• Genomics & Informatics
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• v.16 no.4
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• pp.24.1-24.4
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• 2018

Taxonomic identification is fundamental to all microbiology studies. Particularly in metagenomics, which identifies the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases-Greengenes, Silva, and EzBioCloud-and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy. We show that EzBioCloud performs well compared with other existing databases.

• Ocean and Polar Research
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• v.37 no.3
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• pp.189-200
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• 2015

Mesozooplankton biomass including total biomass and size-fractionated biomass and the abundance of major taxonomic groups of copepods were studied in the Northwestern Subtropical Pacific Warm Pool (NSPWP) and the Northern East China Sea (NECS) from 2006 to 2014. Mesozooplankton biomass ranged from 0.69 to $3.08mgC/m^3$ (mean $1.12mgC/m^3$) in the NSPWP and from 10.60 to $69.10mgC/m^3$ (mean $30.33mgC/m^3$) in the NECS with higher values in spring than fall. Percent composition in the biomass of each size group of mesozooplankton varied interannually both in the NSPWP and in the NECS. The smallest size group (0.2~0.5 mm) contributed the least to total biomass in both regions, but significantly higher in the NSPWP than in the NECS. The percent composition in abundance of copepod taxonomic groups (i.e. Calanoida, Cyclopoida, and Poecilostomatoida) also fluctuated interannually. Mean composition of calanoid copepods was higher in the NECS than in the NSPWP, but the opposite pattern was observed for poecilostomatoid copepods. Mesozooplankton biomass both in the NSPWP and in the NECS was negatively correlated with Oceanic $Ni{\tilde{n}}o$ Index (ONI), indicating declines in biomass during El $Ni{\tilde{n}}o$ periods and vice versa during Na $Ni{\tilde{n}}a$ period. The effect of El $Ni{\tilde{n}}o$ on variation of mesozooplankton biomass was more prominent in the NSPWP than in the NECS. These results suggest that mesozooplankton biomass both in the NSPWP and in the NECS responded to El $Ni{\tilde{n}}o$ events, although the biological process that explain the reduced mesozooplankton biomass might be different in both regions.

• Journal of Environmental Science International
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• v.17 no.10
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• pp.1155-1167
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• 2008

Chlorophyll a (chl a) has been used as an indicator for phytoplankton biomass in pelagic ecosystems due to the relative ease of measurement and selectivity for autotrophs in mixed plankton assemblages. However, the use of chi a as an indicator for phytoplankton biomass is restricted due to its inability to resolve taxonomic differences of phytoplankton and the highly variable relationship of chi a with phytoplankton. Here, we describe the analysis of High-Performance Liquid Chromatography (HPLC) photosynthetic pigment data using CHEMTAX, which is a matrix factorization program that uses chemical taxonomic indices (phytoplankton carotenoids) to quantify the abundance of phytoplankton groups. Compared to direct microscopic counting that can distinguish species within broad groups, the resolution of taxonomic groups by CHEMTAX is generally coarse. It can only distinguish between diatoms, dinoflagellates, cryptophytes, cyanobacteria, chlorophytes, prasinophytes, and haptophytes. However, CHEMTAX analysis is much faster and less expensive than microscopic counting methods. HPLC pigment observations were taken in the spring, summer, fall, and winter in$ 2005\sim2006$ within Gamak Bay, South Korea. CHEMTAX results revealed that diatoms were the dominant taxonomic group in Gamak Bay. In inner Gamak Bay, the ratio between diatoms and cryptophytes was $75\sim80%$, and the ratio between dinoflagellates and cryptophytes was $10\sim15%$. In outer Gamak Bay, the ratio between diatoms and cryptophytes was $85\sim90%$, and the ratio between dinflagellates and cryptophytes was only $1\sim5%$. The population structure was seasonal. Relative diatom populations were less in the summer than the winter season.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.81-85
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• 2015

Since the banning of antibiotic growth promoters (AGPs), the death of livestock has been increased, thus there is a strong demand for AGP-alternatives. Modulation of gut microbiota has been reported to affect host physiological functions and suggested to be a novel approach for developing AGP-alternatives. However, little has been understood about livestock gut microbiota compared to that of humans. We conducted preliminary study provide fundamental information regarding to regional differences in swine gut microbiota. Swine fecal samples were obtained from farms in Jeju (n=40), Gwangju (n=28), and Haenam (n=30). MiSeq was used to sequence 16S rRNA V4 region, and Mothur pipeline (Schloss et al., 2009) was used for data processing. A total of 5,642,125 reads were obtained and 3,868,143 reads were remained after removing erroneous reads. Analysis of taxonomic composition at the phylum level indicated greater abundance of Firmicutes among Jeju swine, and cluster analysis of distribution of operational taxonomic units also showed regional differences among swine gut microbiota. In addition, correlation analysis between non-metric multidimensional scaling and abundance of phyla suggested that the phyla Actinobacter, Verrucomicrobia, Firmicutes, and Fibrobacteres were driving factors for the regional differences. Livestock gut microbiota may be affected by diet and practices in farms. Our results indicated significant regional differences in swine gut microbiota, suggesting that future livestock gut microbiota studies should be designed with the regional differences in mind.

• Journal of Life Science
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• v.32 no.12
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• pp.1005-1012
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• 2022

This study was conducted to investigate the taxonomic composition and diversity of fecal microbiota between birth and weaning stages of Halla horses using 16S rRNA gene amplicon sequencing analysis. Proteobacteria (35.7%) and Firmicutes (45.6%) were identified as the most common phylum in birth and weaning, respectively. Escherichia (19.7%) and Clostridium (14.0%) were observed as the most dominant genus in birth, and Fibrobacter (6.6%) was the highest in weaning. The results of α-diversity showed that the richness and evenness in microbial communities were statistically significant (p<0.001) in birth and weaning. The results of β-diversity indicated that the birth and weaning stages were clearly divided into two groups at the genus and species levels. Permutational multivariate analysis of variance (PERMANOVA) showed that the microbiota composition differences between birth and weaning were statistically significant (q<0.001). A linear discriminant analysis effect (LEfSe) was performed to select taxonomic makers between the birth and weaning stages. On the genus level, Escherichia, Bacteroides, Clostridium, and Methylobacterium were relatively abundant at birth, whereas Fibrobacter was more abundant at weaning. We expect that this research can be utilized as basic data in the identification of microbial communities involved in disease prevention and nutrient absorption in Halla horses.

• Mycobiology
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• v.45 no.4
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• pp.392-400
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• 2017

Peanut yield and quality are seriously affected by pod rot pathogens worldwide, especially in China in recent years. The goals of this study are to analyze the structure of fungal communities of peanut pod rot in soil in three peanut cultivars and the correlation of pod rot with environmental variables using 454 pyrosequencing. A total of 46,723 internal transcribed spacer high-quality sequences were obtained and grouped into 1,706 operational taxonomic units at the 97% similarity cut-off level. The coverage, rank abundance, and the Chao 1 and Shannon diversity indices of the operational taxonomic units were analyzed. Members of the phylum Ascomycota were dominant, such as Fusarium, Chaetomium, Alternaria, and Sordariomycetes, followed by Basidiomycota. The results of the heatmap and redundancy analysis revealed significant variation in the composition of the fungal community among the three cultivar samples. The environmental conditions in different peanut cultivars may also influence on the structure of the fungal community. The results of this study suggest that the causal agent of peanut pod rot may be more complex, and cultivars and environmental conditions are both important contributors to the community structure of peanut pod rot fungi.

• Mycobiology
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• v.41 no.3
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• pp.121-125
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• 2013

Arbuscular mycorrhizal fungi (AMF) have mutualistic relationships with more than 80% of terrestrial plant species. This symbiotic relationship is ancient and would have had important roles in establishment of plants on land. Despite their abundance and wide range of relationship with plant species, AMF have shown low species diversity. However, molecular studies have suggested that diversity of these fungi may be much higher, and genetic variation of AMF is very high within a species and even within a single spore. Despite low diversity and lack of host specificity, various functions have been associated with plant growth responses to arbuscular mycorrhizal fungal colonization. In addition, different community composition of AMF affects plants differently, and plays a potential role in ecosystem variability and productivity. AMF have high functional diversity because different combinations of host plants and AMF have different effects on the various aspects of symbiosis. Consequently, recent studies have focused on the different functions of AMF according to their genetic resource and their roles in ecosystem functioning. This review summarizes taxonomic, genetic, and functional diversities of AMF and their roles in natural ecosystems.

• Journal of Microbiology and Biotechnology
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• v.31 no.11
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• pp.1490-1500
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• 2021

Various microorganisms reside in the human vagina; the vaginal microbiome is closely linked to both vaginal and general health, and for this reason, microbiome studies of the vagina are an area of research. In this study, we analyzed the vaginal microbiome of women before and after menopause to further increase our understanding of the vaginal microbiome and its contribution to general health. We did a 16s rRNA gene-based metagenomic analysis on the vaginal fluids of 11 premenopausal and 19 postmenopausal women in Korea. We confirmed that the taxonomic composition was significantly different between the two groups. In postmenopausal women, species richness was significantly decreased, but species diversity was significantly increased. In particular, among the taxonomic components corresponding to all taxon ranks of the vaginal microbiome, a reduction in Lactobacillus taxa after menopause contributed the most to the difference between the two groups. In addition, we confirmed through metabolic analysis that the lactic-acid concentration was also decreased in the vaginal fluid of women after menopause. Our findings on the correlation between menopause and the microbiome could help diagnose menopause and enhance the prevention and treatment diseases related to menopause.

• Ocean Science Journal
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• v.43 no.3
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• pp.153-160
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• 2008

The distribution of the taxonomical composition and the density of meiobenthos depending on some factors of environment has been studied in bottom sediments of the northern estuary part of Ha Long Bay (Cua Luc estuary). The basic factor of influence on meiobenthic community structure was the granulometric composition of sediment. The greatest taxonomic diversity is noted in the silted sands, lowest - in the silty sediments. The density of meiobenthic community was higher in the silty sediments. Slightly expressed correlation between the density of nematodes and the percentage of silty particles in the sediments is detected (Spearman rank correlation coefficient was $0.49{\pm}0.21$, p=0.035). The nematodes were dominant at all stations. In total, representatives of 66 species of nematodes belonging to 17 families and 52 genera were identified.

• 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.