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For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. However, the 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other nearly-universal prokaryotic marker genes as the number of gene sequences increases in reference databases. This trend was strongly correlated with how represented a taxonomic group was in the database and indicates that, at the gene-level, the boundaries between many species might be fuzzy. Through our study, we argue that any approach that relies on a single marker to distinguish bacterial taxa is fraught even if some markers appear to be discriminative in current databases. Author summary: The use of reference databases for assigning taxonomic labels to genomic and metagenomic sequences is a fundamental bioinformatic task in the characterization of microbial communities. The increasing accessibility of high throughput sequencing has led to a rapid increase in the size and number of sequences in databases. This has been beneficial for improving our understanding of the global microbial genetic diversity. However, there is evidence that as the microbial diversity is more densely sampled, increasingly longer genomic segments are needed to differentiate between distinct bacterial species. The scientific community needs to be aware of this issue and needs to develop methods that better account for it when assigning taxonomic labels to metagenomic sequences from microbial communities. [ABSTRACT FROM AUTHOR]

Background: Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed to correct these errors, but it is uncertain if they obtain the accuracy needed for the high-resolution source tracking of foodborne illness outbreaks. Results: We tested 132 combinations of assembly and short- and long-read polishing tools to assess their accuracy for reconstructing the genome sequences of 15 highly similar Salmonella enterica serovar Newport isolates from a 2020 onion outbreak. While long-read polishing alone improved accuracy, near perfect accuracy (99.9999% accuracy or ~ 5 nucleotide errors across the 4.8 Mbp genome, excluding low confidence regions) was only obtained by pipelines that combined both long- and short-read polishing tools. Notably, medaka was a more accurate and efficient long-read polisher than Racon. Among short-read polishers, NextPolish showed the highest accuracy, but Pilon, Polypolish, and POLCA performed similarly. Among the 5 best performing pipelines, polishing with medaka followed by NextPolish was the most common combination. Importantly, the order of polishing tools mattered i.e., using less accurate tools after more accurate ones introduced errors. Indels in homopolymers and repetitive regions, where the short reads could not be uniquely mapped, remained the most challenging errors to correct. Conclusions: Short reads are still needed to correct errors in nanopore sequenced assemblies to obtain the accuracy required for source tracking investigations. Our granular assessment of the performance of the polishing pipelines allowed us to suggest best practices for tool users and areas for improvement for tool developers. [ABSTRACT FROM AUTHOR]

Background: Globally, prostate cancer is a significant disease that impacts men's health. Objective: We decided to evaluate the position of prostate cancer among oncological pathologies in Mures County during 2022. Material and methods: We used data collected from the county oncology department regarding incidence, mortality, age grouping, origin environments and for 44 cases, informations referring to staging, Gleason score and treatments performed. Results: In 2022 there were 107 cases of which 65(60.74%) were from rural areas. A total of 8(7.47%) deaths were recorded, all in rural areas. The highest incidence was between 71-80 years old(41.12%) followed by 61-70 years old(34.57%). There were no reports under 50 years old. The highest prevalence in rural areas was between the ages of 71-80(41.53%), followed by 61-70(33.84%), and in urban areas between 71-80(40.47%), followed by 61-70(35.71%). In urban areas we had no cases under age of 60. We collected data about 44 patients, 27(61.36%) from rural areas. Gleason scores were between 7 and 8 for 33 out of 44 cases(75%) and ≤6 for 4 cases(9%). In rural areas, 33% of cases were stage III, 30% stage IV and 30% stage II. In urban areas, 35% were stage III, 24% stage IV and 23% stage II. Monotherapy, either as surgery, hormone therapy, radiotherapy, chemotherapy, was done in 34 cases(77.27%) while combination therapies were used in 9 cases(20,45%). Prostatectomy was done in 16 cases(36.36%) and hormone therapy in 26 cases(59.09%). Conclusions: The incidence of prostate cancer is high over the age of 70 and occurs at older ages in rural than in urban areas. The higher mortality rate in rural areas is explained by the advanced stage of detection. The most common Gleason score is intermediate. The main treatments include hormone therapy and prostatectomy at younger ages, with chemotherapy and radiotherapy playing a less important role. [ABSTRACT FROM AUTHOR]

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here we describe the first effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available., Competing Interests: Competing interests The authors declare that they have no competing interests.