• Journal of Microbiology and Biotechnology
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• 제26권5호
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• pp.876-882
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• 2016

Tylosin has been used as a livestock feed additive and antibiotic growth promoter for many years. However, the mode of action by which tylosin enhances animal growth is unclear. We used high-throughput sequencing of 16S rRNA genes to investigate the effects of tylosin as a feed additive on swine gut microbiota. No significant difference in the rate of weight increase was observed between control and tylosin-treated pigs during a 10-week feeding trial. However, tylosin-treated pigs showed rapid increases in the relative abundance of the phylum Firmicutes. Increases in Firmicutes species are associated with (so-called) obese-type gut microbiota. The abundance of species of four families of the phylum Firmicutes (Streptococcaceae, Peptococcaceae, Peptostreptococcaceae, and Clostridiaceae) correlated positively with host weight gain. The abundance of Streptococcaceae family bacteria was least affected by tylosin treatment. Distribution analysis of operational taxonomic units (OTUs) showed that both control and tylosin-treated pigs exhibited similar OTU alterations during growth. However, the tylosin-treated group showed distinctive alterations in gut microbiota when the host weighed approximately 60 kg, whereas similar alterations occurred at around 80 kg in the control group. Our results suggest that use of tylosin accelerates maturation of swine gut microbiota rather than altering its composition.

• 한국토양비료학회지
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• 제49권2호
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• ALGAE
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• 제21권1호
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• pp.83-90
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• 2006

Phytoplankton community in the coastal waters off the northeastern Korean Peninsula were characterized from May 2002 to August 2003. Taxonomic composition, abundance and biomass were determined at two water depths at 10 sample sites. A total of 153 phytoplankton species including 121 diatoms, 28 dinoflagellates, 7 green algae and 7 other species were identified. The mean abundance of phytoplankton varied from 15 to 430 cells mL–1 in the surface layer and from 11 to 545 cells mL–1 in the bottom layer, respectively. Phytoplankton was more abundant in coastal stations relative to those in more open ocean. The most dominant species were marine diatoms such as Thalassionema nitzschioides, Licmorphora abbreviata, Chaetoceros affinis and Chaetoceros socialis. In addition, a few limnotic diatoms including Fragilaria capucina v. rumpens, the green alga Scenedesmus dimorphus, some marine dinoflagellates and Cryptomonas sp. appeared as dominant species. Mean concentration of total chlorophyll-a varied from 0.22 to 7.87 μg chl-a L–1 and from 0.45 to 6.79 μg chl-a L–1 in the surface and bottom layers, respectively. The contribution of phytoplankton each size-fractionated varied highly with season. The contribution of microphytoplankton to total biomass of phytoplankton in the surface and bottom layer was high in February and August 2003, and that of nano-phytoplankton was high in May 2002 in both surface and bottom layers.

• ALGAE
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• 제18권1호
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• pp.49-58
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• 2003

The short-term dynamics of the summer phytoplankton community structure were investigated in coastal waters around Namhae Island, the Southern Sea of Korea. The study was based on a comprehensive survey constituting 39 collections from 13 stations on July 18-22, August 1-2, 14-16 and 27-30, respectively. The community structure was analysed using cluster analysis and important environmental correlates of the assemblage structure were identified with canonical correspondence analysis (CCA). Water temperature, salinity, NO₂, NO₃, NH₄, PO₄, chlorophyll a and transparency were measured as physico-chemical environmental factors which may be associated with the phytoplankton community structure. Variations of salinity and concentrations of NO₃ and chlorophyll a were not significant. In addition to warmer water temperature, concentrations of NO₂, NO₄and PO₄ decreased at the beginning of August. And transparency was deeper and water column became very unstable after the middle of August. A wide taxonomic diversity was encountered during the survey, including a total of 121 taxa which was composed of 72 diatoms, 48 dinoflagellates and 1 euglenoid species. Cluster analysis showed that the Phytoplankton community could be divided into 4 distinct groups, indicating rapid changes of the community in the short course of this survey. These phytoplankton groups also showed distinctive dispersion patterns in 2-dimensional canonical space, indicating distinct groupings for stations at each survey. Dominant taxa of diatoms (Chaetoceros curvisetus, Chaetoceros spp., Leptocylindrus danicus, Leptocylindrus mediteraneus, Skeletonema costanum, and Pseudo-nitzschia pungen) clustered in region of CCA space corresponding to stations surveyed at the middle of July. Dominant taxa of dinoflagellates were tightly associated with stations surveyed at the middle (Karenia breve) and end (Cochlodinium polykrikoides and Polykrikos schwartzii) of August. The CCA also showed that the phytoplankton community compositions were highly associated with water temperature, transparency, NO₂, NH₄ and PO₄, suggesting that gradients in physical and nutrient conditions affect short-term changes in phytoplankton composition.

• Asian-Australasian Journal of Animal Sciences
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• 제28권4호
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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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• 제30권10호
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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.

• KSBB Journal
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• 제11권5호
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• pp.586-592
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• 1996

본 연구에서는 단일 탄소원인 포도당으로부터 P PHA를 생산하는 콩시균 Pseudomonas sp. HJ를 보다 정확하게 동정하기 위하여 수치분류를 실시하 였으며, 또한 보조기질을 첨가하였을때의 PHB/HV 합성 양상을 검토하였다. Pseudomonas sp. HJ는 각 대조균주들중에서 Pseudomonas picketti와 가장 유 사도가 높은 것으로 나타났다(78.8%). 그러나 수치 분류에 서 통일 균종에 포함될 수 있는 유샤도는 85 % 정도인 것으로 얄려져 있으므로, 본 공시균 P Pseudomonas sp. HJ는 Pseudomonas 속의 다른 종 (species)이거나 새로운 종(species)일 가능성이 높 았다. 보조기 질로 hexadecane과 propionic acid를 각각 0.4%씩 첨가했을 경우, 농도증가에 비례하여 H HV 함량은 점차 증가하여 각각 60.8 mol%, 44.9 mol%까지 축적되었다. PHB/HV내의 HV 함량은 p propionic acid냐 hexadecane의 농도를 달리하여 첨가함으로써 조절할 수 있었다. 보조기질로 propl- onic acid 0.2 %를 대수기 중기 인 배양 18시간에 첨 가하였을때 균체 생육이 가장 우수하였으나, HV monomer의 비율은 대수기 말기인 배양 24시간대에 첨가하였을때 49.6 mol%로 가장 높았다.

• Journal of Animal Science and Technology
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• 제62권2호
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• pp.239-246
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• 2020

Microorganism residing in the gut has been known to have important roles in the animal body. Microbes and host microenvironment are highly related with host's health including energy metabolism and immune system. Moreover, it reported that gut microbiome is correlated with diseases like obesity in human and dogs. There have been many studies to identify and characterize microbes and their genes in human body. However, there was little information of microbiome in companion animals. Here, we investigated microbiota communities in feaces from twenty - four Beagles (aged 2 years old) and analyzed the taxonomy profile using metagenomics to study the difference among gut microbiome based on body condition score (BCS). gDNA was isolated from feaces, sequenced and clustered. Taxonomy profiling was performed based on the NCBI database. BCS was evaluated once a week according to the description provided by World Small Animal Veterinary Association. Firmicutes phylum was the most abundant followed by Bacteroidetes, Fusobacteria, Proteobacteria and Actinobacteria. That main microbiota in gut were differently distributed based on the BCS. Fusobacteria has been known to be associated with colon cancer in human. Interestingly, Fusobacteria was in the third level from the top in healthy dog's gut microbiome. In addition, Fusobacteria was especially higher in overweight dogs which had 6 scales of BCS. Species Fusobacterium perfoetens was also more abundant when dogs were in BCS 6. It implied that F. perfoetens would be positively related with overweight in dogs. These finding would contribute to further studies of gut microbiome and their functions to improve dog's diets and health condition.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2000년도 Proceedings of 2000 KSAM International Symposium and Spring Meeting
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• pp.150-156
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• 2000

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. The 30 fatty acids which were identified or characterized are classified. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Cluster 3 and 4-a strains were containing Q-8, these strains are accommodated in the Proteobacteria gamma and beta subdivision. The chemotaxonomic profiles of the cluster 4-a strains showed good agreement with those of the genus Burkholderia. Cluster 3 was characterized by the presence of branched-chain fatty acids, iso-C15:0, iso-C17:1, and iso-C17:0 as the major components. These chemotaxonomy suggested the close relationship of the isolates with Xathomonas/Sterotrophomonas group. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Sterotrophomonas, but were not included in these genera. These strains were even further away from core Xanthomonas, and clearly were seen to branch outside the cluster formed by the Sterotrophomonas maltophilia. MH256 and MA828 16S rDNA sequence was different enough to put new genus on a separate branch. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium.

• Mycobiology
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• 제45권4호
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• pp.270-285
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• 2017

The crustose lichen genus Pertusaria comprises over ca. 800 species worldwide. In total, 20 Pertusaria species were localized to the Mt. Sorak and Jeju-do in Korea. To date, information regarding the distribution of Pertusaria species in the South Korean peninsula is scarce. In this study, we collected Pertusaria species across South Korea and identified them based on morphological, chemical, and molecular characteristics. Of the 387 samples collected, we identified 24 taxa and 1 variety, of which 17 were previously recorded, and 6 taxa were newly found in South Korea (P. leioplaca, P. leucosora var. violascens, P. texana, P. thiospoda, P. thwaitesii, and P. xanthodes), 2 known species were transferred to Varicellaria (Varicellaria lactea and V. velata), one species was transferred to Variolaria as a new record (Variolaria multipunctoides) and one was a new species (P. jogyeensis J. S. Park & J.-S. Hur, sp. nov.). Characteristics of the newly discovered species, P. jogyeensis, are as follows: smooth to bumpy thallus, scattered to crowded poriform apothecia, blackish ostioles, definitely sunken, thin yellowish green rims around ostioles, 8-spored ascus, and the presence of perlatolic acid and thiophaninic acid (chlorinated xanthone). Phylogenetic studies on P. jogyeensis based on the mitochondrial small subunit sequence revealed proximity to P. flavicans and P. texana, and supported its classification as a new species within the genus Pertusaria. Additionally, we describe the chemical composition and morphology of all listed species in detail and provide an artificial key for identification.