Mobilization of Microbiota Commensals and Their Bacteriocins for Therapeutics

Innovative Bacterial Therapies and Genetic Engineering Approaches in Colorectal Cancer: A Review of Emerging Strategies and Clinical Implications

Colorectal cancer (CRC) is considered a widespread cancer, ranking second in mortality and incidence among cancer patients worldwide. CRC develops from adenoma to carcinoma through the dynamic interplay of genetic and environmental factors. The conventional modes of treatment, including operation, chemotherapy, and irradiation, are associated with significant challenges, such as drug resistance and toxicity, necessitating the exploration of new treatment modalities. These difficulties reveal the necessity of the emergence of new therapeutic approaches. This review mainly emphasizes the bacterial-based therapies that have recently developed like the engineered bacteriophage therapy and bacterial immunotherapy that pale the existing chemotherapy in terms of toxicity but are effective in killing tumor cells. Also, it also investigates various molecular genetic engineering strategies such as CRISPR-Cas9, CRISPR prime editing and gene silencing to achieve better targeting of CRC. Implementing these new approaches into the forefront of CRC treatment may bring better, more effective therapy with fewer side effects on patients' quality of life.

Pneumococcal pneumonia is driven by increased bacterial turnover due to bacteriocin-mediated intra-strain competition

Using chromosomal barcoding, we observed that >97% of the Streptococcus pneumoniae (Spn) population turns over in the lung within 2 days post-inoculation in a murine model. This marked collapse of diversity and bacterial turnover was associated with acute inflammation (severe pneumococcal pneumonia), high bacterial numbers in the lungs, bacteremia, and mortality. Intra-strain competition mediated by the blp locus, which expresses bacteriocins in a quorum-sensing-dependent manner, was required for each of these effects. Bacterial turnover from the activity of Blp-bacteriocins increased the release of the pneumococcal toxin, pneumolysin (Ply), which was sufficient to account for the lung pathology. The ability of Ply to evade complement, rather than its pore-forming activity, prevented opsonophagocytic clearance of Spn enabling its multiplication in the lung, facilitating the inflammatory response and subsequent invasion into the bloodstream. Thus, our study demonstrates how an appreciation for bacterial population dynamics during infection provides new insight into pathogenesis.

The Bacteriocins Produced by Lactic Acid Bacteria and the Promising Applications in Promoting Gastrointestinal Health

Bacteriocins produced by lactic acid bacteria (LAB) are promising bioactive peptides. Intriguingly, bacteriocins have health benefits to the host and may be applied safely in the food industry as bio-preservatives or as therapeutic interventions preventing intestinal diseases. In recent years, finding a safe alternative approach to conventional treatments to promote gut health is a scientific hotspot. Therefore, this review aimed to give insight into the promising applications of LAB-bacteriocins in preventing intestinal diseases, such as colonic cancer, Helicobacter pylori infections, multidrug-resistant infection-associated colitis, viral gastroenteritis, inflammatory bowel disease, and obesity disorders. Moreover, we highlighted the recent research on bacteriocins promoting gastrointestinal health. The review also provided insights into the proposed mechanisms, challenges and opportunities, trends and prospects. In addition, a SWOT analysis was conducted on the potential applications. Based on properties, biosafety, and health functions of LAB-bacteriocins, we conclude that the future applications of LAB-bacteriocins are promising in promoting gastrointestinal health. Further in vivo trials are needed to confirm these potential effects of LAB-bacteriocins interventions.

Biopreservation of Food Using Bacteriocins From Lactic Acid Bacteria: Classification, Mechanisms, and Commercial Applications

Food is the primary substance needed by humans to survive. However, food is easily contaminated by spoilage bacteria, which cause a decrease in quality and shelf life. Moreover, spoilage bacteria in food can be pathogenic, leading to foodborne disease that endangers human health. This issue has also driven the widespread use of synthetic preservatives, which have negative effects both in the short and long term. Biopreservation efforts utilizing bacteriocins produced by lactic acid bacteria offer an alternative solution to prevent spoilage and extend the shelf life of food. These bacteriocins are safe to use as they are produced by lactic acid bacteria that are approved for use in food. The application of various types of bacteriocins as biopreservatives has been widely conducted. Several other types of bacteriocins are continuously being researched and developed to ensure their safety and suitability for use as food biopreservatives. This article highlights bacteriocins, including their classification, general overview, mechanisms of action, differences from antibiotics, diversity, applications, prospects, and challenges as future food biopreservatives. Additionally, this article presents commercial bacteriocins, namely, nisin and pediocin, which are frequently used for food preservation.

Isolation of Thermophilic Bacteria Geobacillus subterraneus From Mount Tangkuban Perahu and the Novelty as a Candidate for Streptococcus mutans Anti-Biofilm

Thermophilic bacteria living in extreme areas with high temperatures are capable of producing secondary metabolites, such as antimicrobial peptides (AMPs). AMPs are stable at high temperatures and show good antibacterial activity. Therefore, this study aimed to identify thermophilic bacteria from the crater of Mount Tangkuban Perahu around West Java and assess antibacterial effectiveness of AMPs against Streptococcus mutans, which contribute to oral biofilm formation. The isolate obtained was identified using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, and the supernatant of the isolate was tested against S. mutans American Type Culture Collection (ATCC) 25175 using the disc assay method. To determine AMPs-coding genes, its genome was uploaded to antibiotic and secondary metabolite analysis shell (antiSMASH) 5.0.0 platform and biofilm inhibition was tested using the microtiter plate technique (with a 96-well bottom). Subsequently, the results were assessed using a microplate reader operating at 595 nm wavelength. The isolate was identified as Geobacillus subterraneus, with antibacterial activity against S. mutans, and produced an inhibition zone of 8.40 mm at an optimum pH of 8. The output of AMPs-coding gene showed that AMPs of the isolate were a member of the lanthipeptide class I, or bacteriocin-I group. AMPs of G. subterraneus suppressed the growth of S. mutans biofilm at a supernatant concentration of 5%, with the lowest optical density (OD) value of 0.061 and the highest percentage of biofilm growth inhibition at 28.24%. Based on the results, G. subterraneus derived from the crater of Mount Tangkuban Perahu showed potent antibacterial properties against S. mutans, making it a promising novel S. mutans anti-biofilm candidate.

Uncovering the arsenal of class II bacteriocins in salivarius streptococci

Facing the antibiotic resistance crisis, bacteriocins are considered as a promising alternative to treat bacterial infections. In the human commensal Streptococcus salivarius, the production of unmodified bacteriocins (or salivaricins) is directly controlled at the transcriptional level by quorum-sensing. To discover hidden bacteriocins, we harnessed here the unique molecular signatures of salivaricins not yet used in available computational pipelines and performed genome mining followed by orthogonal reconstitution and expression. From 100 genomes of S. salivarius, we identified more than 50 bacteriocin candidates clustered into 21 groups. Strain-based analysis of bacteriocin combinations revealed significant diversity, reflecting the plasticity of seven independent loci. Activity tests showed both narrow and broad-spectrum bacteriocins with overlapping activities against a wide panel of Gram-positive bacteria, including notorious multidrug-resistant pathogens. Overall, this work provides a search-to-test generic pipeline for bacteriocin discovery with high impact for bacterial ecology and broad applications in the food and biomedical fields.

Understanding of probiotic origin antimicrobial peptides: a sustainable approach ensuring food safety

The practice of preserving and adding value to food dates back to over 10,000 BCE, when unintentional microbial-driven chemical reactions imparted flavor and extended the shelf life of fermented foods. The process evolved, and with the urbanization of society, significant shifts in dietary habits emerged, accompanied by sporadic food poisoning incidents. The repercussions of the COVID-19 pandemic have intensified the search for antibiotic alternatives owing to the rise in antibiotic-resistant pathogens, emphasizing the exploration of probiotic-origin antimicrobial peptides to alleviate human microbiome collateral damage. Often termed 'molecular knives', these peptides outstand as potent antimicrobials due to their compatibility with innate microflora, amenability to bioengineering, target specificity, versatility and rapidity in molecular level mode of action. This review centres on bacteriocins sourced from lactic acid bacteria found in ethnic fermented foods, accentuating their desirable attributes, technological applications as nanobiotics and potential future applications in the modern context of ensuring food safety.

Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities

SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.

The microbiome-derived antibacterial lugdunin acts as a cation ionophore in synergy with host peptides

Lugdunin is a microbiome-derived antibacterial agent with good activity against Gram-positive pathogens in vitro and in animal models of nose colonization and skin infection. We have previously shown that lugdunin depletes bacterial energy resources by dissipating the membrane potential of Staphylococcus aureus. Here, we explored the mechanism of action of lugdunin in more detail and show that lugdunin quickly depolarizes cytoplasmic membranes of different bacterial species and acidifies the cytoplasm of S. aureus within minutes due to protonophore activity. Varying the salt species and concentrations in buffers revealed that not only protons are transported, and we demonstrate the binding of the monovalent cations K+, Na+, and Li+ to lugdunin. By comparing known ionophores with various ion transport mechanisms, we conclude that the ion selectivity of lugdunin largely resembles that of 15-mer linear peptide gramicidin A. Direct interference with the main bacterial metabolic pathways including DNA, RNA, protein, and cell wall biosyntheses can be excluded. The previously observed synergism of lugdunin with dermcidin-derived peptides such as DCD-1 in killing S. aureus is mechanistically based on potentiated membrane depolarization. We also found that lugdunin was active against certain eukaryotic cells, however strongly depending on the cell line and growth conditions. While adherent lung epithelial cell lines were almost unaffected, more sensitive cells showed dissipation of the mitochondrial membrane potential. Lugdunin seems specifically adapted to its natural environment in the respiratory tract. The ionophore mechanism is refractory to resistance development and benefits from synergy with host-derived antimicrobial peptides.

IMPORTANCE

The vast majority of antimicrobial peptides produced by members of the microbiome target the bacterial cell envelope by many different mechanisms. These compounds and their producers have evolved side-by-side with their host and were constantly challenged by the host's immune system. These molecules are optimized to be well tolerated at their physiological site of production, and their modes of action have proven efficient in vivo. Imbalancing the cellular ion homeostasis is a prominent mechanism among antibacterial natural products. For instance, over 120 naturally occurring polyether ionophores are known to date, and antimicrobial peptides with ionophore activity have also been detected in microbiomes. In this study, we elucidated the mechanism underlying the membrane potential-dissipating activity of the thiazolidine-containing cycloheptapeptide lugdunin, the first member of the fibupeptides discovered in a commensal bacterium from the human nose, which is a promising future probiotic candidate that is not prone to resistance development.

Bacteriocin diversity, function, discovery and application as antimicrobials

Bacteriocins are potent antimicrobial peptides that are produced by bacteria. Since their discovery almost a century ago, diverse peptides have been discovered and described, and some are currently used as commercial food preservatives. Many bacteriocins exhibit extensively post-translationally modified structures encoded on complex gene clusters, whereas others have simple linear structures. The molecular structures, mechanisms of action and resistance have been determined for a number of bacteriocins, but most remain incompletely characterized. These gene-encoded peptides are amenable to bioengineering strategies and heterologous expression, enabling metagenomic mining and modification of novel antimicrobials. The ongoing global antimicrobial resistance crisis demands that novel therapeutics be developed to combat infectious pathogens. New compounds that are target-specific and compatible with the resident microbiota would be valuable alternatives to current antimicrobials. As bacteriocins can be broad or narrow spectrum in nature, they are promising tools for this purpose. However, few bacteriocins have gone beyond preclinical trials and none is currently used therapeutically in humans. In this Review, we explore the broad diversity in bacteriocin structure and function, describe identification and optimization methods and discuss the reasons behind the lack of translation beyond the laboratory of these potentially valuable antimicrobials.

Clean-label alternatives for food preservation: An emerging trend

Consumer demand for natural or 'clean-label' food ingredients has risen over the past 50 years and continues growing. Consumers have become more aware of their health and, therefore, insist on transparency in the list of ingredients. Preservatives are the most crucial food additives, ensuring food safety and security. Despite tremendous technological advancements, food preservation remains a significant challenge worldwide, primarily because most are synthetic and non-biodegradable. As a result, the food industry is placing more value on microbiota and other natural sources for bio-preservation, leading to the substitution of conventional processing and chemical preservatives with natural alternatives to ensure 'clean-label.' General Standard for Food Additives (GSFA) includes some of these 'clean-label' options in its list of additives. However, they are very rarely capable of replacing a synthetic preservative on a 'one-for-one' basis, putting pressure on researchers to decipher newer, cleaner, and more economical alternatives. Academic and scientific research has led to the discovery of several plant, animal, and microbial metabolites that may function as effective bio-preservatives. However, most have not yet been put in the market or are under trial. Hence, the present review aims to summarise such relevant and potential metabolites with bio-preservative properties comprehensively. This article will help readers comprehend recent innovations in the 'clean-label' era, provide informed choices to consumers, and improve the business of regulatory approvals.

Antibacterial Activity and Cytotoxicity of the Novel Bacteriocin Pkmh

Bacteriocins are a class of proteins produced by bacteria that are toxic to other bacteria. These bacteriocins play a role in bacterial competition by helping to inhibit potential competitors. In this study, we isolated and purified a novel bacteriocin Pkmh, different from the previously reported bacteriocin PA166, from Pseudomonas sp. strain 166 by ammonium sulfate precipitation, dialysis membrane method, ion exchange chromatography, and gel filtration chromatography. SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) revealed that the molecular weight of Pkmh is approximately 35 kDa. Pkmh exhibited potent antimicrobial activity against bovine Mannheimia haemolytica (M. haemolytica) with low cytotoxicity, and lower hemolytic activity was observed. In addition, Pkmh retained antimicrobial activity at different pH ranges (2-10) and temperature conditions (40, 60, 80, 100 °C). Our analysis of its antimicrobial mechanism showed that Pkmh acts on bacterial cell membranes, increasing their permeability and leading to cell membrane rupture and death. In conclusion, Pkmh exhibited low hemolytic activity, low toxicity, and potent antibacterial effects, suggesting its potential as a promising candidate for clinical therapeutic drugs.

Bacteriocins sourced from traditional fermented foods for ensuring food safety: the microbial guards

Concerns about food safety have consistently driven the exploration of potent antimicrobials with probiotic origins. Identification of probiotic-derived bacteriocins as robust alternatives to antibiotics has gained traction following the COVID-19 pandemic. Additionally, the global market is witnessing an increasing preference for minimally processed food products free from chemical additives. Another contributing factor to the search for potent antimicrobials is the escalating number of infections caused by antibiotic-resistant bacteria and the need to mitigate the significant damage inflicted on the commensal human microbiota by broad-spectrum antibiotics. As an alternative bio-preservation strategy, there is substantial enthusiasm for the use of bacteriocins or starter cultures producing bacteriocins in preserving a variety of food items. This review specifically focuses on bacteriocins originating from lactic acid bacteria associated with fermented foods and explores their technological applications as nanobiotics. The food-grade antibiotic alternatives, whether utilized independently or in combination with other antimicrobials and administered directly or encapsulated, are anticipated to possess qualities of safety, stability and non-toxicity suitable for application in the food sector. © 2024 Society of Chemical Industry.

Safety Assessment of Streptococcus salivarius UBSS-01 in Rats and Double-Blind Placebo-Controlled Study in Healthy Individuals

Streptococcus salivarius is a common, harmless, and prevalent member of the oral microbiota in humans. In the present study, the safety of S. salivarius UBSS-01 was evaluated using in silico methods and preclinical and clinical studies. In an acute toxicity study, rats were administered with 5 g/kg (500 × 109 CFU) S. salivarius UBSS-01. The changes in phenotypic behaviors and hematological, biochemical, electrolytes, and urine analyses were monitored. No toxicity was observed at 14 days post-treatment. The no observable effects limit (NOEL) of S. salivarius UBSS-01 was >5 g/kg in rats. In a 28-day repeat dose toxicity study, rats were administered S. salivarius UBSS-01 once daily at doses of 0.1, 0.5, and 1 g/kg (10, 50, and 100 billion CFU/kg, respectively) body weight. S. salivarius UBSS-01 did not influence any of the hematology parameters and clinical chemistry parameters in plasma and serum samples after 28-day repeated administration. No structural abnormality was observed in the histological examination of organs. Whole genome analysis revealed the absence of virulence factors or genes that may transmit antibiotic resistance. In the double-blind study with 60 human participants (aged 18-60 years), consumption of S. salivarius UBSS-01 for 30 days was found to be safe and results were comparable with placebo treatment These findings indicate that S. salivarius UBSS-01 may be safe for human consumption.

Postbiotics as Metabolites and Their Biotherapeutic Potential

This review highlights the role of postbiotics, which may provide an underappreciated avenue doe promising therapeutic alternatives. The discovery of natural compounds obtained from microorganisms needs to be investigated in the future in terms of their effects on various metabolic disorders and molecular pathways, as well as modulation of the immune system and intestinal microbiota in children and adults. However, further studies and efforts are needed to evaluate and describe new postbiotics. This review provides available knowledge that may assist future research in identifying new postbiotics and uncovering additional mechanisms to combat metabolic diseases.

Anti-caries Streptococcus spp.: A potential preventive tool for special needs patients

INTRODUCTION

Probiotics are living microorganisms that act on the host-microbiome interface to restore the microbiota's physiological homeostasis. Numerous probiotics have been marketed with inhibitory activity against Streptococcus mutans and consequently with a potential anti-caries effect, mainly of the genera Lactobacillus and Bifidobacterium, whose main disadvantage is their limited ability to settle in the oral cavity.

METHODS

This narrative review describes the main Streptococcus spp. with probiotic anti-Streptococcus mutans activity, whose substantivity is greater than that of Lactobacillus spp. and consequently with anti-caries potentiality. We performed a literature review in the PubMed, Science Direct and Google Scholar databases of articles published in English (without time restriction) related to caries and probiotics.

RESULTS

The potential identified anti-caries probiotics included Streptococcus spp. A12, Streptococcus oralis (AJ3), Streptococcus oligofermentans, Streptococcus salivarius (K12, M18, JH, LAB813, 24SMB), Streptococcus spp. with arginolytic activity (S. sanguinis, S. gordonii, S. ratti, S. parasanguinis, S. intermedius, S. australis, and S. cristatus), Streptococcus rattus (JH145), Streptococcus dentisani and Streptococcus downii.

CONCLUSIONS

The possibility of using these Streptococcus spp. as probiotics that inhibit the growth of dental plaque and the development of carious lesions represents a potential tool of particular interest for individuals with physical or intellectual disabilities that impede the routine and effective application of mechanical dental plaque removal techniques.

Bacteriocins: potentials and prospects in health and agrifood systems

Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.

Production of nisin from Lactococcus lactis in acid-whey with nutrient supplementation

The production of Nisin, an FDA-approved food preservative, was attempted by Lactococcus lactis subsp. lactis ATCC® 11454 using the underutilized milk industry effluent, acid-whey, as a substrate. Nisin production was further improved by studying the effect of supplementation of nutrients and non-nutritional parameters. The addition of yeast extract (6% w/v) as nitrogen source and sucrose (4% w/v) as carbon source were found to be suitable nutrients for the maximum nisin production. The changes in the medium pH due to lactic acid accumulation during batch fermentation and its influence on the production of nisin were analyzed in the optimized whey medium (OWM). The production characteristics in OWM were further compared with the nisin production in MRS media. The influence of nisin as an inducer for its own production was also studied and found that the addition of nisin at 0.22 mg/ml promote the nisin production. The analysis of consumption of various metal ions present in the OWM during the nisin production was also analyzed, and found that the copper ions are the most consumed ion. The highest nisin yield of 2.6 × 105 AU/mL was obtained with OWM.

Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation

Bacteriocins, which have narrow-spectrum activity and limited adverse effects, are promising alternatives to antibiotics. In this study, we identified klebicin E (KlebE), a small bacteriocin derived from Klebsiella pneumoniae. KlebE exhibited strong efficacy against multidrug-resistant K. pneumoniae isolates and conferred a significant growth advantage to the producing strain during intraspecies competition. A giant unilamellar vesicle leakage assay demonstrated the unique membrane permeabilization effect of KlebE, suggesting that it is a pore-forming toxin. In addition to a C-terminal toxic domain, KlebE also has a disordered N-terminal domain and a globular central domain. Pulldown assays and soft agar overlay experiments revealed the essential role of the outer membrane porin OmpC and the Ton system in KlebE recognition and cytotoxicity. Strong binding between KlebE and both OmpC and TonB was observed. The TonB-box, a crucial component of the toxin-TonB interaction, was identified as the 7-amino acid sequence (E3ETLTVV9) located in the N-terminal region. Further studies showed that a region near the bottom of the central domain of KlebE plays a primary role in recognizing OmpC, with eight residues surrounding this region identified as essential for KlebE toxicity. Finally, based on the discrepancies in OmpC sequences between the KlebE-resistant and sensitive strains, it was found that the 91st residue of OmpC, an aspartic acid residue, is a key determinant of KlebE toxicity. The identification and characterization of this toxin will facilitate the development of bacteriocin-based therapies targeting multidrug-resistant K. pneumoniae infections.

Synergistic Activity of Ingulados Bacteria with Antibiotics against Multidrug-Resistant Pathogens

Antimicrobial resistance is a critical challenge due to the overuse of conventional antimicrobials, and alternative solutions are urgently needed. This study investigates the efficacy of compounds derived from lactic acid bacteria (LAB) fermentation combined with antibiotics against multidrug-resistant pathogens isolated from clinical cases in a hospital setting. Strains of Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecium and faecalis were isolated and selected from blood, respiratory, and urine samples. They were tested against the fermentation products from the Ingulados LAB collection (BAL5, BAL6, BAL8, BAL13, and BAL16), recognized for their antimicrobial efficacy against veterinary pathogens. The activity against multidrug-resistant (MDR) pathogens was evaluated initially, followed by synergy tests using checkerboard assays and subsequent analysis. Bioinformatic assessments and supernatant treatments were performed to characterize the nature of the compounds responsible for the antimicrobial activity. Notably, BAL16 exhibited significant growth inhibition against multidrug-resistant E. faecium. Synergy tests highlighted its combined activity with tetracycline through FICI and surface analysis and bioinformatic analysis unveiled the protein fraction containing bacteriocins as the underlying mechanism. This study highlights BAL16 fermentation products potential as valuable antimicrobial agents against MDR E. faecium infections, attributed to bacteriocins. Further in-depth studies are necessary for complete bacteriocin characterization.

Molecular identification and safety assessment of the potential probiotic strain Bacillus paralicheniformis HMPM220325 isolated from artisanal fruit dairy products

Bacillus probiotics exhibit considerable economic potential owing to their heightened resilience to external stressors and relatively lower costs related to production and preservation. Although Bacillus paralicheniformis has been acknowledged as a plant-promoting bacterium for a long time, understanding its potential as a probiotic is still in its nascent stages. In this study, the safety and probiotic characteristics of a strain of HMPM220325, isolated from artisanal fruit dairy products, were examined through whole-genome sequencing and phenotypic analysis. The whole genome of HMPM220325 was analyzed for antimicrobial resistance genes, pathogenicity factors, and genes associated with probiotic traits including stress resistance, spore formation, gut adhesion, competitive exclusion of pathogens, bacteriocin expression, and carbohydrate metabolism related to prebiotic utilization. Also, wet lab experiments were conducted for the characterization of probiotics. The identification of the organism as B. paralicheniformis was verified. Its safety was assessed through in silico analysis, the haemolytic activity test, and the acute oral toxicity test. B. paralicheniformis HMPM220325 demonstrated its ability to survive in the pH range of 4-10 and bile salt concentrations of 0-0.9% (w/v), tolerate temperatures between 20 and 60 °C, and exhibit a robust antioxidant capacity. Moreover, B. paralicheniformis HMPM220325 demonstrated a moderate level of hydrophobicity, had the ability to form biofilms, achieved a self-aggregation rate of 51.77 ± 1.01% within 6 hours, and successfully colonized the mouse intestine for a duration of up to 17 days. Additionally, the genome of B. paralicheniformis HMPM220325 contains three gene clusters associated with the biosynthesis of bacteriocins and exhibits co-aggregation with Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica serovar Typhimurium. The findings of the genomic analysis align with those obtained from the experimental investigation, thereby substantiating the potential of B. paralicheniformis HMPM220325 as a probiotic suitable for incorporation in dairy functional foods and feed applications.

Heterologously expressed SacP23, a novel bacteriocin from Paenibacillus polymyxa #23, is active against methicillin resistant Staphylococcus aureus

Antimicrobial peptides have the potential to be used in a range of applications, including as an alternative to conventional antibiotics for the treatment of bacterial infections of humans and animals. Therefore, there is interest in identifying novel bacteriocins which have desirable physico-chemical properties or antimicrobial activities. Paenibacillus polymyxa #23, isolated from a marine sponge, has wide spectrum antimicrobial activity against Gram-negative and Gram-positive bacteria. To explore the basis of this antimicrobial activity, the complete genome sequence of the strain was examined. Multiple genes predicted to encode antimicrobial peptides were identified. One gene was predicted to encode a novel sactipeptide bacteriocin, named SacP23. To confirm that SacP23 does have antimicrobial activity and to explore the antimicrobial spectrum of the peptide it was heterologously expressed in Bacillus subtilis. A cluster of eight genes, encoding a full complement of accessory genes as well as the structural gene expressed from the native promoter, was cloned into B. subtilis BS54A. The recombinant strain displayed antimicrobial activity against several Gram-positive bacteria, including multi-drug resistant Staphylococcus aureus. Heterologous expression of a whole gene cluster offers a powerful way to interrogate and resolve the various antimicrobial activities expressed by native strains that encode multiple compounds of interest.

Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota

Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.

Probiotic and Safety Evaluation of Twelve Lactic Acid Bacteria as Future Probiotics

The human gut flora is highly diverse. Most lactic acid bacteria (LAB) are widely used as probiotics in human and animal husbandry and have a variety of physiological benefits. This article mainly studied the bacteriostatic ability of LAB against four pathogenic bacteria, gastrointestinal environment tolerance, and adhesion ability to Caco-2 cells. The genome of Lactiplantibacillus plantarum L461 was sequenced and analyzed. The results showed that strains F512, L461, and D469 had the most significant inhibitory effects on Escherichia coli, Salmonella enterica B, Staphylococcus aureus, and Listeria monocytogenes. In addition, strains L461, C502, and P231 showed good tolerance after exposure to simulated gastric fluid for 0-4 h. Strains C502, H781, and L461 showed good tolerance in simulated intestinal fluid. Strains L461 and H781 showed good adhesion to Caco-2 cells. The number of viable bacteria was more than 60. Therefore, we screened L. plantarum L461 from 12 LAB strains through three aspects of evaluation, and conducted whole genome sequencing and analysis. Sequencing results showed that L. plantarum L461 had more defense mechanisms and phage annotation genes than L. plantarum WCFS1. Virulence factor studies showed that L. plantarum L461 has iron absorption system and adhesion-related gene annotation, indicating that L. plantarum L461 has survival advantage in intestinal tract. The predicted results showed that there were eight phages with phage resistance in L. plantarum L461. L. plantarum L461 is sensitive to several antibiotics, notably penicillin and oxacillin. In summary, the results of this study prove that L. plantarum L461 has good prebiotic function and is safe. Therefore, L. plantarum L461 can be safely used as a potential functional probiotic.

Anti-Staphylococcal Activity of Ligilactobacillus animalis SWLA-1 and Its Supernatant against Multidrug-Resistant Staphylococcus pseudintermedius in Novel Rat Model of Acute Osteomyelitis

Osteomyelitis caused by staphylococcal infection is a serious complication of orthopedic surgery. Staphylococcus pseudintermedius is the main causative agent of osteomyelitis in veterinary medicine. Methicillin-resistant S. pseudintermedius (MRSP) has been reported in companion animals, especially dogs. Multidrug-resistant S. pseudintermedius is an emerging pathogen and has acquired antibiotic resistance against various commercial antimicrobial agents. New antimicrobial compounds are urgently needed to address antibiotic resistance, and the development of novel agents has become an international research hotspot in recent decades. Antimicrobial compounds derived from probiotics, such as bacteriocins, are promising alternatives to classical antibiotics. In this study, the antibacterial activities of Ligilactobacillus animalis SWLA-1 and its concentrated cell-free supernatant (CCFS) were evaluated in vitro and in vivo. The CCFS of this bacterium showed no toxicity against osteoblast and myoblast cells in vitro, while significantly inhibiting the multidrug-resistant S. pseudintermedius KUVM1701GC strain in a newly established rat model. The CCFS significantly inhibited multidrug-resistant staphylococci both in vitro and in vivo. This suggests that CCFS derived from L. animalis SWLA-1 has potential as an alternative to classic antibiotics for staphylococcal infections in dogs.

Gut microbiota and microbiota-derived metabolites in colorectal cancer: enemy or friend

Colorectal cancer (CRC) is a highly prevalent gastrointestinal cancer worldwide. Recent research has shown that the gut microbiota plays a significant role in the development of CRC. There is mounting evidence supporting the crucial contributions of bacteria-derived toxins and metabolites to cancer-related inflammation, immune imbalances, and the response to therapy. Besides, some gut microbiota and microbiota-derived metabolites have protective effects against CRC. This review aims to summarize the current studies on the effects and mechanisms of gut microbiota and microbiota-produced metabolites in the initiation, progression, and drug sensitivity/resistance of CRC. Additionally, we explore the clinical implications and future prospects of utilizing gut microbiota as innovative approaches for preventing and treating CRC.

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

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

Comparative Analysis of Structural Composition and Function of Intestinal Microbiota between Chinese Indigenous Laiwu Pigs and Commercial DLY Pigs

Intestinal microbiota has an important impact on pig phenotypes. Previous studies mainly focused on the microbiota of feces and worldwide farmed commercial pigs, while research on the microbiota of various intestinal sections and indigenous pig breeds is very limited. This study aimed to characterize and compare the biogeography of intestinal microbiota in pigs of one Chinese indigenous breed and one commercial crossbred. In this study, we sequenced the microbiota of six intestinal segments in the grown-up pigs of a Chinese indigenous breed, Laiwu pigs, and the worldwide farmed crossbred Duroc × Landrace × Yorkshire (DLY) pigs by 16S rRNA sequencing, characterized the biogeography of intestinal microbiota, and compared the compositional and functional differences between the two breeds. The results showed that there were obvious differences in microbial structure and abundance between the small and large intestines. Laiwu pigs had higher large intestinal diversity than DLY pigs, while DLY pigs had higher small intestinal diversity than Laiwu pigs. Moreover, some specific bacterial taxa and Kyoto Encyclopedia of Genes and Genomes pathways were found to be related to the high fat deposition and good meat quality of Laiwu pigs and the high growth speed and lean meat rate of DLY pigs. This study provides an insight into the shifts in taxonomic composition, microbial diversity, and functional profile of intestinal microbiota in six intestinal segments of Laiwu and DLY pigs, which would be essential for exploring the potential influence of the host's genetic background on variation in microbiota composition and diversity.

Bacteriocin-Producing Lactiplantibacillus plantarum YRL45 Enhances Intestinal Immunity and Regulates Gut Microbiota in Mice

Bacteriocins production is one of important beneficial characteristics of probiotics, which has antibacterial property against intestinal pathogens and is helpful for regulating intestinal flora. To investigate the impact of bacteriocin-producing probiotics on gut microecology, bacteriocin-producing Lactiplantibacillus plantarum YRL45 was orally administered to mice. The results revealed that it promoted the release of cytokines and improved the phagocytic activity of peritoneal macrophages to activate the immune regulation system. L. plantarum YRL45 was conducive to maintaining the morphology of colon tissue without inflammation and increasing the ratio of villus height to crypt depth in the ileum. The gene expression levels of Muc2, ZO-1 and JAM-1 were significantly up-regulated in the ileum and colon, and the gene expression of Cramp presented an upward trend with L. plantarum YRL45 intervention. Moreover, L. plantarum YRL45 remarkably enhanced the levels of immunoglobulins sIgA, IgA and IgG in the intestine of mice. The 16S rRNA gene analysis suggested that L. plantarum YRL45 administration up-regulated the relative abundance of the beneficial bacteria Muribaculaceae and Akkermansia, down-regulated the abundance of the pathogenic bacteria Lachnoclostridium, and promoted the production of acetic acid, propionic acid and total short-chain fatty acids (SCFAs) in mice feces. Our findings indicated that L. plantarum YRL45 had the potential to be developed as a novel probiotic to regulate the intestinal barrier by altering gut microbiota to enhance intestinal immunity and ameliorate intestinal flora balance.

Evaluating the Translational Potential of Bacteriocins as an Alternative Treatment for Staphylococcus aureus Infections in Animals and Humans

Antibiotic resistance remains a global threat to human and animal health. Staphylococcus aureus is an opportunistic pathogen that causes minor to life-threatening infections. The widespread use of antibiotics in the clinical, veterinary, and agricultural setting combined with the increasing prevalence of antibiotic-resistant S. aureus strains makes it abundantly clear that alternatives to antibiotics are urgently needed. Bacteriocins represent one potential alternative therapeutic. They are antimicrobial peptides that are produced by bacteria that are generally nontoxic and have a relatively narrow target spectrum, and they leave many commensals and most mammalian cells unperturbed. Multiple studies involving bacteriocins (e.g., nisin, epidermicin, mersacidin, and lysostaphin) have demonstrated their efficacy at eliminating or treating a wide variety of S. aureus infections in animal models. This review provides a comprehensive and updated evaluation of animal studies involving bacteriocins and highlights their translational potential. The strengths and limitations associated with bacteriocin treatments compared with traditional antibiotic therapies are evaluated, and the challenges that are involved with implementing novel therapeutics are discussed.

Environmental insults and compensative responses: when microbiome meets cancer

Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding the functional consequence of the interface between host-microbiome and cancer. Given microbial communities have predominantly been explored through an ecological perspective, it is important that the foundational aspects of ecological stress and the fight to 'survive and thrive' are accounted for tumor-micro(b)environment as well. Building on existing evidence and classical microbial ecology, here we attempt to characterize the ecological stresses and the compensative responses of the microorganisms inside the tumor microenvironment. What insults would microbes experience inside the cancer jungle? How would they respond to these insults? How the interplay of stress and microbial quest for survival would influence the fate of tumor? This work asks these questions and tries to describe this underdiscussed ecological interface of the tumor and its microbiota. It is hoped that a larger scientific thought on the importance of microbial competition sensing vis-à-vis tumor-microenvironment would be stimulated.

Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products

The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.

Microencapsulation of Probiotic Streptococcus salivarius LAB813

Probiotics are living microorganisms that confer a health benefit on the host when administered in adequate amounts. Streptococcus salivarius, a commensal bacterium found in the oral cavity, has been shown to secrete antimicrobial peptides and can be used as probiotics. This study aimed to develop a delivery system for the probiotic LAB813, a novel S. salivarius strain first identified in the laboratory. Probiotics can be delivered and protected through the encapsulation of biomaterials such as polysaccharides. Their biocompatibility, biodegradability, user-friendliness, and ease of access make polysaccharides useful for encapsulating probiotics. Alginate (Alg) and chitosan (Ch) are naturally obtained polysaccharides and, hence, tested for LAB813 encapsulation. An extrusion method of encapsulation was performed to form Alg microcapsules (Alg-LAB813), some of which were coated with Ch (Alg-LAB813-Ch) to provide dual-layered protection. Inhibitory assays of the Alg-LAB813 and Alg-LAB813-Ch microcapsules were assayed against an indicator strain. Alg-LAB813-Ch microcapsules showed superior antibacterial properties compared to Alg-LAB813 microcapsules over 24 h and when subject to temperatures ranging from 4 to 68 °C. In addition, Alg-LAB813-Ch microcapsules retained antibacterial activity for up to 28 days of storage at 4 °C. The strong and sustained inhibitory activities of Ch-coated Alg encapsulated LAB813 signify the potential for their use to improve oral health.

Beneficial modulation of human health in the oral cavity and beyond using bacteriocin-like inhibitory substance-producing streptococcal probiotics

The human oral cavity contains a diversity of microbial habitats that have been adopted and adapted to as homeland by an amazingly heterogeneous population of microorganisms collectively referred to as the oral microbiota. These microbes generally co-habit in harmonious homeostasis. However, under conditions of imposed stress, as with changes to the host’s physiology or nutritional status, or as a response to foreign microbial or antimicrobial incursions, some components of the oral “microbiome” (viz. the in situ microbiota) may enter a dysbiotic state. This microbiome dysbiosis can manifest in a variety of guises including streptococcal sore throats, dental caries, oral thrush, halitosis and periodontal disease. Most of the strategies currently available for the management or treatment of microbial diseases of the oral cavity focus on the repetitive “broad sweep” and short-term culling of oral microbe populations, hopefully including the perceived principal pathogens. Both physical and chemical techniques are used. However, the application of more focused approaches to the harnessing or elimination of key oral cavity pathogens is now feasible through the use of probiotic strains that are naturally adapted for oral cavity colonization and also are equipped to produce anti-competitor molecules such as the bacteriocins and bacteriocin-like inhibitory substances (viz BLIS). Some of these probiotics are capable of suppressing the proliferation of a variety of recognized microbial pathogens of the human mouth, thereby assisting with the restoration of oral microbiome homeostasis. BLIS K12 and BLIS M18, the progenitors of the BLIS-producing oral probiotics, are members of the human oral cavity commensal species Streptococcus salivarius. More recently however, a number of other streptococcal and some non-streptococcal candidate oral probiotics have also been promoted. What is becoming increasingly apparent is that the future for oral probiotic applications will probably extend well beyond the attempted limitation of the direct pathological consequences of oral microbiome dysbiosis to also encompass a plethora of systemic diseases and disorders of the human host. The background to and the evolving prospects for the beneficial modulation of the oral microbiome via the application of BLIS-producing S. salivarius probiotics comprises the principal focus of the present review.

Health Benefits of Consuming Foods with Bacterial Probiotics, Postbiotics, and Their Metabolites: A Review

Over the years, probiotics have been extensively studied within the medical, pharmaceutical, and food fields, as it has been revealed that these microorganisms can provide health benefits from their consumption. Bacterial probiotics comprise species derived from lactic acid bacteria (LAB) (genus Lactobacillus, Leuconostoc, and Streptococcus), the genus Bifidobacterium, and strains of Bacillus and Escherichia coli, among others. The consumption of probiotic products is increasing due to the current situation derived from the pandemic caused by COVID-19. Foods with bacterial probiotics and postbiotics are premised on being healthier than those not incorporated with them. This review aims to present a bibliographic compilation related to the incorporation of bacterial probiotics in food and to demonstrate through in vitro and in vivo studies or clinical trials the health benefits obtained with their metabolites and the consumption of foods with bacterial probiotics/postbiotics. The health benefits that have been reported include effects on the digestive tract, metabolism, antioxidant, anti-inflammatory, anticancer, and psychobiotic properties, among others. Therefore, developing food products with bacterial probiotics and postbiotics is a great opportunity for research in food science, medicine, and nutrition, as well as in the food industry.

Antimicrobial peptide production in response to gut microbiota imbalance

The gut microbiota presents essential functions in the immune response. The gut epithelium acts as a protective barrier and, therefore, can produce several antimicrobial peptides (AMPs) that can act against pathogenic microorganisms, including bacteria. Several factors cause a disturbance in gut microbiota, including the exacerbated and erroneous use of antibiotics. Antibiotic therapy has been closely related to bacterial resistance and is also correlated with undesired side-effects to the host, including the eradication of commensal bacteria. Consequently, this results in gut microbiota imbalance and inflammatory bowel diseases (IBD) development. In this context, AMPs in the gut epithelium play a restructuring role for gut microbiota. Some naturally occurring AMPs are selective for pathogenic bacteria, thus preserving the health microbiota. Therefore, AMPs produced by the host's epithelial cells represent effective molecules in treating gut bacterial infections. Bearing this in mind, this review focused on describing the importance of the host's AMPs in gut microbiota modulation and their role as anti-infective agents against pathogenic bacteria.

Bacteriocins as Potential Therapeutic Approaches in the Treatment of Various Cancers: A Review of In Vitro Studies

Simple Summary

Current cancer treatment strategies such as surgery, chemotherapy, and radiotherapy, have significant drawbacks. There is a need for a breakthrough approach to cancer treatment. Bacteriocin, an antimicrobial peptide, has shown several anticancer properties in vitro. Therefore, this article reviews the effect of bacteriocin on cancer cells and how bacteriocins affect cancer cells in vitro. This article aims to promote additional bacteriocin research, particularly in vivo studies, to fully understand the potential of bacteriocin as a cancer treatment agent.

Abstract

Cancer is regarded as one of the most common and leading causes of death. Despite the availability of conventional treatments against cancer cells, current treatments are not the optimal treatment for cancer as they possess the possibility of causing various unwanted side effects to the body. As a result, this prompts a search for an alternative treatment without exhibiting any additional side effects. One of the promising novel therapeutic candidates against cancer is an antimicrobial peptide produced by bacteria called bacteriocin. It is a non-toxic peptide that is reported to exhibit potency against cancer cell lines. Experimental studies have outlined the therapeutic potential of bacteriocin against various cancer cell lines. In this review article, the paper focuses on the various bacteriocins and their cytotoxic effects, mode of action and efficacies as therapeutic agents against various cancer cell lines.

Effect of a bacteriocin-producing Streptococcus salivarius on the pathogen Fusobacterium nucleatum in a model of the human distal colon

The gut microbiome is a vast reservoir of microbes, some of which produce antimicrobial peptides called bacteriocins that may inhibit specific bacteria associated with disease. Fusobacterium nucleatum is an emerging human bacterial pathogen associated with gastrointestinal diseases including colorectal cancer (CRC). In this study, fecal samples of healthy donors were screened for potential bacteriocin-producing probiotics with antimicrobial activity against F. nucleatum. A novel isolate, designated as Streptococcus salivarius DPC6993 demonstrated a narrow-spectrum of antimicrobial activity against F. nucleatum in vitro. In silico analysis of the S. salivarius DPC6993 genome revealed the presence of genes involved in the production of the bacteriocins salivaricin A5 and salivaricin B. After 6 h in a colon fermentation model, there was a significant drop in the number of F. nucleatum in samples that had been simultaneously inoculated with S. salivarius DPC6993 + F. nucleatum DSM15643 compared to those inoculated with F. nucleatum DSM15643 alone (mean ± SD: 9243.3 ± 3408.4 vs 29688.9 ± 4993.9 copies/μl). Furthermore, 16S rRNA amplicon analysis revealed a significant difference in the mean relative abundances of Fusobacterium between samples inoculated with both S. salivarius DPC6993 and F. nucleatum DSM15643 (0.05%) and F. nucleatum DSM15643 only (0.32%). Diversity analysis indicated minimal impact exerted by S. salivarius DPC6993 on the surrounding microbiota. Overall, this study highlights the ability of a natural gut bacterium to target a bacterial pathogen associated with CRC. The specific targeting of CRC-associated pathogens by biotherapeutics may ultimately reduce the risk of CRC development and positively impact CRC outcomes.

Novel approaches for the treatment of infections due to multidrug-resistant bacterial pathogens

Antimicrobial resistance (AMR), which is a major challenge for global healthcare, emerging because of several reasons including overpopulation, increased global migration and selection pressure due to enhanced use of antibiotics. Antibiotics are the widely used therapeutic options to combat infectious diseases; however, unfortunately, inadequate and irregular antibiotic courses are also major contributing factors in the emergence of AMR. Additionally, persistent failure to develop and commercialize new antibiotics has created the scarcity of effective anti-infective drugs. Thus, there is an urgent need for a new class of antimicrobials and other novel approaches to curb the menace of AMR. Besides the conventional approaches, some novel approaches such as the use of antimicrobial peptides, bacteriophages, immunomodulation, host-directed therapy and antibodies have shown really promising potentials.

Antibacterial activity and cytotoxicity of a novel bacteriocin isolated from Pseudomonas sp. strain 166

Pseudomonas sp. strain 166 was isolated from soil samples from Changbai Mountains. A novel bacteriocin PA166 from Pseudomonas sp. 166 was purified using ammonium sulfate, dextran gel chromatography column and Q-Sepharose column chromatography successively. The molecular mass of bacteriocin PA166 was found to be 49.38 kDa by SDS-PAGE and liquid chromatography-mass spectrometry (MS)/MS. Bacteriocin PA166 showed stability at a wide range of pH (2-10), and thermal stability (40, 60, 80 and 100°C). The bacteriocin PA166 antimicrobial activity was slightly inhibited by Ca²⁺ , K⁺ and Mg²⁺ . The minimum bactericidal concentrations of bacteriocin PA166 against five Pasteurella multocida strains ranged from 2 to 8 μg ml^-1 . Bacteriocin PA166 showed low cytotoxicity and a higher treatment index (TI = 82.51). Fluorescence spectroscopy indicated that bacteriocin PA166 destroyed the cell membrane to exert antimicrobial activity. In summary, bacteriocin PA166 had strong antibacterial activity, high TI and low toxicity, and hence could serve as a potential clinical therapeutic drug.

A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits

The plasmids in gut microbiomes have the potential to contribute to the microbiome community, as well as human health and physiology. Nevertheless, this niche remains poorly explored. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups from South America and Africa, which would represent a link between ancestral and modern human groups. Based on open metagenomic data, we characterized the set of plasmids, including their genes and functions, from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami, semi-isolated groups with a hunter, gather or subsistence lifestyle. Unique plasmid clusters and gene functions for each human group were identified. Moreover, a dozen plasmid clusters circulating in other niches worldwide are shared by these distinct groups. In addition, novel and unique plasmids harboring resistance (encompassing six antibiotic classes and multiple metals) and virulence (as type VI secretion systems) genes were identified. Functional analysis revealed pathways commonly associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza gut plasmids. These results demonstrate the richness of plasmids in semi-isolated human groups’ gut microbiome, which represents an important source of information with biotechnological/pharmaceutical potential, but also on the spread of resistance/virulence genes to semi-isolated groups.

Oropharyngeal Probiotic ENT-K12 as an Effective Dietary Intervention for Children With Recurrent Respiratory Tract Infections During Cold Season

Recurrent respiratory tract infections (RRTi) cause a high burden of disease and lead to negative impact on quality of life, frequent school/work absenteeism, and doctor visits, which remain a great challenge to pediatricians because RRTi can increase the risk of various complications including antibiotic overuse and resistance, which is one of the biggest threats to global health, and there is no confirmed effective treatment. In this study, we aimed to assess the clinical efficacy and safety of oropharyngeal probiotic ENT-K12 as a dietary intervention or a complementary treatment along with standard medical treatment during acute respiratory infections among children with RRTi during cold season. The results of this study show that when comparing to practicing of standard medical treatment only, the complementary intake of oropharyngeal probiotic ENT-K12 can effectively reduce episodes of both acute and RRTi in school children, shorten the course of respiratory symptoms onset, reduce the use of antibiotics and antiviral drugs, and reduce the absence days from both children's school and parents' work. Using oropharyngeal probiotics as a complementary dietary intervention to stabilize oropharyngeal microflora, specifically inhibiting respiratory pathogens and enhancing host immunity, could possibly be a promising approach to reduce RRTi burden and combating antibiotic resistance in long term, more clinical studies will be needed to further confirm the clinical practicing guide to ensure its clinical benefit.

Antibiotic resistant bacteria: current situation and treatment options to accelerate the development of a new antimicrobial arsenal

INTRODUCTION

Antibiotic resistance is one of the biggest public health threats worldwide. Currently, antibiotic-resistant bacteria kill 700,000 people every year. These data represent the near future in which we find ourselves, a "post-antibiotic era" where the identification and development of new treatments are key. This review is focused on the current and emerging antimicrobial therapies which can solve this global threat.

AREAS COVERED

Through a literature search using databases such as Medline and Web of Science, and search engines such as Google Scholar, different antimicrobial therapies were analyzed, including pathogen-oriented therapy, phagotherapy, microbiota and antivirulent therapy. Additionally, the development pathways of new antibiotics were described, emphasizing on the potential advantages that the combination of a drug repurposing strategy with the application of mathematical prediction models could bring to solve the problem of AMRs.

EXPERT OPINION

This review offers several starting points to solve a single problem: reducing the number of AMR. The data suggest that the strategies described could provide many benefits to improve antimicrobial treatments. However, the development of new antimicrobials remains necessary. Drug repurposing, with the application of mathematical prediction models, is considered to be of interest due to its rapid and effective potential to increase the current therapeutic arsenal.

Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development

Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.

Current Status of Probiotics as Supplements in the Prevention and Treatment of Infectious Diseases

Probiotics play an important role against infectious pathogens via their effects on the epithelium, the production of antimicrobial compounds, and competitive exclusion. Administration of probiotic supplements may reduce the risk of infectious diseases and the use of antibiotics, hence contributing to a reduction or a delay of the development of multi-resistant bacteria. Infection is a constant concern for people who experience recurrent infections, and antibiotic treatment usually fails due to antibiotic resistance. Therefore, an infection can lead to severe illness and hospitalization if left untreated. A growing number of studies have demonstrated promising results for a variety of probiotic strains used to prevent or treat acute and recurrent infectious diseases, but additional standardized clinical research is needed.

Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice

With obesity and type 2 diabetes (T2D) at epidemic levels, we need to understand the complex nature of these diseases to design better therapeutics. The underlying causes of both obesity and T2D are complex, but both are thought to develop, in part, based on contributions from the gut microbiota.

Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.

OUP accepted manuscript

Nowadays, the growing human population exacerbates the need for sustainable resources. Inspiration and achievements in nutrient production or human/animal health might emanate from microorganisms and their adaptive strategies. Here, we exemplify the benefits of lactic acid bacteria (LAB) for numerous biotechnological applications and showcase their natural transformability as a fast and robust method to hereditarily influence their phenotype/traits in fundamental and applied research contexts. We described the biogenesis of the transformation machinery and we analyzed the genome of hundreds of LAB strains exploitable for human needs to predict their transformation capabilities. Finally, we provide a stepwise rational path to stimulate and optimize natural transformation with standard and synthetic biology techniques. A comprehensive understanding of the molecular mechanisms driving natural transformation will facilitate and accelerate the improvement of bacteria with properties that serve broad societal interests.