• 한국유가공학회:학술대회논문집
• /
• 한국유가공기술과힉회 2007년도 추계학술발표대회
• /
• pp.21-29
• /
• 2007

The field of microbiology has in recent years been transformed by huge increasing number of publicly available whole-genome sequences. This sequence information has significantly enhanced our understanding of the physiology, genetics, and evolutionary development of bacteria. Among the gastrointestinal microorganisms, bifidobacteria represent important human commensals because of their perceived contribution to maintaining a balanced gastrointestinal tract microbiota. In recent years bifidobacteria have drawn much scientific attention due to their use as live bacteria in numerous food products with various health-related claims. For this reason, these bacteria constitute a growing area of interest with respect to genomics, molecular biology, and genetics. Recent genome sequencing of a number of bifidobacterial species has allowed access to the complete genetic make-up of these bacteria. This review will focus how genomic data has allowed us to understand bifidobacterial evolution, while also revealing genetic functions that explains their presence in the particular ecological environment of the gastrointestinal tract.

• Animal cells and systems
• /
• 제6권4호
• /
• pp.323-326
• /
• 2002

One hundred and three random complementary DNA clones representing rainbow trout intestine were par1i811y sequenced as an approach to analyze the transcribed sequences of its genome. Of the sequences generated, 60.0% of the ESTs were represented by 40 known genes. Thirty-five clones of unknown gene products potentially represented 34 novel genes. The most Bbundantly represented messages were the 28S ribosomal protein (6.5%) and beta actin (5.8%). The genes involved in ribosome formation (18%) accounted for the major gene expression. Development of EST panels representing the genes expressed in a particular tissue will be useful in determining the role of these genes in normal function and in response to developmental, hormonal, environmental and physiological changes.

• Genomics & Informatics
• /
• 제16권4호
• /
• pp.21.1-21.7
• /
• 2018

Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although affected cows are treated with broad-spectrum antibiotics such as ceftiofur, endometrial and ovarian function are not fully recovered, which results in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica. Recent studies using high-throughput sequencing observed very low relative abundance of Escherichia coli, Trueperella pyogenes, and Prevotella melaninogenica in cows with metritis. Herein, we propose that metritis is associated with a dysbiosis of the uterine microbiota, which is characterized by high abundance of Bacteroides, Porphyromonas, and Fusobacterium.

• Journal of Veterinary Science
• /
• 제21권2호
• /
• pp.30.1-30.11
• /
• 2020

Mycoplasma ovipneumoniae (Mo) is difficult to culture, resulting in many difficulties in related research and application. Since nucleotide metabolism is a basic metabolism affects growth, this study conducted a "point-to-point" comparison of the corresponding growth phases between the Mo NM151 strain and the Mycoplasma mycoides subsp. capri (Mmc) PG3 strain. The results showed that the largest difference in nucleotide metabolism was found in the stationary phase. Nucleotide synthesis in PG3 was mostly de novo, while nucleotide synthesis in NM151 was primarily based on salvage synthesis. Compared with PG3, the missing reactions of NM151 referred to the synthesis of deoxythymine monophosphate. We proposed and validated a culture medium with added serine to fill this gap and prolong the stationary phase of NM151. This solved the problem of the fast death of Mo, which is significant for related research and application.

• Genomics & Informatics
• /
• 제21권1호
• /
• pp.13.1-13.8
• /
• 2023

Importance of accurate molecular diagnosis and quantification of particular disease-related pathogenic microorganisms is highlighted as an introductory step to prevent and care for diseases. In this study, we designed a primer/probe set for quantitative real-time polymerase chain reaction (qRT-PCR) targeting rgpA gene, known as the specific virulence factor of periodontitis-related pathogenic bacteria 'Porphyromonas gingivalis', and evaluated its diagnostic efficiency by detecting and quantifying relative bacterial load of P. gingivalis within saliva samples collected from clinical subjects. As a result of qRT-PCR, we confirmed that relative bacterial load of P. gingivalis was detected and quantified within all samples of positive control and periodontitis groups. On the contrary, negative results were confirmed in both negative control and healthy groups. Additionally, as a result of comparison with next-generation sequencing (NGS)-based 16S metagenome profiling data, we confirmed relative bacterial load of P. gingivalis, which was not identified on bacterial classification table created through 16S microbiome analysis, in qRT-PCR results. It showed that an approach to quantifying specific microorganisms by applying qRT-PCR method could solve microbial misclassification issues at species level of an NGS-based 16S microbiome study. In this respect, we suggest that P. gingivalis-specific primer/probe set introduced in present study has efficient applicability in various oral healthcare industries, including periodontitis-related microbial molecular diagnosis field.

• Asian-Australasian Journal of Animal Sciences
• /
• 제26권8호
• /
• pp.1144-1151
• /
• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• Reproductive and Developmental Biology
• /
• 제35권4호
• /
• pp.435-439
• /
• 2011

Sildenafil citrate (SIL) a phosphodiesterase 5 inhibitor (PDE5I) has been used for long time as a first line oral drug for erectile dysfunction. Though it has beneficial effects on erectile organ it also has some adverse effects in other cells and/or tissues related to reproductive system when exposed to longer duration. The objective of the present study is to evaluate the long term effect of SIL on sperm parameters in Wistar albino rat. The animals are divided into two groups, for group I - rats were treated with saline (vehicle alone) and group - II oral administration of 5 mg/kg b.w. of SIL was administrated orally once in a day for 120 days. At the end of the trial period animals were sacrificed and epididymal sperm were subjected to various analysis. Results showed significant reduction in sperm count, motility, viability and morphologically intact sperm in long term PDE5I exposed animals when compared to control. Acrosomal status and fertility test also showed significant reduction in long term PDE5I exposed animals. The present study clearly indicated that long term SIL has shown to induce alteration in sperm quality and quantity, leading to decline in fertility rate. Indicate that SIL impinge on spermatogenesis as well as epididymal function. Understanding the molecular down-stream events involved in long-term exposure to PDE5 inhibitor can be valuable to supervise on related infertility issues and to suggest corrective measures.

• Genes and Genomics
• /
• 제40권12호
• /
• pp.1331-1338
• /
• 2018

Although there have been plenty of dominance deviation analysis, few studies have dealt with multiple phenotypes. Because researchers focused on multiple phenotypes (final weight and backfat thickness) of Landrace pigs, the classification of the genes was possible. With genome-wide association studies (GWASs), we analyzed the additive and dominance effects of the single nucleotide polymorphisms (SNPs). The classification of the pig genes into four categories (overdominance in final weight, overdominance in backfat thickness and overdominance in final weight, underdominance in backfat thickness, etc.) can enable us not only to analyze each phenotype's dominant effects, but also to illustrate the gene ontology (GO) analysis with different aspects. We aimed to determine the additive and dominant effect in backfat thickness and final weight and performed GO analysis. Using additive model and dominance deviation analysis in GWASs, Landrace pigs' overdominant and underdominant SNP effects in final weight and backfat thickness were surveyed. Then through GO analysis, we investigated the genes that were classified in the GWASs. The major GO terms of the underdominant effects in final weight and overdominant effects in backfat thickness were ion transport with the SLC8A3, KCNJ16, P2RX7 and TRPC3 genes. Interestingly, the major GO terms in the underdominant effects in the final weight and the underdominant effects in the backfat thickness were the regulation of ion transport with the STAC, GCK, TRPC6, UBASH3B, CAMK2D, CACNG4 and SCN4B genes. These results demonstrate that ion transport and ion transport regulation genes have distinct dominant effects. Through GWASs using the mode of linear additive model and dominance deviation, overdominant effects and underdominant effects in backfat thickness was contrary to each other in GO terms (ion transport and ion transport regulation, respectively). Additionally, because ion transport and ion transport regulation genes are associative with adipose tissue accumulation, we could infer that these two groups of genes had to do with unique fat accumulation mechanisms in Landrace pigs.

• 농업과학연구
• /
• 제45권4호
• /
• pp.725-732
• /
• 2018

The vaccination for foot-and-mouth disease (FMD) is an effective way to control FMD. However, the injection of FMD vaccine causes abnormalities in pork meat by the incidence of lesions at the injection site. This study was conducted to investigate the inhibition effects of dietary bromelain, a natural protease derived from pineapple stems, on the incidence of lesions at the vaccination site on pigs. A total of 335 pigs (LYD [Landrace ${\times}$ Yorkshire ${\times}$ Duroc]; 7-week-old) were randomly allotted to two dietary treatments: control (basic diet) and bromelain treatment (diet supplemented with bromelain 1 kg/ton). The injection of FMD vaccine was conducted on 56- and 84-day-old pigs. Pigs with the bromelain treatment were fed a diet supplemented with bromelain for 14 days from 5 days before the vaccine injection. After slaughtering the pigs, the number of carcasses that had abnormal meat at the injection site of the vaccine and the amount of abnormal meat, discarded meat, and trimmings were recorded. Pork from the bromelain treated pigs had a lower incidence of abnormal meat caused by vaccine injection as well as a lower amount of abnormal meat, discarded meat, and trimmings than those of the control (p < 0.05). Our result suggests that dietary bromelain could improve the quality of pork meat by inhibiting incidence of lesions at the vaccine injection site.

• Journal of Animal Science and Technology
• /
• 제63권6호
• /
• pp.1411-1422
• /
• 2021

Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.