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Frontiers in Cellular and Infection... 2018Mounting evidence indicates that microbiome plays an important role in the development and progression of cancer. The dogma that urine in healthy individuals must be...
Mounting evidence indicates that microbiome plays an important role in the development and progression of cancer. The dogma that urine in healthy individuals must be sterile has been overturned. Dysbiosis of the urinary microbiome has been revealed responsible for various urological disorders, including prostate cancer. The link between chronic inflammation, microbiome and solid tumors has been established for various neoplastic diseases. However, a detailed and comprehensive analysis of urinary microenvironment of bladder cancer has not been yet reported. We performed this study to characterize the potential urinary microbial community possibly associated with bladder cancer. Mid-stream urine was collected from 31 male patients with bladder cancer and 18 non-neoplastic controls. DNA was extracted from urine pellet samples and processed for high throughput 16S rRNA amplicon sequencing of the V4 region using Illumina MiSeq. Sequencing reads were filtered using QIIME and clustered using UPARSE. We observed increased bacterial richness (Observed Species, Chao 1 and Ace indexes; cancer vs. control; 120.0 vs. 56.0; 134.5 vs. 68.3; and 139.6 vs. 72.9, respectively), enrichment of some bacterial genera (e.g., ) and decrease of some bacterial genera (e.g., , and ) in cancer group when compared to non-cancer group. Significant difference in beta diversity was found between cancer and non-cancer group, among different risk level, but not among different tumor grade. Enrichment of , and was observed in cancer patients with high risk of recurrence and progression, which means these genera maybe potential biomarkers for risk stratification. The PICRUSt showed that various functional pathways were enriched in cancer group, including infection, glycerolipid metabolism and retinol metabolism. To our knowledge, we performed the most comprehensive study to date to characterize the urinary microbiome associated with bladder cancer. A better understanding of the role of microbiome in the development and progression of bladder cancer could pave a new way for exploring new therapeutic options and biomarkers.
Topics: Aged; Biomarkers, Tumor; Carcinoma; China; DNA, Bacterial; Disease Progression; Humans; Male; Microbiota; Middle Aged; RNA, Ribosomal, 16S; Statistics, Nonparametric; Urinary Bladder; Urinary Bladder Neoplasms; Urothelium
PubMed: 29904624
DOI: 10.3389/fcimb.2018.00167 -
Scientific Reports Jan 2021We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through...
We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.
Topics: Biodiversity; Cluster Analysis; Cytophagaceae; DNA Barcoding, Taxonomic; DNA, Environmental; Forests; Fresh Water; Lactococcus; Mycoplasma; RNA, Ribosomal, 16S
PubMed: 33452291
DOI: 10.1038/s41598-020-80602-9 -
Environmental Science & Technology Jan 2023Bacteria play a crucial role in driving ecological processes in aquatic ecosystems. Studies have shown that bacteria-cyanobacteria interactions contributed significantly...
Bacteria play a crucial role in driving ecological processes in aquatic ecosystems. Studies have shown that bacteria-cyanobacteria interactions contributed significantly to phytoplankton dynamics. However, information on the contribution of bacterial communities to blooms remains scarce. Here, we tracked changes in the bacterial community during the development of a cyanobacterial bloom in an equatorial estuarine reservoir. Two forms of blooms were observed simultaneously corresponding to the lotic and lentic characteristics of the sampling sites where significant spatial variabilities in physicochemical water quality, cyanobacterial biomass, secondary metabolites, and cyanobacterial/bacterial compositions were detected. dominated the upstream sites during peak periods and were succeeded by when the bloom subsided. For the main body of the reservoir, a mixed bloom featuring coccoid and filamentous cyanobacteria (, , , , , and ) was observed. Concentrations of the picocyanobacteria remained high throughout the study, and their positive correlations with cylindrospermopsin and anatoxin-a suggested that they could produce cyanotoxins, which pose more damaging impacts than previously supposed. Succession of different cyanobacteria ( and ) following changes in nutrient composition and ionic strength was demonstrated. The microbiomes associated with blooms were unique to the dominant cyanobacteria. Generic and specialized bloom biomarkers for the and downstream mixed blooms were also identified. Microscillaceae, Chthoniobacteraceae, and were the major heterotrophic bacteria associated with bloom, whereas Phycisphaeraceae and Methylacidiphilaceae were the most prominent groups for the bloom. Collectively, bacterial community can be greatly deviated by the geological condition, monsoon season, cyanobacterial density, and dominant cyanobacteria.
Topics: Microcystis; Synechococcus; Phytoplankton; Microbiota; Water Quality; Lakes
PubMed: 36653016
DOI: 10.1021/acs.est.2c04943 -
Current Issues in Molecular Biology 2019Methanol, commercially generated from methane, is a renewable chemical feedstock that is highly soluble, relatively inexpensive, and easy to handle. The concept of... (Review)
Review
Methanol, commercially generated from methane, is a renewable chemical feedstock that is highly soluble, relatively inexpensive, and easy to handle. The concept of native methylotrophic bacteria serving as whole cell catalysts for production of chemicals and materials using methanol as a feedstock is highly attractive. In recent years, the available omics data for methylotrophic bacteria, especially for , the most well-characterized model methylotroph, have provided a solid platform for rational engineering of methylotrophic bacteria for industrial production. In addition, there is a strong interest in converting the more traditional heterotrophic production platforms toward the use of single carbon substrates, including methanol, through metabolic engineering. In this chapter, we review the recent progress toward achieving the desired growth and production yields from methanol, by genetically engineered native methylotrophic strains and by the engineered synthetic methylotrophs.
Topics: Biological Products; Biotransformation; Metabolic Engineering; Metabolic Networks and Pathways; Methane; Methanol; Methylobacterium extorquens; Organisms, Genetically Modified; Synthetic Biology
PubMed: 31166195
DOI: 10.21775/cimb.033.225 -
Frontiers in Microbiology 2021Four strains belonging to the family of were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three...
Four strains belonging to the family of were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as . The sequence similarity of these three ISS strains, designated as IF7SW-B2, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for gene, with the closest being SE2.11. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble and since they assimilate similar sugars as sole carbon substrate when compared to other species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C -ω7 and C -ω6. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus , and the name sp. nov. is proposed. The type strain is IF7SW-B2 (NRRL B-65601 and LMG 32165).
PubMed: 33790880
DOI: 10.3389/fmicb.2021.639396 -
Frontiers in Microbiology 2021The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: and They have been separated into...
The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: and They have been separated into three major clades: A, B (), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other . The species in clade A, including the type species , were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to species; this finding led us to reunite the two genera into a single genus . Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the HMPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.
PubMed: 34737731
DOI: 10.3389/fmicb.2021.740610 -
Microbiome Mar 2020Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a...
BACKGROUND
Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils.
RESULTS
Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a CO atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere.
CONCLUSION
In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.
Topics: Alcohol Oxidoreductases; Bacteria; DNA, Bacterial; Genetic Variation; Metagenome; Methanol; Methylobacterium; Phylogeny; Plant Physiological Phenomena; Plants; RNA, Ribosomal, 16S; Rhizosphere; Soil Microbiology
PubMed: 32156318
DOI: 10.1186/s40168-020-00801-4 -
Frontiers in Immunology 2022The cutaneous microbiome is increasingly recognized as a contributor to skin diseases like atopic dermatitis (AD) and psoriasis. Although traditionally AD and psoriasis...
The cutaneous microbiome is increasingly recognized as a contributor to skin diseases like atopic dermatitis (AD) and psoriasis. Although traditionally AD and psoriasis have been viewed as having opposing immunologic findings, recent evidence suggests an overlap in ceramide-family lipid production in the protection against symptoms. We recently identified that specific environmental pollutants may drive dysbiosis through direct suppression of ceramide-family lipids produced by health-associated skin bacteria in atopic dermatitis (AD). We further demonstrated that one such bacteria, , generated significant clinical improvement in AD lasting beyond active treatment lipid-mediated modulation of tumor necrosis factor (TNF) signaling. To assess the potential preclinical benefit of in psoriasis we assessed for direct effects on surface TNF signaling in cell cultures and identified direct effects on the TNF axis. We also identified preclinical efficacy of treatment in the imiquimod mouse model of psoriasis. Finally, we expanded our previous environmental assessment for psoriasis to include more traditional markers of air quality and found a strong association between disease rates and ambient carbon monoxide (CO), nitrogen dioxide (NO), and particulate matter (PM). At the current stage this work is speculative but does support consideration of further preclinical models and/or clinical assessments to evaluate any potential for therapeutic benefit through microbial manipulation and/or environmental mitigation.
Topics: Animals; Mice; Dermatitis, Atopic; Environmental Pollutants; Psoriasis; Ceramides; Lipids
PubMed: 36605199
DOI: 10.3389/fimmu.2022.1094376 -
Microorganisms Nov 2023Radiation methods are widely used for disinfection and sterilization applications. Microorganisms demonstrate known, variable tolerance levels to inactivation with lower...
Radiation methods are widely used for disinfection and sterilization applications. Microorganisms demonstrate known, variable tolerance levels to inactivation with lower doses of ionizing and non-ionizing radiation based on multiple mechanisms of resistance in their structures and nucleic acid repair mechanisms. The radiation dose required to ensure microbial inactivation during sterilization is typically based on the understanding and routine monitoring of the natural population and resistance of microorganisms on products exposed to radiation sterilization processes. This report describes the isolation of in a device manufacturing environment that was detected during routine device bioburden and dose verification monitoring. Sources of Gram-negative bacteria in the environment were investigated. Non-sterile examination gloves used during manufacturing were found to be a persistent source of and other microbial contaminants. The source of contamination was determined to be from the glove manufacturing process. Maintenance and routine microbiological controls during glove manufacturing, including water systems, are required to reduce the risks of gloves being a source of unexpected microbiological contamination.
PubMed: 38138003
DOI: 10.3390/microorganisms11122859 -
BMC Microbiology Jan 2022Urogenital microbiota may be associated with the recurrence of bladder cancer, but the underlying mechanism remains unclear. The notion that microbiota can upregulate...
BACKGROUND
Urogenital microbiota may be associated with the recurrence of bladder cancer, but the underlying mechanism remains unclear. The notion that microbiota can upregulate PD-L1 expression in certain epithelial tumors to promote immune escape has been demonstrated. Thus, we hypothesized that the urogenital microbiota may be involved in the recurrence and progression of non-muscle invasive bladder cancer (NMIBC) by upregulating the PD-L1 expression. To test this hypothesis, we investigated the relationship between urogenital microbial community and PD-L1 expression in male patients with NMIBC.
RESULTS
16S rRNA gene sequencing was performed to analyse the composition of urogenital microbiota, and the expression of PD-L1 in cancerous tissues was detected by immunohistochemistry. The subjects (aged 43-79 years) were divided into PD-L1-positive group (Group P, n = 9) and PD-L1-negative group (Group N, n = 19) respectively based on their PD-L1 immunohistochemical results. No statistically significant differences were found in the demographic characteristics between group P and N. We observed that group P exhibited higher species richness (based on Observed species and Ace index, both P < 0.05). Furthermore, subgroup analysis showed that the increase in number of PD-L1 positive cells was accompanied by increased richness of urogenital microbiota. Significantly different composition of urogenital microbiota was found between group P and group N (based on weighted Unifrac and unweighted Unifrac distances metric, both P < 0.05). Enrichment of some bacterial genera (e.g., Leptotrichia, Roseomonas, and Propionibacterium) and decrease of some bacterial genera (e.g., Prevotella and Massilia) were observed in group P as compared with group N. These findings indicated that these genera may affect the expression of PD-L1 through some mechanisms to be studied.
CONCLUSION
Our study provided for the first time an overview of the association between urogenital microbiota and PD-L1 expression in male patients with NMIBC, indicating that urogenital microbiota was an important determinant of PD-L1 expression in male NMIBC patients.
Topics: Adult; Aged; B7-H1 Antigen; Bacteria; Disease Progression; Humans; Male; Microbiota; Middle Aged; Recurrence; Urinary Bladder Neoplasms; Urogenital System
PubMed: 34983384
DOI: 10.1186/s12866-021-02407-8