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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 -
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 -
PloS One 2023We recently used EPA databases to identify that isocyanates, most notably toluene diisocyanate (TDI), were the pollutant class with the strongest spatiotemporal and...
We recently used EPA databases to identify that isocyanates, most notably toluene diisocyanate (TDI), were the pollutant class with the strongest spatiotemporal and epidemiologic association with atopic dermatitis (AD). Our findings demonstrated that isocyanates like TDI disrupted lipid homeostasis and modeled benefit in commensal bacteria like Roseomonas mucosa through disrupting nitrogen fixation. However, TDI has also been established to activate transient receptor potential ankyrin 1 (TRPA1) in mice and thus could directly contribute to AD through induction of itch, rash, and psychological stress. Using cell culture and mouse models, we now demonstrate that TDI induced skin inflammation in mice as well as calcium influx in human neurons; each of these findings were dependent on TRPA1. Furthermore, TRPA1 blockade synergized with R. mucosa treatment in mice to improve TDI-independent models of AD. Finally, we show that the cellular effects of TRPA1 are related to shifting the balance of the tyrosine metabolites epinephrine and dopamine. This work provides added insight into the potential role, and therapeutic potential, or TRPA1 in the pathogenesis of AD.
Topics: Humans; Animals; Mice; Dermatitis, Atopic; Exanthema; Pruritus; Isocyanates; Toluene 2,4-Diisocyanate; Cytoskeletal Proteins; TRPA1 Cation Channel
PubMed: 36877675
DOI: 10.1371/journal.pone.0282569 -
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 -
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 -
Current Issues in Molecular Biology 2019Experimental evolution has become an increasingly common approach for studying evolutionary phenomena, as well as uncovering physiological connections in a manner... (Review)
Review
Experimental evolution has become an increasingly common approach for studying evolutionary phenomena, as well as uncovering physiological connections in a manner complementary to traditional genetics. Here I describe the development of as a model system for using experimental evolution to study questions at the intersection of metabolism and evolution. Each experiment was initiated to address a particular question inspired by patterns in natural methylotrophs, such as tradeoffs between single-carbon and multi-carbon growth, or the challenges involved in incorporating novel metabolic pathways or genes with poor codon usage that are acquired via horizontal gene transfer. What I could not have appreciated initially, however, was just how many fortuitous surprise findings would emerge. These have ranged from the repeatability of evolution, complex dynamics within populations, epistasis between beneficial mutations, and even the ability to use simple mathematical models to generate testable, quantitative hypotheses about the fitness landscape.
Topics: Directed Molecular Evolution; Epistasis, Genetic; Evolution, Molecular; Gene Expression Regulation, Bacterial; Gene Transfer Techniques; Metabolic Engineering; Metabolic Networks and Pathways; Methylobacterium; Models, Biological; Organisms, Genetically Modified; Research
PubMed: 31166197
DOI: 10.21775/cimb.033.249 -
PeerJ 2019We investigated the effects of gastric infection on the daytime and overnight human oral microbiota.
BACKGROUND
We investigated the effects of gastric infection on the daytime and overnight human oral microbiota.
METHODS
Twenty four volunteers were recruited. Ten tested positive for infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of gene amplicons. The microbial abundance and composition were analysed in relation to infection status.
RESULTS
-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both and , while , , and were significantly decreased in the UBT-positive samples.
DISCUSSION
Our data demonstrated that infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to infection require more studies to examine their potential health effects on affected individuals.
PubMed: 30713820
DOI: 10.7717/peerj.6336 -
Biotechnology Journal Aug 2018Developing methylotrophic bacteria into cell factories that meet the chemical demand of the future could be both economical and environmentally friendly. Methane is not... (Review)
Review
Developing methylotrophic bacteria into cell factories that meet the chemical demand of the future could be both economical and environmentally friendly. Methane is not only an abundant, low-cost resource but also a potent greenhouse gas, the capture of which could help to reduce greenhouse gas emissions. Rational strain design workflows rely on the availability of carefully combined knowledge often in the form of genome-scale metabolic models to construct high-producer organisms. In this review, the authors present the most recent genome-scale metabolic models in aerobic methylotrophy and their applications. Further, the authors present models for the study of anaerobic methanotrophy through reverse methanogenesis and suggest organisms that may be of interest for expanding one-carbon industrial biotechnology. Metabolic models of methylotrophs are scarce, yet they are important first steps toward rational strain-design in these organisms.
Topics: Anaerobiosis; Biotechnology; Industrial Microbiology; Methane; Methanococcus; Methylobacterium; Models, Biological
PubMed: 29917330
DOI: 10.1002/biot.201800011 -
Microbial Ecology Feb 2022The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon...
The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.
Topics: Antarctic Regions; Biodiversity; Cyanobacteria; Humans; Lichens; Sunlight
PubMed: 34081148
DOI: 10.1007/s00248-021-01769-w -
BMC Infectious Diseases Dec 2023Roseomonas mucosa (R. mucosa) is a pink-pigmented, Gram-negative short rod bacterium. It is isolated from moist environments and skin, resistant to multiple drugs,...
BACKGROUND
Roseomonas mucosa (R. mucosa) is a pink-pigmented, Gram-negative short rod bacterium. It is isolated from moist environments and skin, resistant to multiple drugs, including broad-spectrum cephalosporins, and a rare cause of infection with limited reports. R. mucosa mostly causes catheter-related bloodstream infections, with even fewer reports of skin and soft tissue infections.
CASE PRESENTATION
A 10-year-old boy received topical steroid treatment for sebum-deficient eczema. A few days before the visit, he was bitten by an insect on the front of his right lower leg and scratched it due to itching. The day before the visit, redness, swelling, and mild pain in the same area were observed. Based on his symptoms, he was diagnosed with cellulitis. He was treated with sulfamethoxazole/trimethoprim, and his symptoms improved. Pus culture revealed R. mucosa.
CONCLUSIONS
We report a rare case of cellulitis caused by R. mucosa. Infections caused by rare organisms that cause opportunistic infections, such as R. mucosa, should be considered in patients with compromised skin barrier function and regular topical steroid use. Gram stain detection of organisms other than Gram-positive cocci should be considered.
Topics: Male; Child; Humans; Cellulitis; Soft Tissue Infections; Methylobacteriaceae; Steroids
PubMed: 38082373
DOI: 10.1186/s12879-023-08875-9