• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.342-342
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• 2017

Rice seeds are a home to endophytic bacterial communities which serve as a source of the plant's endophytes. As rice undergo physiological and adaptive modifications through cross breeding in the process of attaining salinity tolerance, this may also lead to changes in the endophytic bacterial community especially those residing in the seeds. This study explores the community structure of seed bacterial endophytes as influenced by rice parental lineage, genotype and physiological adaptation to salinity stress. Endophytic bacterial diversity was studied through culture dependent technique, cloning and Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Results revealed considerably diverse communities of bacterial endophytes in the interior of rice seeds. The richness of ribotypes ranges from 5-14 T-RFs corresponding to major groups of bacterial endophytes in the seeds. Endophytic bacterial diversity of the salt-sensitive IR29 is significantly more diverse compared to those of salt-tolerant cultivars. Proteobacteria followed by Actinobacteria and Firmicutes dominated the overall endophytic bacterial communities of the indica rice seeds based on 16S rDNA analysis of clones and isolates. Community profiles show common ribotypes found in all cultivars of the indica subspecies representing potential core microbiota belonging to Curtobacterium, Flavobacterium, Enterobacter, Xanthomonas, Herbaspirillum, Microbacterium and Stenotrophomonas. Multivariate analysis showed that the bacterial endophytic community and diversity of rice seeds are mainly influenced by their host's genotype, physiological adaptation to salt stress and parental lineage.

• Journal of Microbiology and Biotechnology
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• 제24권7호
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• pp.888-897
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• 2014

A bacterial community analysis of the gut of Tenebrio molitor larvae was performed using pyrosequencing of the 16S rRNA gene. A predominance of genus Spiroplasma species in phylum Tenericutes was observed in the gut samples, but there was variation found in the community composition between T. molitor individuals. The gut bacteria community structure was not significantly affected by the presence of antibiotics or by the exposure of T. molitor larvae to a highly diverse soil bacteria community. A negative relationship was identified between bacterial diversity and ampicillin concentration; however, no negative relationship was identified with the addition of kanamycin. Ampicillin treatment resulted in a reduction in the bacterial community size, estimated using the 16S rRNA gene copy number. A detailed phylogenetic analysis indicated that the Spiroplasma-associated sequences originating from the T. molitor larvae were distinct from previously identified Spiroplasma type species, implying the presence of novel Spiroplasma species. Some Spiroplasma species are known to be insect pathogens; however, the T. molitor larvae did not experience any harmful effects arising from the presence of Spiroplasma species, indicating that Spiroplasma in the gut of T. molitor larvae do not act as a pathogen to the host. A comparison with the bacterial communities found in other insects (Apis and Solenopsis) showed that the Spiroplasma species found in this study were specific to T. molitor.

• Journal of Veterinary Science
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• 제24권2호
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• pp.27.1-27.15
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• 2023

Background: The relationships between the postpartum subacute ruminal acidosis (SARA) occurrence and predicted bacterial functions during the periparturient period are still not clear in Holstein cows. Objectives: The present study was performed to investigate the alterations of rumen fermentation, bacterial community structure, and predicted bacterial functional pathways in Holstein cows. Methods: Holstein cows were divided into the SARA (n = 6) or non-SARA (n = 4) groups, depending on whether they developed SARA during the first 2 weeks after parturition. Reticulo-ruminal pH was measured continuously during the study period. Reticulo-ruminal fluid samples were collected 3 weeks prepartum, and 2 and 6 weeks postpartum, and blood samples were collected 3 weeks before, 0, 2, 4 and 6 weeks postpartum. Results: The postpartum decline in 7-day mean reticulo-ruminal pH was more severe and longer-lasting in the SARA group compared with the non-SARA group. Changes in predicted functional pathways were identified in the SARA group. A significant upregulation of pathway "PWY-6383" associated with Mycobacteriaceae species was identified at 3 weeks after parturition in the SARA group. Significantly identified pathways involved in denitrification (DENITRIFICATION-PWY and PWY-7084), detoxification of reactive oxygen and nitrogen species (PWY1G-0), and starch degradation (PWY-622) in the SARA group were downregulated. Conclusions: The postpartum SARA occurrence is likely related to the predicted functions of rumen bacterial community rather than the alterations of rumen fermentation or fluid bacterial community structure. Therefore, our result suggests the underlying mechanisms, namely functional adaptation of bacterial community, causing postpartum SARA in Holstein cows during the periparturient period.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제19권4호
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• pp.221-228
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• 2016

The gastrointestinal exposome represents the integration of all xenobiotic components and host-derived endogenous components affecting the host health, disease progression and ultimately clinical outcomes during the lifespan. The human gut microbiome as a dynamic exposome of commensalism continuously interacts with other exogenous exposome as well as host sentineling components including the immune and neuroendocrine circuit. The composition and diversity of the microbiome are established on the basis of the luminal environment (physical, chemical and biological exposome) and host surveillance at each part of the gastrointestinal lining. Whereas the chemical exposome derived from nutrients and other xenobiotics can influence the dynamics of microbiome community (the stability, diversity, or resilience), the microbiomes reciprocally alter the bioavailability and activities of the chemical exposome in the mucosa. In particular, xenobiotic metabolites by the gut microbial enzymes can be either beneficial or detrimental to the host health although xenobiotics can alter the composition and diversity of the gut microbiome. The integration of the mucosal crosstalk in the exposome determines the fate of microbiome community and host response to the etiologic factors of disease. Therefore, the network between microbiome and other mucosal exposome would provide new insights into the clinical intervention against the mucosal or systemic disorders via regulation of the gut-associated immunological, metabolic, or neuroendocrine system.

• 한국축산식품학회지
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• 제38권5호
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• pp.936-949
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• 2018

Changes in microbial community and physicochemical traits of chicken summer sausage made from spent layer thigh added with different level (0%, 0.1%, 0.3%, and 0.5% w/w) of ground chopi (Zanthoxylum piperitum) during manufacture were analyzed. The microbial community was profiled and analyzed by sequencing 16S rRNA gene using Illumina MiSeq. Samples were taken from raw sausage batter, after 15 h of fermentation, 8 h of cooking including cooling down, and 7 d of drying. The final pH of the sausage was reduced by the addition of ground chopi. However, no clear effect on water activity was observed. Ground chopi inhibited the development of red curing color after fermentation as it exhibited antimicrobial effect. However, the effect on species richness and microbial composition after cooking was unclear. Ground chopi delayed lipid oxidation during manufacture and the effect was dependent on the addition level. Fermentation reduced the species richness with a dominancy of lactic acid bacteria. The profile of microbiota in the raw batter was different from other stages, while the closest relationship was observed after cooking and drying. Proteobacteria was predominant, followed by Firmicutes and Bacteroidetes in raw samples. Firmicutes became dominating after fermentation and so forth, whereas other predominant phylum decreased. At genus level, unclassified Lactobacillales was the most abundant group found after fermentation and so forth. Therefore, the overall microbial composition aspects were mainly controlled during fermentation by the abundance of lactic acid bacteria, while bacterial counts and lipid oxidation were controlled by cooking and the addition of ground chopi.

• 한국축산식품학회지
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• 제37권4호
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• pp.535-541
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• 2017

This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat. From the Illumina sequencing, a total of 187,671 reads were obtained from 12 chicken samples. Regardless of the type of chicken meat (i.e., whole meat and chicken breast) and storage temperatures ($4^{\circ}C$ and $10^{\circ}C$), Pseudomonas weihenstephanensis and Pseudomonas congelans were the most prominent bacterial species. Serratia spp. and Acinetobacter spp. were prominent in chicken breast and whole chicken meat, respectively. The 118 isolated strains of psychrotrophic bacteria comprised Pseudomonas spp. (58.48%), Serratia spp. (10.17%), and Morganella spp. (6.78%). All isolates grew well at $10^{\circ}C$ and they induced different proteolytic activities depending on the species and strains. Parallel analysis of the next generation sequencing and culture dependent approach provides in-depth information on the biodiversity of the spoilage microbiota in chicken meat. Further study is needed to develop better preservation methods against these spoilage bacteria.

• Journal of Animal Science and Technology
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• 제63권6호
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• pp.1386-1396
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• 2021

Copper is an essential mineral for pigs, thus it is used as a feed additive in the forms of copper sulfate. Therefore, this study aimed at characterizing the fecal microbiota shifts in pigs as fed by different forms of copper supplementation. 40 growing pigs aged 73 ± 1 days with an average weight of 30.22 ± 1.92kg were randomly divided into 5 groups. The control group (CON) fed with basal diet, while treatment groups were fed a basal diet supplemented with 100 ppm/kg of copper sulfate (CuSO₄), Cu-glycine complex (CuGly), Cu-amino acid complex (CuAA), and Cu-hydroxy(4methylthio)butanoate chelate complex (CuHMB) for 28 days of trial, respectively. The data presented the comparison between inorganic and organic copper supplementation through gut microbiota in growing pigs. Alpha and Beta diversity anaylsis resulted in copper supplementation did shifted gut microbioal community structure. At the phylum level, Firmicutes and Bacteroidetes were the most abundant phyla at all times regardless of treatment. At the genus level, the relative abundances of Prevotella, Lactobacillus, Megasphaera, and SMB53 of the CuGly and CuHMB groups were significantly higher than those of copper sulfate and basal diet groups. Overall, this study may provide the potential role of organic copper replacing inorganic copper, resulting in increased beneficial bacteria in the pig gut.

• Journal of Animal Science and Technology
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• 제64권6호
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• pp.1144-1172
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• 2022

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

• Asian-Australasian Journal of Animal Sciences
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• 제30권7호
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• pp.957-966
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• 2017

Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Methods: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database. Results: Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways. Conclusion: Yaks' age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks' growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

• Animal Bioscience
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• 제37권7호
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• pp.1213-1224
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• 2024

Objective: Enterotypes (ETs) are the clustering of gut microbial community structures, which could serve as indicators of growth performance and carcass traits. However, ETs have been sparsely investigated in waterfowl. The objective of this study was to identify the ileal ETs and explore the correlation of the ETs with growth performance and carcass traits in Muscovy ducks. Methods: A total of 200 Muscovy ducks were randomly selected from a population of 5,000 ducks at 70-day old, weighed and slaughtered. The growth performance and carcass traits, including body weight, dressed weight and evidenced weight, dressed percentage, percentage of apparent yield, breast muscle weight, leg muscle weight, percentage of leg muscle and percentage of breast muscle, were determined. The contents of ileum were collected for the isolation of DNA and 16S rRNA gene sequencing. The ETs were identified based on the 16S rRNA gene sequencing data and the correlation of the ETs with growth performance and carcass traits was performed by Spearman correlation analysis. Results: Three ETs (ET1, ET2, and ET3) were observed in the ileal microbiota of Muscovy ducks with significant differences in number of features and α-diversity among these ETs (p<0.05). Streptococcus, Candida Arthritis, and Bacteroidetes were the presentative genus in ET1 to ET3, respectively. Correlation analysis revealed that Lactococcus and Bradyrhizobium were significantly correlated with percentage of eviscerated yield and leg muscle weight (p<0.05) while ETs were found to have a close association with percentage of eviscerated yield, leg muscle weight, and percentage of leg muscle in Muscovy ducks. However, the growth performance of ducks with different ETs did not show significant difference (p>0.05). Lactococcus were found to be significantly correlated with leg muscle weight, dressed weight, and percentage of eviscerated yield. Conclusion: Our findings revealed a substantial variation in carcass traits associated with ETs in Muscovy ducks. It is implied that ETs might have the potential to serve as a valuable biomarker for assessing duck carcass traits. It would provide novel insights into the interaction of gut microbiota with growth performance and carcass traits of ducks.