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Biotechnology Reports (Amsterdam,... Jun 2024The environmental and economic impact of an oil spill can be significant. Biotechnologies applied during a marine oil spill involve bioaugmentation with immobilised or...
The environmental and economic impact of an oil spill can be significant. Biotechnologies applied during a marine oil spill involve bioaugmentation with immobilised or encapsulated indigenous hydrocarbonoclastic species selected under laboratory conditions to improve degradation rates. The environmental factors that act as stressors and impact the effectiveness of hydrocarbon removal are one of the challenges associated with these applications. Understanding how native microbes react to environmental stresses is necessary for effective bioaugmentation. Herein, isolated from a marine oil spill mooring system showed hydrocarbonoclastic activity on Maya crude oil in a short time by means of total petroleum hydrocarbons (TPH) at 144 h: up to 98.79 % and 97.77 % removal. The assessment of biofilms at different temperature (30 °C and 50 °C), pH (5, 6, 7, 8, 9), salinity (30, 50, 60, 70, 80 g/L), and crude oil concentration (1, 5, 15, 25, 35 %) showed different response to the stressors depending on the strain. According to response surface analysis, the main effect was temperature > salinity > hydrocarbon concentration. The hydrocarbonoclastic biofilm architecture was characterised using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Subtle but significant differences were observed: pili in by SEM and the topographical differences measured by AFM Power Spectral Density (PSD) analysis, roughness was higher in than in In all three domains of life, the Universal Stress Protein (Usp) is crucial for stress adaptation. Herein, the A gene expression was analysed in biofilm under environmental stressors. The A expression increased up to 2.5-fold in biofilms at 30 °C, and 1.3-fold at 50 °C. The highest A expression was recorded in M. biofilms at 50 °C with 2.5 and 3-fold with salinities of 50, 60, and 80 g/L at hydrocarbon concentrations of 15, 25, and 35 %. biofilms showed greater resilience than biofilms when exposed to harsh environmental stressors. biofilms were thicker than biofilms. Both biofilm responses to environmental stressors through A gene expression were consistent with the behaviours observed in the response surface analyses. The gene is a suitable biomarker for assessing environmental stressors of potential microorganisms for bioremediation of marine oil spills and for biosensing the ecophysiological status of native microbiota in a marine petroleum environment.
PubMed: 38948351
DOI: 10.1016/j.btre.2024.e00834 -
BMC Microbiology Jun 2024Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer...
BACKGROUND
Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied.
RESULTS
We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin.
CONCLUSIONS
This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
Topics: Paenibacillus; Anti-Bacterial Agents; Multigene Family; Genome, Bacterial; Peptide Synthases; Polyketide Synthases; Bacteriocins; Biosynthetic Pathways; Bacterial Proteins; Drug Discovery
PubMed: 38937695
DOI: 10.1186/s12866-024-03375-5 -
Molecules (Basel, Switzerland) Jun 2024Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy...
Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography-mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, ( 0.01), unclassified class ( 0.05), and ( 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk ( > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation ( > 0.8), such as and , was the main factor causing milk spoilage and that the group with lower correlation ( < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk's initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.
Topics: Microbiota; Animals; Milk; Food Storage; Pasteurization; High-Throughput Nucleotide Sequencing; Dairy Products; Metagenomics; Gas Chromatography-Mass Spectrometry; Food Handling; Bacteria; Metabolome
PubMed: 38930811
DOI: 10.3390/molecules29122745 -
BMC Chemistry Jun 2024The antibacterial characteristics of graphene oxide (GO-SB) nano-sheets generated by charring sugarcane bagasse (SB) are described in this study. The antibacterial...
Fluffy-like amphiphilic graphene oxide and its effects on improving the antibacterial activity and thermal outstanding of ethyl cellulose /polyvinyl alcohol hydrogel film.
The antibacterial characteristics of graphene oxide (GO-SB) nano-sheets generated by charring sugarcane bagasse (SB) are described in this study. The antibacterial capability of GO-SB was improved when it was grafted with ethyl cellulose (EC) and polyvinyl alcohol (PVA) to form GO-SB/EC/PVA hydrogels. Characterization of GO-SB nanosheets and GO-SB/EC/PVA hydrogels was accomplished by using FTIR, SEM, XRD, and thermal studies. The antimicrobial activity was carried out against Gram positive bacteria [Micrococcus leutus & Staphylococcus aureus], Gram negative bacteria [Escherichia coli, Pseudomonas aeruginosa] and pathogenic fungal yeast [Candida albicans] applying the disc diffusion method. The disc diffusion method results showed that the improved GO-SB/EC/PVA exhibited a reasonable level of antimicrobial capability against Micrococcus leutus, demonstrating that the antimicrobial improvement of GO-SB was more effective in the GO-SB/EC/PVA hydrogels by increasing the inhibition zone of Gram-positive bacteria, Micrococcus leutus from (13.0 to 16.0 mm).
PubMed: 38926782
DOI: 10.1186/s13065-024-01221-3 -
Chemistry & Biodiversity Jun 2024Antimicrobial films were prepared with chitosan containing the methanolic extract of M. tenuiflora leaves (FECT20%, FECT30%, and FECT40%), and their antimicrobial...
Antimicrobial films were prepared with chitosan containing the methanolic extract of M. tenuiflora leaves (FECT20%, FECT30%, and FECT40%), and their antimicrobial activities were evaluated by agar diffusion. The films were characterized by IR spectroscopy, scanning electron microscopy (SEM) and TG/DTG curves. TG/DTG curves showed thermal stability of chitosan-extract films up to 166 ºC. Micrographs of chitosan-extract films revealed an increase in porosity with the addition of extract. The FECT40% film showed inhibition zone diameters (IZ) against Micrococcus luteus, Staphylococcus aureus, Bacillus subtilis, and B. cereus, ranging from 1.0 ± 0.02 to 0.72 ± 0.09 cm. Only FECT30% and FECT40% inhibited the P. aeruginosa with IZs of 0.68 ± 0.02 and 0.77 ± 0.06 cm, respectively. In turn, the extract showed inhibition against B. subtilis and B. cereus, with IZs values of 0.92 ± 0.2 cm and 0.72 ± 0.05 cm, respectively. Additionally, the crude extract presented antioxidant potential with inhibition percentages of 32.74% ± 0.90 for ABTS and 27.04% ± 1.36 for DPPH. The antimicrobial and antioxidant activities of the crude extract, as well as the antimicrobial property of chitosan-extract films, suggests the potential of these biopolymers for the development of wound healing bandages and new food packaging alternatives.
PubMed: 38923658
DOI: 10.1002/cbdv.202400645 -
Environmental Microbiology Reports Jun 2024Human activities are a significant contributor to the spread of antibiotic resistance genes (ARGs), which pose a serious threat to human health. These ARGs can be...
Human activities are a significant contributor to the spread of antibiotic resistance genes (ARGs), which pose a serious threat to human health. These ARGs can be transmitted through various pathways, including air, within the context of One Health. This study used metagenomics to monitor the resistomes in urban air from two critical locations: a wastewater treatment plant and a hospital, both indoor and outdoor. The presence of cell-like structures was confirmed through fluorescence microscopy. The metagenomic analysis revealed a wide variety of ARGs and a high diversity of antibiotic-resistant bacteria in the airborne particles collected. The wastewater treatment plant showed higher relative abundances with 32 ARG hits per Gb and m, followed by the main entrance of the hospital (indoor) with ≈5 ARG hits per Gb and m. The hospital entrance exhibited the highest ARG richness, with a total of 152 different ARGs classified into nine categories of antibiotic resistance. Common commensal and pathogenic bacteria carrying ARGs, such as Moraxella, Staphylococcus and Micrococcus, were detected in the indoor airborne particles of the hospital. Interestingly, no ARGs were shared among all the samples analysed, indicating a highly variable dynamic of airborne resistomes. Furthermore, the study found no ARGs in the airborne viral fractions analysed, suggesting that airborne viruses play a negligible role in the dissemination of ARGs.
Topics: Air Microbiology; Bacteria; Humans; Metagenomics; Drug Resistance, Bacterial; One Health; Metagenome; Wastewater; Genes, Bacterial; Hospitals; Anti-Bacterial Agents; Cities
PubMed: 38923122
DOI: 10.1111/1758-2229.13306 -
AIMS Microbiology 2024Transcriptomic and proteomic analysis were performed on 72 h biofilms of the acneic strain and planktonic cultures in the presence of epinephrine. Epinephrine...
Transcriptomic and proteomic analysis were performed on 72 h biofilms of the acneic strain and planktonic cultures in the presence of epinephrine. Epinephrine predominantly downregulated genes associated with various transporter proteins. No correlation was found between proteomic and transcriptomic profiles. In control samples, the expression of 51 proteins differed between planktonic cultures and biofilms. Addition of 5 nM epinephrine reduced this number, and in the presence of 5 µM epinephrine, the difference in proteomic profiles between planktonic cultures and biofilms disappeared. According to the proteomic profiling, epinephrine itself was more effective in the case of biofilms and potentially affected the tricarboxylic acid cycle (as well as alpha-ketoglutarate decarboxylase Kgd), biotin synthesis, cell division, and transport of different compounds in cells. These findings are consistent with recent research on , suggesting that the effects of epinephrine on actinobacteria may be universal.
PubMed: 38919714
DOI: 10.3934/microbiol.2024019 -
Microbiology Resource Announcements Jun 2024Endophytes play important roles in potato production. The whole genome of endophytic sp. Strain HOU01, isolated from potato root grown at Vietnam National University of...
Endophytes play important roles in potato production. The whole genome of endophytic sp. Strain HOU01, isolated from potato root grown at Vietnam National University of Agriculture, Hanoi, Vietnam, was sequenced using Oxford Nanopore's PromethION platform. The complete circular genome is 2,552,707 bp with a GC content of 72.5%.
PubMed: 38916298
DOI: 10.1128/mra.00268-24 -
Frontiers in Microbiology 2024The concept of a sterile uterus was challenged by recent studies that have described the microbiome of the virgin and pregnant uterus for species including humans and...
INTRODUCTION
The concept of a sterile uterus was challenged by recent studies that have described the microbiome of the virgin and pregnant uterus for species including humans and cattle. We designed two studies that tested whether the microbiome is introduced into the uterus when the virgin heifer is first inseminated and whether the origin of the microbiome is the vagina/cervix.
METHODS
The uterine microbiome was measured immediately before and after an artificial insemination (AI; Study 1; = 7 AI and = 6 control) and 14 d after insemination (Study 2; = 12 AI and = 12 control) in AI and non-AI (control) Holstein heifers. A third study (Study 3; = 5 Holstein heifers) that included additional negative controls was subsequently conducted to support the presence of a unique microbiome within the uterus despite the low microbial biomass and regardless of insemination. Traditional bacteriological culture was performed in addition to 16S rRNA gene sequencing on the same samples to determine whether there were viable organisms in addition to those detected based on DNA sequencing (16S rRNA gene sequence).
RESULTS AND DISCUSSION
Inseminating a heifer did not lead to a large change in the microbiome when assessed by traditional methods of bacterial culture or metataxonomic (16S rRNA gene) sequencing (results of Studies 1 and 2). Very few bacteria were cultured from the body or horn of the uterus regardless of whether an AI was or was not (negative control) performed. The cultured bacterial genera (e.g., , and ) were typical of those found in the soil, environment, skin, mucous membranes, and urogenital tract of animals. Metataxonomic sequencing of 16S rRNA gene generated a large number of amplicon sequence variants (ASV), but these larger datasets that were based on DNA sequencing did not consistently demonstrate an effect of AI on the abundance of ASVs across all uterine locations compared with the external surface of the tract (e.g., perimetrium; positive control samples for environment contamination during slaughter and collection). Major genera identified by 16S rRNA gene sequencing overlapped with those identified with bacterial culture and included , and .
PubMed: 38903779
DOI: 10.3389/fmicb.2024.1385505 -
Skin Research and Technology : Official... Jun 2024Ultraviolet (UV)-induced fluorescence technology is widely used in dermatology to identify microbial infections. Our clinical observations under an ultraviolet-induced...
BACKGROUND
Ultraviolet (UV)-induced fluorescence technology is widely used in dermatology to identify microbial infections. Our clinical observations under an ultraviolet-induced fluorescent dermatoscope (UVFD) showed red fluorescence on the scalps of androgenetic alopecia (AGA) patients. In this study, based on the hypothesis that microbes are induced to emit red fluorescence under UV light, we aimed to explore the microbial disparities between the AGA fluorescent area (AF group) and AGA non-fluorescent area (ANF group).
METHODS
Scalp swab samples were collected from 36 AGA patients, including both fluorescent and non-fluorescent areas. The bacterial communities on the scalp were analyzed by 16S rRNA gene sequencing and bioinformatics analysis, as well as through microbial culture methods.
RESULTS
Significant variations were observed in microbial evenness, abundance composition, and functional predictions between fluorescent and non-fluorescent areas. Sequencing results highlighted significant differences in Cutibacterium abundance between these areas (34.06% and 21.36%, respectively; p < 0.05). Furthermore, cultured red fluorescent colonies primarily consisted of Cutibacterium spp., Cutibacterium acnes, Staphylococcus epidermidis, and Micrococcus spp.
CONCLUSIONS
This is the first study to investigate scalp red fluorescence, highlighting microbial composition variability across different scalp regions. These findings may provide novel insights into the microbiological mechanisms of AGA.
Topics: Humans; Alopecia; Ultraviolet Rays; Male; Adult; Middle Aged; Scalp; Female; Dermoscopy; Fluorescence; Microbiota; RNA, Ribosomal, 16S; Bacteria
PubMed: 38899718
DOI: 10.1111/srt.13777