Antibiotic Resistance of LACTOBACILLUS Strains

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.

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.

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.

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.

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.

Revealing antimicrobial resistance profile of the novel probiotic candidate Faecalibacterium prausnitzii DSM 17677

Faecalibacterium prausnitzii, a resident anaerobic bacterium commonly found in healthy gut microbiota, has been proposed as a next generation probiotic with high potential for application in food matrices and pharmaceutical formulations. Despite its recognized health benefits, detailed information regarding its antimicrobial susceptibility profile is still lacking. However, this information is crucial to determine its safety, since the absence of acquired antimicrobial resistance is required to qualify a probiotic candidate as safe for human and animal consumption. Herein, the antimicrobial susceptibility profile of F. prausnitzii DSM 17677 strain was evaluated by integrating both phenotypic and in silico data. Phenotypic antimicrobial susceptibility was evaluated by determining minimum inhibitory concentrations of 9 antimicrobials using broth microdilution and E-test® methods. Also, the whole genome of F. prausnitzii DSM 17677 was analysed, using several databases and bioinformatics tools, to identify possible antibiotic resistance genes (ARG), genomic islands (GI) and mobile genetic elements (MGE). With exception of erythromycin, the same classification (susceptible or resistant) was obtained in both broth microdilution and E-test® methods. Phenotypic resistance to ampicillin, gentamycin, kanamycin and streptomycin were detected, which was supported by the genomic context. Other ARG were also identified but they seem not to be expressed under the tested conditions. F. prausnitzii DSM 17677 genome contains 24 annotated genes putatively involved in resistance against the following classes of antimicrobials: aminoglycosides (such as gentamycin, kanamycin and streptomycin), macrolides (such as erythromycin), tetracyclines and lincosamides. The presence of putative ARG conferring resistance to β-lactams could only be detected using a broader homology search. The majority of these genes are not encoded within GI or MGE and no plasmids were reported for this strain. Despite the fact that most genes are related with general resistance mechanisms, a streptomycin-specific ARG poses the only potential concern identified. This specific ARG is encoded within a GI and a MGE, meaning that it could have been laterally acquired and might be transferred to other bacteria present in the same environment. Thus, our findings provide relevant insights regarding the phenotypic and genotypic antimicrobial resistance profiles of the probiotic candidate F. prausnitzii DSM 17677.

Incidence of Tetracycline and Erythromycin Resistance in Meat-Associated Bacteria: Impact of Different Livestock Management Strategies

The extensive use of antibiotics as growth promoters, or their continued abusive misuse to cure or prevent the onset of bacterial infections as occurs in the intensive farming, may have played a pivotal role in the spread of reservoirs of antibiotic resistance (AR) among food-associated bacteria including pathogens representing risks to human health. The present study compares the incidence of tetracycline and erythromycin resistances in lactic acid bacteria (LAB) and coagulase negative staphylococci (CNS) from fermented products manufacturing using meat from intensive animal husbandry (industrialized manufacturing Italian salami) and from extensive farms (artisanal sausages facilities pork and llama Argentinean sausages). A higher incidence of tetracycline resistance (TET-R) compared to erythromycin resistance (ERY-R) was observed among the 205 isolates. Unlike CNS strains, the LAB showed a significant correlation between the TET-R and the ERY-R phenotypes. Genotypic assessment shows a high correlation with tetK and tetM for the TET-R strains and with ermB and ermC for the ERY-R strains. Multiple correspondence analyses have highlighted the association between AR phenotypes and CNS species isolated from Italian salami, while the susceptible phenotypes were associated with the LAB species from Argentinean sausages. Since antibiotic resistance in meat-associated bacteria is a very complex phenomenon, the assessment of bacterial resistance in different environmental contexts with diverse farming practices and food production technologies will help in monitoring the factors influencing AR emergence and spread in animal production.

Protective Effects of Probiotics on Cognitive and Motor Functions, Anxiety Level, Visceral Sensitivity, Oxidative Stress and Microbiota in Mice with Antibiotic-Induced Dysbiosis

Accumulating clinical and preclinical data indicate a prominent role of gut microbiota in regulation of physiological functions. The gut-brain axis imbalance due to gut dysbiosis is associated with a range of neurodegenerative diseases. Probiotics were suggested not only to restore intestinal dysbiosis but also modulate stress response and improve mood and anxiety symptoms. In this study, we assessed the effects of probiotic lactobacilli on behavioral reactions, the level of oxidative stress and microbiota content in mice administered to broad-spectrum antibiotics. Our study demonstrates that antibiotic treatment of adolescent mice for two weeks resulted in higher mortality and lower weight gain and induced significant changes in behavior including lower locomotor and exploratory activity, reduced muscle strength, visceral hypersensitivity, higher level of anxiety and impaired cognitive functions compared to the control group. These changes were accompanied by decreased diversity and total amount of bacteria, abundance of Proteobacteria and Verrucomicrobia phyla, and reduced Firmicutes/Bacteroides ratio in the gut microbiota. Moreover, a higher level of oxidative stress was found in brain and skeletal muscle tissues of mice treated with antibiotics. Oral administration of two Lactobacillus strains prevented the observed changes and improved not only microbiota content but also the behavioral alterations, suggesting a neuroprotective and antioxidant role of probiotics.

Antimicrobial Susceptibility of Lactic Acid Bacteria Strains of Potential Use as Feed Additives - The Basic Safety and Usefulness Criterion

The spread of resistance to antibiotics is a major health concern worldwide due to the increasing rate of isolation of multidrug resistant pathogens hampering the treatment of infections. The food chain has been recognized as one of the key routes of antibiotic resistant bacteria transmission between animals and humans. Considering that lactic acid bacteria (LAB) could act as a reservoir of transferable antibiotic resistance genes, LAB strains intended to be used as feed additives should be monitored for their safety. Sixty-five LAB strains which might be potentially used as probiotic feed additives or silage inoculants, were assessed for susceptibility to eight clinically relevant antimicrobials by a minimum inhibitory concentration determination. Among antimicrobial resistant strains, a prevalence of selected genes associated with the acquired resistance was investigated. Nineteen LAB strains displayed phenotypic resistance to one antibiotic, and 15 strains were resistant to more than one of the tested antibiotics. The resistance to aminoglycosides and tetracyclines were the most prevalent and were found in 37 and 26% of the studied strains, respectively. Phenotypic resistance to other antimicrobials was found in single strains. Determinants related to resistance phenotypes were detected in 15 strains as follows, the aph(3″)-IIIa gene in 9 strains, the lnu(A) gene in three strains, the str(A)-str(B), erm(B), msr(C), and tet(M) genes in two strains and the tet(K) gene in one strain. The nucleotide sequences of the detected genes revealed homology to the sequences of the transmissible resistance genes found in lactic acid bacteria as well as pathogenic bacteria. Our study highlights that LAB may be a reservoir of antimicrobial resistance determinants, thus, the first and key step in considering the usefulness of LAB strains as feed additives should be an assessment of their antibiotic resistance. This safety criterion should always precede more complex studies, such as an assessment of adaptability of a strain or its beneficial effect on a host. These results would help in the selection of the best LAB strains for use as feed additives. Importantly, presented data can be useful for revising the current microbiological cut-off values within the genus Lactobacillus and Pediococcus.

Lactic Acid Bacteria Diversity and Characterization of Probiotic Candidates in Fermented Meats

Probiotics are defined as live microorganisms which confer health benefits to the host when administered in adequate amounts. Many lactic acid bacteria (LAB) strains have been classified as probiotics and fermented foods are an excellent source of such LAB. In this study, novel probiotic candidates from two fermented meats (pancetta and prosciutto) were isolated and characterized. LAB populations present in pancetta and prosciutto were evaluated and Lactiplantibacillus plantarum was found to be the dominant species. The antagonistic ability of selected isolates against LAB and non-LAB strains was investigated, in particular, the ability to produce anti-microbial compounds including organic acids and bacteriocins. Probiotic characteristics including antibiotic susceptibility, hydrophobicity and autoaggregation capacity; and ability to withstand simulated gastric juice, bile salt, phenol and NaCl were assessed. Among the characterized strains, L. plantarum 41G isolated from prosciutto was identified as the most robust probiotic candidate compared. Results from this study demonstrate that artisanal fermented meat is a rich source of novel strains with probiotic potential.

Characterization of a bacterial strain Lactobacillus paracasei LP10266 recovered from an endocarditis patient in Shandong, China

Background

Lactobacilli are often recognized as beneficial partners in human microbial environments. However, lactobacilli also cause diseases in human, e.g. infective endocarditis (IE), septicaemia, rheumatic vascular disease, and dental caries. Therefore, the identification of potential pathogenic traits associated with lactobacilli will facilitate the prevention and treatment of the diseases caused by lactobacilli. Herein, we investigated the genomic traits and pathogenic potential of a novel bacterial strain Lactobacillus paracasei LP10266 which has caused a case of IE. We isolated L. paracasei LP10266 from an IE patient’s blood to perform high-throughput sequencing and compared the genome of strain LP10266 with those of closely related lactobacilli to determine genes associated with its infectivity. We performed the antimicrobial susceptibility testing on strain LP10266. We assessed its virulence by mouse lethality and serum bactericidal assays as well as its serum complement- and platelet-activating ability. The biofilm formation and adherence of strain LP10266 were also studied.

Results

Phylogenetic analysis revealed that strain LP10266 was allied with L. casei and L. paracasei. Genomic studies revealed two spaCBA pilus clusters and one novel exopolysaccharides (EPS) cluster in strain LP10266, which was sensitive to ampicillin, penicillin, levofloxacin, and imipenem, but resistant to cefuroxime, cefazolin, cefotaxime, meropenem, and vancomycin. Strain LP10266 was nonfatal and sensitive to serum, capable of activating complement 3a and terminal complement complex C5b-9 (TCC). Strain LP10266 could not induce platelet aggregation but displayed a stronger biofilm formation ability and adherence to human vascular endothelial cells (HUVECs) compared to the standard control strain L. paracasei ATCC25302.

Conclusion

The genome of a novel bacterial strain L. paracasei LP10266 was sequenced. Our results based on various types of assays consistently revealed that L. paracasei LP10266 was a potential pathogen to patients with a history of cardiac disease and inguinal hernia repair. Strain LP10266 showed strong biofilm formation ability and adherence, enhancing the awareness of L. paracasei infections.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02253-8.

Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems

Prophage integration, release, and dissemination exert various effects on host bacteria. In the genus Lactobacillus, they may cause bacteriophage contamination during fermentation and even regulate bacterial populations in the gut. However, little is known about their distribution, genetic architecture, and relationships with their hosts. Here, we conducted prophage prediction analysis on 1,472 genomes from 16 different Lactobacillus species and found prophage fragments in almost all lactobacilli (99.8%), with 1,459 predicted intact prophages identified in 64.1% of the strains. We present an uneven prophage distribution among Lactobacillus species; multihabitat species retained more prophages in their genomes than restricted-habitat species. Characterization of the genome features, average nucleotide identity, and landscape visualization presented a high genome diversity of Lactobacillus prophages. We detected antibiotic resistance genes in more than 10% of Lactobacillus prophages and validated that the occurrence of resistance genes conferred by prophage integration was possibly associated with phenotypic resistance in Lactobacillus plantarum. Furthermore, our broad and comprehensive examination of the distribution of CRISPR-Cas systems across the genomes predicted type I and type III systems as potential antagonistic elements of Lactobacillus prophage.

IMPORTANCE Lactobacilli are inherent microorganisms in the human gut and are widely used in the food processing industries due to their probiotic properties. Prophages were reportedly hidden in numerous Lactobacillus genomes and can potentially contaminate entire batches of fermentation or modulate the intestinal microecology once they are released. Therefore, a comprehensive scanning of prophages in Lactobacillus is essential for the safety evaluation and application development of probiotic candidates. We show that prophages are widely distributed among lactobacilli; however, intact prophages are more common in multihabitat species and display wide variations in genome feature, integration site, and genomic organization. Our data of the prophage-mediated antibiotic resistance genes (ARGs) and the resistance phenotype of lactobacilli provide evidence for deciphering the putative role of prophages as vectors of the ARGs. Furthermore, understanding the association between prophages and CRISPR-Cas systems is crucial to appreciate the coevolution of phages and Lactobacillus.

Safety and robustness aspects analysis of Lactobacillus delbrueckii ssp. bulgaricus LDB-C1 based on the genome analysis and biological tests

Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a microaerophylic anaerobe, which is widely used in the production of yogurt, cheese, and other fermented dairy products. L. bulgaricus and its partner Streptococcus thermophilus were used as starter cultures of yogurt in the world for thousands of years. In our previous study, L. bulgaricus LDB-C1 was obtained from traditional fermented milk, and possessed some characteristics like high exopolysaccharide yield and good fermentation performance. The analysis of its CRISPR-Cas system, antibiotic resistance, virulence factors, and mobile elements, was performed to reveal the stability of the strain LDB-C1. It was found that LDB-C1 contains a plenty of spacers in the CRISPR region, indicating it might have better performance against the infection of phages and plasmids. Furthermore, the acquired or transmittable antibiotic resistance/virulence factor genes were absent in the tested L. bulgaricus strain LDB-C1.

In Vitro Evaluation of Probiotic Properties of Lactobacillus plantarum UBLP40 Isolated from Traditional Indigenous Fermented Food

In this study, traditional indigenous fermented food isolate Lactobacillus plantarum UBLP40 was screened for in vitro probiotic properties, antibiotic susceptibility, hemolytic activity, production of lactic acid, hydrogen peroxide, bile salt hydrolase and phytase, and antioxidative activity. Results showed that Lact. plantarum UBLP40 can survive simulated gastrointestinal conditions, adhere to mucin, possess a hydrophobic cell surface, ability to auto-aggregation, and possessed antimicrobial activity against Micrococcus luteus MTCC 106, methicillin-resistant Staphylococcus aureus subsp. aureus ATCC® BAA-1720, Pseudomonas aeruginosa MTCC 1688, and Escherichia coli MTCC 1687. Lact. plantarum UBLP40 produced 48.59 U/mg phytase and 1.78 ± 0.01 gm % lactic acid and showed the ability to produce hydrogen peroxide and bile salt hydrolase. Moreover, the usual antibiotic susceptible profile and non-hemolytic activity indicated the safety of the strain. The intracellular extract of UBLP40 showed 13.8 ± 1.4% (equivalent to ~8 µM butylated hydroxytoluene) α,α-diphenyl-β-picrylhydrazyl (DPPH) radical scavenging activity, reducing activity equivalent to 1 µg L-cysteine, Fe²⁺ chelation equivalent to 5 µM ethylenediaminetetraacetic acid, and exhibited 17.73 ± 4.40 µM glutathione per gram of protein. In conclusion, this study demonstrates that Lact. plantarum UBLP40 is a potential probiotic candidate.

Prebiotic Maltose Gel Can Promote the Vaginal Microbiota From BV-Related Bacteria Dominant to Lactobacillus in Rhesus Macaque

The high incidence of bacterial vaginosis recurrence is common after treatment with an antibiotic agent and suggests the need for new treatments to prevent this. We conducted a randomized trial to evaluate the ability of maltose gel to treat bacterial vaginosis. Eighteen female rhesus macaques were randomly assigned, in a 2:1 ratio, to receive maltose gel or placebo gel by syringe to the fornix of the vagina for five consecutive days. We used 16S rRNA sequencing data from 70 swab samples of vaginal secretions in two groups in total on days 0, 3, and 5 after medication initiation and days 3 and 5 after medication withdrawal for the study of microbiome composition. We found that, in the placebo control group, there was no significant change in the composition and abundance of vaginal microbiota during the follow-up period. In the maltose gel test group, the abundance of Lactobacillus in the vagina microbiota increased gradually with the prolongation of the treatment time on Days 3 and 5 (ANOVA p = 6.99e−5 < 0.01) but began to decrease after the withdrawal of maltose gel, which was different from that of the control group. Correspondingly, the diversity and abundance of BV-related bacteria, Fusobacterium, Parvimonas, Mobiluncus, Campylobacter, Prevotella, and Sneathia, decreased on Day 0 to Day 5 of medication and increased after drug withdrawal in the maltose gel test group. The study confirms that maltose gel can facilitate the proliferation of Lactobacillus and promote the transition of the vaginal microbiota from BV-related bacteria dominant to Lactobacillus dominant in the rhesus macaque.

Characterization of Lactic Acid Bacteria in Raw Buffalo Milk: a Screening for Novel Probiotic Candidates and Their Transcriptional Response to Acid Stress

Lactic acid bacteria (LAB) are important microorganisms for the food industry due to their functional activity, as starters and potential probiotic strains. With that in mind, we explored the LAB diversity in raw buffalo milk, screening for novel potential probiotic strains. A total of 11 strains were identified by combination of MALDI-TOF and partial 16S rDNA sequencing and selected as potential probiotic candidates. Bacteria innocuity assessment was performed by determining antimicrobial susceptibility and the presence of virulence factors. Antagonism activity against Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes and Staphylococcus aureus was assessed, as well as milk proteolytic activity and exopolysaccharides production. Seven strains were identified as innocuous and two of them, Lactobacillus rhamnosus LB1.5 and Lactobacillus paracasei LB6.4 were selected for further probiotic potential analyses. Both strains demonstrated adhesion ability to Caco-2 cells, coaggregated with S. aureus and E. coli and maintained cell viability after gastrointestinal simulation in vitro, suggesting their probiotic potential. Furthermore, the transcriptional response of Lact. rhamnosus LB1.5 and Lact. paracasei LB6.4 to in vitro acid stress was assessed by RT-qPCR targeting seven genes related to adhesion, aggregation, stress tolerance, DNA repair and central metabolism. The association between the transcriptional responses and the maintenance of cell viability after gastrointestinal simulation highlights the genetic ability as probiotic of the two selected strains. Finally, we have concluded that Lact. rhamnosus LB1.5 and Lact. paracasei LB6.4 are important probiotic candidates to further in vivo studies.