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International Journal of Systematic and... Apr 2024As required by Rule 54 of the International Code of Nomenclature of Prokaryotes, the authors propose the replacement specific epithet '' for the illegitimate prokaryotic...
Proposal of nom. nov., subsp. nom. nov. and subsp. nom. nov. as new names with replacement specific or subspecific epithets, respectively, for three illegitimate prokaryotic names Yoo . 2007, subsp. Kim . 2017 and subsp. Kudo . 2012; proposal of comb. nov. and comb. nov. as replacement...
As required by Rule 54 of the International Code of Nomenclature of Prokaryotes, the authors propose the replacement specific epithet '' for the illegitimate prokaryotic name Yoo . 2007, the replacement subspecific epithet '' for subsp. Kim 2017 and the replacement subspecific epithet '' for subsp. Kudo . 2012. Meanwhile, new combinations and are also proposed as replacements for the illegitimate prokaryotic names Yang . 2023 and Zhang . 2023, respectively.
Topics: Mycobacterium chelonae; Lactobacillus delbrueckii; Sphingobacterium; Sequence Analysis, DNA; DNA, Bacterial; Phylogeny; Bacterial Typing Techniques; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Lactobacillus; Mycobacteriaceae
PubMed: 38578275
DOI: 10.1099/ijsem.0.006319 -
Annals of Surgical Oncology Jul 2024This study aimed to characterize the urinary and tumor microbiomes in patients with non-muscle-invasive bladder cancer (NMIBC) before and after transurethral resection... (Observational Study)
Observational Study
BACKGROUND
This study aimed to characterize the urinary and tumor microbiomes in patients with non-muscle-invasive bladder cancer (NMIBC) before and after transurethral resection of the bladder tumor (TURBT).
METHODS
This single-center prospective study included 26 samples from 11 patients with low-grade Ta papillary NMIBC. Urine samples were collected at the index TURBT and at a 1-year follow-up cystoscopy. The metagenomic analysis of bacterial and archaeal populations was performed based on the highly variable V3-V4 region of the 16S rRNA gene.
RESULTS
Phylogenetic alpha diversity of the bladder microbiome detected in urine was found to be lower at the 1-year follow-up cystoscopy compared to the time of the index TURBT (p < 0.01). Actinomyces, Candidatus cloacimonas, Sphingobacterium, Sellimonas, Fusobacterium, and Roseobacter were more differentially enriched taxa in urine at the follow-up cystoscopy than at the index TURBT. Beta diversity of urine microbiome significantly changed over time (p < 0.05). Phylogenetic alpha diversity of the microbiome was greater in tumor tissues than in paired urine samples (p<0.01). Sphingomonas, Acinetobacter, Candidatus, and Kocuria were more differentially overrepresented in tumor tissues than in urine. The enrichment of the abundance of Corynebacterium and Anaerococcus species in urine collected at TURBT was observed in patients who experienced recurrence within the follow-up period.
CONCLUSIONS
In patients with low-grade NMIBC, the urine microbiome undergoes changes over time after removal of the tumor. The microbiome detected in tumor tissues is more phylogenetically diverse than in paired urine samples collected at TURBT. The interplay between bladder microbiome, tumor microbiome, and their alterations requires further studies to elucidate their predictive value and perhaps therapeutic implications.
Topics: Humans; Urinary Bladder Neoplasms; Prospective Studies; Male; Female; Microbiota; Aged; Middle Aged; Follow-Up Studies; Prognosis; Cystectomy; Neoplasm Invasiveness; RNA, Ribosomal, 16S; Bacteria; Phylogeny; Non-Muscle Invasive Bladder Neoplasms
PubMed: 38570378
DOI: 10.1245/s10434-024-15198-9 -
Chemosphere May 2024Environmental challenges arising from organic pollutants pose a significant problem for modern societies. Efficient microbial resources for the degradation of these...
Environmental challenges arising from organic pollutants pose a significant problem for modern societies. Efficient microbial resources for the degradation of these pollutants are highly valuable. In this study, the bacterial community structure of sludge samples from Taozi Lake (polluted by urban sewage) was studied using 16S rRNA sequencing. The bacterial phyla Proteobacteria, Bacteroidetes, and Chloroflexi, which are potentially important in organic matter degradation by previous studies, were identified as the predominant phyla in our samples, with relative abundances of 48.5%, 8.3%, and 6.6%, respectively. Additionally, the FAPROTAX and co-occurrence network analysis suggested that the core microbial populations in the samples may be closely associated with organic matter metabolism. Subsequently, sludge samples from Taozi Lake were subjected to enrichment cultivation to isolate organic pollutant-degrading microorganisms. The strain Sphingobacterium sp. GEMB-CSS-01, tolerant to sulfanilamide, was successfully isolated. Subsequent investigations demonstrated that Sphingobacterium sp. GEMB-CSS-01 efficiently degraded the endocrine-disrupting compound 17β-Estradiol (E2). It achieved degradation efficiencies of 80.0% and 53.5% for E2 concentrations of 10 mg/L and 20 mg/L, respectively, within 10 days. Notably, despite a reduction in degradation efficiency, Sphingobacterium sp. GEMB-CSS-01 retained its ability to degrade E2 even in the presence of sulfanilamide concentrations ranging from 50 to 200 mg/L. The findings of this research identify potential microbial resources for environmental bioremediation, and concurrently provide valuable information about the microbial community structure and patterns within Taozi Lake.
Topics: Sewage; Sphingobacterium; Lakes; RNA, Ribosomal, 16S; Estradiol; Biodegradation, Environmental; Environmental Pollutants; Sulfanilamides
PubMed: 38548087
DOI: 10.1016/j.chemosphere.2024.141806 -
The Science of the Total Environment May 2024Hermetia illucens larvae are recognized for their ability to mitigate or eliminate contaminants by biodegradation. However, the biodegradation characteristics of...
Hermetia illucens larvae are recognized for their ability to mitigate or eliminate contaminants by biodegradation. However, the biodegradation characteristics of microplastics and phthalic acid esters plasticizers, as well as the role of larval gut microorganisms, have remained largely unrevealed. Here, the degradation kinetics of plasticizers, and biodegradation characteristics of microplastics were examined. The role of larval gut microorganisms was investigated. For larval development, microplastics slowed larval growth significantly (P < 0.01), but the effect of plasticizer was not significant. The degradation kinetics of plasticizers were enhanced, resulting in an 8.11 to 20.41-fold decrease in degradation half-life and a 3.34 to 3.82-fold increase in final degradation efficiencies, compared to degradation without larval participation. The depolymerization and biodeterioration of microplastics were conspicuously evident, primarily through a weight loss of 17.63 %-25.52 %, variation of chemical composition and structure, bio-oxidation and bioerosion of microplastic surface. The synergistic effect driven by larval gut microorganisms, each with various functions, facilitated the biodegradation. Specifically, Ignatzschineria, Paenalcaligenes, Moheibacter, Morganella, Dysgonomonas, Stenotrophomonas, Bacteroides, Sphingobacterium, etc., appeared to be the key contributors, owing to their xenobiotic biodegradation and metabolism functions. These findings offered a new perspective on the potential for microplastics and plasticizers biodegradation, assisted by larval gut microbiota.
Topics: Animals; Larva; Microplastics; Plastics; Plasticizers; Diptera; Esters; Phthalic Acids
PubMed: 38479533
DOI: 10.1016/j.scitotenv.2024.171674 -
Journal of Hazardous Materials Apr 2024Biodegradation is an efficient and cost-effective approach to remove residual penicillin G sodium (PGNa) from the environment. In this study, the effective...
Biodegradation is an efficient and cost-effective approach to remove residual penicillin G sodium (PGNa) from the environment. In this study, the effective PGNa-degrading strain SQW1 (Sphingobacterium sp.) was screened from contaminated soil using enrichment technique. The effects of critical operational parameters on PGNa degradation by strain SQW1 were systematically investigated, and these parameters were optimized by response surface methodology to maximize PGNa degradation. Comparative experiments found the extracellular enzyme to completely degrade PGNa within 60 min. Combined with whole genome sequencing of strain SQW1 and LC-MS analysis of degradation products, penicillin acylase and β-lactamase were identified as critical enzymes for PGNa biodegradation. Moreover, three degradation pathways were postulated, including β-lactam hydrolysis, penicillin acylase hydrolysis, decarboxylation, desulfurization, demethylation, oxidative dehydrogenation, hydroxyl reduction, and demethylation reactions. The toxicity of PGNa biodegradation intermediates was assessed using paper diffusion method, ECOSAR, and TEST software, which showed that the biodegradation products had low toxicity. This study is the first to describe PGNa-degrading bacteria and detailed degradation mechanisms, which will provide new insights into the PGNa biodegradation.
Topics: Sphingobacterium; Penicillin Amidase; Penicillin G; Biodegradation, Environmental
PubMed: 38377898
DOI: 10.1016/j.jhazmat.2024.133485 -
The Journal of Biological Chemistry Mar 2024Serine palmitoyltransferase (SPT) catalyzes the pyridoxal-5'-phosphate (PLP)-dependent decarboxylative condensation of l-serine and palmitoyl-CoA to form...
Serine palmitoyltransferase (SPT) catalyzes the pyridoxal-5'-phosphate (PLP)-dependent decarboxylative condensation of l-serine and palmitoyl-CoA to form 3-ketodihydrosphingosine (KDS). Although SPT was shown to synthesize corresponding products from amino acids other than l-serine, it is still arguable whether SPT catalyzes the reaction with d-serine, which is a question of biological importance. Using high substrate and enzyme concentrations, KDS was detected after the incubation of SPT from Sphingobacterium multivorum with d-serine and palmitoyl-CoA. Furthermore, the KDS comprised equal amounts of 2S and 2R isomers. H-NMR study showed a slow hydrogen-deuterium exchange at Cα of serine mediated by SPT. We further confirmed that SPT catalyzed the racemization of serine. The rate of the KDS formation from d-serine was comparable to those for the α-hydrogen exchange and the racemization reaction. The structure of the d-serine-soaked crystal (1.65 Å resolution) showed a distinct electron density of the PLP-l-serine aldimine, interpreted as the racemized product trapped in the active site. The structure of the α-methyl-d-serine-soaked crystal (1.70 Å resolution) showed the PLP-α-methyl-d-serine aldimine, mimicking the d-serine-SPT complex prior to racemization. Based on these enzymological and structural analyses, the synthesis of KDS from d-serine was explained as the result of the slow racemization to l-serine, followed by the reaction with palmitoyl-CoA, and SPT would not catalyze the direct condensation between d-serine and palmitoyl-CoA. It was also shown that the S. multivorum SPT catalyzed the racemization of the product KDS, which would explain the presence of (2R)-KDS in the reaction products.
Topics: Catalytic Domain; Crystallization; Deuterium Exchange Measurement; Electrons; Hydrogen; Palmitoyl Coenzyme A; Serine; Serine C-Palmitoyltransferase; Sphingobacterium; Sphingosine; Stereoisomerism; Substrate Specificity
PubMed: 38325740
DOI: 10.1016/j.jbc.2024.105728 -
PLoS Pathogens Jan 2024Microbes associated with an organism can significantly modulate its susceptibility to viral infections, but our understanding of the influence of individual microbes...
Microbes associated with an organism can significantly modulate its susceptibility to viral infections, but our understanding of the influence of individual microbes remains limited. The nematode Caenorhabditis elegans is a model organism that in nature inhabits environments rich in bacteria. Here, we examine the impact of 71 naturally associated bacteria on C. elegans susceptibility to its only known natural virus, the Orsay virus. Our findings reveal that viral infection of C. elegans is significantly influenced by monobacterial environments. Compared to an Escherichia coli environmental reference, the majority of tested bacteria reduced C. elegans susceptibility to viral infection. This reduction is not caused by virion degradation or poor animal nutrition by the bacteria. The repression of viral infection by the bacterial strains Chryseobacterium JUb44 and Sphingobacterium BIGb0172 does not require the RIG-I homolog DRH-1, which is known to activate antiviral responses such as RNA interference and transcriptional regulation. Our research highlights the necessity of considering natural biotic environments in viral infection studies and opens the way future research on host-microbe-virus interactions.
Topics: Animals; Caenorhabditis elegans; Caenorhabditis elegans Proteins; RNA Interference; Virus Diseases; Viruses
PubMed: 38232128
DOI: 10.1371/journal.ppat.1011947 -
Applied Microbiology and Biotechnology Dec 2024In recent years organic food is gaining popularity as it is believed to promote better human health and improve soil sustainability, but there are apprehensions about...
In recent years organic food is gaining popularity as it is believed to promote better human health and improve soil sustainability, but there are apprehensions about pathogens in organic produces. This study was designed to understand the effect of different composts and soils on the status of the microbiome present in organically grown leafy vegetables. 16S rRNA metagenomic profiling of the leaves was done, and data were analyzed. It was found that by adding composts, the OTU of the microbiome in the organic produce was higher than in the conventional produce. The beneficial genera identified across the samples included plant growth promoters (Achromobacter, Paenibacillus, Pseudomonas, Sphingobacterium) and probiotics (Lactobacillus), which were higher in the organic produce. Some pathogenic genera, viz., plant pathogenic bacteria (Cellvibrio, Georgenia) and human pathogenic bacteria (Corynebacterium, Acinetobacter, Streptococcus, Streptomyces) were also found but with relatively low counts in the organic produce. Thus, the present study highlights that organic produce has lesser pathogen contamination than the conventional produce. KEY POINTS: • 16S rRNA metagenomics profiling done for organic red amaranth cultivar • Microbial richness varied with respect to the soil and compost type used • The ratio of beneficial to pathogenic genera improves with the addition of compost.
Topics: Humans; Composting; RNA, Ribosomal, 16S; Soil; Bacteria; Metagenome
PubMed: 38229333
DOI: 10.1007/s00253-023-12982-7 -
Environmental Research Mar 2024The primary objectives of this study were to explore the community-level succession of bacteria, fungi, and protists during cow-dung-driven composting and to elucidate...
The primary objectives of this study were to explore the community-level succession of bacteria, fungi, and protists during cow-dung-driven composting and to elucidate the contribution of the biodiversity and core microbiota of key-stone microbial clusters on compost maturity. Herein, we used high-throughput sequencing, polytrophic ecological networks, and statistical models to visualize our hypothesis. The results showed significant differences in the richness, phylogenetic diversity, and community composition of bacteria, fungi, and eukaryotes at different composting stages. The ASV191 (Sphingobacterium), ASV2243 (Galibacter), ASV206 (Galibacter), and ASV62 (Firmicutes) were the core microbiota of key-stone bacterial clusters relating to compost maturity; And the ASV356 (Chytridiomycota), ASV470 (Basidiomycota), and ASV299 (Ciliophora) were the core microbiota of key-stone eukaryotic clusters relating to compost maturity based on the data of this study. Compared with the fungal taxa, the biodiversity and core microbiota of key-stone bacterial and eukaryotic clusters contributed more to compost maturity and could largely predict the change in the compost maturity. Structural equation modeling revealed that the biodiversity of total microbial communities and the biodiversity and core microbiota of the key-stone microbial clusters in the compost directly and indirectly regulated compost maturity by influencing nutrient availability (e.g., NH-N and NO-N), hemicellulose, humic acid content, and fulvic acid content, respectively. These results contribute to our understanding of the biodiversity and core microbiota of key-stone microbial clusters in compost to improve the performance and efficiency of cow-dung-driven composting.
Topics: Animals; Cattle; Soil; Composting; Phylogeny; Bacteria; Microbiota; Biodiversity; Manure
PubMed: 38147920
DOI: 10.1016/j.envres.2023.118034 -
Environmental Science and Pollution... Jan 2024With the accelerated modernization of agriculture and industry, sulfides have been released into the environment as a by-products of various production processes....
Desulfurization properties, pathways, and potential applications of two novel and efficient chemolithotrophic sulfur-oxidizing strains of Pseudomonas sp. GHWS3 and Sphingobacterium sp. GHWS5.
With the accelerated modernization of agriculture and industry, sulfides have been released into the environment as a by-products of various production processes. Elevated levels of sulfide pose a threat to organisms' health and disrupt ecosystem equilibrium. This study successfully isolated two highly efficient sulfur-oxidizing strains, namely Pseudomonas aeruginosa GHWS3 and Sphingobacterium sp. GHWS5. Neither strain exhibited hemolytic activity or pathogenicity. Additionally, GHWS3 inhibited the common aquaculture pathogen Vibrio anguillarum, while GHWS5 exhibited inhibitory effects against Vibrio harveyi. GHWS3 and GHWS5 demonstrated effective removal of sulfide under the following conditions: temperature range of 20-40 °C, pH level of 4.5-8.5, salinity range of 0-50‰, C/N ratio of 5-15, and sulfide concentration of 20-200 mg/L. By amplifying the key functional genes of the sulfur-oxidizing Sox and rDsr systems in both GHWS3 and GHWS5 strains, potential desulfurization pathways were analyzed. Furthermore, both strains displayed high efficiency in removing sulfides from actual aquaculture pond substrate mixtures. The findings of this study provide two promising candidate strains for sulfides removal from farm tailwater, industrial wastewater, and domestic wastewater.
Topics: Wastewater; Sphingobacterium; Pseudomonas; Ecosystem; Bioreactors; Oxidation-Reduction; Sulfur; Sulfides
PubMed: 38085488
DOI: 10.1007/s11356-023-31404-9