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.

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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.

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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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The importance of probiotics in pig production is widely recognized. However, the precise role of probiotics in regulating the gut microbiota of piglets has not been assessed extensively. Therefore, we intend to examine whether suckling pigs ingesting with synthetic milk (SM) and probiotics along with mother milk has a carryover effect on its growth and gut health at the post-weaning stage. A total of 40 [Duroc× (Yorkshire× Landrace)] neonates with an initial BW of 1.49 ± 0.28 kg were assigned to one of two treatments groups: control (CON) and treatment (TRT). Control group piglets were nourished with synthetic milk, while TRT group piglets were nourished SM with (1 × 109 CFU/g) Lactobacillus sp. probiotics. The treatment group piglets showed higher (p < 0.05) body weight and daily gain at week 3 than the CON group piglets. 16S metagenome sequencing showed average demultiplexed reads and denoised reads counts of 157,399 and 74,945, respectively. The total ASV taxonomy number classified with a confidence threshold > 70% (default) on sequence alignment with the SILVA v138 reference database was 4,474. During week 1, Escherichia-Shigella, Clostridium sensu stricto 1, and Bacteroides were confirmed as the major dominant bacterial genera in both the groups at the genus level. However, during week 2, the relative proportion of Escherichia-Shigella, Clostridium sensu stricto 1, and Proteobacteria was decreased, while that of Lactobacillus and Bacteroidota was increased in pigs receiving the probiotic supplement. During weeks 2 and 3, Firmicutes, Proteobacteria, and Bacteroidota phyla were dominant in both groups. During week 6, the relative proportion of Proteobacteria was slightly increased in both groups. Furthermore, Prevotella was confirmed as the major dominant bacterial genus in both groups during weeks 3 and 6. This study suggests that nourishing neonatal piglets with synthetic milk and Lactobacillus sp. probiotics from birth to 21 days would be beneficial to enhance the gut health of piglets and to overcome post-weaning mortality.

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.