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International Journal of Molecular... Oct 2023Transmembrane carriers of the Slc11 family catalyze proton (H)-dependent uptake of divalent metal ions (Me) such as manganese and iron-vital elements coveted during...
Transmembrane carriers of the Slc11 family catalyze proton (H)-dependent uptake of divalent metal ions (Me) such as manganese and iron-vital elements coveted during infection. The Slc11 mechanism of high-affinity Me cell import is selective and conserved between prokaryotic (MntH) and eukaryotic (Nramp) homologs, though processes coupling the use of the proton motive force to Me uptake evolved repeatedly. Adding bacterial piracy of genes spread in distinct environmental niches suggests selective gain of function that may benefit opportunistic pathogens. To better understand Slc11 evolution, Alphafold (AF2)/Colabfold (CF) 3D predictions for bacterial sequences from sister clades of eukaryotic descent (MCb and MCg) were compared using both native and mutant templates. AF2/CF model an array of native MCb intermediates spanning the transition from outwardly open (OO) to inwardly open (IO) carriers. In silico mutagenesis targeting (i) a set of (evolutionarily coupled) sites that may define Slc11 function (putative synapomorphy) and (ii) residues from networked communities evolving during MCb transition indicates that Slc11 synapomorphy primarily instructs a Me-selective conformation switch which unlocks carrier inner gate and contributes to Me binding site occlusion and outer gate locking. Inner gate opening apparently proceeds from interaction between transmembrane helix (h) h5, h8 and h1a. MCg1 xenologs revealed marked differences in carrier shape and plasticity, owing partly to an altered intramolecular H network. Yet, targeting Slc11 synapomorphy also converted MCg1 IO models to an OO state, apparently mobilizing the same residues to control gates. But MCg1 response to mutagenesis differed, with extensive divergence within this clade correlating with MCb-like modeling properties. Notably, MCg1 divergent epistasis marks the emergence of the genus -. Slc11 synapomorphy localizes to the 3D areas that deviate least among MCb and MCg1 models (either IO or OO) implying that it constitutes a 3D network of residues articulating a Me-selective carrier conformation switch which is maintained in fast-evolving clades at the cost of divergent epistatic interactions impacting carrier shape and dynamics.
Topics: Furylfuramide; Iron; Manganese; Biological Transport; Bacteria; Protons
PubMed: 37894758
DOI: 10.3390/ijms242015076 -
Microorganisms Sep 2023The fungicide iprodione (IPR) (3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide) is a highly toxic compound. Although IPR has been restricted, it...
The fungicide iprodione (IPR) (3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide) is a highly toxic compound. Although IPR has been restricted, it is still being applied in many places around the world, constituting an environmental risk. The biodegradation of IPR is an attractive option for reducing its residues. In this study, we isolated thirteen IPR-tolerant bacteria from a biopurification system designed to treat pesticides. A study of biodegradation using different strains was comparatively evaluated, and the best degradation rate of IPR was presented by sp. C1 with a half-life (T) of 9 days. Based on a nano-LC-MS/MS analysis for the strains, proteins solely expressed in the IPR treatment were identified by highlighting the strain sp. C1, with 445 proteins primarily involved in the biosynthesis of secondary metabolites and microbial metabolism in diverse environments. Differentially expressed protein amidases were involved in six metabolic pathways. Interestingly, formamidase was inhibited while other cyclases, i.e., amidase and mandelamide hydrolase, were overexpressed, thereby minimizing the effect of IPR on the metabolism of strain C1. The dynamic changes in the protein profiles of bacteria that degrade IPR have been poorly studied; therefore, our results offer new insight into the metabolism of IPR-degrading microorganisms, with special attention paid to amidases.
PubMed: 37894025
DOI: 10.3390/microorganisms11102367 -
Microbiology Resource Announcements Nov 2023We report the complete genome of strain H1_3_1, which was isolated from a reactor of a hybrid biological-inorganic system. The complete genome comprised 7,071,873 bp,...
We report the complete genome of strain H1_3_1, which was isolated from a reactor of a hybrid biological-inorganic system. The complete genome comprised 7,071,873 bp, including 6,428 codings, 10 rRNA, and 70 tRNA, with 67.4% G + C content.
PubMed: 37889011
DOI: 10.1128/MRA.00612-23 -
Cureus Sep 2023is a rare bacteria that causes bacteremia in immune-compromised patients. In this case, a 26-year-old male patient with major burns with a positive blood culture for...
is a rare bacteria that causes bacteremia in immune-compromised patients. In this case, a 26-year-old male patient with major burns with a positive blood culture for is presented. A rare bacterium, , and , was detected in the blood culture of a patient who was hospitalized due to major burn trauma and had delayed wound healing and had no graft take. After treatment with culture-specific antibiotics, the patients' acute phase reactants decreased, and he was discharged with 100% graft-take. Sepsis is the most common cause of death in major burns. Endogenous and exogenous bacteria cause sepsis. Bacteremia and sepsis are the most important factors affecting wound healing in burn patients. This case shows that rare opportunistic bacteria such as should be considered in major burn patients with delayed wound healing and recurrent graft lysis.
PubMed: 37885507
DOI: 10.7759/cureus.45909 -
Journal of Natural Products Nov 2023Through genome mining efforts, two lasso peptide biosynthetic gene clusters (BGCs) within two different species of , a genus that contains pathogenic organisms that can...
Through genome mining efforts, two lasso peptide biosynthetic gene clusters (BGCs) within two different species of , a genus that contains pathogenic organisms that can infect patients with cystic fibrosis, were discovered. Using gene-refactored BGCs in , these lasso peptides, which were named achromonodin-1 and achromonodin-2, were heterologously expressed. Achromonodin-1 is naturally encoded by certain isolates from the sputum of patients with cystic fibrosis. The NMR structure of achromonodin-1 was determined, demonstrating that it is a threaded lasso peptide with a large loop and short tail structure, reminiscent of previously characterized lasso peptides that inhibit RNA polymerase (RNAP). Achromonodin-1 inhibits RNAP and has potent, focused activity toward , another isolate from the sputum of a cystic fibrosis patient. These efforts expand the repertoire of antimicrobial lasso peptides and provide insights into how isolates from certain ecological niches interact with each other.
Topics: Humans; Escherichia coli; Cystic Fibrosis; Peptides; Antimicrobial Peptides; Achromobacter; DNA-Directed RNA Polymerases
PubMed: 37870195
DOI: 10.1021/acs.jnatprod.3c00536 -
The Science of the Total Environment Jan 2024Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly...
Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.
Topics: Microbial Consortia; Creosote; Sand; Polycyclic Aromatic Hydrocarbons; Biodegradation, Environmental; Carbon; Soil Pollutants; Soil Microbiology; Soil
PubMed: 37863223
DOI: 10.1016/j.scitotenv.2023.167832 -
Frontiers in Plant Science 2023The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some...
The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: , , and . In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. , , , , , , , , , , , , , , , among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of was the highest, while the alpha diversity in subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as , , , , , , , , , among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.
PubMed: 37860235
DOI: 10.3389/fpls.2023.1247814 -
Access Microbiology 2023is a Gram-negative, motile, obligate aerobic and non-fermentative bacterium. It is an emerging pathogen in the hospital environment as it is frequently found in various...
INTRODUCTION
is a Gram-negative, motile, obligate aerobic and non-fermentative bacterium. It is an emerging pathogen in the hospital environment as it is frequently found in various solutions.
HYPOTHESIS/GAP STATEMENT
Information about the incidence and risk factors of bacteremia from India is limited.
AIM
We conducted this study to identify the risk factors and underlying conditions predisposing to bacteremia by spp. and analyse the antibiotic resistance pattern of the isolates.
METHODOLOGY
We performed a retrospective observational study where automated blood cultures positive for spp. were assessed for clinical characteristics and antibiotic susceptibility patterns from January 2022 to December 2022 in the microbiology laboratory of a tertiary care centre in Northern India.
RESULTS
A total of 14 cases (14/2435, 0.57 %) of spp. were identified from bloodstream infections in one year. The mean age of the patients was 37.59±23.17 years with a male predominance (8/14, 57.1 %). All patients were managed on intravenous antibiotics and intravenous access as peripheral line catheters and only 5(5/14, 35.7 %) patients were managed on central line catheters. The isolates were found highly susceptible to ticarcillin-clavulanic acid (14/14, 100.0 %) followed by fluoroquinolones (12/14, 85.72 %) and trimethoprim-sulphamethoxazole (12/14, 85.72 %). Only 57.14 % (8/14, 57.14 %) of the patients were susceptible to piperacillin-tazobactam. The all-cause 40 day mortality was observed in 35.7 % (5/14, 35.7 %) with two deaths that were directly attributable to sepsis.
CONCLUSION
This study provides insight into the incidence of bacteremia at our centre and the necessary antibiotic therapy to combat it.
PubMed: 37841106
DOI: 10.1099/acmi.0.000588.v3 -
Scientific Reports Oct 2023Interspecific and intraspecific competition and facilitation have been a focus of study in plant-plant interactions, but their influence on plant recruitment of soil...
Interspecific and intraspecific competition and facilitation have been a focus of study in plant-plant interactions, but their influence on plant recruitment of soil microbes is unknown. In this greenhouse microcosm experiment, three cover crops (alfalfa, brassica, and fescue) were grown alone, in paired mixtures, and all together under different densities. For all monoculture trials, total pot biomass increased as density increased. Monoculture plantings of brassica were associated with the bacteria Azospirillum spp., fescue with Ensifer adhaerens, and alfalfa with both bacterial taxa. In the polycultures of cover crops, for all plant mixtures, total above-ground alfalfa biomass increased with density, and total above ground brassica biomass remained unchanged. For each plant mixture, differential abundances highlighted bacterial taxa which had not been previously identified in monocultures. For instance, mixtures of all three plants showed an increase in abundance of Planctomyces sp. SH-PL14 and Sandaracinus amylolyticus which were not represented in the monocultures. Facilitation was best supported for the alfalfa-fescue interaction as the total above ground biomass was the highest of any mixture. Additionally, the bulk soil microbiome that correlated with increasing plant densities showed increases in plant growth-promoting rhizobacteria such as Achromobacter xylosoxidans, Stentotrophomonas spp., and Azospirillum sp. In contrast, Agrobacterium tumefaciens, a previously known generalist phytopathogen, also increased with alfalfa-fescue plant densities. This could suggest a strategy by which, after facilitation, a plant neighbor could culture a pathogen that could be more detrimental to the other.
Topics: Soil; Medicago sativa; Biomass; Microbiota; Crops, Agricultural; Festuca; Bacteria
PubMed: 37816810
DOI: 10.1038/s41598-023-44104-8 -
Frontiers in Microbiology 2023is a local Brassicaceae in China, while most of it is directly mowed and discarded after the ornamental period. In order to develop forage resources, this study firstly...
is a local Brassicaceae in China, while most of it is directly mowed and discarded after the ornamental period. In order to develop forage resources, this study firstly evaluated the potential preservation of silage. was harvested at full-bloom stage, and ensiled without (CK) or with maize meal (Y5), lactic acid bacteria inoculant (Z) and compound additive (Y5Z) for 60 d. Results of chemical and microbiological analysis showed that a large amount of lactic acid was produced and the final pH value was below 4.1 in silages regardless of additive application. CK silage was well preserved as indicated by the low levels of dry matter loss and butyric acid content, and the predominant genus were identified as and . Y5 silage had potential health risks for humans and animals as seen by frequent occurrence of pathogenic bacteria and . Z and Y5Z silages were poorly preserved, resulting in great dry matter loss and butyric acid content. Considering the abundant acetic acid production, the dominant might possess a heterofermentative pathway in Z and Y5Z silages. In conclusion, has the potential to be long stored as silage because of its sufficient water-soluble carbohydrates, while exogenous lactic acid bacteria and maize meal generally provided little positive effect. In future research, efficient homofermentative strains were suggested to be screened to further enhance the ensiling process of silage.
PubMed: 37808300
DOI: 10.3389/fmicb.2023.1276493