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Purpose: To review experimental peri-implantitis studies using rat models and summarize different peri-implantitis induction techniques and evaluate their effectiveness. Materials and Methods: Electronic searches were conducted by two independent examiners to address the following issues. Meta-analyses explored the marginal bone loss (MBL) of four types of peri-implantitis induction methods in rats. The detailed induction tactics--such as the implant design, implant size, surgical process, time cost, induction methods, and endpoint measurements--were summarized. Results: Of the 18 included studies, 38.9% of the studies placed implants at the maxillary first molar, and 44.4% placed them at the alveolar ridge region anterior to the maxillary first molar. As for the induction method, the numbers of published studies on ligature methods, bacterial inoculation, and bacterial lipopolysaccharide inoculation were equally high among all selected studies. The total implant survival rate at the end was 160 out of 213 implants (75.11%). Eight studies with high pooled heterogeneity (I2 = 98, P < .01) in the meta-analysis reported an overall MBL (µ-CT) of 0.47 mm (95% CI = 0.14 to 0.81). A subgroup analysis estimated an MBL of 0.31 mm (95% CI = 0.12 to 0.50) for bacterial inoculation and 0.66 mm (95% CI = 0.07 to 1.26) for the ligature method. Histopathologic analysis revealed that peri-implantitis in rats was similar to peri-implantitis lesions in humans. Conclusions: Implant placement at the maxillary first molar with bacterial inoculation and the silk ligature method to build peri-implantitis rat models is reliable to use for research on peri-implantitis. [ABSTRACT FROM AUTHOR]

The study aimed to determine the effects of two differing amino acid beverage interventions on biomarkers of intestinal epithelial integrity and systemic inflammation in response to an exertional-heat stress challenge. One week after the initial assessment, participants (n = 20) were randomly allocated to complete two exertional-heat stress trials, with at least 1 week washout. Trials included a water control trial (CON), and one of two possible amino acid beverage intervention trials (VS001 or VS006). On VS001 (4.5 g/L) and VS006 (6.4 g/L), participants were asked to consume two 237-ml prefabricated doses daily for 7 days before the exertional-heat stress, and one 237-ml dose immediately before, and every 20 min during 2-hr running at 60% maximal oxygen uptake in 35 °C ambient conditions. A water volume equivalent was provided on CON. Whole blood samples were collected pre-, immediately post-, 1 and 2 hr postexercise, and analyzed for plasma concentrations of cortisol, intestinal fatty acid protein, soluble CD14, and immunoglobulin M (IgM) by ELISA, and systemic inflammatory cytokines by multiplex. Preexercise resting biomarker concentrations for all variables did not significantly differ between trials (p >.05). A lower response magnitude for intestinal fatty acid protein (mean [95% CI]: 249 [60, 437] pg/ml, 900 [464, 1,336] pg/ml), soluble CD14 (−93 [−458, 272] ng/ml, 12 [−174, 197] ng/ml), and IgM (−6.5 [−23.0, 9.9] MMU/ml, −10.4 [−16.2, 4.7] MMU/ml) were observed on VS001 and V006 compared with CON (p <.05), respectively. Systemic inflammatory response profile was lower on VS001, but not VS006, versus CON (p <.05). Total gastrointestinal symptoms did not significantly differ between trials. Amino acid beverages' consumption (i.e., 4.5–6.4 g/L), twice daily for 7 days, immediately before, and during exertional-heat stress ameliorated intestinal epithelial integrity and systemic inflammatory perturbations associated with exercising in the heat, but without exacerbating gastrointestinal symptoms. [ABSTRACT FROM AUTHOR]

Purpose: The objective of this in vitro study was to evaluate the activity of local gel containing metronidazole (MN) in the leakage area, which was analyzed by the DNA-DNA checkerboard hybridization method. Materials and Methods: Thirty-six sets of Morse taper/mini-pillar implants were used in this study. These implants were equally divided into the following three groups: MN gel (test group), no MN gel (negative test group), and no gel (control). The gel was prepared with metronidazole (15%). Unstimulated saliva samples were collected, transferred to a Falcon tube, and stored at 37°C. The sets were partially immersed in microtubes containing 300 µL of saliva and were incubated at 37°C ± 1°C for 7 days. Microbial infiltration was evaluated (37 bacterial species and 5 species of Candida). The results were analyzed with Wald-Type, ANOVA, and multiple comparisons analysis between groups. Results: After comparing the quantity of microorganisms, both gel-treated groups (no MN gel and MN gel) had more significant microorganism presence than the control group (P < .001), and no significant result was found between the no MN gel and MN gel groups (P > .05). Regarding the bacteria found, the most common were Aggregatibacter actinomycetemcomitans, Prevotella melaninogenica, Bacteroides fragilis, and Candida tropicalis. Conclusion: Within the limitations of this study, it was concluded that the gel containing metronidazole used in this study was not effective in preventing the infiltration of microorganisms through the Morse taper implant-abutment interface. [ABSTRACT FROM AUTHOR]

Background: Engaging in anal sexual intercourse markedly increases the risk of developing HIV among men who have sex with men (MSM); oral sexual activities tend to uniquely introduce gut-derived microbes to salivary microbiota, which, combined with an individual's positive HIV status, may greatly perturb oral microecology. However, till date, only a few published studies have addressed this aspect. Methods: Based on 16S rRNA sequencing data of bacterial taxa, MicroPITA picks representative samples for metagenomic analysis, effectively revealing how the development and progression of the HIV disease influences oral microbiota in MSM. Therefore, we collected samples from 11 HIV-negative and 44 HIV-positive MSM subjects (stage 0 was defined by HIV RNA positivity, but negative or indeterminate antibody status; stages 1, 2, and 3 were defined by CD4+ T lymphocyte counts = 500, 200-499, and = 200 or opportunistic infection) and selected 25 representative saliva samples (5 cases/stage) using MicroPITA. Metagenomic sequencing analysis were performed to explore whether positive HIV status changes salivary bacterial KEGG function and metabolic pathway in MSM. Results: The core functions of oral microbiota were maintained across each of the five groups, including metabolism, genetic and environmental information processing. All HIV-positive groups displayed KEGG functions of abnormal proliferation, most prominently at stage 0, and others related to metabolism. Clustering relationship analysis tentatively identified functional relationships between groups, with bacterial function being more similar between stage 0-control groups and stage 1-2 groups, whereas the stage 3 group exhibited large functional changes. Although we identified most metabolic pathways as being common to all five groups, several unique pathways formed clusters for certain groups; the stage 0 group had several, while the stage 2 and 3 groups had few, such clusters. The abundance of K03046 was positively correlated with CD4 counts. Conclusion: As HIV progresses, salivary bacterial function and metabolic pathways in MSM progressively changes, which may be related to HIV promoting abnormal energy metabolism and exacerbate pathogen virulence. Further, infection and drug resistance of acute stage and immune cell destruction of AIDS stage were abnormally increased, predicting an increased risk for MSM individuals to develop systemic and oral diseases. [ABSTRACT FROM AUTHOR]

Current rates of ocean warming are predicted to exacerbate ongoing declines in seagrass populations. Above-ground responses of seagrass to increasing temperatures have been studied from a direct physiological perspective while indirect effects, including changes to microbially-mediated below-ground processes, remain poorly understood. To test potential effects of increased temperature on seagrass growth and associated microbial communities, we sampled seagrass beds experiencing ambient and elevated water temperatures at Lake Macquarie, Australia. Sites with warmer water were associated with a plume from a power station discharge channel with temperatures analogous to conditions predicted by 2100 under current rates of ocean warming (+3°C). The microbial community composition in both sediments and leaf tissues varied significantly between warm and ambient water temperatures with higher relative abundances of putative sulphate-reducing bacteria such as Desulfocapsaceae, Desulfobulbaceae and Desulfosarcinaceae in sedimentary communities in warm water. Above-ground biomass and seagrass growth rates were greater at warm sites while below-ground biomass and detrital decomposition rates showed no difference suggesting potential buffering of temperature effects below-ground. These findings suggest a 3°C rise in temperate regions is unlikely to induce mortality in seagrass however, it may shift microbial communities towards more homogenous structure and composition. [ABSTRACT FROM AUTHOR]

Background: Soil salinity is one of the major menaces to food security, particularly in dealing with the food demand of the ever-increasing global population. Production of cereal crops such as wheat is severely affected by soil salinity and improper fertilization. The present study aimed to examine the effect of selected microbes and poultry manure (PM) on seedling emergence, physiology, nutrient uptake, and growth of wheat in saline soil. A pot experiment was carried out in research area of Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan. Saline soil (12 dS m− 1 w/w) was developed by spiking using sodium chloride, and used in experiment along with two microbial strains (i.e., Alcaligenes faecalis MH-2 and Achromobacter denitrificans MH-6) and PM. Finally, wheat seeds (variety Akbar-2019) were sown in amended and unamended soil, and pots were placed following a completely randomized design. The wheat crop was harvested after 140 days of sowing. Results: The results showed a 10–39% increase (compared to non-saline control) in agronomic, physiological, and nutritive attributes of wheat plants when augmented with PM and microbes. Microbes together with PM significantly enhanced seedling emergence (up to 38%), agronomic (up to 36%), and physiological (up to 33%) in saline soil as compared to their respective unamended control. Moreover, the co-use of microbes and PM also improved soil's physicochemical attributes and enhanced N (i.e., 21.7%-17.1%), P (i.e., 24.1-29.3%), and K (i.e., 28.7%-25.3%) availability to the plant (roots and shoots, respectively). Similarly, the co-use of amendments also lowered the Na+ contents in soil (i.e., up to 62%) as compared to unamended saline control. This is the first study reporting the effects of the co-addition of newly identified salt-tolerant bacterial strains and PM on seedling emergence, physiology, nutrient uptake, and growth of wheat in highly saline soil. Conclusion: Our findings suggest that co-using a multi-trait bacterial culture and PM could be an appropriate option for sustainable crop production in salt-affected soil. [ABSTRACT FROM AUTHOR]

Introduction: The study into the interplay between foodborne pathogens and human health, particularly their effects on intestinal cells, is crucial. The importance of lactic acid bacteria (LAB) in promoting a healthy balance of gut microbiota, inhibiting harmful bacteria, and supporting overall gastrointestinal health is becoming more apparent. Methods: Our study delved into the impact of fermenting Woodfordia fruticosa (WF), a plant known for its antimicrobial properties against gastrointestinal pathogens, with LAB. We focused on the influence of this fermentation process on the binding of foodborne pathogens to the gut lining and cytokine production, aiming to enhance gut health and control foodborne infections in HT-29 cells. Results and discussion: Post-fermentation, the WF exhibited improved antimicrobial effects when combined with different LAB strains. Remarkably, the LAB-fermented WF (WFLC) substantially decreased the attachment of pathogens such as L. monocytogenes (6.87% ± 0.33%) and V. parahaemolyticus (6.07% ± 0.50%) in comparison to the unfermented control. Furthermore, WFLC was found to upregulate IL-6 production in the presence of pathogens like E. coli O157:H7 (10.6%) and L. monocytogenes (19%), suggesting it may activate immune responses. Thus, LAB-fermented WF emerges as a potential novel strategy for fighting foodborne pathogens, although additional studies are warranted to thoroughly elucidate WF's phytochemical profile and its contribution to these beneficial outcomes. [ABSTRACT FROM AUTHOR]

The concentration of antimicrobial agents in environments like water and food has increased rapidly, which led to a rapid increase in antimicrobial resistance levels in the environment. Monitoring of bacterial resistance levels is considered as a necessary means to control the bacterial resistance. Reference standards are critical for antimicrobial susceptibility testing. CLSI M45 A3 standard defines pathogenic microorganisms that cause infections less frequently than those covered by CLSI M02, M07, and M100 as Infrequently Isolated or Fastidious Bacteria and specifies antimicrobial susceptibility testing methods. Our study investigated the epidemiology and antimicrobial susceptibility testing data of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in 70 hospitals in Guangdong Province between 2017 and 2021. We defined testing methods other than those specified in CLSI M45 A3 as "Non-Standardized." The proportion of standardized antimicrobial susceptibility testing for penicillin increased significantly (Corynebacterium spp. 17.4% vs. 50.0% p < 0.05; Micrococcus spp. 50.0% vs. 77.8% p < 0.05; Abiotrophia spp. and Granulicatella spp. 21.4% vs. 90.9% p < 0.001), while for cefotaxime (Corynebacterium spp. 0.0% vs. 45.2% p < 0.05; Abiotrophia spp. and Granulicatella spp. 0.0% vs. 14.3% p = 0.515) and vancomycin increased finitely. Non-standardized methods were used for all other antimicrobials. Due to limitations in the economic and medical environment, some clinical laboratories are unable to fully comply with CLSI M45 A3 standard. We recommend that CLSI should add breakpoints for disk diffusion method to improve the standardization of antimicrobial susceptibility testing. [ABSTRACT FROM AUTHOR]

Biological soil crusts, or biocrusts, are microbial communities found in soil surfaces in drylands and in other locations where vascular plant cover is incomplete. They are functionally significant for numerous ecosystem services, most notably in the C fixation and storage due to the ubiquity of photosynthetic microbes. Whereas carbon fixation and storage have been well studied in biocrusts, the composition, function and characteristics of other organisms in the biocrust such as heterotrophic bacteria and especially fungi are considerably less studied and this limits our ability to gain a holistic understanding of biocrust ecology and function. In this research we characterised the fungal community in biocrusts developed on Kalahari Sand soils from a site in southwest Botswana, and combined these data with previously published bacterial community data from the same site. By identifying organisational patterns in the community structure of fungi and bacteria, we found fungi that were either significantly associated with biocrust or the soil beneath biocrusts, leading to the conclusion that they likely perform functions related to the spatial organisation observed. Furthermore, we showed that within biocrusts bacterial and fungal community structures are correlated with each other i.e., a change in the bacterial community is reflected by a corresponding change in the fungal community. Importantly, this correlation but that this correlation does not occur in nearby soils. We propose that different fungi engage in short-range and long-range interactions with dryland soil surface bacteria. We have identified fungi which are candidates for further studies into their potential roles in biocrust ecology at short ranges (e.g., processing of complex compounds for waste management and resource provisioning) and longer ranges (e.g., translocation of resources such as water and the fungal loop model). This research shows that fungi are likely to have a greater contribution to biocrust function and dryland ecology than has generally been recognised. [ABSTRACT FROM AUTHOR]

Currently, there are many different therapies available for inflammatory bowel disease (IBD), including engineered live bacterial therapeutics. However, most of these studies focus on producing a single therapeutic drug using individual bacteria, which may cause inefficacy. The use of dual drugs can enhance therapeutic effects. However, expressing multiple therapeutic drugs in one bacterial chassis increases the burden on the bacterium and hinders good secretion and expression. Therefore, a dual-bacterial, dual-drug expression system allows for the introduction of two probiotic chassis and enhances both therapeutic and probiotic effects. In this study, we constructed a dual bacterial system to simultaneously neutralize pro-inflammatory factors and enhance the anti-inflammatory pathway. These bacteria for therapy consist of Escherichia coli Nissle 1917 that expressed and secreted anti-TNF-α nanobody and IL-10, respectively. The oral administration of genetically engineered bacteria led to a decrease in inflammatory cell infiltration in colon and a reduction in the levels of pro-inflammatory cytokines. Additionally, the administration of engineered bacteria did not markedly aggravate gut fibrosis and had a moderating effect on intestinal microbes. This system proposes a dual-engineered bacterial drug combination treatment therapy for inflammatory bowel disease, which provides a new approach to intervene and treat IBD. Key points: • The paper discusses the effects of using dual engineered bacteria on IBD • Prospects of engineered bacteria in the clinical treatment of IBD [ABSTRACT FROM AUTHOR]

Background: Gut bacteria, which serve as essential modulators, exert a significant impact on insect physiology and behavior and have substantial application potential in pest management. The dynamics of gut bacteria and their impact on Phortica okadai behavior remain unclear. Methods: In this study, the dynamics of gut bacteria at different developmental stages in P. okadai were analyzed using 16S ribosomal RNA (rRNA) gene sequencing, and the species and abundance of gut bacteria that affect host behavior were examined via behavioral experiments. Results: A total of 19 phyla, 29 classes, 74 orders, 101 species, and 169 genera were identified. The results of the behavioral experiments indicated that the species Lactiplantibacillus argentoratensis, Acetobacter tropicalis, Leuconostoc citreum, and Levilactobacillus brevis effectively influenced the feeding preference of P. okadai, and the single-bacterium-seeded P. okadai exhibited feeding preferences distinct from those of the germ-free (GF) and wild-type P. okadai. Conclusions: The species and relative abundance of gut bacteria together positively impact P. okadai behavior. Lactiplantibacillus argentoratensis, as the most attractive bacteria to P. okadai, presents opportunities for novel pest control strategies targeting this vector and agricultural pest. [ABSTRACT FROM AUTHOR]

Pneumonia is a common comorbidity in patients with severe traumatic brain injury (TBI), and is associated with increased morbidity and mortality. In this study, we established a model of intratracheal Klebsiella pneumoniae administration in young adult male and female mice, at 4 days following an experimental TBI, to investigate how K. pneumoniae infection influences acute post-TBI outcomes. A dose-response curve determined the optimal dose of K. pneumoniae for inoculation (1 x 10^6 colony forming units), and administration at 4 days post-TBI resulted in transient body weight loss and sickness behaviors (hypoactivity and acute dyspnea). K. pneumoniae infection led to an increase in pro-inflammatory cytokines in serum and bronchoalveolar lavage fluid at 24 h post-infection, in both TBI and sham (uninjured) mice. By 7 days, when myeloperoxidase + neutrophil numbers had returned to baseline in all groups, lung histopathology was observed with an increase in airspace size in TBI + K. pneumoniae mice compared to TBI + vehicle mice. In the brain, increased neuroinflammatory gene expression was observed acutely in response to TBI, with an exacerbated increase in Ccl2 and Hmox1 in TBI + K. pneumoniae mice compared to either TBI or K. pneumoniae alone. However, the presence of neuroinflammatory immune cells in the injured brain, and the extent of damage to cortical and hippocampal brain tissue, was comparable between K. pneumoniae and vehicle-treated mice by 7 days. Examination of the fecal microbiome across a time course did not reveal any pronounced effects of either injury or K. pneumoniae on bacterial diversity or abundance. Together, these findings demonstrate that K. pneumoniae lung infection after TBI induces an acute and transient inflammatory response, primarily localized to the lungs with some systemic effects. However, this infection had minimal impact on secondary injury processes in the brain following TBI. Future studies are needed to evaluate the potential longer-term consequences of this dual-hit insult. [ABSTRACT FROM AUTHOR]

Environmental changes and increasing population are major concerns for crop production and food security as a whole. To address this, researchers had focussed on the improvement of cereals and pulses and have made considerable progress till the beginning of this decade. However, cereals and pulses together, without vegetables and fruits, are inadequate to meet the dietary and nutritional demands of human life. Production of good quality vegetables and fruits is highly challenging owing to their perishable nature and short shelf life as well as abiotic and biotic stresses encountered during pre- and post-harvest. Genetic engineering approaches to produce good quality, to increase shelf life and stress-resistance, and to change the time of flowering and fruit ripening by introducing foreign genes to produce genetically modified crops were quite successful. However, several biosafety concerns, such as the risk of transgeneoutcrossing, limited their production, marketing, and consumption. Modern genome editing techniques, like the CRISPR/Cas9 system, provide a perfect solution in this scenario, as it can produce transgene-free genetically edited plants. Hence, these genetically edited plants can easily satisfy the biosafety norms for crop production and consumption. This review highlights the potential of the CRISPR/Cas9 system for the successful generation of abiotic and biotic stress resistance and thereby improving the quality, yield, and overall productivity of vegetables and fruits. [ABSTRACT FROM AUTHOR]

The Hyphomicrobiales bacterial order (previously Rhizobiales) exhibits a wide range of lifestyle characteristics, including free-living, plant-association, nitrogen-fixing, and association with animals (Bartonella and Brucella). This study explores the diversity and evolutionary strategies of bacteriophages within the Hyphomicrobiales order, comparing animal-associated (AAB) with non-animal-associated bacteria (NAAB). We curated 560 high-quality complete genomes of 58 genera from this order and used the PHASTER server for prophage annotation and classification. For 19 genera with representative genomes, we curated 96 genomes and used the Defense-Finder server to summarize the type of anti-phage systems (APS) found in this order. We analyzed the genetic repertoire and length distributions of prophages, estimating evolutionary rates and comparing intact, questionable, and incomplete prophages in both groups. Analyses of best-fit parameters and bootstrap sensitivity were used to understand the evolutionary processes driving prophage gene content. A total of 1860 prophages distributed in Hyphomicrobiales were found, 695 in AAB and 1165 in the NAAB genera. The results revealed a similar number of prophages per genome in AAB and NAAB and a similar length distribution, suggesting shared mechanisms of genetic acquisition of prophage genes. Changes in the frequency of specific gene classes were observed between incomplete and intact prophages, indicating preferential loss or enrichment in both groups. The analysis of best-fit parameters and bootstrap sensitivity tests indicated a higher selection coefficient, induction rate, and turnover in NAAB genomes. We found 68 types of APS in Hyphomicrobiales; restriction modification (RM) and abortive infection (Abi) were the most frequent APS found for all Hyphomicrobiales, and within the AAB group. This classification of APS showed that NAAB genomes have a greater diversity of defense systems compared to AAB, which could be related to the higher rates of prophage induction and turnover in the latter group. Our study provides insights into the distributions of both prophages and APS in Hyphomicrobiales genomes, demonstrating that NAAB carry more defense systems against phages, while AAB show increased prophage stability and an increased number of incomplete prophages. These results suggest a greater role for domesticated prophages within animal-associated bacteria in Hyphomicrobiales. [ABSTRACT FROM AUTHOR]

Background: Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. Results: To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. Conclusions: This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. FPVwQXB65-N4idcpgwJZ6_ Video Abstract [ABSTRACT FROM AUTHOR]

Antibacterial resistance is a major threat for human health. There is a need for new antibacterials to stay ahead of constantly‐evolving resistant bacteria. Nucleic acid therapeutics hold promise as powerful antibiotics, but issues with their delivery hamper their applicability. Here, we exploit the siderophore‐mediated iron uptake pathway to efficiently transport antisense oligomers into bacteria. We appended a synthetic siderophore to antisense oligomers targeting the essential acpP gene in Escherichia coli. Siderophore‐conjugated PNA and PMO antisense oligomers displayed potent antibacterial properties. Conjugates bearing a minimal siderophore consisting of a mono‐catechol group showed equally effective. Targeting the lacZ transcript resulted in dose‐dependent decreased β‐galactosidase production, demonstrating selective protein downregulation. Applying this concept to Acinetobacter baumannii also showed concentration‐dependent growth inhibition. Whole‐genome sequencing of resistant mutants and competition experiments with the endogenous siderophore verified selective uptake through the siderophore‐mediated iron uptake pathway. Lastly, no toxicity towards mammalian cells was found. Collectively, we demonstrate for the first time that large nucleic acid therapeutics can be efficiently transported into bacteria using synthetic siderophore mimics. [ABSTRACT FROM AUTHOR]

Antibacterial resistance is a major threat for human health. There is a need for new antibacterials to stay ahead of constantly‐evolving resistant bacteria. Nucleic acid therapeutics hold promise as powerful antibiotics, but issues with their delivery hamper their applicability. Here, we exploit the siderophore‐mediated iron uptake pathway to efficiently transport antisense oligomers into bacteria. We appended a synthetic siderophore to antisense oligomers targeting the essential acpP gene in Escherichia coli. Siderophore‐conjugated PNA and PMO antisense oligomers displayed potent antibacterial properties. Conjugates bearing a minimal siderophore consisting of a mono‐catechol group showed equally effective. Targeting the lacZ transcript resulted in dose‐dependent decreased β‐galactosidase production, demonstrating selective protein downregulation. Applying this concept to Acinetobacter baumannii also showed concentration‐dependent growth inhibition. Whole‐genome sequencing of resistant mutants and competition experiments with the endogenous siderophore verified selective uptake through the siderophore‐mediated iron uptake pathway. Lastly, no toxicity towards mammalian cells was found. Collectively, we demonstrate for the first time that large nucleic acid therapeutics can be efficiently transported into bacteria using synthetic siderophore mimics. [ABSTRACT FROM AUTHOR]

Spiders host a diverse range of bacteria in their guts and other tissues, which have been found to play a significant role in their fitness. This study aimed to investigate the community diversity and functional characteristics of spider-associated bacteria in four tissues of Heteropoda venatoria using HTS of the 16S rRNA gene and culturomics technologies, as well as the functional verification of the isolated strains. The results of HTS showed that the spider-associated bacteria in different tissues belonged to 34 phyla, 72 classes, 170 orders, 277 families, and 458 genera. Bacillus was found to be the most abundant bacteria in the venom gland, silk gland, and ovary, while Stenotrophomonas, Acinetobacter, and Sphingomonas were dominant in the gut microbiota. Based on the amplicon sequencing results, 21 distinct cultivation conditions were developed using culturomics to isolate bacteria from the ovary, gut, venom gland, and silk gland. A total of 119 bacterial strains, representing 4 phyla and 25 genera, with Bacillus and Serratia as the dominant genera, were isolated. Five strains exhibited high efficiency in degrading pesticides in the in vitro experiments. Out of the 119 isolates, 28 exhibited antibacterial activity against at least one of the tested bacterial strains, including the pathogenic bacteria Staphylococcus aureus, Acinetobacter baumanii, and Enterococcus faecalis. The study also identified three strains, GL312, PL211, and PL316, which exhibited significant cytotoxicity against MGC-803. The crude extract from the fermentation broth of strain PL316 was found to effectively induce apoptosis in MGC-803 cells. Overall, this study offers a comprehensive understanding of the bacterial community structure associated with H. venatoria. It also provides valuable insights into discovering novel antitumor natural products for gastric cancer and xenobiotic-degrading bacteria of spiders. [ABSTRACT FROM AUTHOR]

Bovine abortion is a critical problem in the cattle industry. Identifying causes of abortion is key to establishing appropriate herd management and prevention strategies. We used pathology examinations, detection of etiologic agents, and serology to determine the cause of bovine abortions in Korea. We analyzed 360 abortion and stillbirth cases submitted to the Animal and Plant Quarantine Agency from December 2014 to January 2020. The putative cause of abortion was identified in 140 of 360 (38.9%) cases; 124 of the 140 (88.6%) cases were attributed to infections. The most common etiologic agents detected were bovine viral diarrhea virus (65 of 360; 18.1%), Coxiella burnetii (19 of 360; 5.3%), Leptospira spp. (13 of 360; 3.6%), Listeria monocytogenes (9 of 360; 2.5%), and Neospora caninum (8 of 360; 2.2%). Minor abortifacient pathogens included Brucella abortus (2 of 360; 0.6%), bovine alphaherpesvirus 1 (2 of 360; 0.6%), Akabane virus (2 of 360, 0.6%), and bovine ephemeral fever virus (1 of 360; 0.3%). Non-infectious conditions included congenital anomalies (7 of 360; 1.9%), goiter (7 of 360; 1.9%), and vitamin A deficiency (2 of 360; 0.6%). Our diagnostic rate in cases with placenta submitted (42 of 86; 48.8%) was significantly higher than in cases without placenta (98 of 274; 35.8%), which highlights the value of submitting placentas. Our results confirm the status of the large variety of causative agents associated with abortions in cattle in Korea. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) in pathogens important to aquatic animal health is of increasing concern but vastly understudied. Antimicrobial therapy is used to both treat and prevent bacterial disease in fish and is critical for a viable aquaculture industry and for maintenance of wild fish populations. Unfortunately, phenotypic antimicrobial susceptibility testing is technically difficult for bacteria recovered from aquatic animal hosts resulting in challenges in resistance monitoring using traditional methods. Whole-genome sequencing provides an appealing methodology for investigation of putative resistance. As part of the ongoing efforts of the FDA CVM Vet-LIRN to monitor AMR, source laboratories cultured and preliminarily identified pathogenic bacteria isolated from various fish species collected in 2019 from across the United States. Sixty-one bacterial isolates were evaluated using whole-genome sequencing. We present here the assembled draft genomes, AMR genes, predicted resistance phenotypes, and virulence factors of the 61 isolates and discuss concurrence of the identifications made by source laboratories using matrix-assisted laser desorption/time-of-flight mass spectrometry. [ABSTRACT FROM AUTHOR]

Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola. [ABSTRACT FROM AUTHOR]

To address the need for facile, rapid detection of pathogens in water supplies, a fluorescent sensing array platform based on antibiotic-stabilized metal nanoclusters was developed for the multiplex detection of pathogens. Using five common antibiotics, eight different nanoclusters (NCs) were synthesized including ampicillin stabilized copper NCs, cefepime stabilized gold and copper NCs, kanamycin stabilized gold and copper NCs, lysozyme stabilized gold NCs, and vancomycin stabilized gold/silver and copper NCs. Based on the different interaction of each NC with the bacteria strains, unique patterns were generated. Various machine learning algorithms were employed for pattern discernment, among which the artificial neural networks proved to have the highest performance, with an accuracy of 100%. The developed prediction model performed well on an independent test dataset and on real samples gathered from drinking water, tap water and the Anzali Lagoon water, with prediction accuracy of 96.88% and 95.14%, respectively. This work demonstrates how generic antibiotics can be implemented for NC synthesis and used as recognition elements for pathogen detection. Furthermore, it displays how merging machine learning techniques can elevate sensitivity of analytical devices. [ABSTRACT FROM AUTHOR]

An ultra-sensitive fluorescent biosensor based on CDs/QDs@ZIF-8 and microfluidic fluidized bed was developed for rapid and ultra-sensitive detection of multiple target bacteria. The zeolitic imidazolate frameworks (ZIF-8) act as the carrier to encapsulate three kinds of fluorescence signal molecules from the CDs/QDs@ZIF-8 signal amplification system. Besides, three kinds of target pathogenic bacteria were automatically, continuously, and circularly captured by the magnetic nanoparticles (MNPs) in the microfluidic fluidized bed. The neutral Na2EDTA solution was the first time reported to not only dissolve the ZIF-8 frameworks from the MNPs-bacteria-CDs/QDs@ZIF-8 sandwich complexes, but also release the CDs/QDs from sandwich complexes with no loss of fluorescence signal. Due to the advantages of signal amplification and automated sample pretreatment, the proposed fluorescent biosensor can simultaneously detect Escherichia coli O157:H7, Salmonella paratyphi A, and Salmonella paratyphi B as low as 101 CFU/mL within 1.5 h, respectively. The mean recovery in spiked milk samples can reach 99.18%, verifying the applicability of this biosensor in detecting multiple bacteria in real samples. [ABSTRACT FROM AUTHOR]

The traditional practice of harvesting and processing raw date palm sap is not only culturally significant but also provides an essential nutritional source in South Asia. However, the potential for bacterial or viral contamination from animals and environmental sources during its collection remains a serious and insufficiently studied risk. Implementing improved food safety measures and collection techniques could mitigate the risk of these infections. Additionally, the adoption of advanced food analytical methods offers the potential to identify pathogens and uncover the natural bacterial diversity of these products. The advancement of next-generation sequencing (NGS) technologies, particularly nanopore sequencing, offers a rapid and highly mobile solution. In this study, we employed nanopore sequencing for the bacterial metabarcoding of a set of raw date palm sap samples collected without protective coverage against animals in Bangladesh in 2021. We identified several bacterial species with importance in the natural fermentation of the product and demonstrated the feasibility of this NGS method in the surveillance of raw palm sap products. We revealed two fermentation directions dominated by either Leuconostoc species or Lactococcus species in these products at the first 6 h from harvest, along with opportunistic human pathogens in the background, represented with lower abundance. Plant pathogens, bacteria with the potential for opportunistic human infection and the sequences of the Exiguobacterium genus are also described, and their potential role is discussed. In this study, we demonstrate the potential of mobile laboratory solutions for food safety purposes in low-resource areas. [ABSTRACT FROM AUTHOR]

This comprehensive review explores the potential of using lactobacilli as a probiotic in the management of COVID-19. Our findings suggest that lactobacilli show promise in reducing the risk of death, gastrointestinal and overall symptoms, and respiratory failure, as well as in lowering cytokines and inflammatory markers associated with the disease. The molecular mechanisms by which lactobacilli protect against COVID-19 and other viral infections may be related to the reduction in inflammation, modulation of the immune response, and direct interaction with viruses to produce antiviral substances. However, the selected studies demonstrate the presence of mixed findings for various clinical, biochemical, hematological, and immunological parameters, which may be attributed to methodological differences among studies. We highlight the importance of clearly describing randomization processes to minimize bias and caution against small sample sizes and inappropriate statistical tests that could lead to errors. This review offers valuable insights into the therapeutic potential of lactobacilli in the context of COVID-19 and identifies avenues for further research and applications. These findings hold promise for the development of novel approaches to managing COVID-19 and warrant further investigation into the potential benefits of lactobacilli in combating the disease. [ABSTRACT FROM AUTHOR]

Simple Summary: The combination of atezolizumab and bevacizumab is a standard treatment for unresectable hepatocellular carcinoma. This study investigated the relationship between the gut microbiome and treatment efficacy. Fecal samples from 37 patients with hepatocellular carcinoma treated with this combination were analyzed. Patients were divided into responders (n = 28) and non-responders (n = 9). While overall microbiome diversity was similar, certain bacteria, such as Bacteroides stercoris and Parabacteroides merdae were more abundant in responders. Patients lacking these bacteria had worse prognoses. This suggests that differences in gut microbiota play a role in the effectiveness of atezolizumab and bevacizumab therapy. The combination of atezolizumab and bevacizumab has become the first-line treatment for patients with unresectable hepatocellular carcinoma (HCC). However, no studies have reported on specific intestinal microbiota associated with the efficacy of atezolizumab and bevacizumab. In this study, we analyzed fecal samples collected before treatment to investigate the relationship between the intestinal microbiome and the efficacy of atezolizumab and bevacizumab. A total of 37 patients with advanced HCC who were treated with atezolizumab and bevacizumab were enrolled. Fecal samples were collected from the patients, and they were divided into responder (n = 28) and non-responder (n = 9) groups. We compared the intestinal microbiota of the two groups and analyzed the intestinal bacteria associated with prognosis using QIIME2. The alpha and beta diversities were not significantly different between both groups, and the proportion of microbiota was similar. The relative abundance of Bacteroides stercoris and Parabacteroides merdae was higher in the responder group than in the non-responder group. When the prognosis was analyzed by the presence or absence of those bacteria, patients without both had a significantly poorer prognosis. Differences in intestinal microbiome are involved in the therapeutic effect of atezolizumab and bevacizumab. [ABSTRACT FROM AUTHOR]

HIV infection results in marked alterations in the gut microbiota (GM), such as the loss of microbial diversity and different taxonomic and metabolic profiles. Despite antiretroviral therapy (ART) partially ablating gastrointestinal alterations, the taxonomic profile after successful new ART has shown wide variations. Our objective was to determine the GM composition and functions in people living with HIV (PLWHIV) under ART in comparison to seronegative controls (SC). Fecal samples from 21 subjects (treated with integrase strand-transfer inhibitors, INSTIs) and 18 SC were included. We employed 16S rRNA amplicon sequencing, coupled with PICRUSt2 and fecal short-chain fatty acid (SCFA) quantification by gas chromatography. The INSTI group showed a decreased α-diversity (p < 0.001) compared to the SC group, at the expense of increased amounts of Pseudomonadota (Proteobacteria), Segatella copri, Lactobacillus, and Gram-negative bacteria. Concurrently, we observed an enrichment in Megasphaera and Butyricicoccus, both SCFA-producing bacteria, and significant elevations in fecal butyrate in this group (p < 0.001). Interestingly, gut dysbiosis in PLWHIV was characterized by a proinflammatory environment orchestrated by Pseudomonadota and elevated levels of butyrate associated with bacterial metabolic pathways, as well as the evident presence of butyrogenic bacteria. The role of this unique GM in PLWHIV should be evaluated, as well as the use of butyrate-based supplements and ART regimens that contain succinate, such as tenofovir disoproxil succinate. This mixed profile is described for the first time in PLWHIV from Mexico. [ABSTRACT FROM AUTHOR]

Infectious diseases account for about 3 million deaths per year. The advent of molecular techniques has led to an enormous improvement in their diagnosis, both in terms of sensitivity and specificity and in terms of the speed with which a clinically useful result can be obtained. Digital PCR, or 3rd generation PCR, is based on a series of technical modifications that result in more sensitive techniques, more resistant to the action of inhibitors and capable of direct quantification without the need for standard curves. This review presents the main applications that have been developed for the diagnosis of viral, bacterial, and parasitic infections and the potential prospects for the clinical use of this technology. [ABSTRACT FROM AUTHOR]

Acute Oak Decline (AOD) is an oak disease that was first described in the United Kingdom. From the time the first symptoms appear, the disease can kill trees even within 6 years. One of the factors causing this disease is the action of the pathogenic bacteria Brenneria goodwinii, Rahnella victoriana and Gibbsiella quercinecans. In recent years, a deterioration in the condition of oak stands has been observed throughout Slovakia. These trees show exudates characteristic of AOD, which may indicate the presence of pathogenic bacteria. Samples of such symptomatic exudates from tree trunks were collected and analysed on 20 different plots in central and western Slovakia. Using real-time PCR, the presence of Brenneria goodwinii and Gibbsiella quercinecans was confirmed in ten and three stands, respectively. This report is the first information about the observation of these bacteria in weakened stands of Quercus robur in Slovakia. [ABSTRACT FROM AUTHOR]

Background Helicobacter pylori is an important public health concern due to its status as a carcinogenic bacterium. Well adapted to the acidic environment of the human stomach, the variety of strains and virulence factors of the organism when interacting with the host immune system creates an individualistic response. Although estimates suggest that approximately half of the global population is infected with H pylori , the majority of infected persons remain asymptomatic while harboring an increased risk of intestinal metaplasia and gastric cancers. Therefore, appropriate diagnostic testing protocols are imperative. Methods This study compared labeling methodologies, including Wright stain, alcian yellow toluidine blue (AYTB), and immunohistochemistry (IHC) on formalin-fixed paraffin-embedded stomach resections from sleeve gastrectomy patients, to detect H pylori infection. Results Although all 3 labeling methods evidenced similar specificity in H pylori detection, the IHC method was significantly more sensitive. However, the IHC cost per test was approximately 5-fold higher than that of the Wright or AYTB stains, and the technical time required per test was at least 6-fold that of Wright or AYTB. Conclusion Despite the higher cost per test, IHC is the most sensitive and preferred method for determination of H pylori infection. [ABSTRACT FROM AUTHOR]

Objective This study retrospectively compared false-positive result frequencies of 3 syphilis serology screening tests and assessed whether false positivity was associated with pregnancy and age. Methods Results for 3 screening tests were retrieved from the laboratory database, including rapid plasma reagin (RPR) assay between October 2016 and September 2019, BioPlex 2200 Syphilis Total immunoassay between May 2020 and January 2022, and Alinity i Syphilis TP assay between February 2022 and April 2023. The false-positive result frequencies were calculated based on testing algorithm criteria. Results False-positive result frequency for BioPlex was 0.61% (90/14,707), significantly higher than 0.29% (50/17,447) for RPR and 0.38% (55/14,631) for Alinity (both P <.01). Patients with false-positive results were significantly older than patients with nonreactive results for RPR (median age: 36 vs 28, P <.001), but not for BioPlex or Alinity. For all 3 tests, the positive predictive values in pregnant women were lower than those in nonpregnant women or men. However, pregnant women did not exhibit a higher false-positive result frequency. Conclusion Although false-positive result frequencies were low overall for all 3 syphilis serology tests, there is a significant difference between different tests. Pregnancy was not associated with more false-positive results for all 3 tests. [ABSTRACT FROM AUTHOR]

Background: Dioscorea bulbifera Linn. has been used for wound care in Thailand. However, a comprehensive evaluation of its antibacterial activity is required. This study aimed to investigate the antibacterial efficacy of D. bulbifera extract against skin-associated bacteria and isolate and characterize its active antibacterial agent, flavanthrinin. Methods: Air-dried bulbils of D. bulbifera were pulverised and extracted with hexane, dichloromethane, ethyl acetate, methanol, ethanol, and distilled water; vacuum filtered; concentrated; freeze-dried; and stored at -20 ºC. Antibacterial activity of the extracts was assessed using microdilution techniques against several skin-associated bacteria. Thin-layer chromatography (TLC) bioautography was used to identify the active compounds in the extract, which were fractionated by column chromatography and purified by preparative TLC. The chemical structures of the purified compounds were analysed using nuclear magnetic resonance (NMR). The cytotoxicity of the extract and its active compounds was evaluated in Vero cells. Results: The ethyl acetate extract exhibited distinct inhibition zones against bacteria compared to other extracts. Therefore, the ethyl acetate extract of D. bulbifera in the ethyl acetate layer was used for subsequent analyses. D. bulbifera extract exhibited antibacterial activity, with minimum inhibitory concentrations (MICs) of 0.78–1.56 mg/mL. An active compound, identified through TLC-bioautography, demonstrated enhanced antibacterial activity, with MICs of 0.02–0.78 mg/mL. NMR analysis identified this bioactive compound as flavanthrinin. Both D. bulbifera extract and flavanthrinin-containing fraction demonstrated potent antibacterial activity against Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), and S. epidermidis. The flavanthrinin containing fraction demonstrated low cytotoxicity against Vero cells, showing CC50 values of 0.41 ± 0.03 mg/mL. These values are lower than the MIC value, indicating that this fraction is safer than the initial ethyl acetate extract. Conclusions: Dioscorea bulbifera extract and its bioactive component flavanthrinin demonstrated significant antibacterial activity against the skin-associated bacteria Staphylococci, including MRSA. Flavanthrinin has potential as a complementary therapeutic agent for managing skin infections owing to its potent antibacterial effects and low cytotoxicity. [ABSTRACT FROM AUTHOR]

Background: The folate cycle of one-carbon (C1) metabolism, which plays a central role in the biosynthesis of nucleotides and amino acids, demonstrates the significance of metabolic adaptation. We investigated the evolutionary history of the methylenetetrahydrofolate dehydrogenase (mTHF) gene family, one of the main drivers of the folate cycle, across life. Results: Through comparative genomic and phylogenetic analyses, we found that several lineages of Archaea lacked domains vital for folate cycle function such as the mTHF catalytic and NAD(P)-binding domains of FolD. Within eukaryotes, the mTHF gene family diversified rapidly. For example, several duplications have been observed in lineages including the Amoebozoa, Opisthokonta, and Viridiplantae. In a common ancestor of Opisthokonta, FolD and FTHFS underwent fusion giving rise to the gene MTHFD1, possessing the domains of both genes. Conclusions: Our evolutionary reconstruction of the mTHF gene family associated with a primary metabolic pathway reveals dynamic evolution, including gene birth-and-death, gene fusion, and potential horizontal gene transfer events and/or amino acid convergence. [ABSTRACT FROM AUTHOR]

Climate change is a universal issue and plastic trash is the major cause of global warming. The present study was specifically designed to address the escalating plastic waste problem, the biodegradation of low-density polyethylene (LDPE) bags was investigated over an 8-week period using liquid culture approach. Bacterial strain (Pseudomonas putida) capable of degrading LDPE was isolated from common plastic garbage dumping sites. The strain was identified after sequencing analysis, as P. putida was evaluated for its effectiveness in degrading LDPE. Various analytical techniques, including weight loss, SEM, FTIR and GC-MS were employed to assess the degradation process. Results revealed that bacterial strain achieved 0.0776 % degradation. SEM and FTIR confirmed surface and chemical changes, while GC MS identified degradation by products in comparison to the control (where no bacteria was used). [ABSTRACT FROM AUTHOR]

Melanins are ubiquitous pigments distributed throughout the biosphere in different forms and structures based on the substrate (phenolic and indolic) from which they are derived. Melanins are predominantly black/brown and sometimes melanins of color yellow/red have also been observed. Though melanins are widespread, at present their applications are only limited because commercially available melanins are often made through the synthetic process which impedes their application due to poor sensitivity. Melanins from biological sources are of great interest because of their biocompatibility and availability in microbes, especially bacteria. Owing to its rising demand, bacterial melanin can be easily produced and optimized in mass by proper fermentation conditions or by overexpressing the genes encoding enzymes such as polyketide synthase, tyrosinase, and laccase responsible for melanin production cost-effectively. Melanins are produced as a secondary metabolite in bacteria which aids in their survival under stressful environments. Besides providing pigmentation to the cells, many other biological properties, types, and potential applications of melanin in the fields of the textile, food industry, nanotechnology, and biomedical and the research gap that needs to be filled in previous discoveries for better application of melanin has been discussed in this review. [ABSTRACT FROM AUTHOR]

Two oxygenated ergostane-type steroids including one new compound, 3β-hydroxy-5α,6β-methoxyergosta-7,22-dien-15-one (1) along with a known analogue ergosta-6,22-dien-3β,5α,8α-triol (2) were isolated from the crude extracts of the marine sponge-derived fungus Aspergillus sp. Their structures were elucidated on the basis of combined NMR and MS spectroscopic methods. Compound 1 was a marine ergostane-type steroid with two methoxy groups at C-5 and C-6, respectively. These oxygenated ergostane-type steroids were evaluated for their antibacterial activities against human or aquatic pathogens. Among them, compound 1 exhibited antibacterial activity against Staphylococcus aureus. [ABSTRACT FROM AUTHOR]

Under adverse environmental conditions, microorganisms are able to enter a state of cellular dormancy which consists of cell cycle arrest and interruption of multiplication. This process ensures their perpetuation in the infected host organism and enables the spread of disease. Throughout biological evolution, dormancy allowed microorganisms to persist in a harsh niche until favorable conditions for their reactivation were re‐established. Here, we propose to discuss the dormancy of bacteria and protozoa pathogens focusing on the potential mechanisms and components associated with dormancy. [ABSTRACT FROM AUTHOR]

Background: Microbial communities are crucial for ecosystems. A central goal of microbial ecological research is to simplify the biodiversity in natural environments and quantify the functional roles to explore how the ecosystems respond under different environmental conditions. However, the research on the stability and dynamics of lake microbes in response to repeated warming stress is limited. Methods: To exclude confounding environmental factors, we conducted a 20-day repeated warming simulation experiment to examine the composition and function dynamics of lake microbial communities. Results: Experimental warming significantly altered the community structure of bacteria instead of fungi. Microbial community structure, together with microbial biomass, jointly regulated the function of microbial communities. The plummeting of aerobic denitrifiers Pseudomonadaceae decreased by 99% (P < 0.001) after high temperature, leading to reduced microbial nitrogen metabolism on nitrogen respiration and nitrate respiration. Under warming conditions, the microbial community with higher adaptability showed more positive correlations and less competitive relationships in co-occurrence networks to acclimate to warming. Conclusion: Microbiome composition controlled carbon and nitrogen metabolism, thus determining lake microbial communities' adaptability to heat stress. This study extended our insights on the lake microbial community response and adaptability under warming drivers. [ABSTRACT FROM AUTHOR]

Tomatoes hold considerable significance in Nigeria due to their substantial contributions to the employment sector, income generation for cultivators, and satisfaction of domestic and nutritional food requirements. Nonetheless, postharvest deterioration of a considerable quantity of tomato produce occurs in Nigeria as a result of the growth of spoilage organisms. The diversity of microorganisms associated with the deterioration of tomato fruits sold by vendors in four major markets in Owerri was analyzed. One hundred and twenty samples were randomly drawn from the various markets and subjected to standard microbiological techniques Total viable count (2.6 × 104 CFU/g), total coliform count (4.2 × 104 CFU/g), and total fungi count (7.0 × 105 CFU/g) were highest from deteriorated tomato samples analyzed from the relief market. A total of six bacteria genera belonging to Micrococcus sp., Klebsiella sp., Escherichia coli, Proteus sp., Bacillus sp., and Staphylococcus spp. were identified. Staphylococcus spp (31.75%) was the most predominant bacteria isolate associated with the deteriorated tomato samples. This was followed by Escherichia coli 4 (25%), Bacillus sp. 3 (18.75%), Proteus sp. 2 (12.5%), Enterobacter sp. 1 (6.25%), and Micrococcus sp. Penicillium sp., Aspergillus sp., and Rhizopus sp. were also isolated from the deteriorated tomatoes, with Rhizopus sp. being the most predominant isolate 6 (40%) while Aspergillus sp. 4 (26.7%) was the least predominant isolate. The isolation of potential pathogens from deteriorated tomatoes sold by vendors in the four major markets in Owerri represents a significant health risk to consumers. A robust measure to combat post-harvest deterioration of tomatoes should be put in place by government agencies at all levels. Additionally, public enlightenment and awareness campaigns on the consequences of consuming deteriorated tomatoes should be encouraged. [ABSTRACT FROM AUTHOR]

Background: Microbial keratitis is one of the leading causes of blindness globally. An overactive immune response during an infection can exacerbate damage, causing corneal opacities and vision loss. This study aimed to identify the differentially expressed genes between corneal infection patients and healthy volunteers within the cornea and conjunctiva and elucidate the contributing pathways to these conditions' pathogenesis. Moreover, it compared the corneal and conjunctival transcriptomes in corneal-infected patients to cytokine levels in tears. Methods: Corneal and conjunctival swabs were collected from seven corneal infection patients and three healthy controls under topical anesthesia. RNA from seven corneal infection patients and three healthy volunteers were analyzed by RNA sequencing (RNA-Seq). Tear proteins were extracted from Schirmer strips via acetone precipitation from 38 cases of corneal infection and 14 healthy controls. The cytokines and chemokines IL-1b, IL-6, CXCL8 (IL-8), CX3CL1, IL-10, IL-12 (p70), IL-17A, and IL-23 were measured using an antibody bead assay. Results: A total of 512 genes were found to be differentially expressed in infected corneas compared to healthy corneas, with 508 being upregulated and four downregulated (fold-change (FC) <-2 or > 2 and adjusted p <0.01). For the conjunctiva, 477 were upregulated, and 3 were downregulated (FC <-3 or = 3 and adjusted p <0.01). There was a significant overlap in cornea and conjunctiva gene expression in patients with corneal infections. The genes were predominantly associated with immune response, regulation of angiogenesis, and apoptotic signaling pathways. The most highly upregulated gene was CXCL8 (which codes for IL-8 protein). In patients with corneal infections, the concentration of IL-8 protein in tears was relatively higher in patients compared to healthy controls but did not show statistical significance. Conclusions: During corneal infection, many genes were upregulated, with most of them being associated with immune response, regulation of angiogenesis, and apoptotic signaling. The findings may facilitate the development of treatments for corneal infections that can dampen specific aspects of the immune response to reduce scarring and preserve sight. [ABSTRACT FROM AUTHOR]

The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read sequencing data that can bridge repetitive and problematic regions. Oxford Nanopore Technologies (ONT) produce long-read sequencing platforms and they are continually improving their technology to obtain higher quality read data that is approaching the quality obtained from short-read platforms such as Illumina. As these innovations continue, we evaluated how much ONT read coverage produced by the Rapid Barcoding Kit v14 (SQK-RBK114) is necessary to generate high-quality hybrid and long-read-only genome assemblies for a panel of carbapenemase-producing Enterobacterales bacterial isolates. We found that 30× long-read coverage is sufficient if Illumina data are available, and that more (at least 100× long-read coverage is recommended for long-read-only assemblies. Illumina polishing is still improving single nucleotide variants (SNVs) and INDELs in long-read-only assemblies. We also examined if antimicrobial resistance genes could be accurately identified in long-read-only data, and found that Flye assemblies regardless of ONT coverage detected >96% of resistance genes at 100% identity and length. Overall, the Rapid Barcoding Kit v14 and long-read-only assemblies can be an optimal sequencing strategy (i.e., plasmid characterization and AMR detection) but finer-scale analyses (i.e., SNV) still benefit from short-read data. [ABSTRACT FROM AUTHOR]

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Pneumonia is a global health concern, causing significant morbidity and mortality, particularly among vulnerable populations. This study, conducted at Dr. Soetomo Regional Public Hospital (RSUD Dr. Soetomo), Surabaya, Indonesia, aimed to assess the causative pathogens, antibiotic sensitivity patterns, and the impact of empiric therapy on the clinical outcomes of pneumonia patients. The present study analyzed 324 cases from January to March 2023, categorizing pneumonia as communityacquired (CAP), hospital-acquired (HAP), and ventilator-associated (VAP). Gram-negative bacteria, predominantly Klebsiella pneumoniae, were the primary pathogens, with 44% being multidrug-resistant. Antibiotic sensitivity patterns highlighted the efficacy of amikacin, cefoperazone sulbactam, and meropenem against Gram-negative bacteria. Empiric therapy, mainly monotherapy, showed varied outcomes across pneumonia types. Clinical improvement was observed in 72.5% of CAP patients, while HAP and VAP patients faced challenges, with high mortality rates of 47.2% and 89.1%, respectively. Clinical stability in CAP correlated with age, culture results, multidrug resistance, pneumonia severity, and antibiotic class. In HAP, appropriate empiric therapy and pneumonia severity influenced clinical outcomes. Notably, VAP patients experienced poor outcomes irrespective of the variables studied. This study underscores the importance of local pathogen prevalence awareness and tailored empiric therapy to enhance pneumonia management, especially in HAP and VAP cases. Further research is warranted to refine treatment strategies and improve patient outcomes. [ABSTRACT FROM AUTHOR]

This study investigates the feasibility of utilizing ureolytic-type bacteria in lightweight foamed concrete to enhance its compressive strength. Previous research focused on microorganisms in different types of concrete, but there is a lack of study on microorganism incorporation in low-density foamed concrete. Bacillus megaterium was introduced in the production of microbial-based lightweight foamed concrete, inducing mineral precipitation through microbial activities. Four mix proportions were prepared: a control mix (LFC-CM) and LFCs incorporated with varying concentrations of B. megaterium. All specimens underwent water curing. Results show significant improvements in compressive, flexural, and splitting tensile strengths of microbial-based LFC compared to control samples due to microbial-induced calcite precipitation. This research has implications for sustainable construction materials. The potential future directions include optimizing microbial dosage, exploring different ureolytic bacteria, and investigating the long-term durability and performance of microbial-based lightweight foamed concrete. This study contributes to knowledge on microbial-based construction materials, providing insights for sustainable concrete solutions. [ABSTRACT FROM AUTHOR]

Bioremediation aspects of crude oil-polluted fields can be achieved by isolating and identifying bacterial species from oil-contaminated soil. This allows for the selection of the most active isolates and the enhancement of the effectiveness of other bacteria. This project will be a base to use green technology for clean the oil contaminated soil in Jordan. This study involved the isolation and identification of oil-degrading microbes from soil samples contaminated with oil in the northeastern region of Jordan. The morphological and biochemical tests were used to characterize twenty-five bacterial isolates. Molecular identification of a universal primer 16S rDNA gene was used to identify bacterial isolates. Total petroleum hydrocarbons were analyzed using gas chromatography for soil samples. All soil samples were analyzed for heavy metal contamination (Cu, Cd, Mn, Zn, and Pb). The bacterial growth count (CFU/g) was between 1.06×105 and 2.80×1017. The identified bacterial genera included: Staphylococcus, Citrobacter, Lactobacillus, Alcaligin's, Pseudomonas, Micrococcus, Serratia, Enterobacter, Bacillus, Salmonella, Mycobacterium, Corynebacterium, and, Microbacterium. The most species showed high growth rates on different types of hydrocarbons such as toluene, naphthalene, and hexane were Lactobacillus casei, Staphylococcus intermedius, Micrococcus luteus, Pseudomonas putida, Mycobacterium phlei, Corynebacterium xerosis. Soil sample M1A contains the highest levels of Fe, Cd, and Pb and Cu,. While M1C contains the highest levels of Fe and Mn. On the other hand, M2A, and M2C have the least levels of Mn and Fe. While M3C has the least level of Zn and Pb. our study conclude the bacterial isolates could be used for in situ and ex situ cleanup of oil-contaminated desert soil in northeastern part of Jordan. [ABSTRACT FROM AUTHOR]

Nutrient subsidy of methane‐oxidising bacteria (MOB), an alternative basal resource, to plankton communities through pelagic‐benthic coupling is expected to alter carbon‐to‐nitrogen (C/N) ratios and biomass of zooplankton, and affect biological processes in aquatic food webs. Previous studies indicate that most MOB nutrient subsidies to zooplankton are focused largely on C subsidies; nevertheless, considering that N is important to zooplankton and phytoplankton growth, a better understanding of MOB N subsidies to plankton communities is needed.We examined changes in nutrients, phytoplankton mass‐specific productivity, MOB reliance, C/N ratios and biomass of zooplankton between summer stratification and winter mixing periods based on in situ investigation in a subtropical deep oligotrophic freshwater ecosystem during 2010–2014.The results revealed that with increasing reliance on MOB during the winter mixing period, zooplankton C/N ratios decreased and had a significantly nonlinearly inverse relationship with zooplankton biomass. The negative relationship between zooplankton biomass and phytoplankton mass‐specific productivity was further observed in synchronous time.The profundal MOB enhanced pelagic‐profundal coupling and served as an alternative N support for pelagic plankton food webs during the winter and/or less productive seasons, adding to greater understanding of the role of methanotrophs in aquatic food webs. [ABSTRACT FROM AUTHOR]

Information on microbial biomass carbon (MBC) is crucial to assess their stocks and role for plant nutrient release in soil. Next to fumigation-extraction, molecular methods are routinely used to estimate the contribution of fungi, bacteria, and archaea to the soil microbial community. However, more information on the links between these different indices would deepen the understanding of microbial processes. The current study is based on 11 datasets, which contain MBC and MBN data obtained by fumigation-extraction and information on bacterial, archaeal, and fungal gene abundance, totalling 765 data points from agricultural, forest, and rangeland soils. Some of these datasets additionally provide information on double-stranded deoxyribonucleic acid (dsDNA) and fungal ergosterol. MBC varied around the median of 206 µg g−1 soil. MBN followed with a median MB-C/N ratio of 4.1. Median microbial gene abundance declined from bacteria (96 × 108) to archaea (4.4 × 108) to fungi (1.8 × 108). The median ratio of MBC/dsDNA was 15.8 and that of bacteria/dsDNA was 5.8 × 108 µg−1. The relationships between MBC and dsDNA as well as between bacterial gene abundance and dsDNA were both negatively affected by soil pH and positively by clay content. The median ergosterol/MBC and fungi/ergosterol ratios were 0.20% and 4.7 (n × 108 µg−1), respectively. The relationship between fungal gene abundance and ergosterol was negatively affected by soil pH and clay content. Our study suggests that combining fumigation-extraction with molecular tools allows more precise insights on the physiological interactions of soil microorganisms with their surrounding environment. [ABSTRACT FROM AUTHOR]