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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 -
International Journal of Systematic and... Oct 2017A Gram-stain-negative, strictly aerobic bacterium, designated HC1, was isolated from an air conditioner in South Korea. Cells were orange, non-motile cocci with oxidase-...
A Gram-stain-negative, strictly aerobic bacterium, designated HC1, was isolated from an air conditioner in South Korea. Cells were orange, non-motile cocci with oxidase- and catalase-positive activities and did not contain bacteriochlorophyll a. Growth of strain HC1 was observed at 10-45 °C (optimum, 30 °C), pH 4.5-9.5 (optimum, pH 7.0) and 0-3 % (w/v) NaCl (optimum, 0 %). Strain HC1 contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0 and cyclo-C19 : 0ω8c as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid were detected as the major polar lipids. The major carotenoid was hydroxyspirilloxanthin. The G+C content of the genomic DNA was 70.1 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain HC1 formed a phylogenetic lineage within the genus Roseomonas. Strain HC1 was most closely related to the type strains of Roseomonas oryzae, Roseomonas rubra, Roseomonas aestuarii and Roseomonas rhizosphaerae with 98.1, 97.9, 97.6 and 96.8 % 16S rRNA gene sequence similarities, respectively, but the DNA-DNA relatedness values between strain HC1 and closely related type strains were less than 70 %. Based on phenotypic, chemotaxonomic and molecular properties, strain HC1 represents a novel species of the genus Roseomonas, for which the name Roseomonas aerofrigidensis sp. nov. is proposed. The type strain is HC1 (=KACC 19097=JCM 31878).
Topics: Air Conditioning; Bacterial Typing Techniques; Base Composition; Carotenoids; DNA, Bacterial; Fatty Acids; Methylobacteriaceae; Nucleic Acid Hybridization; Phosphatidylcholines; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Ubiquinone
PubMed: 28905700
DOI: 10.1099/ijsem.0.002246 -
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 -
Bioscience, Biotechnology, and... Dec 2022C1-microorganisms that can utilize C1-compounds, such as methane and methanol, are ubiquitous in nature, and contribute to drive the global carbon cycle between two... (Review)
Review
C1-microorganisms that can utilize C1-compounds, such as methane and methanol, are ubiquitous in nature, and contribute to drive the global carbon cycle between two major greenhouse gases, CO2 and methane. Plants emit C1-compounds from their leaves and provide habitats for C1-microorganisms. Among C1-microorganisms, Methylobacterium spp., representative of methanol-utilizing methylotrophic bacteria, predominantly colonize the phyllosphere and are known to promote plant growth. This review summarizes the interactions between C1-mircroorganisms and plants that affect not only the fixation of C1-compounds produced by plants but also CO2 fixation by plants. We also describe our recent understanding of the survival strategy of C1-microorganisms in the phyllosphere and the application of Methylobacterium spp. to improve rice crop yield.
Topics: Methanol; Carbon Dioxide; Plants; Methane; Methylobacterium; Plant Leaves; Carbon
PubMed: 36367545
DOI: 10.1093/bbb/zbac176 -
International Journal of Systematic and... Mar 2018An aerobic, Gram-negative, motile by means of a single polar flagellum, and ovoid-shaped bacterium, designated D3, was isolated from shallow stream sediments in...
An aerobic, Gram-negative, motile by means of a single polar flagellum, and ovoid-shaped bacterium, designated D3, was isolated from shallow stream sediments in Sinan-gun, South Korea. Growth occurred at 15-40 °C (optimum 35 °C), at pH 7.0-8.0 (optimum pH 7.0), and at an optimum NaCl concentration of 0.5 % (w/v). The major cellular fatty acids (>7 % of the total) were C16 : 0, C18 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant quinone was ubiquinone-10, and the G+C content of the genomic DNA of strain D3 was 73.1 mol%. The major polyamine was spermidine. The major polar lipids of the isolate were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D3 clustered with Roseomonas aquatica TR53 within the genus Roseomonas. The 16S rRNA gene sequence of strain D3 showed the highest sequence similarity to R. aquatica TR53 (95.9 %), followed by Roseomonas rosea 173-96 (95.7 %) and Roseomonas aerilata 5420S-30 (95.0 %). Based on the phenotypic, phylogenetic and chemotaxonomic characterization, strain D3 represents a novel species of the genus Roseomonas, for which the name Roseomonas fluminis sp. nov. is proposed. The type strain is D3 (=KACC 19269=JCM 31968).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Methylobacteriaceae; Nucleic Acid Hybridization; Phosphatidylglycerols; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Rivers; Sequence Analysis, DNA; Ubiquinone
PubMed: 29458474
DOI: 10.1099/ijsem.0.002578 -
Photochemical & Photobiological... Dec 2023Methylotrophs are a diverse group of bacteria that abundantly colonize the phyllosphere and have great potential to withstand UV irradiation because of their pigmented...
Methylotrophs are a diverse group of bacteria that abundantly colonize the phyllosphere and have great potential to withstand UV irradiation because of their pigmented nature and ability to promote plant growth through various mechanisms. The present study investigated the effects of UVB radiation on plant growth-promoting (PGP) properties of methylotrophic bacteria and the growth of Vigna radiata L. A total of 55 methylotrophic bacteria were isolated from desert plants, and 15 methylotrophs were resistant to UVB radiation for 4 h. All UVB-resistant methylotrophs possess a methyldehydrogenase gene. Identification based on 16S rRNA gene sequencing revealed that all 15 UVB-resistant methylotrophs belonged to the genera Methylorubrum (07), Methylobacterium (07), and Rhodococcus (01). Screening of methylotrophs for PGP activity in the presence and absence of UVB radiation revealed that all isolates showed ACC deaminase activity and growth on a nitrogen-free medium. Furthermore, the production of IAA-like substances ranged from 8.62 to 85.76 µg/mL, siderophore production increased from 3.47 to 65.75% compared to the control. Seed germination assay with V. radiata L. (mung bean) exposed to UVB radiation revealed that methylotrophs improved seed germination, root length, and shoot length compared to the control. The present findings revealed that the isolates SD3, SD2, KD1, KD5, UK1, and UK3 reduced the deleterious effects of UVB radiation on mung bean plants and can be used to protect seedlings from UVB radiation for sustainable agriculture.
Topics: Vigna; RNA, Ribosomal, 16S; Methylobacterium; Seedlings
PubMed: 37838625
DOI: 10.1007/s43630-023-00490-6 -
Molecular Microbiology Oct 2021Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as...
Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE and crtB we disrupted the production of squalene and phytoene in M. extorquens PA1, which are the presumed precursors for hopanoids and carotenoids respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C backbone, rather than the previously predicted canonical C phytoene-derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1.
Topics: Bacterial Outer Membrane; Biosynthetic Pathways; Carotenoids; Gene Knockdown Techniques; Geranylgeranyl-Diphosphate Geranylgeranyltransferase; Methylobacterium extorquens; Oxidative Stress; Oxidoreductases; Phylogeny; Planctomycetes; Sequence Deletion; Squalene
PubMed: 34387371
DOI: 10.1111/mmi.14794 -
Methods in Enzymology 2021Recent work has revealed that certain lanthanides-in particular, the more earth-abundant, lighter lanthanides-play essential roles in pyrroloquinoline quinone (PQQ)...
Recent work has revealed that certain lanthanides-in particular, the more earth-abundant, lighter lanthanides-play essential roles in pyrroloquinoline quinone (PQQ) dependent alcohol dehydrogenases from methylotrophic and non-methylotrophic bacteria. More recently, efforts of several laboratories have begun to identify the molecular players (the lanthanome) involved in selective uptake, recognition, and utilization of lanthanides within the cell. In this chapter, we present protocols for the heterologous expression in Escherichia coli, purification, and characterization of many of the currently known proteins that comprise the lanthanome of the model facultative methylotroph, Methylorubrum extorquens AM1. In addition to the methanol dehydrogenase XoxF, these proteins include the associated c-type cytochrome, XoxG, and solute binding protein, XoxJ. We also present new, streamlined protocols for purification of the highly selective lanthanide-binding protein, lanmodulin, and a solute binding protein for PQQ, PqqT. Finally, we discuss simple, spectroscopic methods for determining lanthanide- and PQQ-binding stoichiometry of proteins. We envision that these protocols will be useful to investigators identifying and characterizing novel members of the lanthanome in many organisms.
Topics: Alcohol Dehydrogenase; Bacterial Proteins; Lanthanoid Series Elements; Methylobacterium extorquens; PQQ Cofactor
PubMed: 33867019
DOI: 10.1016/bs.mie.2021.02.004 -
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 -
Archives of Microbiology Aug 2021A Gram-negative, aerobic, flagellated, rod-shaped, and pink-pigmented bacterium, strain 17Sr1-43, was isolated from a soil sample collected in Nowongu, Seoul, Korea. The...
A Gram-negative, aerobic, flagellated, rod-shaped, and pink-pigmented bacterium, strain 17Sr1-43, was isolated from a soil sample collected in Nowongu, Seoul, Korea. The isolate could grow at 18-37 °C (optimum, 28-30 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0-1.0% (w/v) NaCl (optimum, 0%) with aeration. The major cellular fatty acids were summed feature 8 (C ω7c and/or C ω6c) and summed feature 2 (iso-C I and/or C 3-OH). The predominant respiratory quinone was Q-10 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and diphosphatidylglycerol. The G + C content of genomic DNA was 69.1 mol%. Strain 17Sr1-43 was closely related to Methylobacterium gregans KACC 14808 (98.4% 16S rRNA gene sequence similarity), Methylobacterium hispanicum KACC 11432 (97.9%), and Methylobacterium phyllosphaerae CBMB27 (96.1%). The complete genome of strain 17Sr1-43 contains essential genes related to DNA repair processes including bacterial RecBCD dependent pathway and UmuCD system. Based on the phenotypic, genotypic, and chemotaxonomic characteristics, strain 17Sr1-43 represents a novel species in the genus Methylobacterium, for which the name Methylobacterium radiodurans sp. nov. is proposed. The type strain is strain 17Sr1-43 (= KCTC 52906 = NBRC 112875).
Topics: DNA Repair; Methylobacterium; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Radiation Tolerance; Soil Microbiology; Species Specificity
PubMed: 33895889
DOI: 10.1007/s00203-021-02293-8