• Title/Summary/Keyword: microbial community analysis

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Bacterial communities in the feces of insectivorous bats in South Korea

  • Injung An;Byeori Kim;Sungbae Joo;Kihyun Kim;Taek-Woo Lee
    • Journal of Ecology and Environment
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    • v.48 no.2
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    • pp.120-127
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    • 2024
  • Bats serve as vectors and natural reservoir hosts for various infectious viruses, bacteria, and fungi. These pathogens have also been detected in bat feces and can cause severe illnesses in hosts, other animals, and humans. Because pathogens can easily spread into the environment through bat feces, determining the bacterial communities in bat guano is crucial to mitigate potential disease transmission and outbreaks. This study primarily aimed to examine bacterial communities in the feces of insectivorous bats living in South Korea. Fecal samples were collected after capturing 84 individuals of four different bat species in two regions of South Korea, and the bacterial microbiota was assessed through next generation sequencing of the 16S rRNA gene. The results revealed that, with respect to the relative abundance at the phylum level, Myotis bombinus was dominated by Firmicutes (47.24%) and Proteobacteria (42.66%) whereas Miniopterus fuliginosus (82.78%), Rhinolophus ferrumequinum (63.46%), and Myotis macrodactylus (78.04%) were dominated by Proteobacteria. Alpha diversity analysis showed no difference in abundance between species and a significant difference (p < 0.05) between M. bombinus and M. fuliginosus. Beta-diversity analysis revealed that Clostridium, Asaia, and Enterobacteriaceae_g were clustered as major factors at the genus level using principal component analysis. Additionally, linear discriminant analysis effect size was conducted based on relative expression information to select bacterial markers for each bat species. Clostridium was relatively abundant in M. bombinus, whereas Mycoplasma_g10 was relatively abundant in R. ferrumequinum. Our results provide an overview of bat guano microbiota diversity and the significance of pathogenic taxa for humans and the environment, highlighting a better understanding of preventing emerging diseases. We anticipate that this research will yield bioinformatic data to advance our knowledge of overall microbial genetic diversity and clustering characteristics in insectivorous bat feces in South Korea.

Analysis of Bacterial Community Composition in Wastewater Treatment Bioreactors Using 16S rRNA Gene-Based Pyrosequencing (16S rRNA 유전자 기반의 Pyrosequencing을 이용한 하수처리시설 생물반응기의 세균군집구조 분석)

  • Kim, Taek-Seung;Kim, Han-Shin;Kwon, Soon-Dong;Park, Hee-Deung
    • Korean Journal of Microbiology
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    • v.46 no.4
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    • pp.352-358
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    • 2010
  • Bacterial community composition in activated sludge wastewater treatment bioreactors were analyzed using 16S rRNA gene-based pyrosequencing for the four different wastewater treatment processes. Sequences within the orders Rhodocyclales, Burkholderiales, Sphingobacteriales, Myxococcales, Xanthomonadales, Acidobacteria group 4, Anaerolineales, Methylococcales, Nitrospirales, and Planctomycetales constituted 54-68% of total sequences retrieved in the activated sludge samples, which demonstrated that a few taxa constituted majority of the activated sludge bacterial community. The relative ratio of the order members was different for each treatment process, which was assumed to be affected by different operational and environmental conditions of each treatment process. In addition, activated sludge had very diverse bacterial species (Chao1 richness estimate: 1,374-2,902 operational taxonomic units), and the diversity was mainly originated from rare species. Particularly, the bacterial diversity was higher in membrane bioreactor than conventional treatment processes, and the long solids retention time of the operational strategy of the membrane bioreactor appeared to be appropriate for sustaining diverse slow growing bacteria. This study investigating bacterial communities in different activated sludge processes using a high-throughput pyrosequencing technology would be helpful for understanding microbial ecology in activated sludge and for improving wastewater treatment in the future.

Analysis of Bacterial Community Structure in the Soil and Root System by 168 rRNA Genes (16S rDNA를 이용한 토양, 작물근계의 세균군집 구조해석)

  • Kim, Jong-Shik;Kwon, Soon-Wo;Ryu, Jin-Chang;Yahng, Chang-Sool
    • Korean Journal of Soil Science and Fertilizer
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    • v.33 no.4
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    • pp.266-274
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    • 2000
  • Understanding of microbial community structure in soil-root system is necessary to use beneficial soil and rhizosphere microbes for improvement of crop production and biocontrol. The knowledge of behavior and function of microbes in soil-root system plays a key role for the application of beneficial inocula. Because the majority of the intact bacteria in soil are unable to grow on nutrient media, both culturable and nonculturable bacteria have to be studied together. In our study, culture-independent survey of bacterial community in the soil-root system of red pepper fields was conducted by the sequence analysis of three universal clone libraries of genes which code for small-subunit rRNA (rDNA). Universal small subunit rRNA primers were used to amplify DNA extracted from each sample and PCR products were cloned into pGEM-T. Out of 27 clones sequenced, 25 clones were from domain bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Within the domain bacteria, several kingdoms were represented : the Proteobacteria (16 clones). Cytophyga-Flexibacter-Bacteroides group (2 clones). the high G+C content gram-positive group(1 clone) and 4 unknown clones.

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Analysis of Microbiota in Bellflower Root, Platycodon grandiflorum, Obtained from South Korea

  • Kim, Daeho;Hong, Sanghyun;Na, Hongjun;Chun, Jihwan;Guevarra, Robin B.;Kim, You-Tae;Ryu, Sangryeol;Kim, Hyeun Bum;Lee, Ju-Hoon
    • Journal of Microbiology and Biotechnology
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    • v.28 no.4
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    • pp.551-560
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    • 2018
  • Bellflower root (Platycodon grandiflorum), which belongs to the Campanulaceae family, is a perennial grass that grows naturally in Korea, northeastern China, and Japan. Bellflower is widely consumed as both food and medicine owing to its high nutritional value and potential therapeutic effects. Since foodborne disease outbreaks often come from vegetables, understanding the public health risk of microorganisms on fresh vegetables is pivotal to predict and prevent foodborne disease outbreaks. We investigated the microbial communities on the bellflower root (n = 10). 16S rRNA gene amplicon sequencing targeting the V6-V9 regions of 16S rRNA genes was conducted via the 454-Titanium platform. The sequence quality was checked and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using the weighted Fast UniFrac distance. The average number of sequence reads generated per sample was 67,192 sequences. At the phylum level, bacterial communities from the bellflower root were composed primarily of Proteobacteria, Firmicutes, and Actinobacteria in March and September samples. Genera Serratia, Pseudomonas, and Pantoea comprised more than 54% of the total bellflower root bacteria. Principal coordinate analysis plots demonstrated that the microbial community of bellflower root in March samples was different from those in September samples. Potential pathogenic genera, such as Pantoea, were detected in bellflower root samples. Even though further studies will be required to determine if these species are associated with foodborne illness, our results indicate that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria on fresh vegetables.

Municipal Wastewater Treatment and Microbial Diversity Analysis of Microalgal Mini Raceway Open Pond (미세조류 옥외 배양시스템을 이용한 도시하수 정화 및 미생물 군집다양성 분석)

  • Kang, Zion;Kim, Byung-Hyuk;Shin, Sang-Yoon;Oh, Hee-Mock;Kim, Hee-Sik
    • Korean Journal of Microbiology
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    • v.48 no.3
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    • pp.192-199
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    • 2012
  • Microalgal biotechnology has gained prominence because of the ability of microalgae to produce value-added products including biodiesel through photosynthesis. However, carbon and nutrient source is often a limiting factor for microalgal growth leading to higher input costs for sufficient biomass production. Use of municipal wastewater as a low cost alternative to grow microalgae as well as to treat the same has been demonstrated in this study using mini raceway open ponds. Municipal wastewater was collected after primary treatment and microalgae indigenous in the wastewater were encouraged to grow in open raceways under optimum conditions. The mean removal efficiencies of TN, TP, COD-$_{Mn}$, $NH_3$-N after 6 days of retention time was 80.18%, 63.56%, 76.34%, and 96.74% respectively. The 18S rRNA gene analysis of the community revealed the presence of Chlorella vulgaris and Scenedesmus obliquus as the dominant microalgae. In addition, 16S rRNA gene analysis demonstrated that Rhodobacter, Luteimonas, Porphyrobacter, Agrobacterium, and Thauera were present along with the microalgae. From these results, it is concluded that microalgae could be used to effectively treat municipal wastewater without aerobic treatment, which incurs additional energy costs. In addition, municipal wastewater shall also serve as an excellent carbon and nitrogen source for microalgal growth. Moreover, the microalgal biomass shall be utilized for commercial purposes.

Change of Sludge Consortium in Response to Sequential Adaptation to Benzene, Toluene, and o-Xylene

  • Park, Jae-Yeon;Sang, Byoung-In
    • Journal of Microbiology and Biotechnology
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    • v.17 no.11
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    • pp.1772-1781
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    • 2007
  • Activated sludge was sequentially adapted to benzene, toluene, and o-xylene (BTX) to study the effects on the change of microbial community. Sludge adapted to BTX separately degraded each by various rates in the following order; toluene>o-xylene>benzene. Degradation rates were increased after exposure to repeated spikes of substrates. Eleven different kinds of sludge were prepared by the combination of BTX sequential adaptations. Clustering analyses (Jaccard, Dice, Pearson, and cosine product coefficient and dimensional analysis of MDS and PCA for DGGE patterns) revealed that acclimated sludge had different features from nonacclimated sludge and could be grouped together according to their prior treatment. Benzene- and xylene-adapted sludge communities showed similar profiles. The sludge profile was affected from the point of the final adaptation substrate regardless of the adaptation sequence followed. In the sludge adapted to 50 ppm toluene, Nitrosomonas sp. and bacterium were dominant, but these bands were not dominant in benzene and benzene after toluene adaptations. Instead, Flexibacter sp. was dominant in these cultures. Dechloromonas sp. was dominant in the culture adapted to 50 ppm benzene. Thauera sp. was the main band in the sludge adapted to 50 ppm xylene, but became vaguer as the xylene concentration was increased. Rather, Flexibacter sp. dominated in the sludge adapted to 100 ppm xylene, although not in the culture adapted to 250 ppm xylene. Two bacterial species dominated in the sludge adapted to 250 ppm xylene, and they also existed in the sludge adapted to 250 ppm xylene after toluene and benzene.

Molecular Profiling of Rhizosphere Bacterial Communities Associated with Prosopis juliflora and Parthenium hysterophorus

  • Jothibasu, K.;Chinnadurai, C.;Sundaram, S.P.;Kumar, K.;Balachandar, D.
    • Journal of Microbiology and Biotechnology
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    • v.22 no.3
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    • pp.301-310
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    • 2012
  • Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

Correlation analysis between elderly oral myofunction, oral microorganisms, and cognitive function

  • Kim, Seol-Hee
    • Journal of Korean society of Dental Hygiene
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    • v.19 no.2
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    • pp.161-172
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    • 2019
  • Objectives: This study aimed to analyze the correlation between oral function, oral environment, and brain cognitive function in the elderly. Methods: The subjects were 60 users of senior community center and elderly day care center. The survey was conducted from November to December 2018. Subjects were assessed by oral examination and myofunction test. Oral myofunction was measured using $IOPI^R$ and Lip de $Cum^R$. Survey data were analyzed using the statistical programs of PASW Statistics ver. 18.0. Results: Tongue muscle strength and lips muscle strength was higher in males than in females. The tongue and lip strengths were higher in the <81 years old group than the ${\geq}81$ years old group. Functional tooth analysis showed that there was a ${\geq}15$ teeth group ($40.91{\pm}7.36$) and a <15 teeth group ($32.52{\pm}7.14$). Lip muscle strength analysis showed that the ${\geq}15$ teeth group ($10.54{\pm}3.40$) was higher than the <15 teeth group ($8.20{\pm}2.41$, p<0.05). Tongue muscle strength, lumbar muscle strength, and functional tooth number were lower in the elderly subjects with mild cognitive impairment. Cognitive function was significantly correlated with functional tooth number (r=0.386, p<0.001), tongue strength (r=0.478, p<0.001), and lip strength (r=0.281, p<0.05). Tongue strength was significantly correlated with lip strength (r=0.360, p<0.001) and functional tooth number (r=0.633, p<0.001). Lip strength was significantly correlated with functional tooth number (r=0.376, p<0.001). Conclusions: These results showed that age and functional tooth number influenced oral muscle strength and that the number of functional teeth and oral muscle strength were low in the elderly with mild cognitive impairment. Oral myofunction training and oral care program are suggested to improve the quality of life of the elderly.

Comparison of mice gut microbiota before and after fasting for a day (절식이 마우스 장내미생물에 미치는 영향)

  • Hong, Jiwan;Jo, Hyejun;Unno, Tatsuya
    • Journal of Applied Biological Chemistry
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    • v.62 no.4
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    • pp.333-337
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    • 2019
  • In this study, we investigated the effects of fasting on gut microbiota of mice fed normal (CTL) or high-fat diets (HF). Mice were raised for 16 weeks and fasted for a day at the end of the experiment. Fecal samples were collected one day before and after fasting, which were analyzed using MiSeq. Our results showed that the species richness and evenness were decreased in fasted HF group, whereas no difference was observed for CTL groups. Moreover, HF fed mice gut microbiota showed different microbial communities after fasting, while CTL groups did not show microbiota shifts. Differential abundance analysis showed that fasting CTL group mice increased and decreased one operational taxonomic unit (OTU) in S24_7 and one OTU in Ruminococcaceae, respectively. On the other hand, fasting HF group mice decreased 10 OTUs and increased 3 OTUs most of which were classified to Ruminococcaceae. Our results suggest that fasting mice may affect the abundance of Ruminococcaceae species and effects of fasting seem to be more obvious for HF-fed mice compared to those of mice fed CTL-diet.

Effect of Soil Microbial Diversity in Paddy Wetland under Organic Rice-Fish Mixed Farming System (유기농 복합생태 논습지의 토양 미생물 다양성 증진 효과)

  • Han, Yangsoo;Park, Choongbae;Cho, Jung-Lai;Park, Sang-Gu;Kong, Min-Jae;Nam, Hong-Shik;Son, Jinkwan
    • Journal of Wetlands Research
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    • v.24 no.2
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    • pp.69-82
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    • 2022
  • In this study, we investigated the bacterial community structure in organic rice-fish mixed farming paddy soil by using high-throughput sequencing technology. The results showed that compared with the organic rice cultivated soil, the content of AP (available phosphorus) increased by 310.23 % and the content of OM (organic matter) increased by 168.83%. The most abundant phyla in paddy soils were Proteobacteria, Bacteriodetes, and Chloroflexi, whose relative abundance was above 47.83%. Among the dominant genera, the relative abundance of Limisphaera in paddy soils was observed. Alpha diversity indicated that the bacterial diversity of paddy soils was similar among each other. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Principal Coordinated Analysis (PCoA) results showed that the bacterial communities in organic rice-fish mixed farming soil and organic paddy soil were correlated to each other; the bacterial community structure was distinctively grouped by four different systems (paddy soil under organic rice-fish mixed farming system, organic rice cultivation, and conventional rice cultivation), where the first two are closely related to each other than the third one. The results provide basal support for organic agri-cultivation while improving an ecological value at the same time.