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Microorganisms Aug 2023The aim was to evaluate the relationship between gut dysbiosis and hemodynamic changes (hyperdynamic circulation) in cirrhosis, and between hemodynamic changes and...
The aim was to evaluate the relationship between gut dysbiosis and hemodynamic changes (hyperdynamic circulation) in cirrhosis, and between hemodynamic changes and complications of this disease. This study included 47 patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. Echocardiography with a simultaneous assessment of blood pressure and heart rate was performed to assess systemic hemodynamics. Patients with hyperdynamic circulation had more severe cirrhosis, lower albumin, sodium and prothrombin levels, higher C-reactive protein, aspartate aminotransferase and total bilirubin levels, and higher incidences of portopulmonary hypertension, ascites, overt hepatic encephalopathy, hypoalbuminemia, hypoprothrombinemia, systemic inflammation, and severe hyperbilirubinemia than patients with normodynamic circulation. Patients with hyperdynamic circulation compared with those with normodynamic circulation had increased abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Fusobacteria, Micrococcaceae, Intestinobacter, Clostridium sensu stricto, Proteus and Rumicoccus, and decreased abundance of Bacteroidetes, Bacteroidaceae, Holdemanella, and Butyrivibrio. The systemic vascular resistance and cardiac output values correlated with the abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Micrococcaceae, and Fusobacteria. Heart rate and cardiac output value were negatively correlated with the abundance of Bacteroidetes. The mean pulmonary artery pressure value was positively correlated with the abundance of Proteobacteria and Micrococcaceae, and negatively with the abundance of Holdemanella.
PubMed: 37764046
DOI: 10.3390/microorganisms11092202 -
Polish Journal of Microbiology Sep 2023Uricase (or Urate oxidase), a key enzyme involved in purine metabolism, is commonly used in treating conditions such as gout, hyperuricemia, and tumor lysis syndrome. In...
Uricase (or Urate oxidase), a key enzyme involved in purine metabolism, is commonly used in treating conditions such as gout, hyperuricemia, and tumor lysis syndrome. In this study, a uricase-producing strain (named CSAJ-16) was isolated from the soil sample of Cangshan Mountain, Yunnan Province, China. This strain was identified as sp. CSAJ-16. Based on the gene sequence alignment, the uricase gene (named ) of sp. CSAJ-16 was amplified and heterologously expressed. The recombinant uricase (ArUOX) was about 32 kDa. The optimal pH and temperature of ArUOX were pH 7 and 20°C, respectively. The ArUOX remained above 50% relative activity after incubation at 37°C for 100 min or at pH 6.0-8.6 for 24 h. Moreover, metal ions such as K, Mg, Ca, Ba and Pb can significantly enhance the activity of ArUOX (> 200%). These enzymatic properties indicate that ArUOX has potential applications in pharmaceutical enzymes and uric acid detection kits.
Topics: Arthrobacter; China; Urate Oxidase; Sequence Alignment; Cloning, Molecular
PubMed: 37725900
DOI: 10.33073/pjm-2023-027 -
BMC Genomics Sep 2023Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing...
BACKGROUND
Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids.
RESULTS
In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway.
CONCLUSIONS
The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.
Topics: Nicotine; Micrococcaceae; Soil; DNA
PubMed: 37697273
DOI: 10.1186/s12864-023-09644-3 -
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 -
PeerJ 2023The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel () is protected...
The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel () is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3-V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.
Topics: Humans; Animals; Raptors; Beijing; RNA, Ribosomal, 16S; Falconiformes; Microbiota; Micrococcaceae; Firmicutes; Feces; Regulatory-Associated Protein of mTOR
PubMed: 37637157
DOI: 10.7717/peerj.15789 -
Ecotoxicology and Environmental Safety Sep 2023Cadmium (Cd) removal from soil to reduce Cd accumulation in plants is essential for agroecology, food safety, and human health. Cd enters plants from soil and affects...
Cadmium (Cd) removal from soil to reduce Cd accumulation in plants is essential for agroecology, food safety, and human health. Cd enters plants from soil and affects plant growth and development. Hydrogels can easily combine with Cd, thereby altering its bioavailability in soil. However, few studies have evaluated the effects of hydrogel on the complex phytotoxicity caused by Cd uptake in plants and the microbial community structure. Herein, a new poly (acrylic acid)-grafted starch and potassium humate composite (S/K/AA) hydrogel was added to soil to evaluate its impact on tobacco growth and the soil microenvironment. The results indicate that the addition of S/K/AA hydrogel can significantly improve the biomass, chlorophyll (Chl) content, and photosynthetic capacity of tobacco plants during Cd stress conditions, and decrease Cd concentration, probably by affecting Cd absorption through the expression of Cd absorption transporters (e.g., NRAMP5, NRAMP3, and IRT1). Moreover, the application of S/K/AA hydrogel not only reduced the accumulation of reactive oxygen species (ROS), but also reduced the antioxidant activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), suggesting that S/K/AA hydrogel alleviates Cd toxicity via a non-antioxidant pathway. Notably, we further analyzed the effectiveness of the hydrogel on microbial communities in Cd-contaminated soil and found that it increased the Cd-tolerant microbial community (Arthrobacter, Massilia, Streptomyces), enhancing the remediation ability of Cd-contaminated soil and helping tobacco plants to alleviate Cd toxicity. Overall, our study provides primary insights into how S/K/AA hydrogel affects Cd bioavailability and alleviates Cd toxicity in plants.
Topics: Humans; Cadmium; Biological Availability; Nicotiana; Hydrogels; Arthrobacter
PubMed: 37597289
DOI: 10.1016/j.ecoenv.2023.115361 -
Cells Aug 2023is an opportunistic pathogen, particularly life-threatening for the immunocompromised. It is associated with pneumonia, endocarditis, peritonitis and many other serious...
is an opportunistic pathogen, particularly life-threatening for the immunocompromised. It is associated with pneumonia, endocarditis, peritonitis and many other serious infections, including septicemia. Of note, produces metabolites that support and increase overgrowth of , one of the ESKAPE bacteria. Endolysins are considered as antibacterial enzymes derived from bacteriophages that selectively and efficiently kill susceptible bacteria without harming human cells or the normal microbiome. Here, we applied a computational analysis of metagenomic sequencing data of the gastric mucosa phageome extracted from human patients' stomach biopsies. A selected candidate anti- sequence was produced in an expression system, purified and confirmed as a - and -specific endolysin PolaR, able to destroy bacterial cells even when aggregated, as in a biofilm. PolaR had no cytotoxic or antiproliferative effects on mammalian cells. PolaR is the first described endolysin selectively targeting species, with a high potential to combat infections caused by and , and possibly other bacterial groups. PolaR is the first antibacterial enzyme selected from the gastric mucosa phageome, which underlines the biological complexity and probably underestimated biological role of the phageome in the human gastric mucosa.
Topics: Animals; Humans; Bacteriophages; Micrococcaceae; Bacteria; Anti-Bacterial Agents; Mammals
PubMed: 37566076
DOI: 10.3390/cells12151997 -
Chemosphere Nov 2023BTEX (benzene, toluene, ethylbenzene, xylene) are common pollutants often found in former gasworks sites together with some other contaminants like indene, indane and...
BTEX (benzene, toluene, ethylbenzene, xylene) are common pollutants often found in former gasworks sites together with some other contaminants like indene, indane and naphthalene (Ie, Ia, N). This study aimed to evaluate the inhibitory or stimulative substrate interactions between BTEX, and Ie, Ia, N during aerobic biodegradation. For this, batch bottles, containing originally anaerobic subsurface sediments, groundwater and indigenous microorganisms from a contaminated former gasworks site, were spiked with various substrate combinations (BTEX, BTEXIe, BTEXIa, BTEXN, BTEXIeIa, BTEXIeN, BTEXIaN, BTEXIeIaN). Subsequently concentrations were monitored over time. For the BTEXIeIaN mixture, initial concentrations were between 1 and 5 mg L, and all compounds were completely degraded by the microbial consortia within 39 days of incubation. The experimental data were fitted to a first order kinetic degradation model for interpretation of inhibition/stimulation between the compounds. Results showed that indene, indane, and naphthalene inhibited the degradation of benzene, toluene, ethylbenzene, o-xylene, with benzene being the most affected. M/p-xylene is the only compound whose biodegradation is stimulated by the presence of indene and indane (individually or mixed) but inhibited by the presence of naphthalene. 16S rRNA amplicon sequencing revealed differentiation in the microbial communities within the batches with different substrate mixtures, especially within the two microbial groups Micrococcaceae and Commamonaceae. Indene had more effect on the BTEX microbial community than indane or naphthalene and the presence of indene increased the relative abundance of Micrococcaceae family. In conclusion, co-presence of various pollutants leads to differentiation in degradation processes as well as in microbial community development. This sheds some light on the underlying reasons for that organic compounds present in mixtures in the subsurface of former gasworks sites are either recalcitrant or subjective towards biodegradation, and this understanding helps to further improve the bioremediation of such sites.
Topics: Benzene; Biodegradation, Environmental; Kinetics; RNA, Ribosomal, 16S; Benzene Derivatives; Xylenes; Toluene; Indenes; Environmental Pollutants; Naphthalenes; Microbiota
PubMed: 37558001
DOI: 10.1016/j.chemosphere.2023.139761 -
Journal of Industrial Microbiology &... Feb 2023Historically, bacteria of the phylum, Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera,... (Review)
Review
Historically, bacteria of the phylum, Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera, Micrococcus has not generally been prioritized in the search for novel drugs. The bacteria in this genus are known to have very small genomes (generally < 3 Mb). Actinobacteria with small genomes seldom contain the well-characterized biosynthetic gene clusters such as those encoding polyketide synthases and nonribosomal peptide synthetases that current genome mining algorithms are optimized to detect. Nevertheless, there are many reports of substantial pharmaceutically relevant bioactivity of Micrococcus extracts. On the other hand, there are remarkably few descriptions of fully characterized and structurally elucidated bioactive compounds from Micrococcus spp. This review provides a comprehensive summary of the bioactivity of Micrococcus spp. that encompasses antibacterial, antifungal, cytotoxic, antioxidant, and anti-inflammatory activities. This review uncovers the considerable biosynthetic potential of this genus and highlights the need for a re-examination of these bioactive strains, with a particular emphasis on marine isolates, because of their potent bioactivity and high potential for encoding unique molecular scaffolds.
Topics: Micrococcus; Actinobacteria; Bacteria; Anti-Bacterial Agents; Polyketide Synthases; Drug Discovery
PubMed: 37460166
DOI: 10.1093/jimb/kuad017 -
International Journal of Molecular... Jun 2023The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The...
The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The present study aimed to map the blood microbiota of outpatients with Crohn's disease (CD) or with ulcerative colitis (UC) by 16S metagenomics. A diverse microbiota was observed in the blood samples. Regardless of the type of disease, the alpha diversity of the microbiota was positively associated with C-reactive protein (CRP). The blood microbiota had a surprisingly high proportion of in comparison with human oral and colonic microbiotas. There was no clear difference in the overall pattern of the microbiota between CD and UC. A non-template control (NTC) was included in the whole process to control for the potential contamination from the environment and reagents. Certain bacterial taxa were concomitantly detected in both blood samples and NTC. However, , , and were found in blood from both CD and UC patients but not in NTC, indicating the existence of a specific blood-borne microbiota in the patients. dominated in all blood samples, but a minor amount was also found in NTC. was significantly enriched in CD, but it was also detected in high abundance in NTC. Whether the composition of the blood microbiota could be a marker of a particular phenotype in inflammatory bowel disease (IBD) or whether the blood microbiota could be used for diagnostic or therapeutic purposes deserves further attention.
Topics: Humans; C-Reactive Protein; Outpatients; Inflammatory Bowel Diseases; Colitis, Ulcerative; Crohn Disease; Microbiota
PubMed: 37446076
DOI: 10.3390/ijms241310899