Interaction Of Bacteria Research Articles

New Obolenskvirus Phages Brutus and Scipio: Biology, Evolution, and Phage-Host Interaction.

Two novel virulent phages of the genus Obolenskvirus infecting Acinetobacter baumannii, a significant nosocomial pathogen, have been isolated and studied. Phages Brutus and Scipio were able to infect A. baumannii strains belonging to the K116 and K82 capsular types, respectively. The biological properties and genomic organization of the phages were characterized. Comparative genomic, phylogenetic, and pangenomic analyses were performed to investigate the relationship of Brutus and Scipio to other bacterial viruses and to trace the possible origin and evolutionary history of these phages and other representatives of the genus Obolenskvirus. The investigation of enzymatic activity of the tailspike depolymerase encoded in the genome of phage Scipio, the first reported virus infecting A. baumannii of the K82 capsular type, was performed. The study of new representatives of the genus Obolenskvirus and mechanisms of action of depolymerases encoded in their genomes expands knowledge about the diversity of viruses within this taxonomic group and strategies of Obolenskvirus-host bacteria interaction.

The mammary gland is intolerant to bacterial intrusion

Mammals depend on the secretion of milk to rear their offspring, which exposes the organ in charge of the function, the mammary gland (MG), to bacterial threat. The essential driving force that conditions the interactions of bacteria with the MG is the abundant secretion of milk, a nutritious fluid which endows the common mastitis-causing pathogens with a doubling time of less than 30 min. From this angle, mammals rely on a potential bacterial bioreactor for the survival of their offspring. The MG is lined with a two-layered epithelium devoid of protective mucus. This means that the mammary epithelium is exposed directly to bacteria once they have passed through the opening lactiferous canal. To cope with the threat, the MG resorts to neutrophilic inflammation to check bacterial proliferation in its lumen and at its epithelial lining. Promptness of neutrophil recruitment is a necessity, which requires a low threshold of activation on the part of the mammary epithelium. Constrained by natural selection, the MG has evolved an innate and adaptive immunity intolerant to bacteria regardless of their level of virulence. The evolutionary issue has been to find a compromise between the deleterious tissue-damaging side effects of inflammation and the maintenance of the secretory function indispensable for the offspring’s survival. It appears that the MG relies mainly on neutrophilic inflammation for its protection and is regulated by type 3 immunity. Advances in knowledge of type 3 immunity in the MG will be necessary to induce immune protection adapted to the physiology of this peculiar organ.

Early asymptomatic prediction of potato soft rot disease using phytohormone-induced volatile biomarkers.

Potatoes (Solanum tuberosum L.) are one of the world's major staple crops. In stored potatoes, Pectobacterium carotovorum subsp carotovorum causes soft rot. As a result of the rapid spread of the disease during post-harvest storage, potato production suffers huge losses. By detecting disease early and controlling it promptly, losses can be minimized. The profile of volatiles of plants can be altered by phytopathogens. Identifying unique volatile organic compounds (VOCs) as biomarkers for early disease detection has attracted considerable research attention. This study compared the VOC profiles of healthy and soft rot inoculated potatoes (cv. "Kufri Pukhraj") over a time course using gas chromatography-mass spectrometry (GC-MS). It was found that there was a differential emission of 27 VOCs between healthy non-inoculated potatoes and soft rot inoculated potatoes. Among 27 VOCs, only five (1-octen-3-ol, 2-methylisoborneol, 3-octanone, 1,4-dimethyladamantane, and 2-methyl-2-bornene) were found exclusively in soft rot inoculated potatoes, suggesting them potential biomarker for non-destructive prediction of soft rot disease in potatoes. Reactive oxygen species (H2O2) and phytohormone methyl-jasmonate (MeJa) levels increased transiently on infection with soft rot. The analysis of the primary metabolism of soft rot infected tubers at three different stages suggests metabolic reprogramming that occurs at the early stage of infection, possibly leading to biomarker volatile emission. Based on these results, it appears that the initial potato-soft rot bacteria interaction initiates metabolic reprogramming mainly through H2O2 and the MeJa signalling pathway. In asymptomatic potatoes, these biomarkers may be promising candidates for non-destructive detection of soft rot at an early stage. These biomarkers can be used to develop an e-nose sensor to predict soft rot in the future.

Enriching the antimicrobial efficacy of iron oxide with bioderived mesoporous carbon

Bacterial infections keep posing a severe hazard to human health. Investigating efficient innovative antibacterial methods is exceedingly crucial. In this instance, coprecipitation is used to produce iron oxide and mesoporouscarbon-iron oxide nanostructures with surfaces that resemble grains for antibacterial treatment. More importantly, surfaces composed of iron oxide with embedded mesoporous carbon exhibit higher bacterial consistency, which is advantageous due to the efficient interaction of bacteria with nanostructures. In antibacterial studies, nanostructures are shown to have an all-encompassing combinatorial antibacterial action against Gram-positive Bacillus cereus (B. cereus), andStaphylococcus aureus (S. aureus), and Gram-negativeEscherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa). In the current study, a simple method to produce antibacterial agents forantibacterial applications is presented. This method involves constructing acombined formulation and morphological structure. In the successful prevention and cure ofbacterial infections, iron oxide with a small quantity of mesoporous carbon has a lot of potential.

Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes

Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.

Graphene oxide and bacteria interactions: what is known and what should we expect?

Graphene oxide (GO) and graphene-based materials (GBMs) have gained over the last two decades considerable attention due to their intrinsic physicochemical properties and their applications. Besides, a lot of concern regarding the potential toxicity of GBMs has emerged. One of the aspects of concern is the interactions between GBMs and different environmental compartments, especially indigenous microbial and, in particular, bacterial communities. Recent research showed that GO and GBMs impacted bacterial pure culture or bacterial communities; therefore, these interactions have to be further studied to better understand and assess the fate of these materials in the environment. Here, we present our opinion and hypotheses related to possible degradation mechanisms of GO that can be used by environmental bacteria. This work is the first attempt to deduce and summarize plausible degradation pathways of GO, from structurally similar recalcitrant and toxic compounds, such as polyaromatic hydrocarbons.

Inactivation pathways of Escherichia coli and Staphylococcus aureus induced by transient spark discharge in liquids

AbstractCold plasma finds considerable interest in biodecontamination. A major issue is to elucidate the pathways of plasma–bacteria interaction. The present work aims at studying inactivation mechanisms for planktonic bacteria Escherichia coli and Staphylococcus aureus induced by cold plasma generated by a transient spark discharge. Changes in bacterial viability, metabolic activity, membrane integrity, intracellular reactive oxygen species level, and cell morphology reveal different patterns of cellular damage of the bacteria. Our results emphasize the importance of cell membrane integrity and maintenance of intracellular redox balatnce to resist plasma treatment. The physicochemical properties of the plasma‐treated liquid (PTL) are monitored. Acidification and accumulation of various reactive species including •OH, H2O2, ONOOH, and NO3− in PTL play crucial roles in bacterial inactivation.

Diversities and interactions of phages and bacteria in deep-sea sediments as revealed by metagenomics.

Phages are found virtually everywhere, even in extreme environments, and are extremely diverse both in their virion structures and in their genomic content. They are thought to shape the taxonomic and functional composition of microbial communities as well as their stability. A number of studies on laboratory culture and viral metagenomic research provide deeper insights into the abundance, diversity, distribution, and interaction with hosts of phages across a wide range of ecosystems. Although most of these studies focus on easily accessible samples, such as soils, lakes, and shallow oceans, little is known about bathypelagic phages. In this study, through analyzing the 16S rRNA sequencing and viral metagenomic sequencing data of 25 samples collected from five different bathypelagic ecosystems, we detected a high diversity of bacteria and phages, particularly in the cold seep and hydrothermal vent ecosystems, which have stable chemical energy. The relative abundance of phages in these ecosystems was higher than in other three abyssal ecosystems. The low phage/host ratios obtained from host prediction were different from shallow ecosystems and indicated the prevalence of prophages, suggesting the complexity of phage-bacteria interactions in abyssal ecosystems. In the correlation analysis, we revealed several phages-bacteria interaction networks of potential ecological relevance. Our study contributes to a better understanding of the interactions between bathypelagic bacteria and their phages.

Leveraging genome-scale metabolic models to understand aerobic methanotrophs.

Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.

Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials

BackgroundAs part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms.ResultsWSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release.ConclusionAll the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.

Extraction and Purification of Outer Membrane Vesicles and Their Associated RNAs.

Outer membrane vesicles (OMVs), produced by Gram negative-bacteria and sRNAs, are key players in cell-to-cell communication and interactions of bacteria with the environment. OMVs act as information carriers and encapsulate various molecules such as proteins, lipids, metabolites, and RNAs. OMVs and sRNAs play a broad range of functions from pathogenesis to stress resistance, to biofilm formation and both mediate interkingdom signaling. Various studies indicate that there is a mechanism of intercellular communication mediated by OMV-derived bacterial RNAs that is conserved among certain bacterial species. Here we describe methods for the extraction and purification of vesicles produced by Gram-negative bacteria, such as Pseudomonas brassicacearum and Escherichia coli, and address methods for the extraction of OMVs-derived sRNA and techniques for the analysis of sRNAs.

Mobile CRISPRi moves through the complexity of bacterial genetics

In this issue of Cell Reports Methods, Rachwalski etal. describe a high-throughput method to screen genetic interactions in bacteria using a conjugative CRISPR interference (CRISPRi) plasmid. The method enables systematic studies of gene essentiality in diverse genomic and environmental contexts and is applicable to Escherichia coli as well as other bacteria.

Quantification of Mixed-Linkage β-Glucan (MLG) in Bacteria.

Prokaryotes are known to produce and secrete a broad range of biopolymers with a high functional and structural heterogeneity, often with critical duties in the bacterial physiology and ecology. Among these, exopolysaccharides (EPS) play relevant roles in the interaction of bacteria with eukaryotic hosts. EPS can help to colonize the host and assist in bacterial survival, making this interaction more robust by facilitating the formation of structured biofilms. In addition, they are often key molecules in the specific recognition mechanisms involved in both beneficial and pathogenic bacteria-host interactions. A novel EPS known as MLG (Mixed-Linkage β-Glucan) was recently discovered in rhizobia, where it participates in bacterial aggregation and biofilm formation and is required for efficient attachment to the roots of their legume host plants. MLG is the first and, so far, the only reported linear Mixed-Linkage β-glucan in bacteria, containing a perfect alternation of β (1→3) and β (1→4) bonds. A phylogenetic study of MLG biosynthetic genes suggests that far from being exclusive of rhizobia, different soil and plant-associated bacteria likely produce MLG, adding this novel polymer to the plethora of surface polysaccharides that help bacteria thrive in the changing environment and to establish successful interactions with their hosts.In this work, a quantification method for MLG is proposed. It relays on the hydrolysis of MLG by a specific enzyme (lichenase), and the subsequent quantification of the released disaccharide (laminaribiose) by the phenol-sulfuric acid method. The protocol has been set up and optimized for its use in 96-well plates, which makes it suitable for high-throughput screening (HTS) approaches. This method stands out by its fast processing, technical simplicity, and capability to handle multiple samples and biological replicates at a time.

ZnO and lactic acid bacteria interaction in yogurt: sensory, surface morphology, and functional group analysis

ZnO and lactic acid bacteria interaction in yogurt: sensory, surface morphology, and functional group analysis

Evaluation of the antibacterial properties of commonly used clays from deposits in central and southern Asia

Abstract One potential solution to the rising threat of antibacterial drug resistance is the application of therapeutic clays to treat wound infections. Clays with antibacterial activity have been identified from a range of sources with their antibacterial properties often attributed to the release of toxic metal ions such as Fe(II) and Al(III). Here, clays from Afghanistan, Azerbaijan and Bangladesh that are utilized for washing and healing purposes were examined. Their antibacterial activities were assessed in suspension and as aqueous leachates against representative Gram-negative, Escherichia coli, and Gram-positive, Bacillus subtilis, bacteria. The majority of the clays conferred no deleterious effect and, in fact, tended to promote bacterial growth, likely as a result of released organic and inorganic nutrients. However, one of the clays, obtained from the Dhaka region of Bangladesh, displayed significant bactericidal activity against E. coli and B. subtilis as a clay suspension but not as an aqueous leachate. Further experiments confirmed that contact between clay and the bacteria was necessary for most of the antibacterial effects. Detailed analysis of bulk and <2 μm clay fraction mineralogy and geochemistry revealed no single defining parameter or mineral component that could be used to easily distinguish natural clays with antibacterial properties from those without. Overall, the results suggest a mechanism of antibacterial action of the Dhaka clay that arises from acidic conditions, likely enabled by the absence of calcite in the bulk clay, metal release, the presence of interstratified chlorite-smectite, and direct clay–bacteria interactions.

Influence of the Complex Bacterial Preparation Azogran on Some Physiological-Biochemical Properties and Productivity of Potato Plants Infected by the Potato Virus X

The problem of increasing the yield of cultivated plants attracts the attention of specialists and prompts scientists to study viral plant diseases as one of the causes of significant crop losses. A virus is an endogenous parasite that, having entered plant cells, uses the functions of cell organoids and biosystems for its reproduction, which leads to plant disease and a decrease in their productivity. One of the promising approaches to reducing viral damage to plants is the use of microbial antiviral preparations. The complex bacterial preparation Azogran, developed at the Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, is based on the interaction of phosphate-mobilizing bacteria Bacillus subtilis IMV B-7023, nitrogen-fixing bacteria Azotobacter vinelandii IMV B-7076, and clay mineral — bentonite. Phosphate-mobilizing bacteria and nitrogen-fixing bacteria significantly improve the growth and development of plants, essentially increasing the yield of agricultural crops. However, the effect of Azogran on the development and yield of potato plants infected with the X-virus has not been sufficiently studied. Taking this into account, the aim of the work was to study the effect of the complex bacterial preparation Azogran on the growth, some physiological and biochemical properties, and productivity of potato plants, uninfected and infected by the potato virus X. Methods. Microbiological (obtaining the bacterial preparation Azogran, used in granular form (0.25 g)), virological (isolation of potato virus X, inoculation of plants with potato virus X), serological (testing for the presence or absence of the virus), biochemical (determination of chlorophylls a, b and carotenoids), spectrophotometric, and statistical analysis. Results. In the conducted experiments, the Azogran was used in granular form in the amount of one and two granules. The effectiveness of the use of the preparation, which stimulates the intensive growth of plants of two varieties of potatoes (early variety Spokusa and medium variety Diva), which leads to an increase in their yield, is shown. The positive effect of Azogran was observed on the development of both infected and non-infected plants. It was found that when two granules of the preparation were applied, the yield of potatoes of the Diva variety increased by 27.02%, and the yield of potatoes of the Spokusa variety under the same conditions increased by 29.46%. A similar effect of Azogran was observed on plants infected with the potato virus X, only to a lesser extent: in the Diva variety, the yield was 16.3% higher compared to the control (control — plants not infected by the virus), and in the Spokusa variety it was higher by 22.59%. When studying the content of chlorophylls a and b and carotenoids in virus-infected potato plants, it was established that the content of chlorophylls at different stages of virus infection was different, but the content of chlorophylls and carotenoids was higher in plants bacterized with Azogran. Conclusions. The complex bacterial preparation Azogran has a positive effect on the development of uninfected and infected plants, reducing the harmfulness of viral infections and contributing to the increase in potato productivity. Azogran can be successfully used in crop production to increase the quality and quantity of crop yields.

Inconsistent dilution: experimental but not field evidence for a dilution effect in Daphnia-bacteria interactions.

The dilution effect hypothesis, which suggests greater host biodiversity can reduce infectious disease transmission, occurs in many systems but is not universal. Most studies only investigate the dilution of a single parasite in a community, but many host communities have multiple parasites circulating. We studied a zooplankton host community with prior support for a dilution effect in laboratory- and field-based studies of a fungal parasite, Metschnikowia bicuspidata. We used paired experiments and field studies to ask whether dilution also occurred for a bacterial parasite, Pasteuria ramosa. We hypothesized that the similarities between the parasites might mean the dilution pattern seen in Metschnikowia would also be seen in Pasteuria. However, because Daphnia-Pasteuria interactions have strong host-parasite genotype specificity, dilution may be less likely if diluter host genotypes vary in their capacity to dilute Pasteuria. In a lab experiment, Pasteuria prevalence in susceptible Daphnia dentifera was reduced strongly by higher densities of D. pulicaria and marginally by higher densities of D. retrocurva. In a second experiment, different D. pulicaria genotypes had a similar capacity to dilute both Metschnikowia and Pasteuria, suggesting that Pasteuria's strong host-parasite genotype specificity should not prevent dilution. However, we found no evidence of an impact of the dilution effect on the size of Pasteuria epidemics in D. dentifera in Midwestern U.S. lakes. Our finding that a second parasite infecting the same host community does not show a similar dilution effect in the field suggests the impact of biodiversity can differ even among parasites in the same host community.

Dynamic Interactions between Diarrhoeagenic Enteroaggregative Escherichia coli and Presumptive Probiotic Bacteria: Implications for Gastrointestinal Health.

This study delves into the temporal dynamics of bacterial interactions in the gastrointestinal tract, focusing on how probiotic strains and pathogenic bacteria influence each other and human health. This research explores adhesion, competitive exclusion, displacement, and inhibition of selected diarrhoeagenic Escherichia coli (D-EAEC) and potential probiotic strains under various conditions. Key findings reveal that adhesion is time-dependent, with both D-EAEC K2 and probiotic L. plantarum FS2 showing increased adhesion over time. Surprisingly, L. plantarum FS2 outperformed D-EAEC K2 in adhesion and exhibited competitive exclusion and displacement, with inhibition of adhesion surpassing competitive exclusion. This highlights probiotics' potential to slow pathogen attachment when not in competition. Pre-infecting with L. plantarum FS2 before pathogenic infection effectively inhibited adhesion, indicating probiotics' ability to prevent pathogen attachment. Additionally, adhesion correlated strongly with interleukin-8 (IL-8) secretion, linking it to the host's inflammatory response. Conversely, IL-8 secretion negatively correlated with trans-epithelial electrical resistance (TEER), suggesting a connection between tight junction disruption and increased inflammation. These insights offer valuable knowledge about the temporal dynamics of gut bacteria interactions and highlight probiotics' potential in competitive exclusion and inhibiting pathogenic bacteria, contributing to strategies for maintaining gastrointestinal health and preventing infections.

Comparing Vegetation and Substrate Performances on Nutrient Removal and Biomass Establishment Using a Natural Swimming Pool Experiment

Natural swimming pools (NSPs) rely on the interaction of bog vegetation, bacteria, and substrate to maintain water quality. Nitrogen (N) and phosphorus (P) levels in NSPs are critical because of their involvement in eutrophication. We conducted a 15-week greenhouse study to address the significant literature gap regarding nutrient removal capabilities of substrates and vegetation in the low-nutrient environment of NSPs. We used mass balance analyses to compare the performances of four substrates [river gravel (control), recycled glass, expanded clay, expanded shale] and two plant species [blue flag iris (Iris versicolor) and lizard’s tail (Saururus cernuus)] under two flow conditions: free water surface and subsurface flow. At the end of the experiment, except for the recycled glass group, all other substrate groups reduced water nitrate (NO3) levels to less than 30 mg⋅L−1, the standard of the 2011 Forschungsgesellschaft Landschaftsentwicklung Landschaftsbau (FLL) guidelines. However, only the expanded clay group closely approached the P standard (≤0.01 mg⋅L−1). Expanded clay and expanded shale demonstrated potential as substrates for NSP bogs. The final aboveground biomass dry weight was strongly negatively correlated with the final NO3 and P water concentrations. However, direct plant uptake proved insufficient to remove all nutrient inputs, especially for P. Except for the recycled glass group (34%), a significant portion of N (79%–90%) from total N added was removed by aboveground biomass. However, P uptake by biomass was substantially lower (18%–37%). With acceptable vigor and biomass accumulation, blue flag iris may be a suitable species for vegetated NSPs, whereas lizard’s tail is not because of uncertain establishment. Compared with controlling N, managing P for FLL standards in NSPs will be more challenging. Our work begins to fill the essential gap in the NSP literature regarding nutrient removal capabilities of substrates and vegetation. Future work should continue to study alternative substrates and plant species for P removal, particularly in field conditions and over longer periods.

Exploring the impact of oral bacteria remnants on stem cells from the Apical papilla: mineralization potential and inflammatory response.

Bacterial persistence is considered one of the main causal factors for regenerative endodontic treatment (RET) failure in immature permanent teeth. This interference is claimed to be caused by the interaction of bacteria that reside in the root canal with the stem cells that are one of the essentials for RET. The aim of the study was to investigate whether prolonged exposure of stem cells from the apical papilla (SCAP) to bacterial remnants of Fusobacterium nucleatum, Actinomyces gerensceriae, Slackia exigua, Enterococcus faecalis, Peptostreptococcaceae yurii, commonly found in infected traumatized root canals, and the probiotic bacteria Lactobacillus gasseri and Limosilactobacillus reuteri, can alter SCAP's inflammatory response and mineralization potential. To assess the effect of bacterial remnants on SCAP, we used UV-C-inactivated bacteria (as cell wall-associated virulence factors) and bacterial DNA. Histochemical staining using Osteoimage Mineralization Assay and Alizarin Red analysis was performed to study SCAP mineralization, while inflammatory and osteo/odontogenic-related responses of SCAPs were assessed with Multiplex ELISA. We showed that mineralization promotion was greater with UV C-inactivated bacteria compared to bacterial DNA. Immunofluorescence analysis detected that the early mineralization marker alkaline phosphatase (ALP) was increased by the level of E. coli lipopolysaccharide (LPS) positive control in the case of UV-C-inactivated bacteria; meanwhile, DNA treatment decreased the level of ALP compared to the positive control. SCAP's secretome assessed with Multiplex ELISA showed the upregulation of pro-inflammatory factors IL-6, IL-8, GM-CSF, IL-1b, neurotrophic factor BDNF, and angiogenic factor VEGF, induced by UV-C-killed bacteria. The results suggest that long term stimulation (for 21 days) of SCAP with UV-C-inactivated bacteria stimulate their mineralization and inflammatory response, while DNA influence has no such effect, which opens up new ideas about the nature of RET failure.