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Communicative & Integrative Biology 2024The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a... (Review)
Review
The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a dominance of divalent cations, with magnesium chloride (MgCl) levels approaching the predicted 2.3 M upper limit for life, an acidic pH of 6.0, and high levels of absorbed ultraviolet radiation. Consequently, only organisms adapted to such a polyextreme environment can survive in the surface, sinkholes, sediments, muds, and underwater springs of the Dead Sea. Metagenomic sequence analysis and amino acid profiling indicated that the Dead Sea is predominantly composed of halophiles that have various adaptation mechanisms and produce metabolites that can be utilized for biotechnological purposes. A variety of products have been obtained from halophilic microorganisms isolated from the Dead Sea, such as antimicrobials, bioplastics, biofuels, extremozymes, retinal proteins, colored pigments, exopolysaccharides, and compatible solutes. These resources find applications in agriculture, food, biofuel production, industry, and bioremediation for the detoxification of wastewater and soil. Utilizing halophiles as a bioprocessing platform offers advantages such as reduced energy consumption, decreased freshwater demand, minimized capital investment, and continuous production.
PubMed: 38919836
DOI: 10.1080/19420889.2024.2369782 -
AIMS Microbiology 2024In this study, we used 16S rRNA gene sequence analysis to describe the diversity of cultivable endophytic bacteria associated with fennel ( Mill.) and determined their...
In this study, we used 16S rRNA gene sequence analysis to describe the diversity of cultivable endophytic bacteria associated with fennel ( Mill.) and determined their plant-beneficial traits. The bacterial isolates from the roots of fennel belonged to four phyla: (BRN1 and BRN3), (BRN5, BRN6, and BRN7), (BRN2), and (BRN4). The bacterial isolates from the shoot of fennel represented the phyla (BSN1, BSN2, BSN3, BSN5, BSN6, BSN7, and BSN8), (BSN4, BRN1, and BRN3), and (BRN4). The bacterial species , , and were found both in the roots and shoots of fennel. The bacterial isolates were found to produce siderophores, HCN, and indole-3-acetic acid (IAA), as well as hydrolytic enzymes such as chitinase, protease, glucanase, and lipase. Seven bacterial isolates showed antagonistic activity against , , and . Our findings show that medicinal plants with antibacterial activity may serve as a source for the selection of microorganisms that exhibit antagonistic activity against plant fungal infections and may be considered as a viable option for the management of fungal diseases. They can also serve as an active part of biopreparation, improving plant growth.
PubMed: 38919721
DOI: 10.3934/microbiol.2024022 -
AIMS Microbiology 2024The oral microbiome represents an essential component of the oral ecosystem whose symbiotic relationship contributes to health maintenance. The biofilm represents a... (Review)
Review
The oral microbiome represents an essential component of the oral ecosystem whose symbiotic relationship contributes to health maintenance. The biofilm represents a state of living of microorganisms surrounding themselves with a complex and tridimensional organized polymeric support and defense matrix. The substrates where the oral biofilm adhere can suffer from damages due to the microbial community metabolisms. Therefore, microbial biofilm represents the main etiological factor of the two pathologies of dental interest with the highest incidence, such as carious pathology and periodontal pathology. The study, analysis, and understanding of the characteristics of the biofilm, starting from the macroscopic structure up to the microscopic architecture, appear essential. This review examined the morphological methods used through the years to identify species, adhesion mechanisms that contribute to biofilm formation and stability, and how the action of microbicidal molecules is effective against pathological biofilm. Microscopy is the primary technique for the morphological characterization of biofilm. Light microscopy, which includes the stereomicroscope and confocal laser microscopy (CLSM), allows the visualization of microbial communities in their natural state, providing valuable information on the spatial arrangement of different microorganisms within the biofilm and revealing microbial diversity in the biofilm matrix. The stereomicroscope provides a three-dimensional view of the sample, allowing detailed observation of the structure, thickness, morphology, and distribution of the various species in the biofilm while CLSM provides information on its three-dimensional architecture, microbial composition, and dynamic development. Electron microscopy, scanning (SEM) or transmission (TEM), allows the high-resolution investigation of the architecture of the biofilm, analyzing the bacterial population, the extracellular polymeric matrix (EPS), and the mechanisms of the physical and chemical forces that contribute to the adhesion of the biofilm to the substrates, on a nanometric scale. More advanced microscopic methodologies, such as scanning transmission electron microscopy (STEM), high-resolution transmission electron microscopy (HR-TEM), and correlative microscopy, have enabled the evaluation of antibacterial treatments, due to the potential to reveal the efficacy of different molecules in breaking down the biofilm. In conclusion, evidence based on scientific literature shows that established microscopic methods represent the most common tools used to characterize biofilm and its morphology in oral microbiology. Further protocols and studies on the application of advanced microscopic techniques are needed to obtain precise details on the microbiological and pathological aspects of oral biofilm.
PubMed: 38919718
DOI: 10.3934/microbiol.2024020 -
Frontiers in Microbiology 2024Commensal intestinal bacteria shape our microbiome and have decisive roles in preserving host metabolic and immune homeostasis. They conspicuously impact disease...
Longitudinal microbiome investigation throughout prion disease course reveals pre- and symptomatic compositional perturbations linked to short-chain fatty acid metabolism and cognitive impairment in mice.
Commensal intestinal bacteria shape our microbiome and have decisive roles in preserving host metabolic and immune homeostasis. They conspicuously impact disease development and progression, including amyloid-beta (Aβ) and alpha (α)-synuclein pathology in neurodegenerative diseases, conveying the importance of the brain-gut-microbiome axis in such conditions. However, little is known about the longitudinal microbiome landscape and its potential clinical implications in other protein misfolding disorders, such as prion disease. We investigated the microbiome architecture throughout prion disease course in mice. Fecal specimens were assessed by 16S ribosomal RNA sequencing. We report a temporal microbiome signature in prion disease and uncovered alterations in Lachnospiraceae, Ruminococcaceae, Desulfovibrionaceae, and Muribaculaceae family members in this disease. Moreover, we determined the enrichment of Bilophila, a microorganism connected to cognitive impairment, long before the clinical manifestation of disease symptoms. Based on temporal microbial abundances, several associated metabolic pathways and resulting metabolites, including short-chain fatty acids, were linked to the disease. We propose that neuroinflammatory processes relate to perturbations of the intestinal microbiome and metabolic state by an interorgan brain-gut crosstalk. Furthermore, we describe biomarkers possibly suitable for early disease diagnostics and anti-prion therapy monitoring. While our study is confined to prion disease, our discoveries might be of equivalent relevance in other proteinopathies and central nervous system pathologies.
PubMed: 38919500
DOI: 10.3389/fmicb.2024.1412765 -
Medical Science Monitor Basic Research Jun 2024BACKGROUND Urogenital bacterial infections have a high incidence in humans. The most frequent cause of infections of the urogenital tract is gram-negative bacteria.... (Comparative Study)
Comparative Study
A Comparison of Outcomes from Antibiotic Treatment with and without Probiotics in 897 Patients with Lower Urogenital Tract Infections, Including Cystitis, Urethritis, Prostatitis, and Vulvovaginitis.
BACKGROUND Urogenital bacterial infections have a high incidence in humans. The most frequent cause of infections of the urogenital tract is gram-negative bacteria. Antibiotics are very effective in curing infectious diseases but they are accompanied by health complications. Probiotics are live microorganisms that are believed to confer a beneficial effect on human health when consumed in adequate amounts. This study aimed to compare outcomes from antibiotic treatment with and without the use of probiotics in 897 patients with lower urogenital tract infections, including cystitis, urethritis, prostatitis, and vulvovaginitis. MATERIAL AND METHODS A total of 897 patients aged 18 to 55 years were included in this research. Patients were divided into an intervention group including 460 patients (254 women, 206 men) and a comparison group including 437 patients (240 women, 197 men). The probiotics received by patients were capsules of ProBalans®. The diagnosis of cystitis, urethritis, prostatitis, vulvovaginitis, and sexually transmitted infection was done using several tests, and antibiotics were used for treatment. Qualitative data were analyzed using the chi-square or Fisher exact test. RESULTS We found a significant difference regarding patients' impressions of improvement after therapy between patients in the intervention group and the comparison group. CONCLUSIONS Use of probiotics together with antibiotics in the treatment of urogenital tract infection can help to reduce the adverse effects of antibiotics, increase the efficiency of antibiotic therapy, and reduce bacterial resistance to antibiotics. However, further research is needed to confirm these potential health benefits.
Topics: Humans; Adult; Probiotics; Male; Female; Middle Aged; Anti-Bacterial Agents; Cystitis; Adolescent; Young Adult; Prostatitis; Urethritis; Vulvovaginitis; Treatment Outcome; Urinary Tract Infections
PubMed: 38918937
DOI: 10.12659/MSMBR.943939 -
Microbiome Jun 2024Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via...
BACKGROUND
Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the "salt-in" strategy, involving inorganic ion uptake, or the "salt-out" strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem.
RESULTS
Here, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline-specific to low-, intermediate-, or high-salinity-based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the "inorganic ion transport and metabolism" COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the "salt-in" strategy, three to the "salt-out" strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K transporter related to the "salt-in" strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla.
CONCLUSIONS
We demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the "salt-in" strategy mediated by Trk-type K transporters for microorganisms thriving under osmotic stress in the short residence-time estuary. Video Abstract.
Topics: Estuaries; Salinity; Metagenomics; Bacteria; Archaea; Metagenome; Adaptation, Physiological; Microbiota; Seawater; Water Microbiology
PubMed: 38918820
DOI: 10.1186/s40168-024-01817-w -
BMC Infectious Diseases Jun 2024Healthcare-Associated Infections (HAIs) are a global public health issue, representing a significant burden of disease that leads to prolonged hospital stays,...
BACKGROUND
Healthcare-Associated Infections (HAIs) are a global public health issue, representing a significant burden of disease that leads to prolonged hospital stays, inappropriate use of antimicrobial drugs, intricately linked to the development of resistant microorganisms, and higher costs for healthcare systems. The study aimed to measure the prevalence of HAIs, the use of antimicrobials, and assess healthcare- and patient-related risk factors, to help identify key intervention points for effectively reducing the burden of HAIs.
METHODS
A total of 28 acute care hospitals in the Lombardy region, Northern Italy, participated in the third European Point Prevalence Survey (PPS-3) coordinated by ECDC for the surveillance of HAIs in acute care hospitals (Protocol 6.0).
RESULTS
HAIs were detected in 1,259 (10.1%, 95% CI 9.6-10.7%) out of 12,412 enrolled patients. 1,385 HAIs were reported (1.1 HAIs per patient on average). The most common types of HAIs were bloodstream infections (262 cases, 18.9%), urinary tract infections (237, 17.1%), SARS-CoV-2 infections (236, 17.0%), pneumonia and lower respiratory tract infections (231, 16.7%), and surgical site infections (152, 11.0%). Excluding SARS-CoV-2 infections, the overall prevalence of HAIs was 8.4% (95% CI 7.9-8.9%). HAIs were significantly more frequent in patients hospitalized in smaller hospitals and in intensive care units (ICUs), among males, advanced age, severe clinical condition and in patients using invasive medical devices. Overall, 5,225 patients (42.1%, 95% CI 41.3-43.0%) received systemic antimicrobial therapy. According to the WHO's AWaRe classification, the Access group accounted for 32.7% of total antibiotic consumption, while Watch and Reserve classes accounted for 57.0% and 5.9% respectively. From a microbiological perspective, investigations were conducted on only 64% of the HAIs, showing, however, a significant pattern of antibiotic resistance.
CONCLUSIONS
The PPS-3 in Lombardy, involving data collection on HAIs and antimicrobial use in acute care hospitals, highlights the crucial need for a structured framework serving both as a valuable benchmark for individual hospitals and as a foundation to effectively channel interventions to the most critical areas, prioritizing future regional health policies to reduce the burden of HAIs.
Topics: Humans; Italy; Male; Cross Infection; Female; Aged; Middle Aged; Prevalence; Adult; Aged, 80 and over; Adolescent; Young Adult; Hospitals; Child, Preschool; Child; Risk Factors; Infant; Infant, Newborn; COVID-19; Anti-Infective Agents; Anti-Bacterial Agents; Surveys and Questionnaires; Urinary Tract Infections
PubMed: 38918691
DOI: 10.1186/s12879-024-09487-7 -
Nature Medicine Jun 2024The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design....
The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.
PubMed: 38918632
DOI: 10.1038/s41591-024-03067-7 -
Nature Microbiology Jun 2024Tryptophan is catabolized by gut microorganisms resulting in a wide range of metabolites implicated in both beneficial and adverse host effects. How gut microbial...
Tryptophan is catabolized by gut microorganisms resulting in a wide range of metabolites implicated in both beneficial and adverse host effects. How gut microbial tryptophan metabolism is directed towards indole, associated with chronic kidney disease, or towards protective indolelactic acid (ILA) and indolepropionic acid (IPA) is unclear. Here we used in vitro culturing and animal experiments to assess gut microbial competition for tryptophan and the resulting metabolites in a controlled three-species defined community and in complex undefined human faecal communities. The generation of specific tryptophan-derived metabolites was not predominantly determined by the abundance of tryptophan-metabolizing bacteria, but rather by substrate-dependent regulation of specific metabolic pathways. Indole-producing Escherichia coli and ILA- and IPA-producing Clostridium sporogenes competed for tryptophan within the three-species community in vitro and in vivo. Importantly, fibre-degrading Bacteroides thetaiotaomicron affected this competition by cross-feeding monosaccharides to E. coli. This inhibited indole production through catabolite repression, thus making more tryptophan available to C. sporogenes, resulting in increased ILA and IPA production. The fibre-dependent reduction in indole was confirmed using human faecal cultures and faecal-microbiota-transplanted gnotobiotic mice. Our findings explain why consumption of fermentable fibres suppresses indole production but promotes the generation of other tryptophan metabolites associated with health benefits.
PubMed: 38918470
DOI: 10.1038/s41564-024-01737-3 -
Applied Microbiology and Biotechnology Jun 2024Smokeless tobacco products (STPs) are attributed to oral cancer and oral pathologies in their users. STP-associated cancer induction is driven by carcinogenic compounds...
Smokeless tobacco products (STPs) are attributed to oral cancer and oral pathologies in their users. STP-associated cancer induction is driven by carcinogenic compounds including tobacco-specific nitrosamines (TSNAs). The TSNAs synthesis could enhanced due to the metabolic activity (nitrate metabolism) of the microbial populations residing in STPs, but identifying microbial functions linked to the TSNAs synthesis remains unexplored. Here, we rendered the first report of shotgun metagenomic sequencing to comprehensively determine the genes of all microorganisms residing in the Indian STPs belonging to two commercial (Moist-snuff and Qiwam) and three loose (Mainpuri Kapoori, Dohra, and Gudakhu) STPs, specifically consumed in India. Further, the level of nicotine, TSNAs, mycotoxins, and toxic metals were determined to relate their presence with microbial activity. The microbial population majorly belongs to bacteria with three dominant phyla including Actinobacteria, Proteobacteria, and Firmicutes. Furthermore, the STP-linked microbiome displayed several functional genes associated with nitrogen metabolism and antibiotic resistance. The chemical analysis revealed that the Mainpuri Kapoori product contained a high concentration of ochratoxins-A whereas TSNAs and Zink (Zn) quantities were high in the Moist-snuff, Mainpuri Kapoori, and Gudakhu products. Hence, our observations will help in attributing the functional potential of STP-associated microbiome and in the implementation of cessation strategies against STPs. KEY POINTS: •Smokeless tobacco contains microbes that can assist TSNA synthesis. •Antibiotic resistance genes present in smokeless tobacco-associated bacteria. •Pathogens in STPs can cause infections in smokeless tobacco users.
Topics: Tobacco, Smokeless; Metagenomics; Bacteria; Microbiota; Nitrosamines; India; Nicotine; Humans
PubMed: 38918238
DOI: 10.1007/s00253-024-13156-9