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International Journal of Infectious... Nov 2023We report the isolation of a rare Gram-positive coccobacillary bacterium from synovial fluids of a patient with periprosthetic joint infection on three occasions over an...
We report the isolation of a rare Gram-positive coccobacillary bacterium from synovial fluids of a patient with periprosthetic joint infection on three occasions over an 8-month period. As routine microbiological methods were not able to identify the isolate definitely, sequence analyses of the bacterial 16S ribosomal RNA gene and whole genome were performed. Analysis of the bacterial 16S ribosomal RNA gene showed the highest similarity (98.1%) with that of Falsarthrobacter (previously known as Arthrobacter) nasiphocae, which was first isolated from the nasal cavities of common seals (Phoca vitulina). The genome size of the strain (designated as UM1) is 2.4 Mb. With a high G+C content (70.4 mol%), strain UM1 is phylogenetically most closely related to F. nasiphocae based on whole genome analysis. Strain UM1 was susceptible to vancomycin, linezolid, trimethoprim-sulfamethoxazole, doxycycline, and intermediate to penicillin and ciprofloxacin. Ceftriaxone resistance was noted. The patient who was also on hemodialysis for his end stage kidney disease died approximately 3 weeks following implant removal and fusion with an external fixator. This study describes the first isolation of F. nasiphocae from human clinical samples. The use of emerging technologies has supported more definitive etiological diagnosis associated with rarely encountered organisms in periprosthetic joint infection.
Topics: Humans; Prosthesis-Related Infections; Micrococcaceae; Bacteria; Arthritis, Infectious; Gram-Positive Bacteria
PubMed: 37660726
DOI: 10.1016/j.ijid.2023.08.025 -
Frontiers in Plant Science 2021The rhizosheath is a critical interface supporting the exchange of resources between plants and their associated environment of soil. Favorable microenvironment of...
The rhizosheath is a critical interface supporting the exchange of resources between plants and their associated environment of soil. Favorable microenvironment of rhizosphere soil provides the rhizosheath formed and then promotes desert plant survival. However, it remains unclear how rhizosheath benefits the colonization of pioneer plants in alpine desert under changing environment. In this study, we investigated the effect of different soil moisture and sterilization treatments (three moisture levels and unsterilized or sterilized soil) on rhizosheath forming process of (), a sand-inhabiting and drought-resistant pioneer plant of the Tibetan Plateau desert. The results showed that in both unsterilized and sterilized soil, increasing soil moisture first increased and then decreased rhizosheath weight, with the highest value is 25%. During rhizosheath formation, developing rhizosheaths were selectively enriched in the bacterial genera and . These suggest the existence of a highly specialized signal recognition system during rhizosheath formation that involves the accumulation of bacteria. These bacterial species exhibited different roles in the process of rhizosheath formation and is an advantageous strategy for .
PubMed: 35154178
DOI: 10.3389/fpls.2021.785971 -
Environmental Microbiology Reports Oct 2023The gram-positive soil bacterium, Arthrobacter nicotianae, uses multiple organic acid functional groups to adsorb lanthanides onto its cell surface. At relevant soil pH...
The gram-positive soil bacterium, Arthrobacter nicotianae, uses multiple organic acid functional groups to adsorb lanthanides onto its cell surface. At relevant soil pH conditions of 4.0-6.0, many of these functional groups are de-protonated and available for cation sorption and metal immobilization. However, among the plethora of naturally occurring site types, A. nicotianae is shown to possess high-affinity amide and phosphate sites that disproportionately affect lanthanide adsorption to the cell wall. We quantify neodymium (Nd)-selective site types, reporting an amide-Nd stability constant of log K = 6.41 ± 0.23 that is comparable to sorption via phosphate-based moieties. These sites are two to three orders of magnitude more selective for Nd than the adsorption of divalent metals to ubiquitous carboxyl-based moieties. This implies the importance of lanthanide biosorption in the context of metal transport in subsurface systems despite trace concentrations of lanthanides found in the natural environment.
Topics: Lanthanoid Series Elements; Soil; Adsorption; Amides; Bacteria; Phosphates
PubMed: 37150598
DOI: 10.1111/1758-2229.13162 -
International Journal of Molecular... Jan 2021Phosphorous, in the form of phosphate, is a key element in the nutrition of all living beings. In nature, it is present in the form of phosphate salts,... (Review)
Review
Phosphorous, in the form of phosphate, is a key element in the nutrition of all living beings. In nature, it is present in the form of phosphate salts, organophosphates, and phosphonates. Bacteria transport inorganic phosphate by the high affinity phosphate transport system PstSCAB, and the low affinity PitH transporters. The PstSCAB system consists of four components. PstS is the phosphate binding protein and discriminates between arsenate and phosphate. In the species, the PstS protein, attached to the outer side of the cell membrane, is glycosylated and released as a soluble protein that lacks its phosphate binding ability. Transport of phosphate by the PstSCAB system is drastically regulated by the inorganic phosphate concentration and mediated by binding of phosphorylated PhoP to the promoter of the PstSCAB operon. In an additional high affinity transport system, PhnCDE, is also under PhoP regulation. Additionally, have a duplicated low affinity phosphate transport system encoded by the genes In this system phosphate is transported as a metal-phosphate complex in simport with protons. Expression of , but not that of in is regulated by PhoP. Interestingly, in many species, three gene clusters (for a polyphosphate kinase), are linked in a supercluster formed by nine genes related to phosphate metabolism. Glycerol-3-phosphate may be transported by the actinobacteria that contains a gene cluster for glycerol-3-P uptake, but the cluster is not present in genomes. Sugar phosphates and nucleotides are used as phosphate source by the species, but there is no evidence of the gene involved in the transport of sugar phosphates. Sugar phosphates and nucleotides are dephosphorylated by extracellular phosphatases and nucleotidases. An isolated gene for a hexose phosphate antiporter is present in several pathogenic corynebacteria, such as , but not in non-pathogenic ones. Phosphonates are molecules that contains phosphate linked covalently to a carbon atom through a very stable C-P bond. Their utilization requires the genes for phosphonates/phosphate transport and genes for degradation, including those for the subunits of the C-P lyase. Strains of the and genera were reported to degrade simple phosphonates, but bioinformatic analysis reveals that whole sets of genes for putative phosphonate degradation are present only in three species and a few species. Genes encoding the C-P lyase subunits occur in several species associated with plant roots or with mangroves, but not in the laboratory model species; however, the genes that encode phosphonates/phosphate transport systems are frequent in species, suggesting that these genes, in the absence of C-P lyase genes, might be used as surrogate phosphate transporters. In summary, and related actinobacteria seem to be less versatile in phosphate transport systems than Enterobacteria.
Topics: Actinobacteria; Arsenates; Bacterial Proteins; Biological Transport; Gene Expression Regulation, Bacterial; Glycosylation; Organophosphonates; Phosphate Transport Proteins; Phosphates; Phosphoric Monoester Hydrolases; Promoter Regions, Genetic; Signal Transduction; Streptomyces; Teichoic Acids
PubMed: 33498785
DOI: 10.3390/ijms22031129 -
Environmental Microbiology Reports Jun 2022Two related salmonids, Arctic char (Salvelinus alpinus) and lake whitefish (Coregonus clupeaformis) sampled from the high Arctic region of Nunavut, Canada are anadromous...
Two related salmonids, Arctic char (Salvelinus alpinus) and lake whitefish (Coregonus clupeaformis) sampled from the high Arctic region of Nunavut, Canada are anadromous fish, migrating annually from the same ice-covered freshwater waterbodies to spend summers in the marine waters of the Arctic Ocean. Microbiota associated with the skin-associated mucus undergo community change coincident with migration, and irrespective of this turnover, antibiotic resistance was detected in mixed bacterial cultures initiated with mucus samples. Although as expected most bacteria were unculturable, however, 5/7 isolates showed susceptibility to a panel of five common antibiotics. The fish were sampled under severe conditions and at remote locations far from human habitation. Regardless, two isolates, 'Carnobacterium maltaromaticum sm-2' and 'Arthrobacter citreus sm', showed multi-resistance to two or more antibiotics including ampicillin and streptomycin indicating multiple resistance genes. It is unknown if these fish bacteria have 'natural' resistance phenotypes or if resistance has been acquired. As result of these observations, we urge long-term monitoring of drug-resistant bacteria in the region and caution the assumption of a lack of drug-resistant organisms even in such extreme environments.
Topics: Animals; Anti-Bacterial Agents; Arctic Regions; Bacteria; Drug Resistance, Microbial; Fresh Water; Salmonidae; Trout
PubMed: 34109745
DOI: 10.1111/1758-2229.12975 -
Frontiers in Microbiology 2022Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major...
Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.
PubMed: 36583041
DOI: 10.3389/fmicb.2022.997832 -
Frontiers in Microbiology 2022Heat stress can have an impact on parental gamete maturation and reproduction functions. According to current research, the microbial composition of the vaginal cavity...
Heat stress can have an impact on parental gamete maturation and reproduction functions. According to current research, the microbial composition of the vaginal cavity is species specific. Pregnancy, menstruation, and genital diseases have been linked to the dynamics of vaginal ecology. In this study, we characterized the vaginal microbiota and metabolites after heat stress. At the phylum level, the rabbit's vaginal microbial composition of rabbit showed high similarity with that of humans. In the Heat group, the relative abundance of the dominant microbiota , , and increased, while the relative abundance of decreased. Furthermore, heat stress significantly increased the relative abundance of , , , , , and , whereas the relative abundance of 12 genera significantly decreased, including , , , , , , , , , , , and Besides, the relative concentrations of 158 metabolites differed significantly between the Heat and Control groups. Among them, the endocrine hormone estradiol (E) increased in the Heat group and was positively associated with a number of metabolites such as linolelaidic acid (C18:2N6T), N-acetylsphingosine, N-oleoyl glycine, trans-petroselinic acid, syringic acid, 2-(1-adamantyl)-1-morpholinoethan-1-one, 5-OxoETE, and 16-heptadecyne-1,2,4-triol. Further, the majority of the differential metabolites were enriched in steroid biosynthesis and endocrine and other factor-regulated calcium reabsorption pathways, reflecting that heat stress may affect calcium metabolism, hormone-induced signaling, and endocrine balance of vaginal ecology. These findings provide a comprehensive depiction of rabbit vaginal ecology and reveal the effects of heat stress on the vagina the analysis of vaginal microbiome and metabolome, which may provide a new thought for low female fertility under heat stress.
PubMed: 35495670
DOI: 10.3389/fmicb.2022.813622 -
Acta Crystallographica. Section F,... Apr 2020Human O-phosphoethanolamine phospho-lyase (hEtnppl; EC 4.2.3.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the degradation of O-phosphoethanolamine...
Human O-phosphoethanolamine phospho-lyase (hEtnppl; EC 4.2.3.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the degradation of O-phosphoethanolamine (PEA) into acetaldehyde, phosphate and ammonia. Physiologically, the enzyme is involved in phospholipid metabolism, as PEA is the precursor of phosphatidylethanolamine in the CDP-ethanolamine (Kennedy) pathway. Here, the crystal structure of hEtnppl in complex with pyridoxamine 5'-phosphate was determined at 2.05 Å resolution by molecular replacement using the structure of A1RDF1 from Arthrobacter aurescens TC1 (PDB entry 5g4i) as the search model. Structural analysis reveals that the two proteins share the same general fold and a similar arrangement of active-site residues. These results provide novel and useful information for the complete characterization of the human enzyme.
Topics: Carbon-Oxygen Lyases; Catalytic Domain; Crystallography, X-Ray; Cytidine Diphosphate; Ethanolamines; Humans; Models, Molecular; Protein Structure, Quaternary; Pyridoxal Phosphate
PubMed: 32254049
DOI: 10.1107/S2053230X20002988 -
Microbiology Resource Announcements Oct 2022Arthrobacter phage Iter was isolated in North Georgia. Its genome is 43,963 bp with 70 open reading frames (ORFs) and a GC content of 67.4%. It shares 89.11%...
Arthrobacter phage Iter was isolated in North Georgia. Its genome is 43,963 bp with 70 open reading frames (ORFs) and a GC content of 67.4%. It shares 89.11% nucleotide identity with phage Phives. Actinobacteriophages that share over 50% nucleotide identity are sorted into clusters, with Iter in cluster AZ.
PubMed: 36066250
DOI: 10.1128/mra.00538-22 -
Bioresources and Bioprocessing Feb 2023Nicotine, a toxic and addictive alkaloid from tobacco, is an environmental pollutant. However, nicotine-degrading bacteria (NDB) and their function in tobacco planting...
Nicotine, a toxic and addictive alkaloid from tobacco, is an environmental pollutant. However, nicotine-degrading bacteria (NDB) and their function in tobacco planting soil are not fully understood. First, 52 NDB strains belonging to seven genera were isolated from tobacco soil. The most dominant genera were Flavobacterium (36.5%), Pseudomonas (30.8%), and Arthrobacter (15.4%), and Chitinophaga and Flavobacterium have not been previously reported. Then, two efficient NDB strains, Arthrobacter nitrophenolicus ND6 and Stenotrophomonas geniculata ND16, were screened and inoculated in the compost fertilizer from tobacco waste. The nicotine concentrations were reduced from 1.5 mg/g (DW) to below the safety threshold of 0.5 mg/g. Furthermore, strain ND6 followed the pyridine pathway of nicotine degradation, but the degrading pathway in strain ND16 could not be determined according to genomic analysis and color change. Finally, the abundance of nicotine-degrading genes in tobacco rhizosphere soil was investigated via metagenomic analysis. Five key genes, ndhA, nctB, kdhL, nboR, and dhponh, represent the whole process of nicotine degradation, and their abundance positively correlated with soil nicotine concentrations (p < 0.05). In conclusion, various NDB including unknown species live in tobacco soil and degrade nicotine efficiently. Some key nicotine-degrading genes could be used in monitoring nicotine degradation in the environment. The fermentation of compost from tobacco waste is a promising application of efficient NDB.
PubMed: 38647817
DOI: 10.1186/s40643-023-00630-x