Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
Purpose
The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples.
Methods
In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis.
Results
When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (
Porphyromonas gingivalis
,
Treponema denticola
, and
Prevotella intermedia
). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples.
Conclusions
In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.
Objectives/Hypothesis: This study aimed to provide evidence of whether unfractionated heparin used as adjuvant therapy in conjunction with systemic corticosteroid therapy improves hearing recovery in patients with profound idiopathic sudden sensorineural hearing loss (ISSNHL), and to compare the effect of this treatment with those of additional intratympanic corticosteroid therapy.Study Design: Retrospective chart review. Methods: Eighty-seven patients with profound ISSNHL (≥90 dB) and who had been admitted at a tertiary referral center between 2010 and 2018 were retrospectively reviewed, 67 patients for additional intratympanic corticosteroid injection (ITSI) (ITSI group) and 21 for adjuvant heparin therapy (heparin group). Hearing recovery was evaluated by grade assessment according to the American Academy of Otolaryngology-Head and Neck Surgery criteria.Results: Of the patients in the heparin group, 42.8% recovered serviceable hearing, which was significantly higher than the recovery rates (19.7%) of those in the ITSI group. Particularly, in patients with pretreatment hearing level of 90 to 100 dB, adjuvant heparin therapy enhanced therapeutic effects with a significant hearing recovery rate of 80%. However, in patients with initial hearing level >100 dB, the rates of significant hearing recovery in the two groups were roughly equal and remained unsatisfactory (8.1% in the ITSI group and 9.1% in the heparin group).Conclusions: The results of this study suggest that the treatment of profound ISSNHL with adjuvant heparin therapy, in combination with systemic steroid therapy, results in higher hearing recovery rates when compared to combined local and systemic corticosteroid therapy, without serious complications.
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