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ACS Chemical Biology Aug 2021Pantothenic acid is an essential metabolite found throughout all branches of life. Although the enzymes responsible for pantothenic biosynthesis have been characterized,...
Pantothenic acid is an essential metabolite found throughout all branches of life. Although the enzymes responsible for pantothenic biosynthesis have been characterized, those leading to its biodegradation remain poorly understood. In the study described herein, we showed that use of a "genomic enzymology" strategy enabled identification of four biodegradation pathway genes, which were then confirmed by using kinetic analysis of the purified recombinant enzymes encoded in . The reconstituted pathway converts pantothenic acid to β-alanine and ()-pantoate, and then ()-pantoate to aldopentoate, which is transformed to ()-3,3-dimethylmalate and hence to α-ketoisovalerate. The pathway genes are common to Proteobacterial genomes in which they are not colocated.
Topics: Amidohydrolases; Genes, Bacterial; Genomics; Multigene Family; NAD (+) and NADP (+) Dependent Alcohol Oxidoreductases; Ochrobactrum anthropi; Pantothenic Acid
PubMed: 34313416
DOI: 10.1021/acschembio.1c00492 -
Journal of Ophthalmic Inflammation and... Feb 2024To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
PURPOSE
To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
FINDINGS
A 70-year-old female patient was diagnosed with acute endophthalmitis following intravitreal aflibercept injection for age-related macular degeneration. A standard tap and inject procedure was performed. Microbiological analyses on the anterior chamber and vitreous samples yielded the presence of three non-fermenting Gram-negative rods: Pseudomonas stutzeri, Stenotrophomonas maltophilia, and Ochrobactrum anthropi. The outcome was favorable after intravitreal injections of vancomycin and ceftazidime, with an almost complete recovery of the visual acuity to its baseline level. No potential source of infection was identified.
CONCLUSION
Endophthalmitis following intravitreal injection can be caused by a wide variety of bacteria, including some rare Gram-negative species. They can sometimes co-exist in a single patient, but their virulence may vary greatly. Due to the variable antibiotic susceptibility and frequent multiresistance associated with non-fermenting Gram-negative rods, a prompt microbiological approach is required. Favorable outcome can be achieved with standard management.
PubMed: 38334879
DOI: 10.1186/s12348-023-00376-9 -
Genomics Sep 2020Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species...
Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species of this genus, O. intermedium and O. anthropi were documented for causing infections mostly in the immunocompromised patients. Despite such ubiquitous presence, study of adaptation in various niches is still lacking. Thus, to gain insights into the niche adaptation strategies, pan-genome analysis was carried out by comparing 67 genome sequences belonging to Ochrobactrum species. Pan-genome analysis revealed it is an open pan-genome indicative of the continuously evolving nature of the genus. The presence/absence of gene clusters also illustrated the unique presence of antibiotic efflux transporter genes and type IV secretion system genes in the clinical strains while the genes of solvent resistance and exporter pumps in the environmental strains. A phylogenomic investigation based on 75 core genes depicted better and robust phylogenetic resolution and topology than the 16S rRNA gene. To support the pan-genome analysis, individual genomes were also investigated for the mobile genetic elements (MGE), antibiotic resistance genes (ARG), metal resistance genes (MRG) and virulence factors (VF). The analysis revealed the presence of MGE, ARG, and MRG in all the strains which play an important role in the species evolution which is in agreement with the pan-genome analysis. The average nucleotide identity (ANI) based on the genetic relatedness between the Ochrobactrum species indicated a distinction between individual species. Interestingly, the ANI tool was able to classify the Ochrobactrum genomes to the species level which were assigned till the genus level on the NCBI database.
Topics: Drug Resistance, Bacterial; Environmental Microbiology; Genes, Bacterial; Genome, Bacterial; Genomics; Humans; Interspersed Repetitive Sequences; Molecular Sequence Annotation; Ochrobactrum; Phylogeny; Virulence Factors
PubMed: 32428556
DOI: 10.1016/j.ygeno.2020.04.030 -
Applied Microbiology and Biotechnology Nov 2019Cost and energy reductions in the production process of bismuth chalcogenide (BC) semiconductor materials are essential to make thermoelectric generators comprised of...
Cost and energy reductions in the production process of bismuth chalcogenide (BC) semiconductor materials are essential to make thermoelectric generators comprised of BCs profitable and CO neutral over their life cycle. In this study, as an eco-friendly production method, bismuth selenide (BiSe) nanoparticles were synthesized using the following five strains of chalcogen-metabolizing bacteria: Pseudomonas stutzeri NT-I, Pseudomonas sp. RB, Stenotrophomonas maltophilia TI-1, Ochrobactrum anthropi TI-2, and O. anthropi TI-3 under aerobic conditions. All strains actively volatilized selenium (Se) by reducing selenite, possibly to organoselenides. In the growth media containing bismuth (Bi) and Se, all strains removed Bi and Se concomitantly and synthesized nanoparticles containing Bi and Se as their main components. Particles synthesized by strain NT-I had a theoretical elemental composition of BiSe, whereas those synthesized by other strains contained a small amount of sulfur in addition to Bi and Se, making strain NT-I the best BiSe synthesizer among the strains used in this study. The particle sizes were 50-100 nm in diameter, which is sufficiently small for nanostructured semiconductor materials that exhibit quantum size effect. Successful synthesis of BiSe nanoparticles could be attributed to the high Se-volatilizing activities of the bacterial strains. Selenol-containing compounds as intermediates of Se-volatilizing metabolic pathways, such as methane selenol and selenocysteine, may play an important role in biosynthesis of BiSe.
Topics: Bismuth; Chalcogens; Metal Nanoparticles; Ochrobactrum anthropi; Organoselenium Compounds; Pseudomonas; Selenium Compounds; Semiconductors; Stenotrophomonas maltophilia
PubMed: 31642950
DOI: 10.1007/s00253-019-10160-2 -
Molecules (Basel, Switzerland) Jul 2020Azole antifungal molecules are broadly used as active ingredients in various products, such as pharmaceuticals and pesticides. This promotes their release into the...
Azole antifungal molecules are broadly used as active ingredients in various products, such as pharmaceuticals and pesticides. This promotes their release into the natural environment. The detailed mechanism of their influence on the biotic components of natural ecosystems remains unexplored. Our research aimed to examine the response of AspCl2.2 to the presence of four azole antifungal agents (clotrimazole, fluconazole, climbazole, epoxiconazole). The experiments performed include analysis of the cell metabolic activity, cell membrane permeability, total glutathione level and activity of glutathione S-transferases. These studies allowed for the evaluation of the cells' oxidative stress response to the presence of azole antifungals. Moreover, changes in the nanomechanical surface properties, including adhesive and elastic features of the cells, were investigated using atomic force microscopy (AFM) and spectrophotometric methods. The results indicate that the azoles promote bacterial oxidative stress. The strongest differences were noted for the cells cultivated with fluconazole. The least toxic effect has been attributed to climbazole. AFM observations unraveled molecular details of bacterial cell texture, structure and surface nanomechanical properties. Antifungals promote the nanoscale modification of the bacterial cell wall. The results presented provided a significant insight into the strategies used by environmental bacterial cells to survive exposures to toxic azole antifungal agents.
Topics: Anti-Bacterial Agents; Azoles; Bacterial Adhesion; Biomechanical Phenomena; Cell Membrane Permeability; Clotrimazole; Epoxy Compounds; Fluconazole; Glutathione; Hydrophobic and Hydrophilic Interactions; Imidazoles; Microbial Sensitivity Tests; Microscopy, Atomic Force; Nanoparticles; Ochrobactrum anthropi; Surface Properties; Triazoles
PubMed: 32717971
DOI: 10.3390/molecules25153348 -
International Journal of Environmental... Jan 2022The phenylurea herbicides are persistent in soil and water, making necessary the de-velopment of techniques for their removal from the environment. To identify new...
The phenylurea herbicides are persistent in soil and water, making necessary the de-velopment of techniques for their removal from the environment. To identify new options in this regard, bacterial strains were isolated from a soil historically managed with pesticides. CD3 showed the ability to remove completely herbicides such as diuron, linuron, chlorotoluron and fluometuron from aqueous solution, and up to 89% of isoproturon. In the case of diuron and linuron, their main metabolite, 3,4-dichloroaniline (3,4-DCA), which has a higher toxicity than the parent compounds, was formed, but remained in solution without further degradation. CD3 was also tested for bioremediation of two different agricultural soils artificially contaminated with diuron, employing bioremediation techniques: (i) biostimulation, using a nutrient solution (NS), (ii) bioaugmentation, using CD3, and iii) bioavailability enhancement using 2-hydroxypropyl-β-cyclodextrin (HPBCD). When bioaugmentation and HPBCD were jointly applied, 50% of the diuron initially added to the soil was biodegraded in a range from 4.7 to 0.7 d. Also, 3,4-DCA was degraded in soil after the strain was inoculated. At the end of the soil biodegradation assay an ecotoxicity test confirmed that after inoculating CD3 the toxicity was drastically reduced.
Topics: Biodegradation, Environmental; Diuron; Feasibility Studies; Herbicides; Ochrobactrum; Soil; Soil Microbiology; Soil Pollutants
PubMed: 35162387
DOI: 10.3390/ijerph19031365 -
Classifying Interactions in a Synthetic Bacterial Community Is Hindered by Inhibitory Growth Medium.MSystems Oct 2022Predicting the fate of a microbial community and its member species relies on understanding the nature of their interactions. However, designing simple assays that...
Predicting the fate of a microbial community and its member species relies on understanding the nature of their interactions. However, designing simple assays that distinguish between interaction types can be challenging. Here, we performed spent medium assays based on the predictions of a mathematical model to decipher the interactions among four bacterial species: Agrobacterium tumefaciens, Comamonas testosteroni, Microbacterium saperdae, and Ochrobactrum anthropi. While most experimental results matched model predictions, the behavior of did not: its lag phase was reduced in the pure spent media of A. tumefaciens and but prolonged again when we replenished our growth medium. Further experiments showed that the growth medium actually delayed the growth of , leading us to suspect that A. tumefaciens and could alleviate this inhibitory effect. There was, however, no evidence supporting such "cross-detoxification," and instead, we identified metabolites secreted by A. tumefaciens and that were then consumed or "cross-fed" by , shortening its lag phase. Our results highlight that even simple, defined growth media can have inhibitory effects on some species and that such negative effects need to be included in our models. Based on this, we present new guidelines to correctly distinguish between different interaction types such as cross-detoxification and cross-feeding. Communities of microbes colonize virtually every place on earth. Ultimately, we strive to predict and control how these communities behave, for example, if they reside in our guts and make us sick. But precise control is impossible unless we can identify exactly how their member species interact with one another. To find a systematic way to measure interactions, we started very simply with a small community of four bacterial species and carefully designed experiments based on a mathematical model. This first attempt accurately mapped out interactions for all species except one. By digging deeper, we understood that our method failed for that species as it was suffering in the growth medium that we chose. A revised model that considered that growth media can be harmful could then make more accurate predictions. What we have learned with these four species can now be applied to decipher interactions in larger communities.
Topics: Bacteria; Comamonas testosteroni; Models, Theoretical; Microbiota; Actinomycetales
PubMed: 36197097
DOI: 10.1128/msystems.00239-22 -
Journal of Economic Entomology Apr 2021Recent studies have revealed multiple roles of insect-associated microbes such as lignin degradation, entomopathogen inhibition, and antibiotic production. These...
Recent studies have revealed multiple roles of insect-associated microbes such as lignin degradation, entomopathogen inhibition, and antibiotic production. These functions improve insect host fitness, and provide a novel source of discovering beneficial microbes for industrial and agricultural production. Previously published research found that in the symbiosis formed by the dipteran pest Delia antiqua (Meigen) (Diptera: Anthomyiidae) and its associated bacteria, the bacteria showed effective inhibition of one fungal entomopathogen, Beauveria bassiana. The antifungal activity of those associated bacteria indicates their potential to be used as biocontrol agents for fungal phytopathogens. In this study, we first isolated and identified bacteria associated with D. antiqua using a culture-dependent method. Second, we tested the antifungal activity of these bacteria against four phytopathogens including Fusarium moniliforme, Botryosphaeria dothidea, and two Fusarium oxysporum strains using the dual-culture method. In total, 74 species belonging to 30 genera, 23 families, eight classes, and four phyla were isolated and identified. Among those bacteria, Ochrobactrum anthropi, Morganella morganii, Arthrobacter sp. 3, and Acinetobacter guillouiae showed significant volatile inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum, respectively. Moreover, bacteria including Rhodococcus equi, Leucobacter aridicollis, Paenibacillus sp. 3, and Lampropedia sp. showed significant contact inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum. Our work provides a new source for discovering biocontrol agents against phytopathogens.
Topics: Acinetobacter; Actinobacteria; Animals; Ascomycota; Bacteria; Diptera; Fusarium; Plant Diseases
PubMed: 33547790
DOI: 10.1093/jee/toab002 -
Chemosphere Jun 2023Applying beneficial bacteria in rice rhizosphere to manage heavy metal behaviour in soil-plant system is a promising strategy. However, colonization/domination of...
Applying beneficial bacteria in rice rhizosphere to manage heavy metal behaviour in soil-plant system is a promising strategy. However, colonization/domination of exogenous bacteria in rhizosphere soils remains a challenge. In this study, a bacterium Ochrobactrum anthropi, which showed the potential of transforming soluble Sb into SbO mineral, was repeatedly inoculated into the rice rhizosphere weekly throughout the rice growth period, and the colonization of this bacterium in rice rhizosphere soils and its effect on Sb accumulation in rice plants were investigated. Results showed that repeated inoculants changed the native bacterial community in rhizosphere soils in comparison with the control, but the inoculated O. anthropi was not identified as an abundant species. With weekly inoculation, the decrease in Sb in rice roots and straws was maintained throughout the rice growth period, with decrease percentages ranging from 36 to 49% and 33-35%. In addition, decrease percentages of Sb in husks and grains at the maturing stage obtained 34 and 37%, respectively. Furthermore, the XRD identified the formation of valentinite (SbO) on rice root in inoculation treatment, and the decrease percentages in aqueous Sb in rhizosphere were 53-100% through the growth period. It demonstrated that weekly inoculants performed their temporary activity of valentinite formation, and reduced Sb accumulation in rice plants efficiently. This study suggests that regardless of successful colonization, repeated inoculation of beneficial bacteria is an option to facilitate the positive effects of inoculated bacteria in the management of heavy metal behaviour.
Topics: Antimony; Oryza; Soil Pollutants; Metals, Heavy; Plant Roots; Bacteria; Rhizosphere; Soil
PubMed: 36948256
DOI: 10.1016/j.chemosphere.2023.138335 -
Marine Drugs Feb 2022Epibiotic bacteria associated with the filamentous marine cyanobacterium were explored as a novel source of antibiotics and to establish whether they can produce...
Epibiotic bacteria associated with the filamentous marine cyanobacterium were explored as a novel source of antibiotics and to establish whether they can produce cyclodepsipeptides on their own. Here, we report the isolation of micrococcin P1 () (CHNOS; obs. / 1144.21930/572.60381) and micrococcin P2 () (CHNOS; obs. / 1142.20446/571.60370) from a strain of isolated from ' filaments. Interestingly, most bacteria isolated from ' filaments were found to be human pathogens. Stalked diatoms on the filaments suggested a possible terrestrial origin of some epibionts. CuSO·5HO assisted differential genomic DNA isolation and phylogenetic analysis showed that a Kenyan strain of differed from strain CCAP 1446/4 and clones. Organic extracts of the epibiotic bacteria and did not produce cyclodepsipeptides. Further characterization of 24 Firmicutes strains from identified extracts of as most active. Our results showed that the genetic basis for synthesizing micrococcin P1 (), discovered in ATCC 14579, is species/strain-dependent and this reinforces the need for molecular identification of species worldwide and their epibionts. These findings indicate that -associated bacteria are an overlooked source of antimicrobial compounds.
Topics: Anti-Infective Agents; Bacillus; Bacteriocins; Cyanobacteria; Depsipeptides; Kenya; Phylogeny; Species Specificity
PubMed: 35200657
DOI: 10.3390/md20020128