• Journal of Applied Biological Chemistry
• /
• v.58 no.4
• /
• pp.369-375
• /
• 2015

Meat from black pigs (BP) is in high demand compared with that from modern white pig (WP) breeds such as Landrace pigs owing to its high quality. However, the growth rate of black pigs is slower than that of white pig breeds. We investigated differences in the fecal microbial composition between white and black pigs to explore whether these breeds differed in the composition of their gut microbial communities. The swine gut microbiota was investigated using Illumina's MiSeq-based sequencing technology by targeting the V4 region of the 16S rRNA gene. Our results showed that the composition of the gut microbiota was significantly different between the two pig breeds. While the composition of the WP microbiota shifted according to the growth stage, fewer shifts in composition were observed for the BP gut microbiota. In addition, the WP gut microbiota showed a higher Firmicutes/Bacteroidetes ratio compared with that of BP. A high ratio between these phyla was previously reported as an obesity-linked microbiota composition. Moreover, the WP microbiota contained a significantly higher abundance of cellulolytic bacteria, suggesting a possibility of higher fiber digestion efficiency in WP compared to BP. These findings may be important factors affecting growth performance and energy-harvesting capacities in pigs. Our findings of differences in the gut microbiota composition between the two breeds may provide new leads to understand growth rate variation across pig breeds.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.1
• /
• pp.78-84
• /
• 2017

Objective: The aim of this study was to examine shifts in the composition of the bacterial population in the intestinal tracts (ITs) of weaning piglets by antibiotic treatment using high-throughput sequencing. Methods: Sixty 28-d-old weaning piglets were randomly divided into two treatment groups. The Control group was treated with a basal diet without antibiotics. The Antibiotic group's basal diet contained colistin sulfate at a concentration of 20 g per ton and bacitracin zinc at a concentration of 40 g per ton. All of the pigs were fed for 28 days. Then, three pigs were killed, and the luminal contents of the jejunum, ileum, cecum, and colon were collected for DNA extraction and high-throughput sequencing. Results: The results showed that the average daily weight gain of the antibiotic group was significantly greater (p<0.05), and the incidence of diarrhea lower (p>0.05), than the control group. A total of 812,607 valid reads were generated. Thirty-eight operational taxonomic units (OTUs) that were found in all of the samples were defined as core OTUs. Twenty-one phyla were identified, and approximately 90% of the classifiable sequences belonged to the phylum Firmicutes. Forty-two classes were identified. Of the 232 genera identified, nine genera were identified as the core gut microbiome because they existed in all of the tracts. The proportion of the nine core bacteria varied at the different tract sites. A heat map was used to understand how the numbers of the abundant genera shifted between the two treatment groups. Conclusion: At different tract sites the relative abundance of gut microbiota was different. Antibiotics could cause shifts in the microorganism composition and affect the composition of gut microbiota in the different tracts of weaning piglets.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.3
• /
• pp.524-534
• /
• 2017

The development and utilization of crop straw biogas resources can effectively alleviate the shortage of energy, environmental pollution, and other issues. This study performed a continuous batch test at $35^{\circ}C$ to assess the methane production potential and volatile organic acid contents using the modified Gompertz equation. Illumina MiSeq platform sequencing, which is a sequencing method based on sequencing-by-synthesis, was used to compare the archaeal community diversity, and denaturing gradient gel electrophoresis (DGGE) was used to analyze the bacterial community diversity in rice straw, dry maize straw, silage maize straw, and tobacco straw. The results showed that cumulative gas production values for silage maize straw, rice straw, dry maize straw, and tobacco straw were 4,870, 4,032.5, 3,907.5, and $3,628.3ml/g{\cdot}VS$, respectively, after 24 days. Maximum daily gas production values of silage maize straw and rice straw were 1,025 and $904.17ml/g{\cdot}VS$, respectively, followed by tobacco straw and dry maize straw. The methane content of all four kinds of straws was > 60%, particularly that of silage maize straw, which peaked at 67.3%. Biogas production from the four kinds of straw was in the order silage maize straw > rice straw > dry maize straw > tobacco straw, and the values were 1,166.7, 1,048.4, 890, and $637.4ml/g{\cdot}VS$, respectively. The microbial community analysis showed that metabolism was mainly carried out by acetate-utilizing methanogens, and that Methanosarcina was the dominant archaeal genus in the four kinds of straw, and the DGGE bands belonged to the phyla Firmicutes, Bacteroidetes, and Chloroflexi. Silage maize is useful for biogas production because it contains four kinds of straw.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.2
• /
• pp.227-235
• /
• 2018

Foodborne illness represents a major threat to public health and is frequently attributed to pathogenic microorganisms on fresh produce. Recurrent outbreaks often come from vegetables that are grown close to or within the ground. Therefore, the first step to understanding the public health risk of microorganisms on fresh vegetables is to identify and describe microbial communities. We investigated the phyllospheres on Chinese cabbage (Brassica rapa subsp. pekinensis, N = 54). 16S rRNA gene amplicon sequencing targeting the V5-V6 region of 16S rRNA genes was conducted by employing the Illumina MiSeq system. Sequence quality was assessed, and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using a weighted Fast UniFrac matrix. The average number of sequence reads generated per sample was 34,584. At the phylum level, bacterial communities were composed primarily of Proteobacteria and Bacteroidetes. The most abundant genera on Chinese cabbages were Chryseobacterium, Aurantimonadaceae_g, Sphingomonas, and Pseudomonas. Diverse potential pathogens, such as Pantoea, Erwinia, Klebsiella, Yersinia, Bacillus, Staphylococcus, Salmonella, and Clostridium were also detected from the samples. Although further epidemiological studies will be required to determine whether the detected potential pathogens are associated with foodborne illness, our results imply that a metagenomic approach can be used to detect pathogenic bacteria on fresh vegetables.

• Journal of Microbiology and Biotechnology
• /
• v.26 no.7
• /
• pp.1320-1332
• /
• 2016

Light hydrocarbons accumulated in subsurface soil by long-term microseepage could favor the anomalous growth of indigenous hydrocarbon-oxidizing microorganisms, which could be crucial indicators of underlying petroleum reservoirs. Here, Illumina MiSeq sequencing of the 16S rRNA gene was conducted to determine the bacterial community structures in soil samples collected from three typical oil and gas fields at different locations in China. Incubation with n-butane at the laboratory scale was performed to confirm the presence of "universal microbes" in light-hydrocarbon microseepage ecosystems. The results indicated significantly higher bacterial diversity in next-to-well samples compared with background samples at two of the three sites, which were notably different to oil-contaminated environments. Variation partitioning analysis showed that the bacterial community structures above the oil and gas fields at the scale of the present study were shaped mainly by environmental parameters, and geographic location was able to explain only 7.05% of the variation independently. The linear discriminant analysis effect size method revealed that the oil and gas fields significantly favored the growth of Mycobacterium, Flavobacterium, and Pseudomonas, as well as other related bacteria. The relative abundance of Mycobacterium and Pseudomonas increased notably after n-butane cultivation, which highlighted their potential as biomarkers of underlying oil deposits. This work contributes to a broader perspective on the bacterial community structures shaped by long-term light-hydrocarbon microseepage and proposes relatively universal indicators, providing an additional resource for the improvement of microbial prospecting of oil and gas.

• Korean Journal of Medicinal Crop Science
• /
• v.28 no.3
• /
• pp.183-194
• /
• 2020

Background: This study investigated the effect of soil properties and soil bacterial community on early growth characteristics of wild-simulated ginseng (Panax ginseng C. A. Meyer) in coniferous and mixed forest experimental fields. Methods and Results: The soil bacterial community was analyzed using a high throughput sequencing technique (Illumina MiSeq sequencing). The relationship between the soil bacterial community, soil properties, and growth characteristics of wild-simulated ginseng were analyzed using principal coordinate analysis (PCoA) and the Pearson's correlation analysis. Soil properties and soil bacterial community showed significant difference with forest physiognomy. Results of Pearson's correlation analysis and PCoA showed that the soil properties (soil pH, organic matter, total nitrogen, and cation exchange capacity) and soil bacterial community had significant correlation with tree species ratio and early growth characteristics of wild-simulated ginseng. Conclusions: This study clearly demonstrated the effect of soil properties and soil bacterial community on early growth characteristics of wild-simulated ginseng in coniferous and mixed forest. Moreover, these results will help in the selection of suitable cultivation sites for wild-simulated ginseng.

• Korean Journal of Medicinal Crop Science
• /
• v.28 no.3
• /
• pp.209-220
• /
• 2020

Background: This study investigated the effects of soil properties on the soil fungal community in first and continuous cultivation areas of Cnidium officinale Makino. Methods and Results: The soil fungal community was analyzed for relative abundance and principal coordinate analysis (PCoA) was conducted using Illumina MiSeq sequencing. The correlation between the soil chemical properties and the soil fungal community was assessed with distance-based linear models (DISTLM). The soil fungal community showed distinct clusters consisting in the continuous cultivation area of C. officinale Makino. PCoA and DISTLM indicated that soil pH, calcium, and available P₂O₅ significantly affected the soil fungal community in the cultivation area of C. officinale Makino. In addition, considering 5 different pathogenic fungi the relative abundance of Fusarium in the continuous cultivation area was significantly higher compared to that in the first cultivation area of C. officinale Makino. Conclusions: This study is important because it has determinined the effects of soil properties on the soil fungal community in both first and continuous cultivation areas of C. officinale Makino. Moreover, these results will be helpful to investigate the cause of continuous cropping obstacle in C. officinale Makino by examining the changes of soil fungal community.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.17
• /
• pp.7935-7941
• /
• 2015

The aim of this study was to implement massive parallel sequencing (MPS) technology in clinical genetics testing. We developed and tested an amplicon-based method for resequencing the BRCA1 and BRCA2 genes on an Illumina MiSeq to identify disease-causing mutations in patients with hereditary breast or ovarian cancer (HBOC). The coding regions of BRCA1 and BRCA2 were resequenced in 96 HBOC patient DNA samples obtained from different sample types: peripheral blood leukocytes, whole blood drops dried on paper, and buccal wash epithelia. A total of 16 random DNA samples were characterized using standard Sanger sequencing and applied to optimize the variant calling process and evaluate the accuracy of the MPS-method. The best bioinformatics workflow included the filtration of variants using GATK with the following cut-offs: variant frequency >14%, coverage ($>25{\times}$) and presence in both the forward and reverse reads. The MPS method had 100% sensitivity and 94.4% specificity. Similar accuracy levels were achieved for DNA obtained from the different sample types. The workflow presented herein requires low amounts of DNA samples (170 ng) and is cost-effective due to the elimination of DNA and PCR product normalization steps.

• Asian-Australasian Journal of Animal Sciences
• /
• v.33 no.10
• /
• pp.1610-1616
• /
• 2020

Objective: This study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions. Methods: A total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment. Results: i) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens. Conclusion: The core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.

• Proceedings of the Korea Contents Association Conference
• /
• 2017.05a
• /
• pp.105-106
• /
• 2017

Background: Atopic dermatitis one of the most common chronic skin diseases, is caused by various environmental and genetic factors. Methods: A total of 2609 healthy newborns who were enrolled in the COCOA study (COCOA) from 2008 to 2015 were surveyed for indoor environmental exposure to fungi during gestation and then diagnosed postnatally for atopic dermatitis. The fungi collected during the gestation of 20 normal subjects and 20 infants that developed atopic dermatitis were identified using Illumina's MiSeq platform and analyzed for their diversity and species. Results: A total of 2,609 respondents were surveyed (52.8% male and 47.2% female) Children, 1, 2, and 3 years old diagnosed with atopic dermatitis comprised 15.2%, 15.7%, and 14.1% of the respondents, respectively. The prevalence of exposure to mold during gestation was 1.46 (95% CI, 1.05-2.04) and 1.52 (95% CI, 0.95-2.43), in the first and third years after birth, respectively. One-year-old children with atopic dermatitis and no fungal markers detected in the bathroom environment during gestation accounted for less than 5% (aOR, 1.51; 95%CI, 0.96-2.38) and in the group less than 5 ~ 30% (aOR, 2.21; 95%CI, 1.00-4.89), 3-year-old children had an increased prevalence of atopic dermatitis of more than 30% (aOR, 9.48, 95%CI 1.42-63.13). Conclusions: Exposure to indoor fungi during gestation and infancy is associated with the development of atopic dermatitis in children. The phyla and genera of the fungi in the indoor house dust differed during gestation. This suggests that exposure to indoor fungi during gestation may be associated with the development of atopic dermatitis in children. Future research will be necessary to establish the underlying mechanisms.