Antibiotic Resistance of LACTOBACILLUS Strains

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.

Antibiotic Resistance in Lactic Acid Bacteria from Dairy Products in Northern Italy

Background: The spread of antibiotic resistance genes (ARGs) from the food chain is a significant public health concern. Dairy products from raw milk containing lactic acid bacteria (LAB) resistant to antimicrobials may serve as vectors for the transfer of resistance to commensal or potentially pathogenic bacteria in the human gut. Detecting ARGs in dairy products and milk is, therefore, crucial and could aid in the development of strategies to mitigate resistance dissemination through the food chain. Objectives: This study aimed to determine the presence of ARGs and assess the antibiotic susceptibility of LAB strains isolated from dairy products made from raw milk. Methods: Fifty-four LAB strains were isolated from 41 dairy samples and were tested for antimicrobial susceptibility using broth microdilution to determine Minimal Inhibitory Concentration (MIC). Moreover, the presence of resistance genes related to tetracyclines, beta-lactams, quinolones, and erythromycin was examined using six multiplex PCR assays. Results: Lactobacillus spp. and Leuconostoc spp. strains exhibited a high level of resistance to vancomycin (93-100%). Low-level resistance (4.2-20%) was observed in Lactococcus spp. and Lactobacillus spp. strains against tetracycline. Additionally, Lactococcus spp. strains showed resistance to trimethoprim/sulfamethoxazole, erythromycin, and clindamycin. Twenty-two out of 54 LAB strains (40.7%) carried at least one antibiotic resistance gene, and five of these were multidrug-resistant. Genes associated with acquired resistance to tetracycline were commonly detected, with tetK being the most frequent determinant. Conclusions: This study demonstrated that LABs in dairy products can act as reservoirs for ARGs, potentially contributing to the horizontal transfer of resistance within microbial communities in food and consumers. These findings highlight the need for the ongoing surveillance of antibiotic resistance in LAB and the implementation of control measures to minimize the dissemination of resistance through dairy products.

Efficacy of Lacticaseibacillus rhamnosus probiotic strains in treating chromate induced dermatitis

Chromate induced dermatitis is a significant occupational health concern. Chromate (Cr) resistant Lacticaseibacillus rhamnosus strains were isolated from commercial probiotic sachets PREPRO and HiFLORA. Among 13 Cr-resistant bacterial isolates, six were selected based on high chromate resistance at 500 ug/ml. Selected isolates were subjected to biochemical and molecular characterization and in vivo analyses. DPC assay was conducted under controlled conditions in order to determine the reduction potential of the isolated bacteria. The selected isolates were identified as L. rhamnosus-L1 (PP493917), L. rhamnosus-L2 (PP493918), L. rhamnosus-L3 (PP493921) L. rhamnosus-L4 (PP493920) L. rhamnosus-L8 (PP493922) and L. rhamnosus-L12 (PP493923). Lacticaseibacillus rhamnosus L1showed highest resistance against Cr (VI) with reduction potential 56%. In vivo experiments were performed to assess the healing effects of isolated bacterial strains on mice skin, with Hematoxylin and Eosin (H&E) staining used to identify severe dermatitis in skin tissue and evaluate therapeutic effects of probiotic strains. The structural determination of flavin reductase protein of L. rhamnosus was carried out using bioinformatics tools. These tools predicted the structural-based functional homology of flavin reductase protein in bacterial Cr (VI)-detoxification system. Lacticaseibacillus rhamnosus can be effectively used against chromate-induced dermatitis due to its high chromate resistance and reduction potential.

The Invisible Threat of Antibiotic Resistance in Food

The continued and improper use of antibiotics has resulted in the emergence of antibiotic resistance (AR). The dissemination of antibiotic-resistant microorganisms occurs via a multitude of pathways, including the food supply. The failure to comply with the regulatory withdrawal period associated with the treatment of domestic animals or the illicit use of antibiotics as growth promoters has contributed to the proliferation of antibiotic-resistant bacteria in meat and dairy products. It was demonstrated that not only do animal and human pathogens act as donors of antibiotic resistance genes, but also that lactic acid bacteria can serve as reservoirs of genes encoding for antibiotic resistance. Consequently, the consumption of fermented foods also presents a potential conduit for the dissemination of AR. This review provides an overview of the potential for the transmission of antibiotic resistance in a range of traditional and novel foods. The literature data reveal that foodborne microbes can be a significant factor in the dissemination of antibiotic resistance.

Genomic Scale Analysis Foresees Enteroprotective and Butyrogenic Properties in Brazilian Isolates of Lactiplantibacillus plantarum

Probiogenomics offers a rapid and comprehensive approach to characterizing the beneficial properties of microorganisms, allowing the identification and selection of specific strains for improving human health. The species Lactiplantibacillus plantarum is highly ubiquitous and presents great genetic diversity making it difficult to conduct massive screening of probiotic strains when using conventional methods. Hence, this work aimed to taxonomically and functionally characterize the complete genomes of six novel L. plantarum strains isolated in Brazil through high-standard NGS. The taxonomy of strains E6, E10, E14, E18, Lpl2, and Lpl4 was investigated through average nucleotide identity analysis using the genome of L. plantarum SK151 from the GENBANK database as a reference. Moreover, multilocus phylogenetic analyses were performed to investigate their genetic relatedness to probiotic L. plantarum strains using a total of 225 complete genomes from the same database. To investigate specific health-promoting and safety properties, the isolates from Brazil were analyzed using several bioinformatic tools to predict antimicrobials and anti-inflammatory biomolecules and potential risk factors including drug resistance, virulence genes, and genetic mobility elements. The results confirmed that all six isolates belong to the species L. plantarum and the phylogenetic analysis suggests high proximity to known probiotics and strains that have demonstrated protective effects against inflammation and pathogens. Several bacteriocin genes were identified in the Brazilian isolates, mostly plantaricins, suggesting antimicrobial properties, especially in the strain E14 that presented 9 bacteriocins genes. Furthermore, the study revealed the potential capacity of these strains to produce anti-inflammatory compounds including metabolites such as butyrate through the fermentation of fructan sugars, and IL-10 stimulation activity mediated by adhesin proteins from the bacterial cell wall. The lpl4 strain glutamate decarboxylase (GADB) gene showed a high degree of genetic and structural conservation prediction and increased stabilization of the predicted protein compared to a functional homologous GADB from L. plantarum Taj-Apis362, suggesting lpl4 potential for the modulation of the gut-brain axis functions by the production of GABA. Regarding the presence of virulence and resistance genes, only one resistance island was observed in strain E6 genome. In conclusion, it is possible to suggest that most of the evaluated strains are safe and we highlight the strains Lpl4 and E14 for presenting outstanding enteroprotective properties such as the potential production of GABA and several bacteriocins.

Antibacterial Activity, Probiotic Potential, and Biocontrol Efficacy of Two Lactic Acid Bacteria Against Penicillium expansum on Fresh Grapes

Lactic acid bacteria are commonly present in various sources and possess significant probiotic properties. They can inhibit pathogenic bacteria and fungi simultaneously, making them promising candidates as bio-preservatives. This study investigated two potential probiotic strains: Lactiplantibacillus plantarum LR5-2 (isolated from fermented meat products) and Lacticaseibacillus rhamnosus SQ63 (isolated from infant feces). The study evaluated their aggregation ability, anti-pathogenic activity, safety, and tolerance to gastrointestinal conditions, phenol, and bile salts. Additionally, their biological control potential against Penicillium expansum on fresh grapes was assessed. The results demonstrated that both strains exhibited high survival rates under extreme gastrointestinal conditions, enhanced Auto-aggregation, co-aggregation, and hydrophobicity. They displayed strong antioxidant activity and significant antibacterial effects against 11 pathogenic fungi and foodborne pathogens. Biosafety testing revealed that both strains are sensitive to most antibiotics, do not produce biogenic amines, and exhibit no hemolytic or DNase activity. In grapes, L. plantarum LR5-2 and L. rhamnosus SQ63 significantly reduced the incidence and disease index of P. expansum infection. In conclusion, the characterization analysis and bio-preservation experiments revealed that LR5-2 and SQ63 have strong potential as probiotics and bio-preservatives.

Characterization and Probiotic Potential of Levilactobacillus brevis DPL5: A Novel Strain Isolated from Human Breast Milk with Antimicrobial Properties Against Biofilm-Forming Staphylococcus aureus

Lactobacillus is a key genus of probiotics commonly utilized for the treatment of oral infections The primary aim of our research was to investigate the probiotic potential of the newly isolated Levilactobacillus brevis DPL5 strain from human breast milk, focusing on its ability to combat biofilm-forming pathogens such as Staphylococcus aureus. Employing in vitro approaches, we demonstrate L. brevis DPL5's ability to endure at pH 3 with survival rates above 30%, and withstand the osmotic stress often found during industrial processes like fermentation and freeze drying, retaining over 90% viability. The lyophilized cell-free supernatant of L. brevis DPL5 had a significant antagonistic effect against biofilm-producing nasal strains of Staphylococcus aureus, and it completely eradicated biofilms at subinhibitory concentrations of 20 mg·mL-1. Higher concentrations of 69 mg·mL-1 were found to have a 99% bactericidal effect, based on the conducted probability analysis, indicating the production of bactericidal bioactive extracellular compounds capable of disrupting the biofilm formation of pathogens like S. aureus. Furthermore, genome-wide sequencing and analysis of L. brevis DPL5 with cutting-edge Nanopore technology has uncovered over 50 genes linked to probiotic activity, supporting its ability to adapt and thrive in the harsh gut environment. The genome also contains multiple biosynthetic gene clusters such as lanthipeptide class IV, Type III polyketide synthase (T3PKS), and ribosomally synthesized, and post-translationally modified peptides (RiPP-like compounds), all of which are associated with antibacterial properties. Our study paves the way for the further exploration of DPL5, setting the stage for innovative, nature-inspired solutions to combat stubborn bacterial infections.

Cefazolin shifts the kidney microbiota to promote a lithogenic environment

Clinical studies of the urinary tract microbiome, termed urobiome, suggest a direct, antibiotic-dependent, impact of the urobiome on kidney physiology. However, evidence for kidney bacteria comes from indirect sources or infected tissue. Further, it is unclear how antibiotics impact kidney bacteria. Here we show direct evidence for the presence of bacteria in the kidneys, with microniches in nephrons. In murine kidneys, administration of cefazolin, a commonly used perioperative antibiotic, led to a loss of uroprotective Lactobacillus spp. and proliferation of Enterobacteriaceae (which includes many known uropathogens). This effect was dependent on treatment duration, with recovery post treatment. Uroprotective L. crispatus and a strain of stone-associated E. coli differentially influenced calcium oxalate (CaOx) crystallization through the incorporation of CaOx inhibitors or promoters, respectively. In humans, microbial signatures were identified in the kidney, with unique niches between the glomeruli and tubules, established through RNA sequencing analysis and direct imaging of two independent populations. Collectively, findings support the hypothesis that the kidneys harbor a stable and antibiotic-responsive microbiota that can influence CaOx lithogenesis. The presence of unique, age-dependent microbial signatures in the glomeruli and tubuli carry implications for non-infectious kidney diseases.

Evaluation of Probiotic Potential and Functional Properties of Lactobacillus Strains Isolated from Dhan, Traditional Algerian Goat Milk Butter

Goat milk butter, locally known as "Dhan", from the Sfisfa region of Algeria, holds significant cultural and economic value. This study investigates the probiotic properties of lactic acid bacteria (LAB) present in Dhan, focusing particularly on Lactobacillus strains. Molecular identification using 16S rRNA revealed a dominance of Levilactobacillus brevis and Lactiplantibacillus plantarum, forming a substantial part of the bacterial profile. Three LAB isolates (DC01-A, DC04, and DC06) were selected from fresh samples, and rigorous analyses were performed to evaluate their probiotic properties. Safety assessments confirmed the absence of gelatinase, DNase, and haemolytic activities in all isolates. The isolates demonstrated high tolerance to bile salts and acidic conditions, along with the ability to survive simulated gastrointestinal digestion. Notably, strain DC06 exhibited exceptional survival at low pH (1.5) and high bile salt concentrations (0.15-0.3%). All isolates showed substantial growth in MRS medium with 2% phenol, although growth was significantly decreased at 5% phenol. Furthermore, our strains exhibited high adhesion rates to various solvents, demonstrating their potential for strong interaction with cell membranes. Specifically, adhesion to chloroform was observed at 98.26% for DC01-A, 99.30% for DC04, and 99.20% for DC06. With xylene, the adhesion rates were 75.94% for DC01-A, 61.13% for DC04, and 76.52% for DC06. The LAB strains demonstrated impressive growth in ethanol concentrations up to 12%, but their tolerance did not exceed this concentration. They also exhibited robust growth across temperatures from 10 °C to 37 °C, with strains DC04 and DC06 able to proliferate at 45 °C, though none survived at 50 °C. Additionally, the isolates showed significant resistance to oxidative stress induced by hydrogen peroxide (H2O2) and displayed medium to high autolytic activity, with rates of 50.86%, 37.53%, and 33.42% for DC01-A, DC04, and DC06, respectively. The cell-free supernatant derived from strain DC04 exhibited significant antimicrobial activity against the tested pathogens, while strain DC06 demonstrated moderate antioxidant activity with the highest DPPH scavenging rate at 68.56%, compared to the probiotic reference strain LGG at 61.28%. These collective findings not only suggest the probiotic viability of LAB strains found in Dhan but also highlight the importance of traditional food practises in contributing to health and nutrition. Consequently, this study supports the potential of traditional Dhan butter as a functional food and encourages further exploration of its health benefits.

Beneficial and Safety Properties of a Bacteriocinogenic and Putative Probiotic Latilactobacillus sakei subsp. sakei 2a Strain

This work aimed to evaluate some of the probiotic features and safety of the bacteriocin-producing Latilactobacillus sakei subsp. sakei 2a. The effect of selected commercial drugs from different generic groups and antibiotics on the growth of Ltb. sakei subsp. sakei 2a was also determined. The presence of virulence factors was determined based on PCR with total DNA from Ltb. sakei subsp. sakei 2a. Good growth of Ltb. sakei subsp. sakei 2a was recorded in MRS broth supplemented with 0.2% or 0.4% oxbile or in MRS broth adjusted to a pH from 5.0-9.0. Auto-aggregation of Ltb. sakei subsp. sakei 2a was 62.59%. Different levels of co-aggregation were recorded between Ltb. sakei subsp. sakei 2a and Enterococcus faecalis ATCC19443, Ltb. sakei ATCC15521 and Listeria monocytogenes ScottA. Growth of Ltb. sakei subsp. sakei 2a was not inhibited by commercial drugs from different generic groups. The inhibitory effect on the growth of Ltb. sakei subsp. sakei 2a was recorded only in the presence of Arotin [selective serotonin reuptake inhibitor antidepressant] Minimal Inhibition Concentration (MIC) 1.0 mg/mL, Atlansil [Antiarrhythmic] MIC 0.625 mg/mL, Diclofenac potassium [non-steroidal anti-inflammatory drug (NSAID)] MIC 2.5 mg/mL and Spidufen [NSAID] MIC 15.0 mg/mL. Only two antibiotics tested in this study, Amoxil and Urotrobel, inhibited the growth of Ltb. sakei subsp. sakei 2a with a MIC of <0.5 mg/mL and 5.0 mg/mL, respectively. However, Ltb. sakei subsp. sakei 2a generated positive PCR results on the DNA level for vanA (vancomycin resistance), hyl (hyaluronidase), esp (enterococcal surface protein), ace (adhesion of collagen) and cilA (cytolisin) and a high virulence profile when examined for the presence of virulence factors. It is important to underline that cytolysis has been described as a virulence and antibacterial factor.

Genomic Face-off: An In Silico Comparison of the Probiotic Potential of Lactobacillus spp. and Akkermansia muciniphila

Introduction

The gut microbiota plays a crucial role in maintaining human health, and probiotics have gained significant attention for their potential benefits. Among the diverse array of gut bacteria, Akkermansia muciniphila, and Lactobacillus spp. have emerged as promising candidates for their putative probiotic properties.

Methods

In this study, we conducted a comprehensive comparative in silico analysis of the genomes of A. muciniphila and Lactobacillus to decipher their probiotic potential. Utilizing a range of bioinformatics tools, we evaluated various genomic attributes, including functional gene content, metabolic pathways, antimicrobial peptide production, adhesion factors, and stress response elements. These findings revealed distinctive genomic signatures between the two genera. A. muciniphila genomes exhibited a high prevalence of mucin-degrading enzymes, suggesting a specialized adaptation for mucin utilization in the gut environment.

Results

Additionally, the presence of specific pathways for short-chain fatty acid production highlighted its potential impact on host health. Lactobacillus genomes, on the other hand, demonstrated a diverse repertoire of functional genes associated with probiotic attributes, including the production of antimicrobial peptides and adhesion factors, indicating potential for host-microbe interactions and immune modulation. Furthermore, this analysis unveiled the genetic basis of stress tolerance in both genera, revealing conserved mechanisms for surviving the dynamic conditions of the gut ecosystem.

Conclusion

This study also shed light on the distribution of antibiotic-resistance genes, allowing us to assess safety concerns associated with their potential use as probiotics. Overall, this comparative in silico exploration provides valuable insights into the genomic foundation of A. muciniphila and Lactobacillus probiotic potential. These findings contribute to the understanding of their respective roles within the gut microbiota and offer a foundation for further experimental investigations. As probiotic applications continue to expand, this study advances our knowledge of the genetic underpinnings that govern their functionality and highlights promising avenues for future therapeutic interventions and personalized health strategies.

Metabolomics analysis of the lactobacillus plantarum ATCC 14917 response to antibiotic stress

BACKGROUND

Lactobacillus plantarum has been found to play a significant role in maintaining the balance of intestinal flora in the human gut. However, it is sensitive to commonly used antibiotics and is often incidentally killed during treatment. We attempted to identify a means to protect L. plantarum ATCC14917 from the metabolic changes caused by two commonly used antibiotics, ampicillin, and doxycycline. We examined the metabolic changes under ampicillin and doxycycline treatment and assessed the protective effects of adding key exogenous metabolites.

RESULTS

Using metabolomics, we found that under the stress of ampicillin or doxycycline, L. plantarum ATCC14917 exhibited reduced metabolic activity, with purine metabolism a key metabolic pathway involved in this change. We then screened the key biomarkers in this metabolic pathway, guanine and adenosine diphosphate (ADP). The exogenous addition of each of these two metabolites significantly reduced the lethality of ampicillin and doxycycline on L. plantarum ATCC14917. Because purine metabolism is closely related to the production of reactive oxygen species (ROS), the results showed that the addition of guanine or ADP reduced intracellular ROS levels in L. plantarum ATCC14917. Moreover, the killing effects of ampicillin and doxycycline on L. plantarum ATCC14917 were restored by the addition of a ROS accelerator in the presence of guanine or ADP.

CONCLUSIONS

The metabolic changes of L. plantarum ATCC14917 under antibiotic treatments were determined. Moreover, the metabolome information that was elucidated can be used to help L. plantarum cope with adverse stress, which will help probiotics become less vulnerable to antibiotics during clinical treatment.

Multidrug resistance profile in Lactobacillus delbrueckii: a food industry species with probiotic properties

Lactobacillus delbrueckii, a widely used lactic acid bacterium in the food industry, has been studied for its probiotic properties and reservoir of antibiotic-resistant genes, raising safety concerns for probiotic formulations and fermented products. This review consolidates findings from 60 articles published between 2012 and 2023, focusing on the global antibiotic resistance profile and associated genetic factors in L. delbrueckii strains. Resistance to aminoglycosides, particularly streptomycin, kanamycin, and gentamicin, as well as resistance to glycopeptides (vancomycin), fluoroquinolones (ciprofloxacin), and tetracyclines was predominant. Notably, although resistance genes have been identified, they have not been linked to mobile genetic elements, reducing the risk of dissemination. However, a significant limitation is the insufficient exploration of responsible genes or mobile elements in 80% of studies, hindering safety assessments. Additionally, most articles originated from Asian and Middle Eastern countries, with strains often isolated from fermented dairy foods. Therefore, these findings underscore the necessity for comprehensive analyses of new strains of L. delbrueckii for potential industrial and biotherapeutic applications and in combating the rise of antibiotic-resistant pathogens.

Comparative Genomics Reveals Genetic Diversity and Variation in Metabolic Traits in Fructilactobacillus sanfranciscensis Strains

Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified. In this research, 14 F. sanfranciscensis strains were isolated from sourdough samples to evaluate the genetic diversity and variation in metabolic traits. These 14 and 31 other strains (obtained from the NCBI database) genomes were compared. The values for genome size and GC content, on average, turned out to 1.31 Mbp and 34.25%, respectively. In 45 F. sanfranciscensis strains, there were 162 core genes and 0 to 51 unique genes present in each strain. The primary functions of core genes were related to nucleotide, lipid transport, and amino acid, as well as carbohydrate metabolism. The size of core genes accounted for 41.18% of the pan-genome size in 14 F. sanfranciscensis strains, i.e., 0.70 Mbp of 1.70 Mbp. There were genetic variations among the 14 strains involved in carbohydrate utilization and antibiotic resistance. Moreover, exopolysaccharides biosynthesis-related genes were annotated, including epsABD, wxz, wzy. The Type IIA & IE CRISPR-Cas systems, pediocin PA-1 and Lacticin_3147_A1 bacteriocins operons were also discovered in F. sanfranciscensis. These findings can help to select desirable F. sanfranciscensis strains to develop standardized starter culture for sourdough fermentation, and expect to provide traditional fermented pasta with a higher quality and nutritional value for the consumers.

An Insider's Perspective about the Pathogenic Relevance of Gut Bacterial Transportomes

BACKGROUND

The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community.

SUMMARY

This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut.

KEY MESSAGES

Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.

Daily fluctuation of Lactobacillus species and their antibiotic resistome in the colon of growing pigs

There are various types of bacteria inhabiting the intestine that help maintain the balance of the intestinal microbiota. Lactobacillus is one of the important beneficial bacteria and is widely used as a food starter and probiotic. In this study, we investigated the daily fluctuation of the colonic Lactobacillus species and their distribution of antibiotic resistance genes (ARGs) as well as antibiotic susceptibility in pigs. Metagenomic analysis revealed that genus Lactobacillus was one of the most dominant genera in the colon of growing pigs. Rhythmicity analysis revealed that 84 out of 285 Lactobacillus species exhibited rhythmic patterns. Lactobacillus johnsonii and Lactobacillus reuteri were the two most abundant lactobacilli with circadian oscillation, which increased during the day and decreased at night. The profile of the antibiotic resistome was modified over time within 24-h period. Elfamycin resistance genes were the most enriched class found in Lactobacillus. Furthermore, the seven strains of Lactobacillus isolated from the pig intestine mainly exhibited resistance to gentamicin, erythromycin, and lincomycin. The whole genome annotation of four Lactobacillus strains indicated the presence of multiple ARGs, including elfamycin resistance genes, however, the most abundant ARG was optrA in genome of four strains. These results indicate the presence of various Lactobacillus species harboring a large number of ARGs in the swine intestine. This implies that when using animal-derived lactobacilli, it is essential to assess antibiotic resistance to prevent further transmission between animals and the environment.

Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.

Prevalence of antibiotic resistance in lactic acid bacteria isolated from traditional fermented Indian food products

The emergence of antimicrobial resistance (AMR) in lactic acid bacteria (LAB) raises questions on qualified presumptive safety status and poses challenge of AMR transmission in food milieu. This study focuses on isolation, identification and characterization of AMR in LAB prevalent in traditional fermented Indian food products. The analysis of 16SrRNA based phylogenetic tree showed placements of isolates among four different genera Lactobacillus, Enterococcus, Weissella and Leuconostoc. In E-strip gradient test of susceptibility to 14 different antibiotics, over 50% of isolates showed resistance to ampicillin, chloramphenicol, ciprofloxacin, erythromycin, kanamycin, linezolid, streptomycin, trimethoprim and vancomycin. A multivariate principal component analysis, an antibiogram and multiple antibiotic resistance index-values (> 0.2) indicated presence of multidrug-resistance among the isolates. This study reports prevalence of an alarmingly high rate of AMR LAB strains in traditional fermented foods and is important to regulators and public health authorities for developing strategies to control transmission in food systems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01305-1.

Ligilactobacillus salivarius CNCM I-4866, a potential probiotic candidate, shows anti-inflammatory properties in vitro and in vivo

INTRODUCTION

The aim of this work was to characterize a new strain of Ligilactobacillus salivarius (CNCM I-4866) (CNCM I-4866) to address its potential as probiotic with a special focus on intestinal inflammation. Potential anti-inflammatory abilities of this strain were evaluated through in vivo and in vitro experiments.

METHODS

Firstly, the strain was tested in a murine acute inflammation colitis model induced by DNBS. In vitro characterization was then performed with diverse tests: modulation capability of intestinal permeability; study of the impact on immunity profile through cytokines dosage; capacity to inhibit pathogens and adhere to intestinal cells lines. Production of metabolites, antibiotic resistance and survival to gastro-intestinal tract conditions were also tested.

RESULTS

In vitro assay has shown a reduction of colonic damage and markers of inflammation after treatment with CNCM I-4866. Transcriptomic analysis performed on colons showed the capacity of the strain to down-regulate pro-inflammatory cytokines. L. salivarius CNCM I-4866 exerted anti-inflammatory profile by reducing IL-8 production by TNF-α stimulated cell and modulated cytokines profile on peripheral blood mononuclear cells (PBMC). It protected intestinal integrity by increasing trans-epithelial electrical resistance (TEER) on Caco-2 TNF-α inflamed cells. Additionally, L. salivarius CNCM I-4866 displayed inhibition capacity on several intestinal pathogens and adhered to eukaryotic cells. Regarding safety and technical concerns, CNCM I-4866 was highly resistant to 0.3% of bile salts and produced mainly L-lactate. Finally, strain genomic characterization allowed us to confirm safety aspect of our strain, with no antibiotic gene resistance found.

DISCUSSION

Taken together, these results indicate that L. salivarius CNCM I-4866 could be a good probiotic candidate for intestinal inflammation, especially with its steady anti-inflammatory profile.

Antioxidant Effects and Probiotic Properties of Latilactobacillus sakei MS103 Isolated from Sweet Pickled Garlic

Fermented vegetable-based foods, renowned for their unique flavors and human health benefits, contain probiotic organisms with reported in vitro antioxidative effects. This study investigates the probiotic properties of Latilactobacillus sakei MS103 (L. sakei MS103) and its antioxidant activities using an in vitro oxidative stress model based on the hydrogen peroxide (H2O2)-induced oxidative damage of RAW 264.7 cells. L. sakei MS103 exhibited tolerance to extreme conditions (bile salts, low pH, lysozyme, H2O2), antibiotic sensitivity, and auto-aggregation ability. Moreover, L. sakei MS103 co-aggregated with pathogenic Porphyromonas gingivalis cells, inhibited P. gingivalis-induced biofilm formation, and exhibited robust hydrophobic and electrostatic properties that enabled it to strongly bind to gingival epithelial cells and HT-29 cells for enhanced antioxidant effects. Additionally, L. sakei MS103 exhibited other antioxidant properties, including ion-chelating capability and the ability to effectively scavenge superoxide anion free radicals, hydroxyl, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid, and 2,2-diphenyl-1-picrylhydrazyl. Furthermore, the addition of live or heat-killed L. sakei MS103 cells to H2O2-exposed RAW 264.7 cells alleviated oxidative stress, as reflected by reduced malondialdehyde levels, increased glutathione levels, and the up-regulated expression of four antioxidant-related genes (gshR2, gshR4, Gpx, and npx). These findings highlight L. sakei MS103 as a potential probiotic capable of inhibiting activities of P. gingivalis pathogenic bacteria and mitigating oxidative stress.

Antibiotic Resistance and Probiotics: Knowledge Gaps, Market Overview and Preliminary Screening

Probiotics are among those products, the use of which is increasing, and they are available primarily as food/dietary supplements, as well as in the form of medicines. This study aims to assess the attitudes and practices of health professionals and students of health sciences, give a short overview of the probiotics currently on the market, and conduct a screening of five food supplements and one drug with respect to antibiotic resistance. Nearly half of the respondents in our survey state that probiotics have no side effects, while only 6.3% believe that the use of probiotics can lead to antibiotic resistance. In addition, more than 40% of the participants throw unused probiotics into municipal waste. The market analysis results indicate that probiotic products on the Serbian market have highly variable CFU counts, while the declared health claims cover numerous beneficial health effects, and they are sometimes even registered as medicines. Lactobacilli are frequently present in probiotic supplements, and are sold in pharmacies and online. The experimental results showed that antibiotic resistance is present in different types of lactobacilli in probiotic products. The risk of using probiotics, regardless of their beneficial health effects, should be taken into account in the future. An update to the regulations governing probiotics, including a stipulation for antimicrobial resistance (AMR) testing, should be established, and guidelines for their proper use and disposal put into place.

Cattle-compost-soil: The transfer of antibiotic resistance in livestock agriculture

Antibiotic resistance is a major global health threat. Agricultural use of antibiotics is considered to be a main contributor to the issue, influencing both animals and humans as defined by the One Health approach. The purpose of the present study was to determine the abundance of antibiotic-resistant bacterial populations and the overall bacterial diversity of cattle farm soils that have been treated with animal manure compost. Soil and manure samples were collected from different sites at Tullimba farm, NSW. Cultures were grown from these samples in the presence of 11 commonly used antibiotics and antibiotic-resistant bacteria (ARB) colonies were identified. Soil and manure bacterial diversity was also determined using 16S ribosomal RNA next-generation sequencing. Results showed that ARB abundance was greatest in fresh manure and significantly lower in composted manure. However, the application of composted manure on paddock soil led to a significant increase in soil ARB abundance. Of the antibiotics tested, the number of ARB in each sample was greatest for antibiotics that inhibited the bacterial cell wall and protein synthesis. Collectively, these results suggest that the transfer of antibiotic resistance from composted animal manure to soil may not be solely mediated through the application of live bacteria and highlight the need for further research into the mechanism of antibiotic resistance transfer.

Whole Genome Sequencing of the Novel Probiotic Strain Lactiplantibacillus plantarum FCa3L

Lactiplantibacillus plantarum is best known for its significant adaptive potential and ability to colonize different ecological niches. Different strains of L. plantarum are widely used as probiotics. To characterize the probiotic potential of the novel L. plantarum FCa3L strain isolated from fermented cabbage, we sequenced its whole genome using the Illumina MiSeq platform. This bacterial isolate had a circular chromosome of 3,365,929 bp with 44.3% GC content and a cyclic phage phiX174 of 5386 bp with 44.7% GC content. The results of in vitro studies showed that FCa3L was comparable with the reference probiotic strain L. plantarum 8PA3 in terms of acid and bile tolerance, adhesiveness, H₂O₂ production, and acidification rate. The strain 8PA3 possessed higher antioxidant activity, while FCa3L demonstrated superior antibacterial properties. The antibiotic resistance of FCa3L was more relevant to the probiotic strain than that of 8PA3, although a number of silent antibiotic resistance genes were identified in its genome. Genomic evidence to support adhesive and antibacterial properties, biosynthesis of bioactive metabolites, and safety of FCa3L was also presented. Thus, this study confirmed the safety and probiotic properties of L. plantarum FCa3L via complete genome and phenotype analysis, suggesting its potential as a probiotic, although further in vivo investigations are still necessary.

Promising biotherapeutic prospects of different probiotics and their derived postbiotic metabolites: in-vitro and histopathological investigation

BACKGROUND

Probiotics and their derived postbiotics, as cell-free supernatants (CFS), are gaining a solid reputation owing to their prodigious health-promoting effects. Probiotics play a valuable role in the alleviation of various diseases among which are infectious diseases and inflammatory disorders. In this study, three probiotic strains, Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, and Pediococcus acidilactici, were isolated from marketed dietary supplements. The antimicrobial activity of the isolated probiotic strains as well as their CFS was investigated. The neutralized CFS of the isolated probiotics were tested for their antibiofilm potential. The anti-inflammatory activity of the isolated Lactobacillus spp., together with their CFS, was studied in the carrageenan-induced rat paw edema model in male Wistar rats. To the best of our knowledge, such a model was not previously experimented to evaluate the anti-inflammatory activity of the CFS of probiotics. The histopathological investigation was implemented to assess the anti-inflammatory prospect of the isolated L. plantarum and L. rhamnosus strains as well as their CFS.

RESULTS

The whole viable probiotics and their CFS showed variable growth inhibition of the tested indicator strains using the agar overlay method and the microtiter plate assay, respectively. When tested for virulence factors, the probiotic strains were non-hemolytic lacking both deoxyribonuclease and gelatinase enzymes. However, five antibiotic resistance genes, blaZ, ermB, aac(6')- aph(2"), aph(3'')-III, and vanX, were detected in all isolates. The neutralized CFS of the isolated probiotics exhibited an antibiofilm effect as assessed by the crystal violet assay. This effect was manifested by hindering the biofilm formation of the tested Staphylococcus aureus and Pseudomonas aeruginosa clinical isolates in addition to P. aeruginosa PAO1 strain. Generally, the cell cultures of the two tested probiotics moderately suppressed the acute inflammation induced by carrageenan compared to indomethacin. Additionally, the studied CFS relatively reduced the inflammatory changes compared to the inflammation control group but less than that observed in the case of the probiotic cultures treated groups.

CONCLUSIONS

The tested probiotics, along with their CFS, showed promising antimicrobial and anti-inflammatory activities. Thus, their safety and their potential use as biotherapeutics for bacterial infections and inflammatory conditions are worthy of further investigation.

Regenerative Potential of Human Breast Milk: A Natural Reservoir of Nutrients, Bioactive Components and Stem cells

Human milk is a complex fluid that contains carbohydrates, lipids, proteins, and other bioactive molecules (immunoglobulins, lactoferrin, human milk oligosaccharides, lysozyme, leukocytes, cytokines, hormones, and microbiome) which provide nutritional, immunological, and developmental benefits to the infant. In addition to their involvement in the development, these bioactive compounds have a key role in anti-oncogenicity, neuro-cognitive development, cellular communication, and differentiation. As a result of technological advancements, it has been discovered that human breast milk contains cells that display many of the characteristics of stem cells with multilineage differentiation potentials. Do these cells have any specific properties or roles? Research efforts on breast milk cells have been mainly focused on leukocytes based on their immunological perspective in the early postpartum period. This review summarizes the nutritional components in human milk, i.e., the macro and micronutrients required for the growth and development of infants. Further, it discusses the research work reported concerning the purification, propagation, and differentiation of breast milk progenitor cells and highlights the advancements made in this newly emerging field of stem cell biology and regenerative medicine.

Isolation and characterization of Lactobacillus casei A14.2, a strain with immunomodulating activity on Apis mellifera

Considering the economic and environmental role played by bees and their present threats it is necessary to develop food supplements favoring their health. The aim of this work was to isolate and characterize an immunomodulating probiotic capable to improve the health of honeybee colonies. For this purpose, bacterial strains were isolated from Apis mellifera bees (N = 180) obtained at three apiaries. A total of 44 strains were isolated and 9 of them were identified as Lactobacillus having the capacity to grow under saccharose osmotic stress, at pH 4.0 and possessing a wide susceptibility to antibiotics. Results allowed to select two strains but finally only one of them, strain A14.2 showed a very significant immunomodulating activity. This strain increased the expression of mRNA codifying the antimicrobial peptides 24 h post-administration. We evaluated its growth kinetics under aerobic and microaerobic conditions and its survival in the presence of high concentrations of saccharose. Results demonstrated that Lactobacillus casei A14.2 strain was highly tolerant to oxygen and that it was able to adapt to saccharose enriched environments (50% and 100% w/v). Finally, L. casei A14.2 strain was administered monthly during summer and early fall to 4 honeybee colonies (2 controls and 2 treatments). The results showed a gradual sustained decrease of infestation (p < 0.05) by the pathogenic Nosema spp. but no reduction in the infestation by the mite Varroa destructor. These results suggest that the administration of this potential probiotic, may increase the resistance of honeybee colonies to infectious diseases caused by Nosema spp.

Characterization of lactic acid bacteria isolated from the poultry intestinal environment with anti-Salmonella activity in vitro

The purpose of this research was the genotypic identification of lactic acid bacteria (LAB), isolated from the gastrointestinal tract (GIT) of healthy adult birds, and the study of their safety regarding antibiotic resistance, physiological and functional properties involved in the colonization of the GIT of poultry, and Salmonella exclusion, as members of a potential mixed probiotic supplement for poultry. The nucleotidic sequence from Lactobacillus crispatus P1, L. animalis L3, and Enterococcus faecium CRL 1385 (ex-J96) showed 100, 99.8, and 99.3% identity with L. crispatus DSM 20584 T, Ligilactobacillus salivarius ATCC 11741 T, and E. faecium ATCC 19434 T, respectively. These strains showed no resistance to relevant antibiotics usually administered to animals proposed by the European Food Safety Authority. They could endure the detrimental conditions of the gastrointestinal tract (pH 2.6 and oxgall 0.1 and 0.4% w/v). In an ex vivo assay, the LAB showed high adherence to the three sections of the GIT, reaching values higher than 70%. The adhesion to mucus was strain-dependent: L. crispatus CRL 1453 evidenced the highest adhesion (> 19%) while Lig. salivarius subsp. salivarius CRL 1417 and E. faecium CRL 1385 adhered to a lower extent (> 9 and 2%, respectively). Moreover, the LAB elicited remarkable anti-Salmonella activity, taking into account that they could inhibit elevated counts of different Salmonella serovars, especially the host-specific serovars S. Gallinarum and S. Pullorum (up to 8 log CFU/mL decrease in Salmonella counts).

Screening for Antifungal Indigenous Lactobacilli Strains Isolated from Local Fermented Milk for Developing Bioprotective Fermentates and Coatings Based on Acid Whey Protein Concentrate for Fresh Cheese Quality Maintenance

The demand for healthy foods without artificial food additives is constantly increasing. Hence, natural food preservation methods using bioprotective cultures could be an alternative to chemical preservatives. Thus, the main purpose of this work was to screen the indigenous lactobacilli isolated from fermented cow milk for their safety and antifungal activity to select the safe strain with the strongest fungicidal properties for the development of bioprotective acid whey protein concentrate (AWPC) based fermentates and their coatings intended for fresh cheese quality maintenance. Therefore, 12 lactobacilli strains were isolated and identified from raw fermented cow milk as protective cultures. The safety of the stains was determined by applying antibiotic susceptibility, haemolytic and enzymatic evaluation. Only one strain, Lacticaseibacillus paracasei A11, met all safety requirements and demonstrated a broad spectrum of antifungal activity in vitro. The strain was cultivated in AWPC for 48 h and grew well (biomass yield 8 log10 cfu mL−1). L. paracasei A11 AWPC fermentate was used as a vehicle for protective culture in the development of pectin-AWPC-based edible coating. Both the fermentate and coating were tested for their antimicrobial properties on fresh acid-curd cheese. Coating with L. paracasei A11 strain reduced yeast and mould counts by 1.0–1.5 log10 cfu mL−1 (p ≤ 0.001) during cheese storage (14 days), simultaneously preserving its flavour and prolonging the shelf life for six days.

Evaluation of Probiotic Properties of Novel Brazilian Lactiplantibacillus plantarum Strains

Beneficial effects of Lactiplantibacillus plantarum strains have been widely reported. Knowing that the effects of probiotic bacteria are strain-dependent, this study aimed to characterize the probiotic properties and investigate the gastrointestinal protective effects of nine novel L. plantarum strains isolated from Bahia, Brazil. The probiotic functionality was first evaluated in vitro by characterizing bile salt and acidic tolerance, antibacterial activity, and adhesion to Caco-2 cells. Antibiotic resistance profile, mucin degradation, and hemolytic activity assays were also performed to evaluate safety features. In vivo analyses were conducted to investigate the anti-inflammatory effects of the strains on a mouse model of 5-Fluorouracil-induced mucositis. Our results suggest that the used L. plantarum strains have good tolerance to bile salts and low pH and can inhibit commonly gastrointestinal pathogens. Lp2 and Lpl1 strains also exhibited high adhesion rates to Caco-2 cells (13.64 and 9.05%, respectively). Phenotypical resistance to aminoglycosides, vancomycin, and tetracycline was observed for most strains. No strain showed hemolytic or mucolytic activity. Seven strains had a protective effect against histopathological and inflammatory damage induced by 5-FU. Gene expression analysis of inflammatory markers showed that five strains upregulated interleukin 10 (Il10), while four downregulated both interleukin 6 (Il6) and interleukin 1b (Il1b). Additionally, all strains reduced eosinophilic and neutrophilic infiltration; however, they could not prevent weight loss or reduced liquid/ food intake. Altogether, our study suggests these Brazilian L. plantarum strains present good probiotic characteristics and safety levels for future applications and can be therapeutically adjuvant alternatives to prevent/treat intestinal mucositis.

Antimicrobial Susceptibility Data for Six Lactic Acid Bacteria Tested against Fifteen Antimicrobials

Antimicrobial resistance is a rising threat in the agrifood sector. The misuse of antibiotics exerts selective pressure, driving resistance mechanisms in bacteria, which could ultimately spread through many routes and render treatments for infectious diseases inefficient in humans and animals. Herein, we report antimicrobial susceptibility data obtained for six lactic acid bacteria, the members of which are commonly used in the food and feed chain. Fifteen antimicrobials were considered for the phenotypic testing: ampicillin, gentamicin, kanamycin, tetracycline, erythromycin, clindamycin, chloramphenicol, streptomycin, vancomycin, quinupristin-dalfopristin, bacitracin, sulfamethoxazole, ciprofloxacin, linezolid, and rifampicin. The reported dataset could be used for the comparison, generation, and reconsideration of new and/or existing cut-off values when considering lactic acid bacteria, particularly lactobacilli and pediococci.

The dangerous transporters: A study of microplastic-associated bacteria passing through municipal wastewater treatment

Microplastics (MPs) provide a stable and protective habitat for diverse wastewater bacteria, including pathogenic and antibiotic-resistant species. Therefore, MPs may potentially transport these bacteria through wastewater treatment steps to the environment and far distances. This study investigated bacterial communities of MP-associated bacteria from different stages of municipal wastewater treatment processes to evaluate the potential negative effect of these biofilms on the environment. The results showed a high diversity of bacteria that were strongly attached to MPs. After all treatment steps, the core bacterial groups remained attached to MPs and escaped from the wastewater treatment plant with effluent water. Several pathogenic bacteria were identified in MP samples from all treatment steps, and most of them were found in effluent water. These data provide new insights into the possible impacts of wastewater-derived MPs on the environment. MP-associated biofilms were proved to be important sources of pathogens and antibiotic-resistant genes in natural waters.

Alarming Antibiotic Resistance of Lactobacilli Isolated from Probiotic Preparations and Dietary Supplements

In this study, we screened eight commercially available brands of Lactobacillus-containing probiotic preparations and dietary supplements for resistance towards commonly administered antibiotics of different classes. According to disc diffusion results, most of the isolates were resistant to vancomycin and susceptible to penicillin-type antibiotics (ampicillin and amoxicillin), carbapenems (imipenem, meropenem, and ertapenem), and inhibitors of protein synthesis (chloramphenicol, erythromycin, tetracycline, clarithromycin, and linezolid). However, based on minimum inhibitory concentration (MIC) values, six strains were reconsidered as resistant to tetracycline. All tested lactobacilli were resistant towards amikacin, ciprofloxacin, and norfloxacin. Resistance to cephalosporins was highly variable and decreased in the following order: ceftazidime/cefepime, ceftriaxone, cefotaxime, cefazolin, and cefoperazone. PCR screening for antibiotic resistance determinants in probiotic lactobacilli revealed a wide occurrence of vancomycin resistance gene vanX, ciprofloxacin resistance gene parC, and extended-spectrum β-lactamase gene blaTEM. We also detected the tetK gene for tetracycline resistance in one isolate. Additionally, we identified discrepancies between the claims of the manufacturers and the identified species composition, as well as the enumerated amount of viable bacteria, for several products. The results of this study raise concerns about the safety of lactobacilli for human consumption as probiotics, as they may act as reservoirs of transferable antibiotic resistance genes.

Characterization, High-Density Fermentation, and the Production of a Directed Vat Set Starter of Lactobacilli Used in the Food Industry: A Review

Lactobacilli have been widely concerned for decades. Bacteria of the genus Lactobacillus have been commonly employed in fermented food to improve the appearance, smell, and taste of food or prolong its shelf-life. They comprise 261 species (by March 2020) that are highly diverse at the phenotypic, ecological, and genotypic levels. Some Lactobacilli strains have been documented to be essential probiotics, which are defined as a group of living microorganisms that are beneficial to the health of the host when ingested in sufficiency. However, the characterization, high-density fermentation, and the production of a directed vat set (DVS) starter of Lactobacilli strains used in the food industry have not been systematically reported. This paper mainly focuses on reviewing Lactobacilli as functional starter cultures in the food industry, including different molecular techniques for identification at the species and strain levels, methods for evaluating Lactobacilli properties, enhancing their performance and improving the cell density of Lactobacilli, and the production techniques of DVS starter of Lactobacilli strains. Moreover, this review further discussed the existing problems and future development prospects of Lactobacilli in the food industry. The viability and stability of Lactobacilli in the food industry and gastrointestinal environment are critical challenges at the industrial scale. The new production equipment and technology of DVS starter of Lactobacilli strains will have the potential for large-scale application, for example, developing low-temperature spray drying, freezing granulation drying, and spray freeze-drying.

Analysis and Characterization of Lactobacillus paragasseri and Lacticaseibacillus paracasei: Two Probiotic Bacteria that Can Degrade Intestinal Oxalate in Hyperoxaluric Rats

In the present study, we characterized the probiotic properties of two commercially available bacterial strains, Lactobacillus paragasseri UBLG-36 and Lacticaseibacillus paracasei UBLPC-87, and evaluated their ability to degrade oxalate in vitro and in a hyperoxaluria-induced nephrolithiasis rat model. UBLG-36 harboring two oxalate catabolizing genes, oxalyl coenzyme A decarboxylase (oxc) and formyl coenzyme A transferase (frc), was previously shown to degrade oxalate in vitro effectively. Here, we show that UBLPC-87, lacking both oxc and frc, could still degrade oxalate in vitro. Both these strains harbored several potential putative probiotic genes that may have conferred them the ability to survive in low pH and 0.3% bile, resist antibiotic stress, show antagonistic activity against pathogenic bacteria, and adhere to epithelial cell surfaces. We further evaluated if UBLG-36 and UBLPC-87 could degrade oxalate in vivo and prevent hyperoxaluria-induced nephrolithiasis in rats. We observed that rats treated with 4.5% sodium oxalate (NaOx) developed hyperoxaluria and renal stones. However, when pre-treated with UBLG-36 or UBLPC-87 before administering 4.5% NaOx, the rats were protected against several pathophysiological manifestations of hyperoxaluria. Compared to the hyperoxaluric rats, the probiotic pre-treated rats showed reduced urinary excretion of oxalate and urea (p < 0.05), decreased serum blood urea nitrogen and creatinine (p < 0.05), alleviated stone formation and renal histological damage, and an overall decrease in renal tissue oxalate and calcium content (p < 0.05). Taken together, both UBLG-36 and UBLPC-87 are effective oxalate catabolizing probiotics capable of preventing hyperoxaluria and alleviating renal damage associated with nephrolithiasis.

ProbResist: a database for drug-resistant probiotic bacteria

Drug resistance remains a global threat, and the rising trend of consuming probiotic-containing foods, many of which harbor antibiotic resistant determinants, has raised serious health concerns. Currently, the lack of accessibility to location-, drug- and species-specific information of drug-resistant probiotics has hampered efforts to combat the global spread of drug resistance. Here, we describe the development of ProbResist, which is a manually curated online database that catalogs reports of probiotic bacteria that have been experimentally proven to be resistant to antibiotics. ProbResist allows users to search for information of drug resistance in probiotics by querying with the names of the bacteria, antibiotic or location. Retrieved results are presented in a downloadable table format containing the names of the antibiotic, probiotic species, resistant determinants, region where the study was conducted and digital article identifiers (PubMed Identifier and Digital Object Identifier) hyperlinked to the original sources. The webserver also presents a simple analysis of information stored in the database. Given the increasing reports of drug-resistant probiotics, an exclusive database is necessary to catalog them in one platform. It will enable medical practitioners and experts involved in policy making to access this information quickly and conveniently, thus contributing toward the broader goal of combating drug resistance.

Insights into the Antimicrobial Resistance Profile of a Next Generation Probiotic Akkermansia muciniphila DSM 22959

Akkermansia muciniphila is a Gram-negative intestinal anaerobic bacterium recently proposed as a novel probiotic candidate to be incorporated in food and pharmaceutical forms. Despite its multiple health benefits, the data addressing its antimicrobial susceptibility profile remain scarce. However, the absence of acquired resistance in probiotic strains is a compulsory criterion for its approval in the qualified presumption of safety list. This study aimed at characterizing the A. muciniphila DSM 22959 strain’s antimicrobial susceptibility profile using phenotypic and in silico approaches. To establish the phenotypic antimicrobial susceptibility profile of this strain, minimum inhibitory concentrations of eight antimicrobials were determined using broth microdilution and E-test methods. Additionally, the A. muciniphila DSM 22959 genome was screened using available databases and bioinformatics tools to identify putative antimicrobial resistance genes (ARG), virulence factors (VF), genomic islands (GI), and mobile genetic elements (MGE). The same categorization was obtained for both phenotypic methods. Resistance phenotype was observed for gentamicin, kanamycin, streptomycin, and ciprofloxacin, which was supported by the genomic context. No evidence was found of horizontal acquisition or potential transferability of the identified ARG and VF. Thus, this study provides new insights regarding the phenotypic and genotypic antimicrobial susceptibility profiles of the probiotic candidate A. muciniphila DSM 22959.

Association of Intrauterine Microbes with Endometrial Factors in Intrauterine Adhesion Formation and after Medicine Treatment

Intrauterine adhesions (IUAs) have caused serious harm to women’s reproductive health. Although emerging evidence has linked intrauterine microbiome to gynecological diseases, the association of intrauterine microbiome with IUA, remains unknown. We performed metagenome-wide association, metabolomics, and transcriptomics studies on IUA and non-IUA uteri of adult rats to identify IUA-associated microbial species, which affected uterine metabolites and endometrial transcriptions. A rat model was used with one side of the duplex uterus undergoing IUA and the other remaining as a non-IUA control. Both 16S rRNA sequencing and metagenome-wide association analysis revealed that instead of Mycoplasmopsis specie in genital tract, murine lung pathogen Mycoplasmopsispulmonis markedly increased in IUA samples and displayed a distinct positive interaction with the host immune system. Moreover, most of the IUA-enriched 58 metabolites positively correlate with M.pulmonis, which inversely correlates with a mitotic progression inhibitor named 3-hydroxycapric acid. A comparison of metabolic profiles of intrauterine flushing fluids from human patients with IUA, endometritis, and fallopian tube obstruction suggested that rat IUA shared much similarity to human IUA. The endometrial gene Tenascin-N, which is responsible for extracellular matrix of wounds, was highly up-regulated, while the key genes encoding parvalbumin, trophectoderm Dkkl1 and telomerase involved in leydig cells, trophectoderm cells, activated T cells and monocytes were dramatically down-regulated in rat IUA endometria. Treatment for rat IUA with estrogen (E2), oxytetracycline (OTC), and a traditional Chinese patent medicine GongXueNing (GXN) did not reduce the incidence of IUA, though inflammatory factor IL-6 was dramatically down-regulated (96–86%) with all three. Instead, in both the E2 and OTC treated groups, IUA became worse with a highly up-regulated B cell receptor signaling pathway, which may be associated with the significantly increased proportions of Ulvibacter or Staphylococcus. Our results suggest an association between intrauterine microbiota alterations, certain uterine metabolites, characteristic changes in endometrial transcription, and IUA and the possibility to intervene in IUA formation by targeting the causal factors, microbial infection, and Tenascin-like proteins.

Analysis of Bacterial Diversity in Different Types of Daqu and Fermented Grains From Danquan Distillery

Bacterial communities in high-temperature Daqu and fermented grains are important for brewing Jiang-flavor Baijiu such as Danquan Baijiu. Daqu is a saccharifying and fermenting agent, which has a significant impact on the flavor of Baijiu. However, bacterial communities in three different types of samples from the Danquan distillery (dqjq_ck, dqjqcp, and dqjp3) were still unclear, which limited further development of Danquan Baijiu. “dqjq_ck” and “dqjqcp” indicate high-temperature Daqu at days 45 and 135, respectively. “dqjp3” indicates fermented grains. In this study, the bacterial communities of three samples were analyzed by Illumina Miseq high-throughput sequencing. The bacterial communities of three samples primarily composed of thermophilic bacteria and bacteria with stress resistance. The most abundant species in dqjq_ck, dqjqcp, and dqjp3 were Comamonas, Bacillus, and unclassified Lactobacillales, respectively. The main bacteria included Bacillus, Comamonas, Myroides, Paenibacillus, Acetobacter, Kroppenstedtia, Staphylococcus, Saccharopolyspora, Planifilum, Lactobacillus, Acinetobacter, Oceanobacillus, Enterococcus, Thermoactinomyces, Lactococcus, Streptomyces, Saccharomonospora, Tepidimicrobium, Anaerosalibacter, unclassified_Lactobacillales, unclassified_Thermoactinomycetaceae_1, unclassified_Bacillaceae_2, unclassified_Bacillales, unclassified_Microbacteriaceae, unclassified_Rhodobacteraceae, unclassified_Actinopolysporineae, and unclassified_Flavobacteriaceae in three samples (percentage was more than 1% in one of three samples). In our study, the succession of microbiota in three samples representing three important stages of Danquan Baijiu brewing was revealed. This article lays a good foundation for understanding the fermentation mechanism and screening some excellent indigenous bacteria to improve the quality of Danquan Baijiu in future.

Fast growth can counteract antibiotic susceptibility in shaping microbial community resilience to antibiotics

SignificanceAntibiotic exposure stands among the most used interventions to drive microbial communities away from undesired states. How the ecology of microbial communities shapes their recovery-e.g., posttreatment shifts toward Clostridioides difficile infections in the gut-after antibiotic exposure is poorly understood. We study community response to antibiotics using a model community that can reach two alternative states. Guided by theory, our experiments show that microbial growth following antibiotic exposure can counteract antibiotic susceptibility in driving transitions between alternative community states. This makes it possible to reverse the outcome of antibiotic exposure through modifying growth dynamics, including cooperative growth, of community members. Our research highlights the relevance of simple ecological models to better understand the long-term effects of antibiotic treatment.

Bacteriocin-Producing Lactic Acid Bacteria Strains with Antimicrobial Activity Screened from Bamei Pig Feces

Lactic acid bacteria (LAB), which are characterized by producing various functional metabolites, including antioxidants, organic acids, and antimicrobial compounds, are widely used in the food industry to improve gut health and prevent the growth of spoilage microorganisms. With the continual incidence of foodborne disease and advocacy of consumers for gut health, LAB have been designated as vital biopreservative agents in recent years. Therefore, LAB with excellent antimicrobial properties and environmental tolerance should be explored further. In this study, we focus on screening the LAB strains from a specialty pig (Bamei pig) feces of the Tibetan plateau region and determine their antimicrobial properties and environmental tolerance to evaluate their potential probiotic values. A total of 116 LAB strains were isolated, from which the LAB strain Qinghai (QP)28-1 was identified as Lactiplantibacillus (L.) plantarum subsp. plantarum using 16S rDNA sequencing and recA amplification, showing the best growth capacity, acid production capacities, environmental tolerance, hydrophobicity, antibiotic susceptibility, and bacteriocin production capacity. Furthermore, this strain inhibited the growth of multiple pathogens by producing organic acids and bacteriocin. These bacteriocin-encoding genes were identified using PCR amplification, including plnS, plnN, and plnW. In conclusion, bacteriocin-producing L. plantarum subsp. plantarum QP28-1 stands out among these 116 LAB strains, and was considered to be a promising strain used for LAB-related food fermentation. Moreover, this study provides a convenient, comprehensive, and shareable profile for screening of superior functional and bacteriocin-producing LAB strains, which can be used in the food industry.

Assessing the drug resistance profiles of oral probiotic lozenges

Background

Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria.

Aim

To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro.

Results

Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128 µg/mL) and chloramphenicol (> 512 µg/mL) for all probiotics but only one was resistant to piperacillin (MIC = 32 µg/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments.

Conclusion

Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.

Antimicrobial Bacillus: Metabolites and Their Mode of Action

The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.

Probiotics: controversial issues

Recent studies have strongly confirmed the health benefits of a variety of probiotic microorganisms. However, some issues regarding the use of probiotics currently remain unresolved or ambiguous. This article highlights some controversial issues of probiotic use in clinical practice such as regulatory status of probiotics, co-administration of probiotics and antibiotics, potential impact of probiotics on antimicrobial resistance emergence and spread, dosing and duration of probiotic use, contraindications and some other debatable topics.

Microbial detoxification of dimethoate through mediated hydrolysis by Brucella sp. PS4: molecular profiling and plant growth-promoting traits

High toxicity of dimethoate requires efficient ways for detoxification and removal of its residues in contaminated environments. Microbial remediation is a process that utilizes the degradation potential of microbes to provide a cost-effective and reliable approach for pesticide abatement. For this purpose, a dimethoate-degrading bacterium Brucella sp. was isolated from a contaminated agricultural soil sample in Multan, Pakistan. This isolate was found to tolerate up to 100 ppm of dimethoate in minimal salt medium and was further evaluated for plant growth-promoting traits. The strain gave positive results for amylase, ammonia, and catalase production, while other traits such as indole acetic acid production and potassium solubilization were also confirmed. Thus, the strain could play an important role for plant nutrient transmission in the plant rhizosphere. Optimization of growth parameters (i.e., pH and temperature) depicted the potential of PS4 to be best tolerating dimethoate, with maximum cell density at λ 600 nm. Optimum pH and temperature for growth were found to be 6 and 35 °C, respectively. Based on optimization results as well as different attributes, the rhizospheric bacterial isolate PS4 was further subjected to a batch degradation experiment under different concentrations of dimethoate (25, 50, 75, and 100 ppm). This promising dimethoate-degrading isolate was found to degrade 83% of dimethoate (at 100 ppm) within a period of 7 days. In addition, it degraded 88% of dimethoate at 50 ppm, indicating that the bacterial isolate utilized dimethoate solely as a source of energy. The strain followed the first order reaction kinetics, depicting its dependence on dimethoate as energy and carbon source. Molecular profiling further supported its role in plant growth promotion and multi-stress tolerance. This research showed that Brucella sp. is capable of degrading dimethoate, and therefore, it would be useful in the investigation of novel bioremediation techniques at pesticide-polluted sites.