• Journal of Life Science
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• v.32 no.12
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• pp.1005-1012
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• 2022

This study was conducted to investigate the taxonomic composition and diversity of fecal microbiota between birth and weaning stages of Halla horses using 16S rRNA gene amplicon sequencing analysis. Proteobacteria (35.7%) and Firmicutes (45.6%) were identified as the most common phylum in birth and weaning, respectively. Escherichia (19.7%) and Clostridium (14.0%) were observed as the most dominant genus in birth, and Fibrobacter (6.6%) was the highest in weaning. The results of α-diversity showed that the richness and evenness in microbial communities were statistically significant (p<0.001) in birth and weaning. The results of β-diversity indicated that the birth and weaning stages were clearly divided into two groups at the genus and species levels. Permutational multivariate analysis of variance (PERMANOVA) showed that the microbiota composition differences between birth and weaning were statistically significant (q<0.001). A linear discriminant analysis effect (LEfSe) was performed to select taxonomic makers between the birth and weaning stages. On the genus level, Escherichia, Bacteroides, Clostridium, and Methylobacterium were relatively abundant at birth, whereas Fibrobacter was more abundant at weaning. We expect that this research can be utilized as basic data in the identification of microbial communities involved in disease prevention and nutrient absorption in Halla horses.

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

• Journal of Microbiology and Biotechnology
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• v.31 no.5
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• pp.747-755
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• 2021

The effects of the gut microbiome on both allergy and autoimmunity in dermatological diseases have been indicated in several recent studies. Chronic spontaneous urticaria (CSU) is a disease involving allergy and autoimmunity, and there is no report detailing the role of microbiota alterations in its development. This study was performed to identify the fecal microbial composition of CSU patients and investigate the different compositions and potential genetic functions on the fecal microbiota between CSU patients and normal controls. The gut microbiota of CSU patients and healthy individuals were obtained by 16s rRNA massive sequencing. Gut microbiota diversity and composition were compared, and bioinformatics analysis of the differences was performed. The gut microbiota composition results showed that Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia were dominant microbiota in CSU patients. The differential analysis showed that relative abundance of the Proteobacteria (p = 0.03), Bacilli (p = 0.04), Enterobacterales (p = 0.03), Enterobacteriaceae (p = 0.03) was significantly increased in CSU patients. In contrast, the relative abundance of Megamonas, Megasphaera, and Dialister (all p < 0.05) in these patients significantly decreased compared with healthy controls. The different microbiological compositions impacted normal gastrointestinal functions based on function prediction, resulting in abnormal pathways, including transport and metabolism. We found CSU patients exhibited gut microbiota dysbiosis compared with healthy controls. Our results indicated CSU is associated with gut microbiota dysbiosis and pointed out that the bacterial taxa increased in CSU patients, which might be involved in the pathogenesis of CSU. These results provided clues for future microbial-based therapies on CSU.

• Journal of Life Science
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• v.31 no.12
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• pp.1079-1087
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• 2021

To analyze gut microbiota of livestock in Korea and compare taxonomic differences, we conducted 16S rRNA metagenomic analysis through next-generation sequencing. Fecal samples from broiler chickens, pigs, and cattle were collected from domestic feedlots randomly. α-diversity results showed that significant differences in estimated species richness estimates (Chao1 and ACE, Abundance-based coverage estimators) and species richness index (OUTs, Operational taxonomic units) were identified among the three groups. However, NPShannon, Shannon, and Simpson indices revealed that abundance and evenness of the species were statistically significant only for poultry (broiler chickens) and mammals (pigs and cattle). Firmicutes was the most predominant phylum in the three groups of fecal samples. Linear discriminant (LDA) effect size (LEfSe) analysis was conducted to reveal the ranking order of abundant taxa in each of the fecal samples. A size-effect over 2.0 on the logarithmic LDA score was used as a discriminative functional biomarker. As shown by the fecal analysis at the genus level, broiler chickens were characterized by the presence of Weissella and Lactobacillus, as well as pigs were characterized by the presence of provetella and cattele were characterized by the presence of Acinetobacter. A permutational multivariate analysis of variance (PERMANOVA) showed that differences of microbial clusters among three groups were significant at the confidence level. (p=0.001). This study provides basic data that could be useful in future research on microorganisms associated with performance growth, as well as in studies on the livestock gut microbiome to increase productivity in the domestic livestock industry.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.10
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• pp.1456-1463
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• 2017

Objective: To investigate the effect of host genetics on gut microbial diversity, we performed a structural survey of the fecal microbiota of four purebred boar pig lines: Duroc, Landrace, Hampshire, and Yorkshire. Methods: The V3-V4 regions of the 16S rRNA genes were amplified and sequenced. Results: A total of 783 operational taxonomic units were shared by all breeds, whereas others were breed-specific. Firmicutes and Bacteroidetes dominated the majority of the fecal microbiota; Clostridia, Bacilli, and Bacteroidia were the major classes. Nine predominant genera were observed in all breeds and eight of them can produce short-chain fatty acids. Some bacteria can secrete cellulase to aid fiber digestion by the host. Butyric, isobutyric, valeric, and isovaleric acid levels were highest in Landrace pigs, whereas acetic and propionic acid were highest in the Hampshire breed. Heatmap was used to revealed breed-specific bacteria. Principal coordinate analysis of fecal bacteria revealed that the Landrace and Yorkshire breeds had high similarity and were clearly separated from the Duroc and Hampshire breeds. Conclusion: Overall, this study is the first time to compare the fecal microbiomes of four breeds of boar pig by high-throughput sequencing and to use Spearman's rank correlation to analyze competition and cooperation among the core bacteria.

• Korean Journal of Environmental Agriculture
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• v.41 no.4
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• pp.335-343
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• 2022

BACKGROUND: Antibiotics used in animal husbandry for disease prevention and treatment have resulted in the rapid progression of antibiotic resistant bacteria which can be introduced into the environment through livestock feces/manure, disseminating antibiotic resistant genes (ARGs). In this study, fecal samples were collected from the livestock farms located in Jeju Island to investigate the relationship between microbial communities and ARGs. METHODS AND RESULTS: Illumina MiSeq sequencing was applied to characterize microbial communities within each fecal sample. Using quantitative PCR (qPCR), ten ARGs encoding tetracycline resistance (tetB, tetM), sulfonamide resistance (sul1, sul2), fluoroquinolone resistance (qnrD, qnrS), fluoroquinolone and aminoglycoside resistance (aac(6')-Ib), beta-lactam resistance (bla_TEM, bla_CTX-M), macrolide resistance (ermC), a class 1 integronsintegrase gene (intI1), and a class 2 integrons-integrase gene (intI2) were quantified. The results showed that Firmicutes and Bacteroidetes were dominant in human, cow, horse, and pig groups, while Firmicutes and Actinobacteria were dominant in chicken group. Among ARGs, tetM was detected with the highest number of copies, followed by sul1 and sul2. Most of the genera belonging to Firmicutes showed positive correlations with ARGs and integron genes. There were 97, 34, 31, 25, and 22 genera in chicken, cow, pig, human, and horse respectively which showed positive correlations with ARGs and integron genes. In network analysis, we identified diversity of microbial communities which correlated with ARGs and integron genes. CONCLUSION(S): In this study, antibiotic resistance patterns in human and livestock fecal samples were identified. The abundance of ARGs and integron genes detected in the samples were associated with the amount of antibiotics commonly used for human and livestocks. We found diverse microbial communities associated with antibiotics resistance genes in different hosts, suggesting that antibiotics resistance can disseminate across environments through various routes. Identifying the routes of ARG dissemination in the environment would be the first step to overcome the challenge of antibiotic resistance in the future.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1321-1334
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• 2020

Beef, pork, chicken and milk are considered representative protein sources in the human diet. Since the digestion of protein is important, the role of intestinal microflora is also important. Despite this, the pure effects of meat and milk intake on the microbiome are yet to be fully elucidated. To evaluate the effect of beef, pork, chicken and milk on intestinal microflora, we observed changes in the microbiome in response to different types of dietary animal proteins in vitro. Feces were collected from five 6-week-old pigs. The suspensions were pooled and inoculated into four different media containing beef, pork, chicken, or skim milk powder in distilled water. Changes in microbial communities were analyzed using 16S rRNA sequencing. The feces alone had the highest microbial alpha diversity. Among the treatment groups, beef showed the highest microbial diversity, followed by pork, chicken, and milk. The three dominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all the groups. The most abundant genera in beef, pork, and chicken were Rummeliibacillus, Clostridium, and Phascolarctobacterium, whereas milk was enriched with Streptococcus, Lactobacillus, and Enterococcus. Aerobic bacteria decreased while anaerobic and facultative anaerobic bacteria increased in protein-rich nutrients. Functional gene groups were found to be over-represented in protein-rich nutrients. Our results provide baseline information for understanding the roles of dietary animal proteins in reshaping the gut microbiome. Furthermore, growth-promotion by specific species/genus may be used as a cultivation tool for uncultured gut microorganisms.

• Journal of Microbiology and Biotechnology
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• v.25 no.7
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• pp.1136-1145
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• 2015

The diverse microbial communities that colonize distinct segments of the gastrointestinal tract are intimately related to aspects of physiology and the pathology of human health. However, most recent studies have focused on the rectal or fecal microbiota, and the microbial signature of the duodenum is poorly studied. In this study, we compared the microbiota in duodenal and rectal samples to illustrate the characteristic microbial signatures of the duodenum in healthy adults. Nine healthy volunteers donated biopsies and luminal contents from the duodenum and rectum. To determine the composition and diversity of the microbiota, 454-pyrosequencing of bacterial 16S rRNA was performed and multiple bioinformatics analyses were applied. The α-diversity and phylogenetic diversity of the microbiota in the duodenal samples were higher than those of the rectal samples. There was higher biodiversity among the microbiota isolated from rectal biopsies than feces. Proteobacteria were more highly represented in the duodenum than in the rectum, both in the biopsies and in the luminal contents from the healthy volunteers (38.7% versus 12.5%, 33.2% versus 5.0%, respectively). Acinetobacter and Prevotella were dominant in the duodenum, whereas Bacteroides and Prevotella were dominant in the rectum. Additionally, the percentage of OTUs shared in biopsy groups was far higher than in the luminal group (43.0% versus 26.8%) and a greater number of genera was shared among the biopsies than the luminal contents. Duodenal samples demonstrated greater biological diversity and possessed a unique microbial signature compared with the rectum. The mucosa-associated microbiota was more relatively conserved than luminal samples.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.4
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• pp.452-461
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• 2012

Four, ruminally fistulated crossbred (Brahman${\times}$native) beef cattle with initial body weight of $420{\pm}15kg$ were randomly assigned according to a $4{\times}4$ Latin square design. The dietary treatments were mulberry leaf pellet (MUP) supplementation at 0, 200, 400 and 600 g/hd/d with rice straw fed to allow ad libitum intake. All steers were kept in individual pens and supplemented with concentrate at 5 g/kg of body weight daily. The experiment was 4 periods, and each lasted 21 d. During the first 14 d, all steers were fed their respective diets ad libitum and during the last 7 d, they were moved to metabolism crates for total urine and fecal collection. It was found that increasing MUP levels resulted in linearly increasing rice straw and total intakes (p<0.05). Ruminal temperature and pH were not significantly affected by MUP supplementation while $NH_3$-N concentration was increased (p<0.05) and maintained at a high level (18.5 mg/dl) with supplementation of MUP at 600 g/hd/d. Similarly, viable total bacteria in the rumen and cellulolytic bacteria were enriched by MUP supplementation at 600 g/hd/d. However, the rumen microbial diversity determined with a PCR-DGGE technique showed similar methanogenic diversity between treatments and sampling times and were similar at a 69% genetic relationship as determined by a UPGMA method. Based on this study, it could be concluded that supplementation of MUP at 600 g/hd/d improved DM intake, ruminal $NH_3$-N, and cellulolytic bacteria thus iimproving rumen ecology in beef cattle fed with rice straw.

• Journal of Microbiology and Biotechnology
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• v.33 no.9
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• pp.1111-1118
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• 2023

As a long-term condition that affects the airways and lungs, chronic obstructive pulmonary disease (COPD) is characterized by inflammation, emphysema, breathlessness, chronic cough, and sputum production. Currently, the bronchodilators and anti-inflammatory drugs prescribed for COPD are mostly off-target, warranting new disease management strategies. Accumulating research has revealed the gut-lung axis to be a bidirectional communication system. Cigarette smoke, a major exacerbating factor in COPD and lung inflammation, affects gut microbiota composition and diversity, causing gut microbiota dysbiosis, a condition that has recently been described in COPD patients and animal models. For this review, we focused on the gut-lung axis, which is influenced by gut microbial metabolites, bacterial translocation, and immune cell modulation. Further, we have summarized the findings of preclinical and clinical studies on the association between gut microbiota and COPD to provide a basis for using gut microbiota in therapeutic strategies against COPD. Our review also proposes that further research on probiotics, prebiotics, short-chain fatty acids, and fecal microbiota transplantation could assist therapeutic approaches targeting the gut microbiota to alleviate COPD.