• Journal of Microbiology and Biotechnology
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• v.33 no.9
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• pp.1162-1169
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• 2023

16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.

• International Journal of Oral Biology
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• v.46 no.3
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• pp.146-153
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• 2021

Accurate identification of microbes facilitates the prediction, prevention, and treatment of human diseases. To increase the accuracy of microbiome data analysis, a long region of the 16S rRNA is commonly sequenced via paired-end sequencing. In paired-end sequencing, a sufficient length of overlapping region is required for effective joining of the reads, and high-quality sequencing reads are needed at the overlapping region. Trimming sequences at the reads distal to a point where sequencing quality drops below a specific threshold enhance the joining process. In this study, we examined the effect of trimming conditions on the number of reads that remained after quality control and chimera removal in the Illumina paired-end reads of the V3-V4 hypervariable region. We also examined the alpha diversity and taxa assigned by each trimming condition. Optimum quality trimming increased the number of good reads and assigned more number of operational taxonomy units. The pre-analysis trimming step has a great influence on further microbiome analysis, and optimized trimming conditions should be applied for Divisive Amplicon Denoising Algorithm 2 analysis in QIIME2 platform.

• Korean Journal of Microbiology
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• v.39 no.1
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• pp.45-50
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• 2003

The diversity and change of microbial communities during kimchi fermentation at $4^{\circ}C$ were analyzed by denaturing gradient gel electrophoresis (DGGE). Kimchi samples were taken every 5 days over the fermentation periods (for 60 days) to extract total DNA for DGGE analysis. Touchdown polymerase chain reaction was performed to amplify the V3 region of 16S rRNA gene. Sequencing results of partial 16S rDNA amplicons from DGGE profiles revealed that lactic acid bacteria (LAB), especially Weissella koreensis, Lactobacillus sakei and Leuconostoc gelidum were dominants in kimchi fermentation at $4^{\circ}C$. And we knew that W. koreensis steadily existed throughout the whole fermentation period, also Lb. sakei and Leuc. gelidum appeared from 10th day and 30th day of fermentation time, respectively and then these species were to be dominant microorganisms.

• Journal of Veterinary Science
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• v.25 no.5
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• pp.65.1-65.11
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• 2024

Importance: Recent developments in genetic analytical techniques have enabled the comprehensive analysis of gastrointestinal symbiotic bacteria as a screening tool for animal health conditions, especially the endangered gibbons at the National Wildlife Rescue Centre (NWRC). Objective: High-throughput sequencing based on 16S ribosomal RNA genes was used to determine the baseline gut bacterial composition and identify potential pathogenic bacteria among three endangered gibbons housed in the NWRC. Methods: Feces were collected from 14 individuals (Hylobates lar, n = 9; Hylobates agilis, n = 4; and Symphalangus syndactylus, n = 1) from March to November 2022. Amplicon sequencing were conducted by targeting V3-V4 region. Results: The fecal microbial community of the study gibbons was dominated by Bacteroidetes and Firmicutes (phylum level), Prevotellaceae and Lachnospiraceae/Muribaculaceae (family level), and Prevotella (and its subgroups) (genera level). This trend suggests that the microbial community composition of the study gibbons differed insignificantly from previously reported conspecific or closely related gibbon species. Conclusions and Relevance: This study showed no serious health problems that require immediate attention. However, relatively low alpha diversity and few potential bacteria related to gastrointestinal diseases and streptococcal infections were detected. Information on microbial composition is essential as a guideline to sustain a healthy gut condition of captive gibbons in NWRC, especially before releasing this primate back into the wild or semi-wild environment. Further enhanced husbandry environments in the NWRC are expected through continuous health monitoring and increase diversity of the gut microbiota through diet diversification.

• Animal Bioscience
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• v.34 no.12
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• pp.1921-1929
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• 2021

Objective: The intestinal microbiota enhances nutrient absorption in the host and thus promotes heath. Qinghai semi-fine wool sheep is an important livestock raised in the Qinghai-Tibetan Plateau; however, little is known about the bacterial microbiota of its intestinal tract. The aim of this study was to detect the microbial characterization in the intestinal tract of the Qinghai semi-fine wool sheep. Methods: The bacterial profiles of the six different intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of Qinghai semi-fine wool sheep were studied using 16S rRNA V3-V4 hypervariable amplicon sequencing. Results: A total of 2,623,323 effective sequences were obtained, and 441 OTUs shared all six intestinal segments. The bacterial diversity was significantly different among the different intestinal segments, and the large intestine exhibited higher bacterial diversity than the small intestine. Firmicutes, Bacteroidetes, and Patescibacteria were the dominant phyla in these bacterial communities. Additionally, at the genus level, Prevotella_1, Candidatus_Saccharimonas, and Ruminococcaceae_UCG-005 were the most predominant genus in duodenal segment, jejunal and ileal segments, and cecal, colonic, and rectal segments, respectively. We predicted that the microbial functions and the relative abundance of the genes involved in carbohydrate metabolism were overrepresented in the intestinal segments of Qinghai semi-fine wool sheep. Conclusion: The bacterial communities and functions differed among different intestinal segments. Our study is the first to provide insights into the composition and biological functions of the intestinal microbiota of Qinghai semi-fine wool sheep. Our results also provide useful information for the nutritional regulation and production development in Qinghai semi-fine wool sheep.