Flavobacterium panaciterrae sp. nov., a β-glucosidase producing bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field.

Jin, Yan,Kim, Yeon-Ju,Hoang, Van-An,Young Jung, Sun,Nguyen, Ngoc-Lan,Woo Min, Jin,Wang, Chao,Yang, Deok-Chun Institute of Applied Microbiology, University of T 2014 The Journal of general and applied microbiology Vol.60 No.2

<P>The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DCY69(T) is JX233806. A Gram-reaction-negative, oxidase- and catalase-positive, non-gliding motile strain, designated strain DCY69(T), was isolated from the soil of a ginseng field in the Republic of Korea. Colonies of strain DCY69(T) were circular, 0.5-1.5 mm diameter, yellow, and convex on an R2A agar plate after 2 days. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DCY69(T) belonged to the genus Flavobacterium with 90.5-98.3% gene sequence similarity. The major predominant quinone was MK-6. The major cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH and summed feature 3 (containing C16:1ω7c and/or C16:1ω6c). The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and unidentified polar lipids (L1, L2). The genomic DNA G+C content of strain DCY69(T) was 35.0mol%. The strain DCY69(T) transformed ginsenoside Rb1 into Rd and F2. Based on the polyphasic taxonomic data, strain DCY69(T) is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium panaciterrae sp. nov. is proposed. The type strain is DCY69(T)(= KCTC 32392(T) = JCM 19161(T)), isolated from the soil of a ginseng field in the Republic of Korea.</P>

Bacterial virulence analysis using brine shrimp as an infection model in relation to the importance of quorum sensing and proteases.

Lee, Mi-Nan,Kim, Soo-Kyoung,Li, Xi-Hui,Lee, Joon-Hee Institute of Applied Microbiology, University of T 2014 The Journal of general and applied microbiology Vol.60 No.5

<P>Brine shrimp are aquatic crustaceans belonging to a genus of Artemia. This organism is widely used for testing the toxicity of chemicals. In this study, brine shrimp were evaluated as an infection model organism to study bacterial virulence. Artemia nauplii were infected with various pathogenic bacteria, such as Vibrio vulnificus, Pseudomonas aeruginosa, Burkholderia vietnamiensis, Staphylococcus aureus, and Escherichia coli, and the susceptibility to these bacteria was investigated by counting the survival of the infected nauplii. While all of the tested bacteria have significant virulence to brine shrimp, killing the nauplii in a few days, V. vulnificus showed the strongest virulence. P. aeruginosa also showed a dose-dependent virulence to brine shrimp, but the virulence was weaker than that of V. vulnificus. The virulence tests using the virulence-attenuated mutants of V. vulnificus and P. aeruginosa, such as quorum sensing (QS) mutants or protease-deficient mutants showed a significant attenuation of virulence, demonstrating that the QS mechanism is important in the virulence of these bacteria to brine shrimp. B. vietnamiensis, S. aureus, and E. coli were also virulent to brine shrimp and the virulence was correlated with dosage within 24 h under our conditions. Salmonella enterica Typhimurium and Bacillus subtilis were also virulent to brine shrimp, but the virulence was weak and slowly exerted compared with that of other bacteria. Taken together, we suggest that brine shrimp are a good infection model to assay bacterial virulence, especially for V. vulnificus and P. aeruginosa, and QS is important in the bacterial virulence to brine shrimp.</P>

Paenibacillus humi sp. nov., isolated from peat-soil.

Kim, Hyun-Sook,Lee, Sang-Seob Institute of Applied Microbiology, University of T 2014 The Journal of general and applied microbiology Vol.60 No.1

<P>A Gram-positive, facultative-anaerobic, rod-shaped and endospore-forming bacterium designated as strain J30-4(T) was isolated from peat-soil collected in Russia. 16S rRNA gene sequence analysis revealed that strain belongs to the genus Paenibacillus, closely related to Paenibacillus terrigena A35(T) (98.1%) and Paenibacillus harenae B519(T) (95.5%). Chemotaxonomic analysis revealed that strain J30-4(T) possessed menaquinone MK-7 as predominant quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-ethanolamine, phosphatidyl-N-methylethanolamine and several unknown lipids were detected in the polar lipid profile. The cell wall peptidoglycan was of the A1γ type (meso-diaminopimelic acid). The major fatty acids were anteiso-C1?:? and iso-C1?:?. The DNA G+C content of J30-4(T) was 55.5 mol%. Based on phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain J30-4(T) (= KEMC 7302-014(T) = JCM 18166(T)) is indicative of a new Paenibacillus species, for which the name Paenibacillus humi sp. nov., is proposed.</P>

Assessment of fecal bacterial diversity among healthy piglets during the weaning transition.

Alain B Pajarillo, Edward,Chae, Jong-Pyo,Balolong, Marilen P,Bum Kim, Hyeun,Kang, Dae-Kyung Institute of Applied Microbiology, University of T 2014 The Journal of general and applied microbiology Vol.60 No.4

<P>The high level of genetic diversity in the microflora of the gastrointestinal tract has the potential to provide numerous beneficial functions to the host. Thus it is now acknowledged that the complexity in animal functioning is linked to the interacting microbiome in the gut. Despite the importance of gut microbiome, there is a lack of information concerning the microbial communities in the pig gut during the weaning transition. This study describes the fecal microbial shifts of healthy piglets during the weaning transition using barcoded pyrosequencing of the prokaryotic 16S rRNA gene. Fecal samples were obtained from 15 piglets during the pre-weaning period (fourth week after birth) and post-weaning (sixth week after birth) and were subjected to community genomic DNA extraction for pyrosequencing analysis. As the piglets underwent the weaning transition a trend toward increased bacterial diversity was observed, based on species abundance as measured by the Shannon-Weaver index. Firmicutes (54.0%) and Bacteroidetes (59.6%) were the most dominant phyla during pre-weaning and post-weaning, respectively. During the weaning transition a distinct shift from Bacteroides to Prevotella as the most abundant genus was observed. Additionally, we detected a number of abundant gut bacterial species that have not been reported previously. Clostridium rectum, C. clostridioforme, C. lactatifermentans and Butyricimonas virosa were uniquely detected prior to weaning while Roseburia cecicola and Blautia wexlerae were detected during the post-weaning period only.</P>

The antioxidant properties of solid-culture extracts of basidiomycetous fungi.

Lee, Jaejung,Hong, Joo-Hyun,Kim, Jeong-Do,Ahn, Byoung Jun,Kim, Beom Seok,Kim, Gyu-Hyeok,Kim, Jae-Jin Institute of Applied Microbiology, University of T 2013 The Journal of general and applied microbiology Vol.59 No.4

<P>Current studies of the antioxidant activity of fungal resources are mainly focused on the fruiting bodies of edible mushrooms. To access the potential of basidiomycetes in culture-state applications, extracts of solid cultures of 83 basidiomycetous fungi newly isolated from woody materials were prepared at the same concentration (10 mg/ml), and their antioxidant activities were measured using ABTS (2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid) and DPPH (2,2-diphenyl-1-picrylhydrazyl) radical-scavenging assays. Among the basidiomycetes tested, Cryptoporus volvatus, Daedalea dickinsii, Gloeophyllum abietinum, G. trabeum, Pseudomerulius curtisii and Stereum hirsutum exhibited good antioxidant activities. The EC50 value for the removal of free radicals was lowest (i.e., most effective) in the crude extract of S. sanguinolentum (19.61 g/ml), and reduced DNA damage based on a DNA nicking assay was observed for the extracts from the six basidiomycetous species above.</P>

The mitochondrial genome of the white-rot fungus Flammulina velutipes.

Yoon, Hyeokjun,You, Young-Hyun,Woo, Ju-Ri,Park, Young-Jin,Kong, Won-Sik,Lee, Byoung-Moo,Kim, Jong-Guk Institute of Applied Microbiology, University of T 2012 The Journal of general and applied microbiology Vol.58 No.4

Metagenomic analysis of bacterial communities on Dokdo Island.

Kim, Ye-Eun,Yoon, Hyeokjun,Kim, Miae,Nam, Yoon-Jong,Kim, Hyun,Seo, Yeonggyo,Lee, Gyeong-Min,Ja Kim, Young,Kong, Won-Sik,Kim, Jong-Guk,Seu, Young-Bae Institute of Applied Microbiology, University of T 2014 The Journal of general and applied microbiology Vol.60 No.2

<P>Dokdo, located east of the mainland of South Korea, is a volcanic island designated as a natural monument of South Korea due to its ecological value. Dokdo is divided into Dongdo and Seodo, islands with geological differences. The soil bacterial communities on Dokdo (Dongdo and Seodo) were analyzed using the pyrosequencing method. There were 1,693 and 1,408 operational taxonomic units (OTU) from Dongdo and Seodo, respectively. The statistical analyses (rarefaction curves as well as Chao1, Shannon, and Simpson indices) showed that bacterial diversity was slightly higher in Dongdo than Seodo. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. From the phylum level down to the species level, the number of classified reads considerably decreased due to the absence of information concerning unculturable or unidentified bacteria to date. Among the 36 phyla identified, three phyla (Proteobacteria, Actinobacteria and Acidobacteria) accounted for around 74.64%. The taxonomic composition was similar at the higher ranks (family and above) between Dongdo and Seodo, but a little different at the genus level. There were also various differences in the relative abundance of taxonomic ranks between Dongdo and Seodo. In particular, the proportion of the genus Acidobacterium (of the phylum Acidobacteria) was about six times higher in Seodo than Dongdo. In addition, the percentage of the genus Mycobacterium (of the phylum Actinobacteria) was nearly three times higher in Seodo than Dongdo, and the proportion of the genus Gaiella was about 3.7 times higher in Dongdo than Seodo. Overall, through the metagenomic analysis, the number of species identified in Dongdo and Seodo was 1,239 and 1,055, respectively. This information on the numerous culturable and unculturable bacteria is expected to help in the screening of new species in Dokdo.</P>