Journal of Microbiology

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Host Species as a Strong Determinant of the Intestinal Microbiota of Fish Larvae: Xuemei Li , Yuhe Yu , Weisong Feng , Qingyun Yan , Yingchun Gong; J. Microbiol. 2012;50(1):29-37. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1340-1

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Abstract: We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models.
Results
showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.

Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis Analysis of Bacterial Community Structure in the Food, Intestines, and Feces of Earthworms: Sung Wook Hong , Ju Sam Lee , Kun Sub Chung; J. Microbiol. 2011;49(4):544-550. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0423-8

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The bacterial communities in the food, intestines, and feces of earthworms were investigated by PCR-denaturing gradient gel electrophoresis (DGGE). In this study, PCR-DGGE was optimized by testing 6 universal primer sets for microbial 16S rRNA in 6 pure culture strains of intestinal microbes in earthworms. One primer set effectively amplified 16S rRNA from bacterial populations that were found in the food, intestines, and feces of earthworms. Compared with the reference markers from the pure culture strains, the resulting DGGE profiles contained 28 unique DNA fragments. The dominant microorganisms in the food, intestines, and feces of earthworms included Rhodobacterales bacterium, Fusobacteria, Ferrimonas marina, Aeromonas popoffii, and soil bacteria. Other strains, such as Acinetobacter, Clostridium, and Veillonella, as well as rumen bacteria and uncultured bacteria also were present. These results demonstrated that PCR-DGGE analysis can be used to elucidate bacterial diversity and identify unculturable microorganisms.

Citations

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Effects of rhamnolipids on bacterial communities in a dioxin-contaminated soil and the gut of earthworms added to the soil
Bing XIA, Dan HUANG, Mao YE, Hao QIU, Hongfeng CHEN, Keqiang ZHAO, Rongliang QIU, Rongrong YING
Pedosphere.2023; 33(6): 927. CrossRef
Analysis of Rhizosphere Soil Bacterial Communities on Seonginbong, Ulleungdo Island
Yoon-Jong Nam, Hyeokjun Yoon, Hyun Kim, Jong-Guk Kim
Journal of Life Science.2015; 25(3): 323. CrossRef
Metagenomic analysis of bacterial communities on Dokdo Island
Ye-Eun Kim, Hyeokjun Yoon, Miae Kim, Yoon-Jong Nam, Hyun Kim, Yeonggyo Seo, Gyeong-Min Lee, Young Ja Kim, Won-Sik Kong, Jong-Guk Kim, Young-Bae Seu
The Journal of General and Applied Microbiology.2014; 60(2): 65. CrossRef
DGGE analysis of buffalo manure eubacteria for hydrogen production: effect of pH, temperature and pretreatments
Petronia Carillo, Claudia Carotenuto, Filomena Di Cristofaro, Ioannis Kafantaris, Carmine Lubritto, Mario Minale, Biagio Morrone, Stefania Papa, Pasqualina Woodrow
Molecular Biology Reports.2012; 39(12): 10193. CrossRef

Impact of cry1AC-Carrying Brassica rapa subsp. pekinensis on Leaf Bacterial Community: Young Tae Kim , Kang Seon Lee , Moon Jung Kim , Seung Bum Kim; J. Microbiol. 2009;47(1):33-39. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0254-4

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Abstract: The effects of Chinese cabbage (Brassica rapa subsp. pekinensis) carrying cry1AC derived from Bacillus thuringiensis (Bt) on leaf bacterial community were examined by analyzing the horizontal transfer of transgene fragments from plants to bacteria. The effect of plant pathogenic bacteria on the gene transfer was also examined using Pseudomonas syringae pathovar. maculicola. The frequency of hygromycin-resistant bacteria did not alter in Bt leaves, though slight increase was observed in Pseudomonas-infected Bt leaves with no statistical significance. The analysis of bacterial community profiles using the denaturing gradient gel electrophoresis (DGGE) fingerprinting indicated that there were slight differences between Bt and control Chinese cabbage, and also that infected tissues were dominated by P. syringae pv. maculicola. However, the cultured bacterial pools were not found to contain any transgene fragments. Thus, no direct evidence of immediate gene transfer from plant to bacteria or acquisition of hygromycin resistance could be observed. Still, long-term monitoring on the possibility of gene transfer is necessary to correctly assess the environmental effects of the Bt crop on bacteria.

Analysis of Vaginal Lactic Acid Producing Bacteria in Healthy Women: Hyeran Nam , Kyunghee Whang , Yeonhee Lee; J. Microbiol. 2007;45(6):515-520.; DOI: https://doi.org/2642 [pii]

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Abstract: Vaginal lactic acid-producing bacteria of 80 pre-menopausal women were studied by isolation on Blood and DeMan-Rogosa-Sharpe agar, PCR with group-specific primers for Lactobacillus-denaturing gradient gel electrophoresis (DGGE), and PCR with specific primers for V3 region in 16S rRNA-temporal temperature gel electrophoresis (TTGE). Conventional isolation method on media detected only one lactobacillus (Lactobacillus brevis) while TTGE detected only Lactobacillus sp. DGGE detected seven Lactobacillus species; L. coleohominis, L. crispatus, L. iners, L. reuteri, L. rhamnosus, L. vaginalis, and Leuconostoc lactis. L. acidophilus and L. gasseri, which are prevalent in Western women, were not detected in Korean women. Furthermore, L. rhamnosus, Leuc. lactis, L. coleohominis, and Weissella cibaria, which were not previously reported in the vaginal microbiota of Korean women, were detected. The five most prevalent LABs in vaginal microbiota in Korean women were L. iners, Enterococcus faecalis, L. crispatus, Leuc. lactis, and W. cibaria.

Denaturing Gradient Gel Electrophoresis Analysis of Bacterial Populations in 5-Stage Biological Nutrient Removal Process with Step Feed System for Wastewater Treatment: Soo-Youn Lee , Hyeon-Guk Kim , Jong Bok Park , Yong Keun Park; J. Microbiol. 2004;42(1):1-8.; DOI: https://doi.org/2009 [pii]

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Abstract: Changes in the bacterial populations of a 5-stage biological nutrient removal (BNR) process, with a step feed system for wastewater treatment, were monitored by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA fragments. DGGE analysis indicated seasonal community changes were observed, however, community profiles of the total bacteria of each reactor showed only minor differences in the samples obtained from the same season. The number of major bands was higher in the summer samples, and decreased during the winter period, indicating that the microbial community structure became simpler at low temperatures. Since the nitrogen and phosphate removal efficiencies were highly maintained throughout the winter operation period, the bacteria which still remaining in the winter sample can be considered important, playing a key role in the present 5-stage BNR sludge. The prominent DGGE bands were excised, and sequenced to gain insight into the identities of the predominant bacterial populations present, and most were found to not be closely related to previously characterized bacteria. These data suggest the importance of culture independent methods for the quality control of wastewater treatment

Denaturing Gradient Gel Electrophoresis Analysis of Bacterial Community Profiles in the Rhizosphere of cry1AC-carrying Brassica rapa subsp. pekinensis: Sera Jung , Semi Park , Daeha Kim , Seung Bum Kim; J. Microbiol. 2008;46(1):12-15.; DOI: https://doi.org/10.1007/s12275-007-0190-8

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Abstract: The effect of genetically modified (GM) Brassica rapa subsp. pekinensis (Chinese cabbage) expressing Bt toxin gene (cry1AC) to the rhizosphere bacterial community was examined using the denaturing gradient gel electrophoresis (DGGE) fingerprinting method. From the visual comparison of the DGGE profiles, there were no significant differences between the profiles of Bt and control rhizosphere in both Suwon and Yesan samples. From the sequence analysis of the individual bands, Sphingomonas sp. of Alphaproteobacteria and several actinobacterial members were identified as the main bacterial taxa in both Suwon and Yesan samples. In the multiple correspondence analysis, no clear separation between Bt and control rhizosphere was seen in both Suwon and Yesan datasets. The profiles of bulk soils were separated from those of rhizosphere. The DGGE fingerprinting analyses indicated that Bt crops did not significantly alter the genetic composition of rhizosphere bacterial communities.

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