• Journal of Species Research
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• v.9 no.2
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• pp.105-116
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• 2020

A total of 37 anaerobic bacteria strains within the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidia, Flavobacteriia, Bacilli, Clostridia, and Fusobacteriia were isolated from freshwater and sediment of the Geum River in Korea. The unreported species were related with Rhizobium and Oleomonas of the class Alphaproteobacteria; Acidovorax, Pseudogulbenkiania, and Aromatoleum of the class Betaproteobacteria; Tolumonas, Aeromonas, Cronobacter, Lonsdalea, and Phytobacter of the class Gammaproteobacteria; Bacteroides, Dysgonomonas, Macellibacteroides, and Parabacteroides of the class Bacteroidia; Flavobacterium of the class Flavobacteriia; Bacillus and Paenibacillus of the class Bacilli; Clostridium, Clostridioides, Paraclostridium, Romboutsia, Sporacetigenium, and Terrisporobacter of the class Clostridia; and Cetobacterium and Ilyobacter of the class Fusobacteriia. A total of 37 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species, but not reported in Korea, were determined to be unrecorded anaerobic bacterial species in Korea.

• Korean Journal of Microbiology
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• v.52 no.2
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• pp.183-191
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• 2016

Marine bacteria have represented unique physiologies and products which are not discovered from terrestrial organisms. There has been great interest to utilize and develop marine bacteria in many industrial sectors. Recently, we isolated and characterized anaerobic bacteria from various marine environments in Korea to search organic acids fermenting strains. From our enrichment performed under anaerobic condition, 65 strains were isolated and identified by the 16S rRNA gene sequence analysis. Among them, eleven strains were selected for phylogenetical and biochemical analysis. All tested strains were affiliated with Class Clostridia except one with Class Bacteroidia. Most of strains produce acetate (6 strains) with butyrate (2 strains) and/or formate (4 strains). Strain MCWD5 transformed 40% of glucose to extracellular polymeric substances. These results indicate that many novel anaerobic microorganisms which have great potential in commercial application are distributed in the marine environments of Korean Peninsula.

• Journal of Animal Reproduction and Biotechnology
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• v.34 no.3
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• pp.157-165
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• 2019

This study was conducted to analyze the diversity census of fecal microbiome in horses using meta-analysis of equine 16S rRNA gene sequences that are available in the Ribosomal Database Project (RDP; Release 11, Update 5). The search terms used were "horse feces (or faeces)" and "equine feces (or faeces)". A total of 842 sequences of equine feces origin were retrieved from the RDP database, where 744 sequences were assigned to 10 phyla placed within Domain Bacteria. Firmicutes (n = 391) and Bacteroidetes (n = 203) were the first and the second dominant phyla, respectively, followed by Verrucomicrobia (n = 58), Proteobacteria (n = 30) and Fibrobacteres (n = 24). Clostridia (n = 319) was the first dominant class placed within Bacteroidetes while Bacteroidia (n = 174) was the second dominant class placed within Bacteroidetes. The remaining 98 sequences were assigned to phylum Euryarchaeota placed within Domain Archaea, where 74 sequences were assigned to class Methanomicrobia. The current results will improve understanding of the diversity of fecal microbiome in horses and may be used to further analyze equine fecal microbiome in future studies.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.584-591
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• 2015

This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

• 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.

• Journal of Species Research
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• v.7 no.2
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• pp.104-113
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• 2018

In order to investigate indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined. Isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species, but not reported in Korea, were selected as unrecorded species. 28 unrecorded bacterial species belonging to the phylum Bacteroidetes were discovered from various habitats including wastewater, freshwater, freshwater sediment, wet land, reclaimed land, plant root, bird feces, seawater, sea sand, tidal flat sediment, a scallop, marine algae, and seaweed. The unrecorded species were assigned to 18 different genera in five families: Flavobacterium, Epilithonimonas, Dokdonia, Gillisia, Flavicella, Chryseobacterium, Algibacter, Aquimarina, Lacinutrix, Gaetbulibacter, Cellulophaga, Tenacibaculum, and Maribacter of Flavobacteriaceae, Dyadobacter of Cytophagaceae, Draconibacterium of Draconibacterium_f, Sunxiuqinia of Prolixibacteraceae, and Fulvivirga of Fulvivirga_f. The selected isolates were subjected to further taxonomic characterization including analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. Descriptive information of the 28 unrecorded species is provided.

• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.971-988
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• 2023

This study evaluated the effects of supplementing solubles from shredded, steam-exploded pine particles (SSPP) on growth performances, plasma biochemicals, and microbial composition in broilers. The birds were reared for 28 days and fed basal diets with or without the inclusion of SSPP from 8 days old. There were a total of three dietary treatments supplemented with 0% (0% SSPP), 0.1% (0.1% SSPP) and 0.4% (0.4% SSPP) SSPP in basal diets. Supplementation of SSPP did not significantly affect growth or plasma biochemicals, but there was a clear indication of diet-induced microbial shifts. Beta-diversity analysis revealed SSPP supplementation-related clustering (ANOSIM: r = 0.31, p < 0.01), with an overall lower (PERMDISP: p < 0.05) individual dispersion in comparison to the control group. In addition, the proportions of the Bacteroides were increased, and the relative abundances of the families Vallitaleaceae, Defluviitaleaceae, Clostridiaceae, and the genera Butyricicoccus and Anaerofilum (p < 0.05) were significantly higher in the 0.4% SSPP group than in the control group. Furthermore, the linear discriminant analysis effect size (LEfSe) also showed that beneficial bacteria such as Ruminococcus albus and Butyricicoccus pullicaecorum were identified as microbial biomarkers of dietary SSPP inclusion (p < 0.05; | LDA effect size | > 2.0). Finally, network analysis showed that strong positive correlations were established among microbial species belonging to the class Clostridia, whereas Erysipelotrichia and Bacteroidia were mostly negatively correlated with Clostridia. Taken together, the results suggested that SSPP supplementation modulates the cecal microbial composition of broilers toward a "healthier" profile.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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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.