Microbial Samples Research Articles

A COVID-19 Outbreak in a Large Meat-Processing Plant in England: Transmission Risk Factors and Controls.

The meat-processing industry had frequent COVID-19 outbreaks reported worldwide. In May 2021, a large meat-processing plant in the UK had an outbreak affecting 4.1% (63/1541) of workers. A rapid on-site investigation was conducted to understand the virus transmission risk factors and control measures. This included observational assessments of work activities, control measures, real-time environmental measurements and surface microbial sampling. The production night-shift attack rate (11.6%, 44/380) was nearly five times higher than the production day-shift (2.4%, 9/380). Shared work transport was provided to 150 staff per dayshift and 104 per nightshift. Production areas were noisy (≥80 dB(A)) and physical distancing was difficult to maintain. Face visors were mandatory, additional face coverings were required for some activities but not always worn. The refrigeration system continuously recirculated chilled air. In some areas, the mean temperature was as low as 4.5 °C and mean relative humidity (RH) was as high as 96%. The adequacy of ventilation in the production areas could not be assessed reliably using CO2, due to the use of CO2 in the packaging process. While there were challenges in the production areas, the observed COVID-19 control measures were generally implemented well in the non-production areas. Sixty surface samples from all areas were tested for SARS-CoV-2 RNA and 11.7% were positive. Multi-layered measures, informed by a workplace specific risk assessment, are required to prevent and control workplace outbreaks of COVID-19 or other similar respiratory infectious diseases.

Built environment microbiomes transition from outdoor to human-associated communities after construction and commissioning

The microbiota of the built environment is linked to usage, materials and, perhaps most importantly, human health. Many studies have attempted to identify ways of modulating microbial communities within built environments to promote health. None have explored how these complex communities assemble initially, following construction of new built environments. This study used high-throughput targeted sequencing approaches to explore bacterial community acquisition and development throughout the construction of a new build. Microbial sampling spanned from site identification, through the construction process to commissioning and use. Following commissioning of the building, bacterial richness and diversity were significantly reduced (P < 0.001) and community structure was altered (R2 = 0.14; P = 0.001). Greater longitudinal community stability was observed in outdoor environments than indoor environments. Community flux in indoor environments was associated with human interventions driving environmental selection, which increased 10.4% in indoor environments following commissioning. Increased environmental selection coincided with a 12% reduction in outdoor community influence on indoor microbiomes (P = 2.00 × 10–15). Indoor communities became significantly enriched with human associated genera including Escherichia, Pseudomonas, and Klebsiella spp. These data represent the first to characterize the initial assembly of bacterial communities in built environments and will inform future studies aiming to modulate built environment microbiota.

Fish Waste: A Potential Source of Biodiesel

The continuously increasing energy requirement on one hand and the incessant depletion of non-renewable fossil fuels on the other urge us to focus on alternative renewable energy sources such as biofuels. Biofuels including biodiesel, bioethanol, biobutanol, biohydrogen, etc., are generated from different biological sources, and their waste which stands as the best alternative in the present scenario. Specifically, the utilization of biological wastes as raw materials for the production of biofuels is considered as best waste management practice. To date, most of the biodiesel production research has been carried out with plant, algal, and microbial samples, or their waste. It is a well-known fact that diesel can also be produced from specific oily fish and their waste using different methods. In addition, fish waste constitutes a major quantity compared to other food waste which is a serious concern. Furthermore, the disposal of fish waste shows an impact on both the environment and the economy. Hence, the development of protocols for the efficient production of biodiesel from fish waste is the ultimate goal. However, insufficient knowledge and less effort in the conversion of fish waste to biodiesel impede the achievement of this goal. Therefore, this review intends to summarize the mechanism of biodiesel production from fish waste. Also, various physico-chemical factors involved in biodiesel production from fish waste were discussed. In addition, research on biodiesel generation from various fish wastes or waste fish oil was also emphasized in detail, which will be helpful for commercial practice. Overall, this information will be useful for improvement in biodiesel production from fish waste.

Molecular Surveillance of Natural Focal Diseases Causative Agents in the Stavropol Territory in 2016–2021

Relevance. Molecular surveillance, aimed at obtaining up-to-date information on the genetic variants of pathogens circulating in the studied region, is an important element of the surveillance of natural focal infections (NFIs). The Stavropol Territory is one of the main recreational regions in the Russian Federation; it is endemic for a number of NFIs, including: Crimean-Congo hemorrhagic fever (CCHF), Q fever, tularemia, Lime disease, etc.The aim of the work is is genomic profiling of NFIs causative agents circulating in the Stavropol Territory in 2016-2021.Materials and methods. Microbial strains and samples of field and clinical material containing genomic DNA/RNA of pathogens were used as material for the study. Genetic typing of strains and isolates of DNA/RNA NFIs causative agents was performed by MLVA (Francisella tularensis and Coxiella burnetii) and genome fragment sequencing (Crimean-Congo hemorrhagic fever virus, West Nile virus, orthohantaviruses, Borrelia burgdorferii s.l., Ricckettsia sp.).Results. As a result of molecular genetic typing in the ST in 2016-2021 confirmed circulation of strains of F. tularensis of genetic subgroups B.I, B.III, B.VI, genetically identical strains of C. burnetii (VNTR-профиль 4-6-6-4-7-6-3-12-3-11), rickettsia belonging to 5 species: R. raoultii, R. aeschlimannii, R. slovaca, R. massiliae, R. helvetica , Borrelia belonging to the species: B. afzelii, B. garinii, B. miyamotoi, B. bavariensis, B. lusitaniae, B. valaisiana, RNA isolates of the CCHF virus of the Europe-1 and Europe-3 genetic lines, Tula orthohantaviruses, West Nile virus genotype 2. For the first time on the territory of the CT, in insectivore lung samples, RNA isolates of orthohantavirus genetically close to Camp Ripley virus (RLPV) were detected.Conclusions. New data have been obtained on the distribution of genetic variants of NFIs causative agents in the S, also in the recreation areas. Genetic structure of the population of NFIs causative agents in the ST in 2016-2021 did not change significantly, which indicates the relative stability of the natural foci of NFIs in the region.

BDE-209-induced genotoxicity, intestinal damage and intestinal microbiota dysbiosis in zebrafish (Danio Rerio)

The environmental presence of polybrominated diphenyl ethers (PBDEs) is ubiquitous due to their wide use as brominated flame retardants in industrial products. As a common congener of PBDEs, decabromodiphenyl ether (BDE-209) can pose a health risk to animals as well as humans. However, to date, few studies have explored BDE-209's toxic effects on the intestinal tract, and its relevant mechanism of toxicity has not been elucidated. In this study, adult male zebrafish were exposed to BDE-209 at 6 μg/L, 60 μg/L and 600 μg/L for 28 days, and intestinal tissue and microbial samples were collected for analysis to reveal the underlying toxic mechanisms. Transcriptome sequencing results demonstrated a dose-dependent pattern of substantial gene differential expression in the group exposed to BDE-209, and the differentially expressed genes were mainly concentrated in pathways related to protein synthesis and processing, redox reaction, and steroid and lipid metabolism. In addition, BDE-209 exposure caused damage to intestinal structure and barrier function, and promoted intestinal oxidative stress, inflammatory response, apoptosis and steroid and lipid metabolism disorders. Mechanistically, BDE-209 induced intestinal inflammation by increasing the levels of TNF-α and IL-1β and activating the NFκB signaling pathway, and might induce apoptosis through the p53-Bax/Bcl2-Caspase3 pathway. BDE-209 also significantly inhibited the gene expression of rate-limiting enzymes such as Sqle and 3βhsd (p < 0.05) to inhibit cholesterol synthesis. In addition, BDE-209 induced lipid metabolism disorders through the mTOR/PPARγ/RXRα pathway. 16S rRNA sequencing results showed that BDE-209 stress reduced the richness and diversity of intestinal microbiota, and reduced the abundance of probiotics (e.g., Bifidobacterium and Faecalibacterium). Overall, the results of this study help to clarify the intestinal response mechanism of BDE-209 exposure, and provide a basis for evaluating the health risks of BDE-209 in animals.

Machine learning-based detection of adventitious microbes in T-cell therapy cultures using long-read sequencing.

Assuring that cell therapy products are safe before releasing them for use in patients is critical. Currently, compendial sterility testing for bacteria and fungi can take 7-14 days. The goal of this work was to develop a rapid untargeted approach for the sensitive detection of microbial contaminants at low abundance from low volume samples during the manufacturing process of cell therapies. We developed a long-read sequencing methodology using Oxford Nanopore Technologies MinION platform with 16S and 18S amplicon sequencing to detect USP <71> organisms and other microbial species. Reads are classified metagenomically to predict the microbial species. We used an extreme gradient boosting machine learning algorithm (XGBoost) to first assess if a sample is contaminated, and second, determine whether the predicted contaminant is correctly classified or misclassified. The model was used to make a final decision on the sterility status of the input sample. An optimized experimental and bioinformatics pipeline starting from spiked species through to sequenced reads allowed for the detection of microbial samples at 10 colony-forming units (CFU)/mL using metagenomic classification. Machine learning can be coupled with long-read sequencing to detect and identify sample sterility status and microbial species present in T-cell cultures, including the USP <71> organisms to 10 CFU/mL. IMPORTANCE This research presents a novel method for rapidly and accurately detecting microbial contaminants in cell therapy products, which is essential for ensuring patient safety. Traditional testing methods are time-consuming, taking 7-14 days, while our approach can significantly reduce this time. By combining advanced long-read nanopore sequencing techniques and machine learning, we can effectively identify the presence and types of microbial contaminants at low abundance levels. This breakthrough has the potential to improve the safety and efficiency of cell therapy manufacturing, leading to better patient outcomes and a more streamlined production process.

1144 Audit of Microbiological Sampling in Patients with Diabetic Foot Infections Presenting to a Tertiary Vascular Centre in the North-East of England

Abstract Aim To identify the practice of microbiology sampling in patients presenting to a Tertiary Vascular Centre in the North East of England in accordance with NICE guideline (NG19) ‘Diabetic foot problems: prevention and management’ and the ‘International Working Group on the Diabetic Foot guidance on the diagnosis and management of foot infections in diabetes’. Method A two-part retrospective audit was completed before and after the introduction of a podiatrist-led 'Hot Foot Clinic'. Patients were identified from the surgical-take handover and admission database by using keywords ‘diabetic’, ‘cellulitis’, ‘erythema’, ‘pain’, ‘wet necrosis’, ‘collection’, 'osteomyelitis’. Route of admission, timing and type of microbial samples and date of antibiotics prescribed were recorded. Results In the first cycle 56.8% (21/37) patients had microbiology samples sent. 47.6% (10/21) of these were sent before antibiotic prescription. 8.1% (3/37) had both a swab and tissue sample taken. 35.1% (13/37) had tissue samples and 21.6% (5/37) had swabs. In the second cycle 74.2% (23/31) had microbiology samples sent. In patients who had tissue samples taken, 23.5% (4/17) were prior to antibiotic initiation. All patients (3/3) admitted from a podiatry-led ‘Hot Foot Clinic’ had microbiology taken prior to antibiotics. 6.3% (1/16) patients admitted through the clinician-led Emergency Admissions Suite had microbiology taken before antibiotics. Conclusions Despite introducing a podiatrist-led clinic, reinforcement of correct microbiological sampling in diabetic foot infections is required for accurate diagnosis and optimal treatment. Further specialist input and audio-visual educational material is being developed to improve practice amongst all staff.

Radiation hazards and extremophiles bioaccumulation of radionuclides from hypersaline lakes and hot springs

Radioactivity measurements for water, sediment, microbial films and the bioaccumulation of radionuclides by extremophiles from hypersaline lakes and hot springs were carried out as scarcity studies in the Siwa Oasis, Egypt. Natural and man-made radionuclides were measured using high-resolution γ-spectrometry. Different radionuclides behaved differently in different environmental samples, while radionuclides were higher in microbial films compared to sediment, but all radionuclide levels except 226Ra in water were generally low. Microbial films from hypersaline lakes had higher concentrations of 40K, while microbial films from freshwater hot springs had the highest concentrations of 226Ra, 232Th and 137Cs. The calculated radiological hazard index parameters of radium equivalent activity (Raeq), absorbed dose rate (D), annual effective dose (AED) and external hazard (Hex) in the sediment were within acceptable limits, but were higher in the microbial film samples. Otherwise, the potential cancer risk of the three freshwater springs was 0.00244 ± 0.000293, 0.00135.6 ± 0.000172 and 0.00155.2 ± 0.000198. In addition, the bioaccumulation factor for microbial films indicated that they are good accumulators of radionuclides, especially for 226Ra and 232Th, which may contribute to their effectiveness in removing radionuclides from ecosystems.

Translocation of vaginal and cervical low-abundance non-Lactobacillus bacteria notably associate with endometriosis: A pilot study

The etiology remains to be understood for endometriosis (EMS) which affected health negatively for 10% of reproductive-age women globally. Emerging studies found the associations of EMS with genital microbiota dysbiosis. However, the role of vaginal and cervical microbiota is not fully understood for Chinese women. This study recruited forty Chinese women (21 healthy women and 19 EMS patients) to analyze vaginal and cervical microbiota using 16S rRNA amplicon sequencing method. For both sites, there were no significant differences for distribution of microbial samples between control and EMS group, which was concordant with dominated Lactobacillus in both groups. In contrast, we observed accumulation of several low-abundance genera in vaginal and cervical microbiota of EMS patients, such as Fannyhessea, Prevotella, Streptococcus, Bifidobacterium, Veillonella, Megasphaera and Sneathia. Random forest analysis found that translocation of these genera had the significant importance in differentiating EMS patients from controls. In addition, cervix/vagina ratio of these genera also associated with EMS severity. And these genera had notable associations with ascending infection-related functional pathways, including flagellar assembly, bacterial motility proteins, bacterial toxins and epithelial cell signaling in Helicobacter pylori infection. These findings suggest that translocation of specific genera between vaginal and cervical sites play a role in EMS.

Refining biome labeling for large-scale microbial community samples: Leveraging neural networks and transfer learning

Microbiome research has generated an extensive amount of data, resulting in a wealth of publicly accessible samples. Accurate annotation of these samples is crucial for effectively utilizing microbiome data across scientific disciplines. However, a notable challenge arises from the lack of essential annotations, particularly regarding collection location and sample biome information, which significantly hinders environmental microbiome research. In this study, we introduce Meta-Sorter, a novel approach utilizing neural networks and transfer learning, to enhance biome labeling for thousands of microbiome samples in the MGnify database that have incomplete information. Our findings demonstrate that Meta-Sorter achieved a remarkable accuracy rate of 96.7% in classifying samples among the 16,507 lacking detailed biome annotations. Notably, Meta-Sorter provides precise classifications for representative environmental samples that were previously ambiguously labeled as “Marine” in MGnify, thereby elucidating their specific origins in benthic and water column environments. Moreover, Meta-Sorter effectively distinguishes samples derived from human-environment interactions, enabling clear differentiation between environmental and human-related studies. By improving the completeness of biome label information for numerous microbial community samples, our research facilitates more accurate knowledge discovery across diverse disciplines, with particular implications for environmental research.

Stevia vs. triple antibiotic paste: An intracanal battle?

Intracanal medicaments are vital in treating the infections of the deciduous dentition due to the large percentage of accessory canals that hasten the microbial spread to the periradicular region. Though countless medicaments have been produced to reduce the microbial load and aid symptomatic relief, they still do not fulfill every function of an ideal medicament. The aim of the present study was to evaluate and compare the antimicrobial efficacy of Stevia rebaudiana (S. rebaudiana) and triple antibiotic paste (TAP) against Enterococcus faecalis (E. faecalis). The present in vitro, parallel, double-blinded study had an equal allocation ratio. The specimens were prepared, randomly divided into 4 groups and inoculated with E. faecalis (ATCC35550). Following incubation, the first 3 groups were treated with S. rebaudiana, triple antibiotic therapy or carbopol gel, respectively, with the 4th negative control group left untreated. The microbial samples were collected before and after treatment, and the counts of colony-forming units (CFUs) were compared. The results were analyzed using the Kruskal-Wallis, Dunn's post-hoc and Wilcoxon's signed rank tests. The first 2 groups displayed a significant decrease in CFUs after drug application, while the carbopol and control groups showed an exponential increase. There was no statistically significant difference between the stevia and TAP groups (p = 0.630). Stevia gel was comparable to TAP in terms of antimicrobial efficacy, and can therefore be considered a new alternative in intracanal treatment.

Is ozonated water a suitable alternative to sodium hypochlorite in root canal disinfection?

Aim: This study evaluated the disinfection ability of ozonated water in comparison to sodium hypochlorite (NaOCl) solution in root canals infected with Enterococcus faecalis. Material and methods: Forty single-rooted bovine teeth were standardized and prepared using K-files. The root canals were contaminated for 21 days and the first microbial sample was collected from root canals (S1). The teeth were divided into 5 groups: Saline solution, 0.5% NaOCl, Ozonated water, and 2 control groups. The root canals were irrigated with 20 mL of the selected solution for an uninterrupted period of 20 minutes, the irrigant solution was maintained resting for 5 minutes and then, samples were collected from root canals (S2). The data was evaluated using Kruskal Wallis and Wilcoxon tests (P&lt;0.05). Results: The NaOCl group had lower microbial counts (P&lt;0.05) and a higher percentage of microbiological reduction than the other groups (P&lt;0.05). Conclusion: It was determined that ozonated water was not a suitable substitute for NaOCl.

Prevalence and Antibiotic Susceptibility Pattern of Bacterial Pathogens in Intensive Care Unit (ICU) of a Tertiary Care Facility

Aim: To determine the prevalence and antibiotic susceptibility pattern of microorganisms in the ICU patients of a tertiary care facility in Karachi, Pakistan. Method: A retrospective study was conducted on the laboratory records of 50 patients with positive culture admitted to a tertiary care facility. A structured questionnaire was used to obtain patients’ records comprising of their name, sex, age, diagnosis, sample source, isolated pathogen culture results and antibiotic susceptibility patterns. Blood, tracheal fluid, urine, sputum, pus, peritoneal fluid and catheter tips were included as specimen sources. Total 94% patients selected had clinically suspected nosocomial infections. Results: Overall, 45% of them had traumatic brain or spinal injury followed by 35% of post-operative cases, 10% respiratory disease related patients, 6% cardiac patients, 2% renal failure and 2% with miscellaneous infections. Majority of the patients admitted to the ICU were in the age range 51- 65 years. Positive microbial growth samples included blood (30%), trachea (24%), urine (26%), sputum (10%), pus (4%), peritoneal fluids (2%) and catheter tip (4%). Amongst the samples tested, Acinetobacter spp. (22%) were predominant, followed by E. coli (14%), P. aeruginosa (10%), S. aureus (10%) and Enterococcus spp. (8%). Majority of the gram negative species were resistant to amoxiclave, cefotaxime, pipercillin and teicoplanin. Conclusions: The incidence of nosocomial infections is high in ICU patients. Thus accurate antimicrobial treatment strategies together with the development of new therapeutic regimens and risk assessment in hospitals and their ICUs is significantly required to prevent antimicrobial drug resistance among microorganisms.

Prevalence and Antibiotic Susceptibility Pattern of Bacterial Pathogens in Intensive Care Unit (ICU) of a Tertiary Care Facility

Aim: To determine the prevalence and antibiotic susceptibility pattern of microorganisms in the ICU patients of a tertiary care facility in Karachi, Pakistan. Method: A retrospective study was conducted on the laboratory records of 50 patients with positive culture admitted to a tertiary care facility. A structured questionnaire was used to obtain patients’ records comprising of their name, sex, age, diagnosis, sample source, isolated pathogen culture results and antibiotic susceptibility patterns. Blood, tracheal fluid, urine, sputum, pus, peritoneal fluid and catheter tips were included as specimen sources. Total 94% patients selected had clinically suspected nosocomial infections. Results: Overall, 45% of them had traumatic brain or spinal injury followed by 35% of post-operative cases, 10% respiratory disease related patients, 6% cardiac patients, 2% renal failure and 2% with miscellaneous infections. Majority of the patients admitted to the ICU were in the age range 51- 65 years. Positive microbial growth samples included blood (30%), trachea (24%), urine (26%), sputum (10%), pus (4%), peritoneal fluids (2%) and catheter tip (4%). Amongst the samples tested, Acinetobacter spp. (22%) were predominant, followed by E. coli (14%), P. aeruginosa (10%), S. aureus (10%) and Enterococcus spp. (8%). Majority of the gram negative species were resistant to amoxiclave, cefotaxime, pipercillin and teicoplanin. Conclusions: The incidence of nosocomial infections is high in ICU patients. Thus accurate antimicrobial treatment strategies together with the development of new therapeutic regimens and risk assessment in hospitals and their ICUs is significantly required to prevent antimicrobial drug resistance among microorganisms.

Microbial diversity on grape epidermis and wine volatile aroma in spontaneous fermentation comprehensively driven by geography, subregion, and variety

On their journey from the wine grape to the resulting wine, microbiota from grape surfaces controlled by multiple factors is transferred to wine spontaneous fermentation process with indisputable consequences for wine quality parameters. The associated microbiota was regionally distinct (defined to microbial terroir) but how these microbial patterns with significantly regional distinctiveness quantitatively drive the wine regional characteristics are not definite within a complete grape ecosystem at different geographical (> 300 km), subregional (< 10 km), and varietal scales. Here, we collected 24 samples (containing two grape varieties) from four subregions of two regions in Xinjiang wine production area to investigate fungal distribution patterns and the association with wine chemical composition at different evaluation scales. Meanwhile, the relationships were established between geographical, subregional, varietal community of fungi, and wine volatile aroma using partial least squares regression (PLSR) and structural equation modeling (SEM). Results show that microbial and volatile samples present the significantly regional difference inside the complete ecosystem. Microbiota showed a stronger heterogeneity at geography scales, which drove the distributions of subregional and varietal microbiota thereby influencing the volatile composition of finished wines. Moreover, geographical microbiota seems to weaken the effects of varietal community on wine aroma compounds. Microbial communities respond to environmental changes within a completely set grape-related ecosystem at different scales, and these responses resulted in the wine regional distinctiveness based on the volatile profiles. Our findings further confirmed the important role of microbial terroir in shaping wine styles and provided the new cerebration for the terroir drivers of microbiota.

Evaluation of pathogen distribution and antimicrobial resistance in breast plastic surgery infection.

The demand for mammaplasty has increased in recent years, and infection remains one of the common and serious post-operative complications. In this study, we analyzed the pathogen distribution and antibiotic susceptibility of breast plastic surgery infections, and compared the differences in pathogenic species between surgical procedures. The number of each species was counted in the microbial samples of breast plastic surgery infections in Plastic Surgery Hospital of Chinese Academy of Medical Sciences from January 2011 to December 2021. The in vitro antibiotic sensitivity testing data were analyzed using WHONET 5.6 software. The surgical techniques, the period of infection, and other details were gathered in accordance with the clinical data. There were a total of 42 cases included, and 43 different types of pathogenic bacteria, mostly gram-positive bacteria, were found. CoNS (13/43) and Staphylococcus aureus (22/43) made up the majority. The most prevalent of the five Gram-negative bacteria was Pseudomonas aeruginosa. Results of drug sensitivity tests indicate that S. aureus is highly sensitive to vancomycin, cotrimoxazole, and linezolid, whereas CoNS is highly sensitive to vancomycin, linezolid, and chloramphenicol. Both of these bacteria show high resistance to erythromycin and penicillin. Breast augmentation, breast reconstruction, and breast reduction surgery were the most frequently associated breast surgery procedures in this study with infections, with the highest number of infections occurring following breast augmentation with fat grafting, breast reduction surgery, and breast reconstruction with autologous tissue. Various breast plastic surgery procedures have different common pathogens of infection, but the most prevalent are CoNS and S. aureus. Additionally, the majority of the infections in this study were in the early stages. Gram-positive bacteria were the predominant cause of breast plastic surgery infections, and the types of infection strains, the period of infection onset, and the antibiotic susceptibility of prevalent strains varied between breast plastic procedures.

Microbiota present in combined endodontic-periodontal diseases and its risks for endocarditis.

Infective endocarditis (IE) is an inflammatory disease usually caused by bacteria that enter the bloodstream and establish infections in the inner linings or valves of the heart, including blood vessels. Despite the availability of modern antimicrobial and surgical treatments, IE continues to cause substantial morbidity and mortality. Oral microbiota is considered one of the most significant risk factors for IE. The objective of this study was to evaluate the microbiota present in root canal (RC) and periodontal pocket (PP) clinical samples in cases with combined endo-periodontal lesions (EPL) to detect species related to IE using NGS. Microbial samples were collected from 15 RCs and their associated PPs, also from 05 RCs with vital pulp tissues (negative control, NC). Genomic studies associated with bioinformatics, combined with structuring of a database (genetic sequences of bacteria reported for infective endocarditis), allowed for the assessment of the microbial community at both sites. Functional prediction was conducted using PICRUSt2. Parvimonas, Streptococcus, and Enterococcus were the major genera detected in the RCs and PPs. A total of 79, 96, and 11 species were identified in the RCs, PPs, and NCs, respectively. From them, a total of 34 species from RCs, 53 from PPs, and 2 from NCs were related to IE. Functional inference demonstrated that CR and PP microbiological profiles may not be the only risk factors for IE but may also be associated with systemic diseases, including myocarditis, human cytomegalovirus infection, bacterial invasion of epithelial cells, Huntington's disease, amyotrophic lateral sclerosis, and hypertrophic cardiomyopathy. Additionally, it was possible to predict antimicrobial resistance variants for broad-spectrum drugs, including ampicillin, tetracycline, and macrolides. Microorganisms present in the combined EPL may not be the only risk factor for IE but also for systemic diseases. Antimicrobial resistance variants for broad-spectrum drugs were inferred based on PICRUSt-2. State-of-the-art sequencing combined with bioinformatics has proven to be a powerful tool for conducting studies on microbial communities and could considerably assist in the diagnosis of serious infections. Few studies have investigated the microbiota in teeth compromised by combined endo-periodontal lesions (EPL), but none have correlated the microbiological findings to any systemic condition, particularly IE, using NGS techniques. In such cases, the presence of apical periodontitis and periodontal disease can increase IE risk in susceptible patients.

Seasonal freeze–thaw processes regulate and buffer the distribution of microbial communities in soil horizons

The freeze–thaw process alters microbial communities in alpine soils. However, soil microbial responses to seasonal freeze–thaw processes have been overlooked under climate change, especially in deep soil. In this study, microbial samples were collected from three alpine meadows on the northeastern Qinghai-Tibet Plateau during four seasonal freeze–thaw periods (TP: thawed period; UFP: unstable freezing period; FP: frozen period; and UTP: unstable thawing period), and the taxa and biomass of living microbes were determined by the phospholipid fatty acid (PLFA) method. The results showed that the microbial biomass in the TP was significantly lower than that in other seasonal freeze–thaw periods. The biomass of fungi and gram-positive bacteria (GP) was high in the UFP and FP, and the biomass of bacteria and gram-negative bacteria (GN) was high in the UTP. The soil microbial biomass decreased with soil depth, and the difference in soil microbial biomass between soil horizons in the FP was smaller than those in the UTP, FP and UFP. The values of GN/GP and fungi/bacteria (F/B) decreased with soil depth during all seasonal freeze–thaw periods and were lower in the UFP and FP than in the TP and UTP. The main controlling factors of the total microbial biomass of the alpine meadow were soil temperature, soil organic carbon (SOC) and total nitrogen (TN) during the seasonal freeze–thaw periods. TN was the critical soil variable affecting the total microbial biomass in the TP. SOC was the critical soil variable affecting the total microbial biomass in the UFP and UTP. With global warming (especially in winter), soil microbial biomass can be expected to decrease in alpine regions. These results could provide a deep understanding of biodiversity and the prediction of carbon cycle in alpine regions.

Potential role of intratumor bacteria outside the gastrointestinal tract: More than passengers.

Tumor-associated bacteria and gut microbiota have gained significant attention in recent years due to their potential role in cancer development and therapeutic response. This review aims to discuss the contributions of intratumor bacteria outside the gastrointestinal tract, in addition to exploring the mechanisms, functions, and implications of these bacteria in cancer therapy. We reviewed current literature on intratumor bacteria and their impact on tumorigenesis, progression, metastasis, drug resistance, and anti-tumor immune modulation. Additionally, we examined techniques used to detect intratumor bacteria, precautions necessary when handling low microbial biomass tumor samples, and the recent progress in bacterial manipulation for tumor treatment. Research indicates that each type of cancer uniquely interacts with its microbiome, and bacteria can be detected even in non-gastrointestinal tumors with low bacterial abundance. Intracellular bacteria have the potential to regulate tumor cells' biological behavior and contribute to critical aspects of tumor development. Furthermore, bacterial-based anti-tumor therapies have shown promising results in cancer treatment. Understanding the complex interactions between intratumor bacteria and tumor cells could lead to the development of more precise cancer treatment strategies. Further research into non-gastrointestinal tumor-associated bacteria is needed to identify new therapeutic approaches and expand our knowledge of the microbiota's role in cancer biology.

Microbial Biofilm Colonizing Plastic Substrates in the Ross Sea (Antarctica): First Overview of Community-Level Physiological Profiles

The microbial colonization of plastic substrates made of polyvinylchloride (PVC) and polyethylene (PE) was studied in Tethys and Road Bays (Ross Sea, Antarctica) in order to evaluate the metabolic profiles of the plastisphere community in comparison with those of the surrounding waters. PVC and PE panels, mounted on stainless steel structures, were deployed in the austral summer 2017 at 5 and 20 m and recovered one year later at four different stations (Amorphous Glacier-AG was potentially impacted by the ice-melting process, and its control site was within Tethys Bay-TB; Road Bay-RB, close to the wastewater plant of the Italian research station Mario Zucchelli and its control site Punta Stocchino-PTS). Additional panels were settled in Road Bay at 5 m and recovered after three months to follow time variability in the microbial colonization process. At the same times and depths as plastic substrates, water samples were also collected. Carbon substrates’ utilization rates were determined on scraped microbial biofilm and water samples, with a fluorimetric assay based on 96-well Biolog Ecoplates. Complex carbon sources, carbohydrate and amines were the organic substrates that mostly fuelled the community metabolism in the RB area, while in the TB area, in addition to carbohydrates, phosphate carbon compounds and amino acids were also actively utilized. Within Road Bay, small differences in the physiological profiles were found, with higher metabolic rates in the biofilm community after 3 months’ deployment (late austral summer period) compared to 12 months, suggesting that autumn to spring period conditions negatively affected foulers’ metabolism. Moreover, different metabolic profiles between the plastisphere and the pelagic microbial community were observed; this last utilized a higher number of carbon sources, while plastic substrates were colonized by a more specialized community. Higher carbon substrate utilization rates were recorded at RB and AG stations, receiving organic supply from anthropic activity or ice melting sources, respectively, compared to their control sites. These results highlighted the functional plasticity of the microbial community, with the adaptive ability to utilize a diversified range of organic substrates.