focuses on the use of cellulose from bacteria as a carrier for active compounds, specifically targeting antibacterial activity against drug-resistant strains. We explore its role in innovative bacterial cellulose-based systems, which present a promising solution for tackling bacterial resistance. This review aims to showcase the potential of bacterial cellulose in developing new devices and treatment strategies that address critical concerns in global health.

Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan

BACKGROUND

Endemic fluorosis refers to the condition when individuals are exposed to excessive amounts of fluoride ion due to living in a region characterized by elevated levels of fluorine in the drinking water, food, and/or air. In Pakistan, a substantial proportion of the population is thereby affected, posing a public health concern.

OBJECTIVES

Assessing how the gut microbiota and its metabolic profiles are impacted by chronic exposure to fluoride in drinking water (that caused Dental Fluorosis) as well as to perceive how this microbiota is connected to adverse health outcomes prevailing with fluoride exposure.

METHODS

Drinking water (n=27) and biological samples (n=100) of blood, urine and feces were collected from 70 high fluoride exposed (with Dental Fluorosis) and 30 healthy control (without Dental Fluorosis) subjects. Water and urinary fluoride concentrations were determined. Serum/plasma biochemical testing was performed. Fecal DNA extraction, 16S rRNA analysis of microbial taxa, their predicted metabolic function and fecal short chain fatty acids (SCFAs) quantification were carried out.

RESULTS

The study revealed that microbiota taxonomic shifts and their metabolic characterization had been linked to certain host clinical parameters under the chronic fluoride exposure. Some sets of genera showed strong specificity to water and urine fluoride concentrations, Relative Fat Mass index and SCFAs. The SCFAs response in fluoride-exposed samples was observed to be correlated with bacterial taxa that could contribute to adverse health effects.

CONCLUSIONS

Microbial dysbiosis as a result of endemic fluorosis exhibits a structure that is associated with risk of metabolic deregulation and is implicated in various diseases. Our results may form the development of novel interventions and may have utility in diagnosis and monitoring.

Beyond Harmful: Exploring Biofilm Formation by Enterococci Isolated from Portuguese Traditional Cheeses

This study investigated the biofilm-forming capabilities of Enterococcus isolates from Portuguese traditional cheeses with protected designation of origin (PDO) status, specifically Azeitão and Nisa. Given the absence of added starter cultures in the cheesemaking process, the characteristics of these cheeses are intrinsically linked to the autochthonous microbiota present in the raw materials and the production environment. Our findings demonstrate that all isolates possess biofilm production abilities, which are crucial for their colonization and persistence within cheese factories, thereby maintaining factory-specific microbial heritage. Through an integrated analysis utilizing principal component analysis (PCA), a direct correlation between biofilm formation and cell viability was established. Notably, these results underscore the adaptive capacity of enterococci to survive environmental fluctuations and their role in the unique characteristics of Portuguese traditional cheeses. Overall, this research enhances our understanding of the microbial dynamics in cheese production and highlights the importance of enterococci in preserving cheese quality and heritage.

Phenotypic and genotypic characterization of Enterococcus faecalis and Enterococcus faecium isolated from fish, vegetables, and humans

Enterococci, common hospital-acquired infections in immunocompromised patients, have garnered attention in clinical microbiology. To determine the clinical relevance of enterococci as food-borne pathogens, 116 fish, 90 vegetables, and 120 human diarrheal samples were tested for E. faecalis and E. faecium pathogenicity. Conventionally, 69 of 326 (21.17%) samples were positive for Enterococcus species, 52 (15.95%) of which were molecularly classified as E. faecalis and 13 (3.99%) as E. faecium. The E. faecalis contamination percentage of fresh fish (19.70%) was higher than frozen fish (4%). Cauliflower had the highest E. faecalis percentage (16.67%) when fish and vegetable samples didn't harbor the E. faecium atpA gene. 23.33% and 10.83% of participants' samples were molecularly confirmed as E. faecalis and E. faecium positive, respectively. E. faecalis isolates had all virulence genes, with gels being the most common (65.38%), while cylA and asa1 genes couldn't be detected in E. faecium isolates. E. faecalis showed the highest resistance against vancomycin and tetracycline (69.23%), whereas E. faecium extremely resisted tetracycline (76.92%) and erythromycin (69.23%) with the recognition of MDR among 44.2% of E. faecalis and 38.5% of E. faecium isolates. The great similarity of our isolates showed the clinical importance of food-borne antibiotic-resistant enterococci.

Linezolid-resistant Enterococcus faecium clinical isolates from Pakistan: a genomic analysis

BACKGROUND

Linezolid-resistant Enterococcus faecium (LRE) is a global priority pathogen. Thirteen LRE were reported from clinical specimens between November 2021 and April 2023 at two laboratories in Karachi, Pakistan. We aimed to investigate the strain types and genes associated with linezolid resistance among these isolates. Whole genome sequencing (WGS) was performed and analyzed by multilocus sequence typing (MLST). The presence of linezolid resistance genes was identified using ResFinder v4.1.11 and the LRE-finder tool.

RESULTS

Twelve isolates belonged to clonal complex 17 (CC17); ST80 (n = 10), ST612 (n = 1) and ST1380 (n = 1). Six isolates showed the presence of optrA gene and G2576T mutations in the 23S rRNA gene, while six showed poxtA and cfr(D) genes. One isolate showed the combination of optrA, cfr(D) and poxtA genes.

CONCLUSION

Our findings show the circulation of CC17 sequence types with a known outbreak potential and we identified molecular mechanisms of resistance that were not previously reported from Pakistan.

Enterococcal-host interactions in the gastrointestinal tract and beyond

The gastrointestinal tract (GIT) is typically considered the natural niche of enterococci. However, these bacteria also inhabit extraintestinal tissues, where they can disrupt organ physiology and cause life-threatening infections. Here, we discuss how enterococci, primarily Enterococcus faecalis, interact with the intestine and other host anatomical locations such as the oral cavity, heart, liver, kidney, and vaginal tract. The metabolic flexibility of these bacteria allows them to quickly adapt to new environments, promoting their persistence in diverse tissues. In transitioning from commensals to pathogens, enterococci must overcome harsh conditions such as nutrient competition, exposure to antimicrobials, and immune pressure. Therefore, enterococci have evolved multiple mechanisms to adhere, colonize, persist, and endure these challenges in the host. This review provides a comprehensive overview of how enterococci interact with diverse host cells and tissues across multiple organ systems, highlighting the key molecular pathways that mediate enterococcal adaptation, persistence, and pathogenic behavior.

Nutritional and microbial profiles of ripened plant-based cheese analogs collected from the European market

Plant-based cheese analogs have emerged as a novel global market trend driven by sustainability concerns for our planet. This study examines eleven soft ripened plant-based cheese analogs produced in Europe, primarily with bloomy rinds and cashew nuts as the main ingredient. First, we focused on exploring the macronutrients and salt content stated on the labels, as well a detailed fatty acid analysis of the samples. Compared to dairy cheeses, plant-based cheeses share similarities in lipid content, but their fatty acid profiles diverge significantly, with higher ratio of mono- and polyunsaturated fatty acids such as oleic and linoleic acids. We also investigated the microbiota of these analog products, employing a culture-dependent and -independent approaches. We identified a variety of microorganisms in the plant-based cheeses, with Lactococcus lactis and Leuconostoc mesenteroides being the dominant bacterial species, and Geotrichum candidum and Penicillium camemberti the dominant fungal species. Most of the species characterized are similar to those present in dairy cheeses, suggesting that they have been inoculated as culture starters to contribute to the sensorial acceptance of plant-based cheeses. However, we also identify several species that are possibly intrinsic to plant matrices or originate from the production environment, such as Pediococcus pentosaceus and Enterococcus spp. This coexistence of typical dairy-associated organisms with plant associated species highlights the potential microbial dynamics inherent in the production of plant-based cheese. These findings will contribute to a better understanding of plant-based cheese alternatives, enable the development of sustainable products, and pave the way for future research exploring the use of plant-based substrates in the production of cheese analogues.