Microbial Strains Research Articles

Efficiency of freeze- and spray-dried microbial preparation as active dried starter culture in kombucha fermentation.

Kombucha is a widely consumed fermented beverage produced by fermenting sweet tea with a symbiotic culture of bacteria and yeast (SCOBY). The dynamic nature of microbial communities in SCOBY may pose challenges to production scale-up due to unpredictable variations in microbial composition. Using identified starter strains is a novel strategy to control microorganism composition, thereby ensuring uniform fermentation quality across diverse batches. However, challenges persist in the cultivation and maintenance of these microbial strains. This study examined the potential of microencapsulated kombucha fermentation starter cultures, specifically Komagataeibacter saccharivorans, Levilactobacillus brevis and Saccharomyces cerevisiae, through spray-drying and freeze-drying. Maltodextrin and gum arabic-maltodextrin were employed as carrier agents. Our results revealed that both spray-dried and freeze-dried samples adhered to physicochemical criteria, with low moisture content (2.18-7.75%) and relatively high solubility (65.75-87.03%) which are appropriate for food application. Freeze-drying demonstrated greater effectiveness in preserving bacterial strain viability (88.30-90.21%) compared to spray drying (74.92-78.66%). Additionally, the freeze-dried starter strains demonstrated similar efficacy in facilitating kombucha fermentation, compared to the SCOBY group. The observations included pH reduction, acetic acid production, α-amylase inhibition and elevated total polyphenol and flavonoid content. Moreover, the biological activity, including antioxidant potential and in vitro tyrosinase inhibition activity, was enhanced in the same pattern. The freeze-dried strains exhibited consistent kombucha fermentation capabilities over a three-month preservation, regardless of storage temperature at 30 or 4 °C. These findings highlight the suitability of freeze-dried starter cultures for kombucha production, enable microbial composition control, mitigate contamination risks and ensure consistent product quality. © 2024 Society of Chemical Industry.

Bifidobacterium breve modulates lactic acid to curtail Escherichia coli expansion and alleviate inflammatory bowel disease

Inhibition of the abnormal proliferation of Escherichia coli is crucial for alleviating inflammatory bowel disease. Due to the complexity of the gut microbiota, specifically targeting and inhibiting particular microbes is a challenging task. One approach involves screening for probiotics that antagonize E. coli; however, this process often requires extensive in vitro experiments using a vast pool of probiotics. In this study, we employed a genome-scale metabolic prediction model to predict the interactions between 803 strains of microbes and E. coli. The results indicated that Bifidobacterium breve and Bifidobacterium animalis exhibited the most potent inhibitory effects. In vitro antibacterial assays and mouse experiments validated the inhibitory efficacy of B. breve CCFM1369. Additionally, B. breve CCFM1369 demonstrated the ability to inhibit key gene Ldha and HIF-2α and reduce the luminal lactate concentration, thereby diminishing the colonization capacity of E. coli. These findings support the potential application of B. breve in the alleviation of colitis.

ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction

Adenosine-5’-triphosphate (ATP), the primary energy currency in cellular processes, drives metabolic activities and biosynthesis. Despite its importance, understanding intracellular ATP dynamics’ impact on bioproduction and exploiting it for enhanced bioproduction remains largely unexplored. Here, we harness an ATP biosensor to dissect ATP dynamics across different growth phases and carbon sources in multiple microbial strains. We find transient ATP accumulations during the transition from exponential to stationary growth phases in various conditions, coinciding with fatty acid (FA) and polyhydroxyalkanoate (PHA) production in Escherichia coli and Pseudomonas putida, respectively. We identify carbon sources (acetate for E. coli, oleate for P. putida) that elevate steady-state ATP levels and boost FA and PHA production. Moreover, we employ ATP dynamics as a diagnostic tool to assess metabolic burden, revealing bottlenecks that limit limonene bioproduction. Our results not only elucidate the relationship between ATP dynamics and bioproduction but also showcase its value in enhancing bioproduction in various microbial species.

Combined treatment of rice bran by solid-state fermentation and extrusion: Effect of processing sequence and microbial strains

Solid-state fermentation (SSF) and extrusion are effective methods to improve the nutritional and sensory quality of rice bran. The effect of the processing sequence of SSF and extrusion and microbial strains on the quality of rice bran was studied. The results showed that the first SSF followed by extrusion increased the contents of phenolic, flavonoid and γ-oryzanol, but the color changed to brown. The first extrusion followed by SSF caused damage to bioactive components and antioxidant activity, but significantly increased the content of arabinoxylans. The difference between the two processing sequences may be related to the process time and the effect of substrate on microbial induction. Aspergillus oryzae and Neurospora sitophila were suitable for increasing the bioactive components of rice bran, while Lactiplantibacillus plantarum was suitable for increasing water-extractable arabinoxylan content. Different processing sequences and microbial strains have their advantages, and these results can provide reference for rice bran processing.

Identification and characterization of microorganisms isolated from noncompliant or atypical dairy products in Canada

Despite good manufacturing practices and rigorous cleaning and sanitizing procedures established in dairy processing plants, microbiological contamination remains the main cause of products being non-compliant and/or atypical and hence not fit for human consumption. The objective of this study was to isolate, identify and characterize bacteria, yeasts and molds associated with substandard dairy products in Canada and to create a collection of reference isolates. In addition to conventional microbiological characterization, each isolate was tested for biofilm-forming ability and susceptibility to heat, antimicrobial agents, and common industrial disinfectants. Among the 105 microbial strains isolated from pasteurized milk, cream, and cheese samples, 24 bacterial isolates, belonging mainly to the genus Pseudomonas, were shown to be moderate or strong biofilm producers in 96-well plates and highly resistant to peracetic acid (100 ppm, 5 min contact time) and sodium hypochlorite (70 ppm, 5 min contact time). In addition, 56 bacterial isolates, including Acinetobacter baumannii, Enterobacter bugandensis, Klebsiella pneumoniae and Pseudomonas spp., were found resistant to ampicillin, fosfomycin and/or ceftriaxone, while 14 others, such as Bacillus spp. and Macrococcus spp., withstood a heat treatment equivalent to low-temperature long-time pasteurization (63°C for 30 min). This descriptive study provides new information on potential problematic microorganisms in dairies and will guide the development of novel control strategies intended to prevent and reduce microbiological contamination and the associated economic losses.

Eco-evolutionary dynamics of cooperative antimicrobial resistance in a population of fluctuating volume and size

Antimicrobial resistance to drugs (AMR), a global threat to human and animal health, is often regarded as resulting from cooperative behaviour. Moreover, microbes generally evolve in volatile environments that, together with demographic fluctuations (birth and death events), drastically alter population size and strain survival. Motivated by the need to better understand the evolution of AMR, we study a population of time-varying size consisting of two competing strains, one drug-resistant and one drug-sensitive, subject to demographic and environmental variability. This is modelled by a binary carrying capacity randomly switching between mild and harsh environmental conditions, and driving the fluctuating volume (total amount of nutrients and antimicrobials at fixed concentration), and thus the size of the community (number of resistant and sensitive cells). We assume that AMR is a shared public good when the concentration of resistant cells exceeds a fixed concentration cooperation threshold, above which the sensitive strain has a growth advantage, whereas resistant cells dominate below it. Using computational means, and devising an analytical treatment (built on suitable quenched and annealed averaging procedures), we fully characterise the influence of fluctuations on the eco-evolutionary dynamics of AMR, and notably obtain specific strain fixation and long-lasting coexistence probabilities as a function of the environmental variation rate and cooperation threshold. We find that microbial strains tend to coexistence, but demographic fluctuations eventually lead to the extinction of resistant or sensitive cells for small or large values of the concentration cooperation threshold, respectively. This also holds for dynamic environments, whose specific properties determine the extinction timescale.

Linking preterm infant gut microbiota to nasograstric enteral feeding tubes: exploring potential interactions and microbial strain transmission.

Preterm birth is a growing problem worldwide. Staying at a neonatal intensive care unit (NICU) after birth is critical for the survival of preterm infants whose feeding often requires the use of nasogastric enteral feeding tubes (NEFT). These can be colonized by hospital-associated pathobionts that can access the gut of the preterm infants through this route. Since the gut microbiota is the most impactful factor on maturation of the immune system, any disturbance in this may condition their health. Therefore, the aim of this study is to assess the impact of NEFT-associated microbial communities on the establishment of the gut microbiota in preterm infants. A metataxonomic analysis of fecal and NEFT-related samples obtained during the first 2 weeks of life of preterm infants was performed. The potential sharing of strains isolated from the same set of samples of bacterial species involved in NICU's outbreaks, was assessed by Random Amplification of Polymorphic DNA (RAPD) genotyping. In the samples taken 48 h after birth (NEFT-1 and Me/F1), Staphylococcus spp. was the most abundant genera (62% and 14%, respectively) and it was latter displaced to 5.5% and 0.45%, respectively by Enterobacteriaceae. Significant differences in beta diversity were detected in NEFT and fecal samples taken at day 17 after birth (NEFT-3 and F3) (p = 0.003 and p = 0.024, respectively). Significant positive correlations were found between the most relevant genera detected in NEFT-3 and F3. 28% of the patients shared at least one RAPD-PCR profile in fecal and NEFT samples and 11% of the total profiles were found at least once simultaneously in NEFT and fecal samples from the same patient. The results indicate a parallel bacterial colonization of the gut of preterm neonates and the NEFTs used for feeding, potentially involving strain sharing between these niches. Moreover, the same bacterial RAPD profiles were found in neonates hospitalized in different boxes, suggesting a microbial transference within the NICU environment. This study may assist clinical staff in implementing best practices to mitigate the spread of pathogens that could threaten the health of preterm infants.

Detection and Characterization of Virulent Pseudomonas aeruginosa genes in Fresh Fish at Al-Diwaniya City Market, Iraq.

Fish meat is more susceptible to pathogen contamination than other protein-rich foodstuffs due to its high deterioration. Pseudomonas aeruginosa is considered one of the most common microbial strains responsible for the deterioration of fish and seafood products. the study's goals are to detecting virulence variables Pseudomonas aeruginosa and estimating the level of contamination in a fish sample, In this research, 120 fresh fish samples, gathered from a the local Diwaniyah city market local fish meat sample. including (60 marine fish and 60 common carp (Cyprinus carpio). The isolates were subjected to numerous biochemical, microbiological, and molecular analyses, and the results showed that about 26 samples were contaminated with Pseudomonas spp. performed on 21.6% of the total sample. Polymerase chain reaction (PCR) was used to amplify 539 bp, 511 bp, and 495 bp, for 16S DNA, Tox A, and Tox S respectively. A total of 21 Tox A genes were identified in 26 P. aeruginosa isolates, whereas the ToxS gene was detected in 17 of the same isolates. According to the results Pseudomonas aeruginosa isolated from fish samples contains multiple virulence factor genes, indicating high pathogenicity, which may affect consumer health because these variants exhibit the capability to increase the pathogenesis of the microorganisms with the severity of the infection and cause economic losses

Unlocking nature's sweet secret for citric acid production from wood sugars: Evaluation of microbial strains and environmental impacts

This study investigates a novel approach by utilizing wood-derived sugars as a substrate for microbial citric acid (CA) production. Additionally, it examines the environmental implications through an ex-ante life cycle assessment (LCA). Various microbial strains including six yeast strains from the Yarrowia genus, three filamentous fungi strains from the Aspergillus genus, and eight bacterial strains were evaluated for their potential in CA production. The investigation primarily focused on optimizing citric acid production by considering various factors such as substrate concentrations, nitrogen levels, alcohols, surfactants, and the potential of non-commercial strains. The study yielded promising results, with the highest CA yields recorded as follows: 5.7 g/L from bacterial fermentation, 36.8 g/L from yeast fermentation, and 67.7 g/L from fungi fermentation. Furthermore, by applying an ex-ante LCA, the study assessed the environmental impact of citric acid production. Results indicated a significant reduction in environmental footprint when scaled up, with emissions decreasing from 235 to 585.8 kgCO2eq/kg at the laboratory scale to 4–6 kgCO2eq/kg at the larger scale.

Evaluation of Salophen-Based Immobilized Copper Nanoparticles Biosynthesized Using Curcuma Longa Extract: Physicochemical Characterization and Biological Study

The treatment of infectious diseases has become more difficult today than in the past, as a result of the increasing resistance of pathogenic bacterial and fungal strains to antibiotics and antifungals. As a solution, it is necessary to design new antimicrobial agents to deal with these strains. Schiff bases and their metallic derivatives, especially silver and copper complexes, have a prominent place in the pharmaceutical industry due to their excellent inhibitory potential against microbial strains. In order to combine these inhibitory effects in a single compound, a novel Cu@Ag-salophen nanocomposite was prepared by immobilizing of biochemical synthesized copper nanoparticles from methanolic extract of Curcuma longa on an Ag(I) salophen Schiff base complex. The physicochemical characterization of prepared nanocomposite was attained by FTIR, UV/Vis, TEM, FESEM, EDAX, ICP-AES, and XRD analyses. All the synthesized compounds, including Schiff base ligand, Ag complex, Cu nanoparticles, and the Cu@Ag-salophen nanocomposite, were assessed for their potential activities on DPPH free radicals and 8 different pathogenic microorganisms. The IC50 values in the range of 4.02–71.49 μg/ml were assessed in DPPH scavinging studies, indicating their potential to be utilized as potent antioxidant agents to treat oxidative stress-related diseases. Among the tested compounds, the Schiff base ligand exhibited excellent antioxidant effects. Regarding the antimicrobial activities, the Schiff base ligand showed a wide spectrum of antimicrobial effects, with MIC, MBC, and MFC values ranging from 256 to 4096 μg/ml. However, the Ag complex alone did not exhibit any inhibitory effect against the tested microbial strains. Interestingly, when the copper nanoparticles were combined with it in the form of the Cu@Ag-salophen nanocomposite, the resulting material was able to prevent the growth of 5 out of 8 tested strains. Synergistic effects were observed with nanocomposite against P. aeruginosa, S. epidermidis, and A. fumigatus strains. These findings suggest that the functionalization of the ligand and the incorporation of additional nanoparticles could further improve the antimicrobial efficacy of the Cu@Ag-salophen nanocomposite, converting it into a more efficient antimicrobial agent.

Microbial Consortia: Promising Tool as Plant Bioinoculants for Agricultural Sustainability.

In the present scenario, growing population demands more food, resulting in the need for sustainable agriculture. Numerous approaches are explored in response to dangers and obstacles to sustainable agriculture. A viable approach is to be exploiting microbial consortium, which generate diverse biostimulants with growth-promoting characteristics for plants. These bioinoculants play an indispensable role in optimizing nutrient uptake efficiency mitigating environmental stress. Plant productivity is mostly determined by the microbial associations that exist at the rhizospheric region of plants. The engineered consortium with multifunctional attributes can be effectively employed to improve crop growth efficacy. A number of approaches have been employed to identify the efficient consortia for plant growth and enhanced crop productivity. Various plant growth-promoting (PGP) microbes with host growth-supporting characteristics were investigated to see if they might work cohesively and provide a cumulative effect for improved growth and crop yield. The effective microbial consortia should be assessed using compatibility tests, pot experimentation techniques, generation time, a novel and quick plant bioassay, and sensitivity to external stimuli (temperature, pH). The mixture of two or more microbial strains found in the root microbiome stimulates plant growth and development. The present review deals with mechanism, formulation, inoculation process, commercialization, and applications of microbial consortia as plant bioinoculants for agricultural sustainability.

Nanofibers Embedded with Nanoparticles as Carriers for the Controlled Release of Anticancer Drug: Promoting the Apoptosis of Breast Cancer Cell Line and Growth Inhibition of Microbial Strains.

The polymeric nanofiber mats were produced from polylactic acid, methylcellulose, and polyethylene glycol with 5-fluorouracil (5Fu) drug and iron oxide (Fe3O4) nanoparticles. Spectral and crystallographic studies clearly elucidated the ionic interactions, structure and nature of the mats. Fe3O4 nanoparticles <10 nm in size, along with methyl cellulose and polyethylene glycol, have significantly reduced the size of nanofiber mats. The mechanical properties for the mats was found to be challenging; however, surface wettability, swelling capacity, and drug encapsulation efficiency results were promising. A controlled drug release pattern was observed from in vitro drug release study, zero-order kinetics, and a Higuchi model. Nanofiber mats showed higher anticancer activity (78%) against MDA-MB 231 cancer cells, which reveals that a small amount of 5Fu drug (15.86%) with high levels of O2••, H2O2, and OH• radicals generated from Fe3O4 have catalyzed the Fenton's reaction to eradicate the cancer cells, in a shorter span of 24 h, itself. In addition, the apoptosis assay by dual AO/PI staining method clearly exhibited the apoptotic cancer cells by fluorescence microscopy. Incorporation of Fe3O4 nanoparticles enhanced the anticancer activity of the mats, compared to the commercially available standard 5Fu drug. Nanofiber mats significantly controlled the growth of selected pathogenic microbial strains by the action of the 5Fu drug and Fe3+ ions. The degradation of mats was investigated by an in vitro mass loss study for a period of 360 days. In a nutshell, promising nanofiber mats were produced as targeted drug delivery devices for chemotherapy.

Evaluation of strain variability of food microorganisms in response to decontamination by pulsed electric fields and thermal treatments

The effect of pulsed electric fields (PEF) and thermal treatments on the inactivation of the population of 40 strains of 4 model microorganisms (Escherichia coli, Listeria monocytogenes, Lactiplantibacillus plantarum, Saccharomyces cerevisiae) were investigated. Microbial samples of McIlvaine buffer pH 7.0 were subjected to pulses with electric field strength 20 kV/cm and total specific energies (88, 136, and 184 kJ/kg). Depending on the species and strain, microorganisms exhibited various resistances. PEF microbial resistance and strain variability data were correlated to the total specific energy used. E. coli strains showed statistical log10 inactivation differences under the 88 and 136 kJ/kg but not under the 184 kJ/kg PEF treatment. In contrast, L. monocytogenes strains showed statistical log10 inactivation differences only under the 184 kJ/kg treatment. L. monocytogenes L6 strain was identified as the most resistant strain at PEF treatment (184 kJ/kg). This result was in accordance with the resistance under thermal treatment (62.8 °C, 30 min). Industrial relevanceThe identification of target microorganisms related to their resistance in one or more technologies can help at establishing treatment conditions that reassure food safety. Data obtained in this research show that species and strain behaviours vary and are dependent on the technology and the applied treatment conditions. Thus, the resistance exhibited by microorganisms of public health importance may be dependent on the used technology and the applied treatment.

Alternanthera sessilis derived fluorescent carbon dots and their sensing and biological applications

Herein, the green synthesis of novel fluorescent carbon dots (CDs) from the Alternanthera sessilis plant by a simple, eco-friendly, and facile hydrothermal method was reported. The developed CDs exhibit green fluorescence and have a size of 5.25 nm. Various analyses reveal outstanding features, including high quantum yield, good photostability, and excellent hydrophilicity of the as-synthesized CDs. It was used as a dual-mode probe for the sensing of Cu2+ ions and Zn2+ ions in an aqueous system. Efficient sensing of Cu2+ ions takes place by static quenching of fluorescence with a detection limit of 28.03 nM. CDs-coated glassy carbon electrode was used to perform the electrochemical detection of Zn2+ ions in an aqueous system with high selectivity and sensitivity, and the LOD value was found to be 2.28 nM. The LC50 value of the fabricated CDs against the human breast cancer cell line is 89.85 µL/mL. Also, the antimicrobial efficacy of the CDs was examined against Escherichia coli, Staphylococcus Aureus, and Aspergillus niger, and the results indicate the high toxicity of the CDs against all tested microbial strains.

Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential

Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.

A Comprehensive Methodology for Microbial Strain Typing Using Fourier-Transform Infrared Spectroscopy.

Timely and accurate detection and characterization of microbial threats is crucial for effective infection and outbreak management. Additionally, in food production, rapid microbe identification is indispensable for maintaining quality control and hygiene standards. Current methods for typing microbial strains often rely on labor-intensive, time-consuming, and expensive DNA- and sera-serotyping techniques, limiting their applicability in rapid-response scenarios. In this context, the IR Biotyper®, utilizing Fourier-transform infrared (FTIR) spectroscopy, offers a novel approach, providing specific spectra for fast strain typing within 3 h. This methodology article serves as a comprehensive resource for researchers and technicians aiming to utilize FTIR spectroscopy for microbial strain typing. It encompasses detailed guidelines on sample preparation, data acquisition, and analysis techniques, ensuring the generation of reliable and reproducible results. We highlight the IR Biotyper®'s rapid and accurate discrimination capabilities, showcasing its potential for real-time pathogen monitoring and source-tracking to enhance public health and food safety. We propose its integration as an early screening method, followed by more detailed analysis with whole-genome sequencing, to optimize detection accuracy and response efficiency in microbial surveillance systems.

Harnessing Green Helpers: Nitrogen-Fixing Bacteria and Other Beneficial Microorganisms in Plant–Microbe Interactions for Sustainable Agriculture

The health of soil is paramount for sustaining life, as it hosts diverse communities of microorganisms that interact with plants, influencing their growth, health, and resilience. Beneficial microorganisms, including fungi and bacteria, form symbiotic relationships with plants, providing essential nutrients, promoting growth, and enhancing stress tolerance. These microorganisms, such as mycorrhizal fungi and plant growth-promoting bacteria, play crucial roles in nutrient cycling, soil health, and plant productivity. Additionally, they help lessen reliance on chemical fertilizers, thereby mitigating the environmental risks associated with their use. Advances in agricultural practices harness the potential of these beneficial microorganisms to improve crop yields while minimizing the environmental impact. However, challenges such as competition with indigenous microbial strains and environmental factors limit the universal utilization of microbial inoculants. Despite these challenges, understanding and leveraging the interactions between plants and beneficial microorganisms hold promise for sustainable agriculture and enhanced food security.

Co-evolution of vaginal microbiome and cervical cancer

BackgroundExploration of adaptive evolutionary changes at the genetic level in vaginal microbial communities during different stages of cervical cancer remains limited. This study aimed to elucidate the mutational profile of the vaginal microbiota throughout the progression of cervical disease and subsequently establish diagnostic models.MethodsThis study utilized a metagenomic dataset consisting of 151 subjects classified into four categories: invasive cervical cancer (CC) (n = 42), cervical intraepithelial neoplasia (CIN) (n = 43), HPV-infected (HPVi) patients without cervical lesions (n = 34), and healthy controls (n = 32). The analysis focused on changes in microbiome abundance and extracted information on genetic variation. Consequently, comprehensive multimodal microbial signatures associated with CC, encompassing taxonomic alterations, mutation signatures, and enriched metabolic functional pathways, were identified. Diagnostic models for predicting CC were established considering gene characteristics based on single nucleotide variants (SNVs).ResultsIn this study, we screened and analyzed the abundances of 18 key microbial strains during CC progression. Additionally, 71,6358 non-redundant mutations were identified, predominantly consisting of SNVs that were further annotated into 25,773 genes. Altered abundances of SNVs and mutation types were observed across the four groups. Specifically, there were 9847 SNVs in the HPV-infected group and 14,892 in the CC group. Furthermore, two distinct mutation signatures corresponding to the benign and malignant groups were identified. The enriched metabolic pathways showed limited similarity with only two overlapping pathways among the four groups. HPVi patients exhibited active nucleotide biosynthesis, whereas patients with CC demonstrated a significantly higher abundance of signaling and cellular-associated protein families. In contrast, healthy controls showed a distinct enrichment in sugar metabolism. Moreover, biomarkers based on microbial SNV abundance displayed stronger diagnostic capability (cc.AUC = 0.87) than the species-level biomarkers (cc.AUC = 0.78). Ultimately, the integration of multimodal biomarkers demonstrated optimal performance for accurately identifying different cervical statuses (cc.AUC = 0.86), with an acceptable performance (AUC = 0.79) in the external testing set.ConclusionsThe vaginal microbiome exhibits specific SNV evolution in conjunction with the progression of CC, and serves as a specific biomarker for distinguishing between different statuses of cervical disease.

In vitro Assessment of the Antimicrobial Properties of Orthodontic Bonding Materials.

Orthodontic bonding materials are extensively used in dentistry, but their antimicrobial properties are of growing concern due to the risk of biofilm formation and associated complications. Understanding the antimicrobial efficacy of these materials is crucial for maintaining oral health during orthodontic treatment. In this in vitro study, we evaluated the antimicrobial properties of various orthodontic bonding materials against common oral pathogens. Samples of bonding materials were prepared and exposed to microbial strains including Streptococcus mutans, Porphyromonas gingivalis, and Candida albicans. Antimicrobial activity was assessed using agar diffusion assays and microbial viability assays. The tested orthodontic bonding materials exhibited varying degrees of antimicrobial activity. Material A showed a zone of inhibition of 12 mm against S. mutans, 8 mm against P. gingivalis, and 6 mm against C. albicans. Material B exhibited slightly higher antimicrobial activity with inhibition zones of 14 mm, 10 mm, and 8 mm against S. mutans, P. gingivalis, and C. albicans, respectively. Material C displayed the highest antimicrobial activity, with inhibition zones of 16 mm against S. mutans, 12 mm against P. gingivalis, and 10 mm against C. albicans. Microbial viability assays confirmed the efficacy of these materials in reducing microbial growth. Our findings demonstrate that orthodontic bonding materials possess varying degrees of antimicrobial properties. Material C exhibited the highest efficacy against the tested microbial strains. Incorporating antimicrobial agents into orthodontic bonding materials may contribute to the prevention of oral infections during orthodontic treatment.

Simultaneous design of fermentation and microbe

AbstractConstraint‐based optimization of microbial strains and model‐based bioprocess design have been used extensively to enhance yields in biotechnological processes. However, strain and process optimization are usually carried out in sequential steps, causing underperformance of the biotechnological process when scaling up to industrial fermentation conditions. Herein, we propose the optimization formulation SimulKnock that combines the optimization of a fermentation process with metabolic network design in a bilevel optimization program. The upper level maximizes space‐time yield and includes mass balances of a continuous fermentation, while the lower level is based on flux balance analysis. SimulKnock predicts optimal gene deletions and finds the optimal trade‐off between growth rate and product yield. Results of a case study with a genome‐scale metabolic model of Escherichia coli indicate higher space‐time yields than a sequential approach using OptKnock for almost all target products considered. By leveraging SimulKnock, we reduce the gap between strain and process optimization.