A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline’s performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.

Clinical analysis and review of literature on pilomatrixoma in pediatric patients

Background@#Pilomatrixoma is a benign tumor that originates from the hair follicle matrix. It usually presents as a hard, slow growing, solitary mass that can be easily misdiagnosed as other skin masses. The aim of this study was to clinically analyze a case series of pilomatrixoma in pediatric patients from Korea. @*Methods@#A total of 165 pediatric patients from 2011 to 2018 with a histological diagnosis of pilomatrixoma were included. A retrospective review was performed using the electronic medical records, including patient demographics, number and location of the mass, clinical and imaging presentation, and postoperative outcomes. @*Results@#There were 61 male and 104 female patients with 152 solitary and 13 multiple pilomatrixomas. Among solitary pilomatrixomas, the lesion commonly occurred in the head and neck (84.2%), followed by upper limbs (11.2%), lower limbs (3.3%), and trunk (1.3%). The pilomatrixoma lesion presented as the following types based on our clinical classification: mass (56.02%), pigmentation (25.31%), mixed (12.65%), ulceration (4.82%), and keloid-like (1.2%). Ultrasonography showed a high positive predictive value (95.56%). There were no specific complications observed except for two cases of recurrence. @*Conclusion@#Pilomatrixoma has various clinical feature presentations and commonly occurs in the head and neck. Ultrasonography is a helpful diagnostic tool. Surgical removal of the lesion is the main treatment method with a low recurrence rate.

Rhabdomyomatous Mesenchymal Hamartoma Presenting as a Midline Mass on a Chin

A 17-month-old boy was evaluated for a midline mass on his chin. The mass was anchored to the mentalis muscle with a stalk-like structure. The pathological diagnosis of the mass was rhabdomyomatous mesenchymal hamartoma. This is the first report of rhabdomyomatous mesenchymal hamartoma presenting as a midline chin mass in Korean pediatric patients.

Rhabdomyomatous Mesenchymal Hamartoma Presenting as a Midline Mass on a Chin

A 17-month-old boy was evaluated for a midline mass on his chin. The mass was anchored to the mentalis muscle with a stalk-like structure. The pathological diagnosis of the mass was rhabdomyomatous mesenchymal hamartoma. This is the first report of rhabdomyomatous mesenchymal hamartoma presenting as a midline chin mass in Korean pediatric patients.