• Journal of Periodontal and Implant Science
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• 제52권5호
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• pp.394-410
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• 2022

Purpose: The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples. Methods: In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis. Results: When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples. Conclusions: In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

• The Plant Pathology Journal
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• 제29권2호
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• pp.144-153
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• 2013

Diverse bacteria are known to colonize plants. However, only a small fraction of that diversity has been evaluated for their biopesticide potential. To date, the criteria for sampling and selection in such bioprospecting endeavors have not been systematically evaluated in terms of the relative amount of diversity they provide for analysis. The present study aimed to enhance the success of bioprospecting efforts by increasing the diversity while removing the genotypic redundancy often present in large collections of bacteria. We developed a multivariate sampling and marker-based selection strategy that significantly increase the diversity of bacteria recovered from plants. In doing so, we quantified the effects of varying sampling intensity, media composition, incubation conditions, plant species, and soil source on the diversity of recovered isolates. Subsequent sequencing and high-throughput phenotypic analyses of a small fraction of the collected isolates revealed that this approach led to the recovery of over a dozen rare and, to date, poorly characterized genera of plant-associated bacteria with significant biopesticide activities. Overall, the sampling and selection approach described led to an approximately 5-fold improvement in efficiency and the recovery of several novel strains of bacteria with significant biopesticide potential.

• 환경생물
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• 제22권
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• pp.38-46
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• 2004

다환 방향족 탄화수소(PAHs)에 의한 오염이 미생물군집구조에 미치는 영향을 파악하기 위하여 연안에 가까운 광양만 퇴적토를 대상으로 하여 2000년 3월과 8월 2회에 걸쳐 PAHs 오염도와 말단제한절편 다형성 (T-RFLP)분석방법을 이용하여 미생물 군집구조를 조사하였다. T-RFLP방법으로 조사한 미생물 군집은 계절에 따라 군집이 구분되었으며 월내천입구에 위치한 정점 1에서 3월에 다른 정점과 다른 독특한 군집구조를 형성하였다. 또한 상대적으로 PAHs 오염도가 높은 정점들에서 미생물 다양성도 높은 것으로 나타났다. PAHs 농후배양시료에서의 미생물군집구조 변화와 비교해 볼 때 조사대상지역 퇴적토의 미생물 군집구조는 PAHs의 오염에 부분적으로는 영향을 받지만 군집구조를 결정하는 주된 요인은 온도, 입도, 유기물 함량 등과 같은 환경요인인 것으로 사료된다.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2005년도 총회 및 춘계학술발표회
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• pp.28-30
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• 2005

Because of high population diversity in soil microbial communities, it is difficult to accurately assess the capability of biodegradation of toxicant by microbes in soil and sediment. Identifying biodegradative microorganisms is an important step in designing and analyzing soil bioremediation. To remove non-important noise information, it is necessary to selectively enrich genomes of biodegradative microorganisms fromnon-biodegradative populations. For this purpose, a stable isotope probing (SIP) technique was applied in selectively harvesting the genomes of biphenyl-utilizing bacteria from soil microbial communities. Since many biphenyl-using microorganisms are responsible for aerobic PCB degradation In soil and sediments, biphenyl-utilizing bacteria were chosen as the target organisms. In soil microcosms, 13C-biphenyl was added as a selective carbon source for biphenyl users, According to $13C-CO_2$ analysis by GC-MS, 13C-biphenyl mineralization was detected after a 7-day of incubation. The heavy portion of DNA(13C-DNA) was separated from the light portion of DNA (12C-DNA) using equilibrium density gradient ultracentrifuge. Bacterial community structure in the 13C-DNAsample was analyzed by t-RFLP (terminal restriction fragment length polymorphism) method. The t-RFLP result demonstates that the use of SIP efficiently and selectively enriched the genomes of biphenyl degrading bacteria from non-degradative microbes. Furthermore, the bacterial diversity of biphenyl degrading populations was small enough for environmental genomes tools (metagenomics and DNA microarrays) to be used to detect functional (biphenyl degradation) genes from soil microbial communities, which may provide a significant progress in assessing microbial capability of PCB bioremediation in soil and groundwater.

• Journal of Microbiology and Biotechnology
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• 제30권9호
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• pp.1310-1320
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• 2020

Low-quality soil for land reuse is a crucial problem in vegetation quality and especially to waste disposal sites in mining areas. It is necessary to find suitable materials to improve the soil quality and especially to increase soil microbial diversity and activity. In this study, pot experiments were conducted to investigate the effect of a mixed material of humic acid, super absorbent polymer and biochar on low-quality soil indexes and the microbial community response. The indexes included soil physicochemical properties and the corresponding plant growth. The results showed that the mixed material could improve chemical properties and physical structure of soil by increasing the bulk density, porosity, macro aggregate, and promote the mineralization of nutrient elements in soil. The best performance was achieved by adding 3 g·kg^-1 super absorbent polymer, 3 g·kg^-1 humic acid, and 10 g·kg^-1 biochar to soil with plant total nitrogen, dry weight and height increased by 85.18%, 266.41% and 74.06%, respectively. Physicochemical properties caused changes in soil microbial diversity. Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, and Proteobacteria were significantly positively correlated with most of the physical, chemical and plant indicators. Actinobacteria and Armatimonadetes were significantly negatively correlated with most measurement factors. Therefore, this study can contribute to improving the understanding of low-quality soil and how it affects soil microbial functions and sustainability.

• 식물병연구
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• 제17권1호
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• pp.38-43
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• 2011

채소류가 소비되기까지 약 10~30%에 이르는 양이 부패에 의해 버려지고 있다. 채소류는 수확 후 수많은 세균이나 곰팡이와 같은 다양한 미생물들에 의해 부패가 이루어진다. 채소류의 부패와 세균과의 관계를 알아보고자 세균의 다양성에 관한 조사를 하였다. 신선한 상추와 깻잎, 치커리에서의 총 호기성 균 수는 각각 $2.6{\sim}2.7{\times}10^6$, $4.6{\times}10^5$, $1.2{\times}10^6\;CFU/g$ of fresh weight이었으며, Pseudomonas spp., Alysiella spp., Burkholderia spp.와 그 외의 18개의 다양한 속들이 확인되었다. 신선한 채소류를 $28^{\circ}C$에서 일주일 동안 배양하였을 때 세균 다양성에 변화가 생겼다. 총 호기성 균의 수는 상추와 깻잎, 치커리에 대하여 각각 $1.1{\sim}4.6{\times}10^8$, $4.9{\times}10^7$, $7.6{\times}10^8\;CFU/g$ of fresh weight로 나타났으며, 이는 약 $10^2$배 정도 증가한 수치이다. 하지만 세균 다양성은 단순해져서 보다 적은 수의 세균이 분리, 동정되었다. Pseudomonas spp.가 대부분을 차지하였으며(~48%), Arthrobacter sp., Bacillus sp.가 그 뒤를 이었다. 동정된 세균 각각의 부패능을 검정하고자 무균배양한 상추에 접종하였으며, 그 결과 Pseudomonas fluorescence와 Pantoea agglomerans가 상당한 부패를 야기하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권4호
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• pp.585-594
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• 2018

Objective: This study was to determine the bacterial diversity and monitor the community dynamic changes during storage of vacuum-packaged sliced raw beef as affected by Lactobacillus sakei and Lactobacillus curvatus. Methods: L. sakei and L. curvatus were separately incubated in vacuumed-packaged raw beef as bio-protective cultures to inhibit the naturally contaminating microbial load. Dynamic changes of the microbial diversity of inoculated or non-inoculated (control) samples were monitored at $4^{\circ}C$ for 0 to 38 days, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Results: The DGGE profiles of DNA directly extracted from non-inoculated control samples highlighted the order of appearance of spoilage bacteria during storage, showing that Enterbacteriaceae and Pseudomonas fragi emerged early, then Brochothrix thermosphacta shared the dominant position, and finally, Pseudomonas putida showed up became predominant. Compared with control, the inoculation of either L. sakei or L. curvatus significantly lowered the complexity of microbial diversity and inhibited the growth of spoilage bacteria (p<0.05). Interestingly, we also found that the dominant position of L. curvatus was replaced by indigenous L. sakei after 13 d for L. curvatus-inoculated samples. Plate counts on selective agars further showed that inoculation with L. sakei or L. curvatus obviously reduced the viable counts of Enterbacteraceae, Pseudomonas spp. and B. thermosphacta during later storage (p<0.05), with L. sakei exerting greater inhibitory effect. Inoculation with both bio-protective cultures also significantly decreased the total volatile basic nitrogen values of stored samples (p<0.05). Conclusion: Taken together, the results proved the benefits of inoculation with lactic acid bacteria especially L. sakei as a potential way to inhibit growth of spoilage-related bacteria and improve the shelf life of vacuum-packaged raw beef.

• Journal of Dairy Science and Biotechnology
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• 제34권1호
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• pp.9-20
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• 2016

Various microflora, including lactic acid bacteria, are important and necessary components of various cheeses and have significant roles in cheese manufacturing and ripening. In general, the starter culture and secondary microflora could affect the physicochemical properties of various cheeses and could contribute to modifications during manufacturing and ripening. Therefore, during cheese manufacturing and ripening, microbial diversity may depend on continuous interactions among microflora and various environmental conditions. The microbial diversity of cheese is very complex and difficult to control using the classical microbiological techniques. However, recent culture-independent methods have been rapidly developed for microflora in cheese, which could be directly detected using DNA (and/or RNA) in combination with culture-dependent methods. Therefore, this review summarizes state-of-the-art molecular methods to analyze microbial communities in order to understand the properties that affect quality and ripening as well as the complex microbial diversity of various raw-milk, long-ripened cheeses.

• Journal of Microbiology and Biotechnology
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• 제25권7호
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• pp.1136-1145
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• 2015

The diverse microbial communities that colonize distinct segments of the gastrointestinal tract are intimately related to aspects of physiology and the pathology of human health. However, most recent studies have focused on the rectal or fecal microbiota, and the microbial signature of the duodenum is poorly studied. In this study, we compared the microbiota in duodenal and rectal samples to illustrate the characteristic microbial signatures of the duodenum in healthy adults. Nine healthy volunteers donated biopsies and luminal contents from the duodenum and rectum. To determine the composition and diversity of the microbiota, 454-pyrosequencing of bacterial 16S rRNA was performed and multiple bioinformatics analyses were applied. The α-diversity and phylogenetic diversity of the microbiota in the duodenal samples were higher than those of the rectal samples. There was higher biodiversity among the microbiota isolated from rectal biopsies than feces. Proteobacteria were more highly represented in the duodenum than in the rectum, both in the biopsies and in the luminal contents from the healthy volunteers (38.7% versus 12.5%, 33.2% versus 5.0%, respectively). Acinetobacter and Prevotella were dominant in the duodenum, whereas Bacteroides and Prevotella were dominant in the rectum. Additionally, the percentage of OTUs shared in biopsy groups was far higher than in the luminal group (43.0% versus 26.8%) and a greater number of genera was shared among the biopsies than the luminal contents. Duodenal samples demonstrated greater biological diversity and possessed a unique microbial signature compared with the rectum. The mucosa-associated microbiota was more relatively conserved than luminal samples.

• 한국해양생명과학회지
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• 제8권1호
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• pp.43-49
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• 2023

본 연구에서는 남극 로스해 연안에 서식하는 아델리펭귄(Pygoscelis adeliae)과 황제펭귄(Aptenodytes forsteri)의 분변 시료를 기반으로 펭귄 장내 미생물 메타지놈 연구를 수행하였다. Taxonomy 분석 결과, 아델리펭귄과 황제펭귄의 장내 미생물에는 주로 7개의 문(phylum), 18개의 과(family)가 존재하는 것으로 나타났다. 또한 미생물 다양성을 평가하기 위해 Alpha diversity 및 OTU abundance 분석을 수행한 결과, 전반적으로 아델리펭귄의 장내 미생물 다양성이 황제펭귄보다 높은 것을 확인하였고, PCoA를 기반으로 한 Beta diversity 분석을 통해 두 개체군 간 장내 미생물 군집에 차이가 존재함을 확인하였다. PICRUSt를 활용한 기능적인 차원의 KEGG pathway 분석을 통해서는 아델리펭귄과 황제펭귄 시료에서 nucleoside and nucleotide biosynthesis pathway가 가장 많이 존재하는 것을 확인하였다. 본 연구를 통해 남극 아델리펭귄과 황제펭귄의 장내미생물 구성과 다양성을 비교분석 할 수 있었다. 본 연구 결과는 향후 펭귄의 먹이 섭식 관련 연구에 활용될 수 있으며, 더 나아가 다양한 남극 생물의 장내미생물 메타지놈 분석에 대한 기초가 될 수 있을 것이다.