• 한국축산식품학회지
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• 제39권5호
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• pp.804-819
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• 2019

Ezine cheese is a non-starter and long-ripened cheese produced in the Mount of Ida region of Canakkale, Turkey, with a protected designation of origin status. Non-starter lactic acid bacteria (NSLAB) have a substantial effect on the quality and final sensorial characteristics of long-ripened cheeses. The dominance of NSLAB can be attributed to their high tolerance to the hostile environment in cheese during ripening relative to many other microbial groups and to its ability to inhibit undesired microorganisms. These qualities promote the microbiological stability of long-ripened cheeses. In this study, 144 samples were collected from three dairies during the ripening period of Ezine cheese. Physicochemical composition and NSLAB identification analyses were performed using both conventional and molecular methods. According to the results of a 16S rRNA gene sequence analysis, 13 different species belonging to seven genera were identified. Enterococcus faecium (38.42%) and E. faecalis (18.94%) were dominant species during the cheese manufacturing process, surviving 12 months of ripening together with Lactobacillus paracasei (13.68%) and Lb. plantarum (11.05%). The results indicate that NSLAB contributes to the microbiological stability of Ezine cheese over 12 months of ripening. The isolation of NSLAB with antimicrobial activity, potential bacteriocin producers, yielded defined collections of natural NSLAB isolates from Ezine cheese that can be used to generate specific starter cultures for the production of Ezine cheese (PDO).

• 미생물학회지
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• 제55권1호
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• pp.58-60
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• 2019

혐기성 그람 음성 세균인 Prevotella intermedia는 사람의 구강 내 정상세균총의 하나이고 다양한 구강 및 전신 질환과 관련이 있다. 본 논문에서는 경부안면형 방선균증으로부터 분리된 P. intermedia ATCC 15032 균주의 유전체 염기서열을 분석하여 보고한다. 이 균주의 유전체는 2,848,426 bp의 크기로 GC 함량은 43.45%이다. 이 유전체 서열 정보는 P. intermedia 종 내에서의 균주 간 유전체 다양성 및 표현형 차이의 유전적 기초를 이해하는데 중요한 정보를 제공할 것이다.

• 농업과학연구
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• 제45권4호
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• pp.655-663
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• 2018

The insect gut microbiome is known to have important roles in host growth, development, digestion, and resistance against pathogens. In addition, the genetic diversity of the insect gut microbiota has recently been recognized as potential genetic resources for industrial bioprocessing. However, there is limited information regarding the insect gut microbiota to better help us understand their potential benefits for enhanced pig production. With the development of next-generation sequencing methods, whole genome sequence analysis has become possible beyond traditional culture-independent methods. This improvement makes it possible to identify and characterize bacteria that are not cultured and located in various environments including the gastrointestinal tract. Insect intestinal microorganisms are known to have an important role in host growth, digestion, and immunity. These gut microbiota have recently been recognized as potential genetic resources for livestock farming which is using the functions of living organisms to integrate them into animal science. The purpose of this literature review is to emphasize the necessity of research on insect gut microbiota and their applicability to pig production or bioindustry. In conclusion, bacterial metabolism of feed in the gut is often significant for the nutrition intake of animals, and the insect gut microbiome has potential to be used as feed additives for enhanced pig performance. The exploration of the structure and function of the insect gut microbiota needs further investigation for their potential use in the swine industry particularly for the improvement of growth performance and overall health status of pigs.

• 미생물학회지
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• 제55권3호
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• pp.280-282
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• 2019

본 논문에서는 농흉 환자의 흉막액에서분리된 Bifidobacterium dentium ATCC 15424균주의 유전체 염기서열을 분석하여 보고한다. 이 균주의 유전체는 구강에서 분리된 다른 B. dentium 균주에 존재하지 않는 type III 및 IV secretion system proteins, N-acetylmuramoyl-L-alanine amidase 그리고 PRTRC system protein E를 암호화하는 유전자 등 247개의 ATCC 15424균주 특이적인 유전자들을 포함한다. 이 유전체의 서열 정보는 B. dentium의 자연적 변이와 세균 종 내의 유전체 다양성을 이해하는 데 유용할 것이다.

• 한국미생물·생명공학회지
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• 제47권3호
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• pp.401-411
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• 2019

All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, $tRNA^{Ile(GAT)}$ and $tRNA^{Ala(TGC)}$, which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the $tRNA^{Ala}$ gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies.

• Parasites, Hosts and Diseases
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• 제61권1호
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• pp.42-52
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• 2023

The genus Babesia includes parasites that can induce human and animal babesiosis, which are common in tropical and subtropical regions of the world. The gut microbiota has not been examined in hamsters infected by Babesia duncani. Red blood cells infected with B. duncani were injected into hamsters through intraperitoneal route. To evaluate the changes in gut microbiota, DNAs were extracted from small intestinal contents, acquired from hamsters during disease development. Then, the V4 region of the 16S rRNA gene of bacteria was sequenced using the Illumina sequencing platform. Gut microbiota alternation and composition were assessed according to the sequencing data, which were clustered with >97.0% sequence similarity to create amplicon sequence variants (ASVs). Bacteroidetes and Firmicutes were made up of the major components of the gut microbiota in all samples. The abundance of Bacteroidetes elevated after B. duncani infection than the B. duncani-free group, while Firmicutes and Desulfobacterota declined. Alpha diversity analysis demonstrated that the shown ASVs were substantially decreased in the highest parasitemia group than B. duncani-free and lower parasitemia groups. Potential biomarkers were discovered by Linear discriminant analysis Effect Size (LEfSe) analysis, which demonstrated that several bacterial families (including Muribaculaceae, Desulfovibrionaceae, Oscillospiraceae, Helicobacteraceae, Clostridia UGG014, Desulfovibrionaceae, and Lachnospiraceae) were potential biomarkers in B. duncani-infected hamsters. This research demonstrated that B. duncani infectious can modify the gut microbiota of hamsters.

• Journal of Periodontal and Implant Science
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• 제53권1호
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• pp.69-84
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• 2023

Purpose: The objective of this study was to analyze the microbial profile of individuals with peri-implantitis (PI) compared to those of periodontally healthy (PH) subjects and periodontitis (PT) subjects using Illumina sequencing. Methods: Buccal, supragingival, and subgingival plaque samples were collected from 109 subjects (PH: 30, PT: 49, and PI: 30). The V3-V4 region of 16S rRNA was sequenced and analyzed to profile the plaque microbiota. Results: Microbial community diversity in the PI group was higher than in the other groups, and the 3 groups showed significantly separated clusters in the buccal samples. The PI group showed different patterns of relative abundance from those in the PH and PT groups depending on the sampling site at both genus and phylum levels. In all samples, some bacterial species presented considerably higher relative abundances in the PI group than in the PH and PT groups, including Anaerotignum lactatifermentans, Bacteroides vulgatus, Faecalibacterium prausnitzii, Olsenella uli, Parasutterella excrementihominis, Prevotella buccae, Pseudoramibacter alactolyticus, Treponema parvum, and Slackia exigua. Network analysis identified that several well-known periodontal pathogens and newly recognized bacteria were closely correlated with each other. Conclusions: The composition of the microbiota was considerably different in PI subjects compared to PH and PT subjects, and these results could shed light on the mechanisms involved in the development of PI.

• Journal of Microbiology and Biotechnology
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• 제33권9호
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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.

• Journal of Veterinary Science
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• 제25권3호
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• pp.44.1-44.13
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• 2024

Importance: The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics. Objective: This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia. Methods: Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder. Results: Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%. Conclusions and Relevance: The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.

• Animal Bioscience
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• 제37권8호
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• pp.1428-1439
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• 2024

Objective: Compared to Mimas pigeons, Shiqi pigeons exhibit greater tolerance to coarse feeding because of their abundant gut microbiota. Here, to investigate the potential of utilizing intestinal flora derived from Shiqi pigeons, the intestinal flora and body indices of Mimas squabs were evaluated after fecal microbiota transplantation (FMT) from donors. Methods: A total of 90 one-day-old squabs were randomly divided into the control group (CON), the low-concentration group (LC) and the high-concentration group (HC): gavaged with 200 μL of bacterial solution at concentrations of 0, 0.1, and 0.2 g/15 mL, respectively. Results: The results suggested that FMT improved the body weight of Mimas squabs in the HC and LC groups (p<0.01), and 0.1 g/15 mL was the optimal dose during FMT. After 16S rRNA sequencing was performed, compared to those in the CON group, the abundance levels of microflora, especially Lactobacillus, Muribaculaceae, and Megasphaera (p<0.05), in the FMT-treated groups were markedly greater. Random forest analysis indicated that the main functions of key microbes involve pathways associated with metabolism, further illustrating their important role in the host body. Conclusion: FMT has been determined to be a viable method for augmenting the weight and intestinal microbiota of squabs, representing a unique avenue for enhancing the economic feasibility of squab breeding.