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Tagele SB, Gachomo EW. Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation. Sci Rep 2024; 14:9867. [PMID: 38684826 PMCID: PMC11058253 DOI: 10.1038/s41598-024-59587-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
Ridomil Gold SL (45.3% a.i. mefenoxam) is a widely used chemical fungicide for the control of oomycetes. However, its impact on fungal communities remains unexplored. Therefore, the goal of this study was to examine the effects of mefenoxam on the temporal dynamics of fungal taxonomic and functional diversities during carrot cultivation under four treatment groups: mefenoxam application with and without Pythium inoculation, and untreated control groups with and without Pythium inoculation. Our in vitro sensitivity assay showed that the maximum recommended concentration of mefenoxam, 0.24 ppm, did not suppress the mycelial growth of P. irregulare. At 100 ppm, mycelial growth was only reduced by 11.4%, indicating that the isolate was resistant to mefenoxam. MiSeq sequencing data revealed transient taxonomic variations among treatments 2 weeks post-treatment. Mortierella dominated the fungal community in the mefenoxam-Pythium combination treatment, as confirmed through PCR using our newly designed Mortierella-specific primers. Conversely, mefenoxam-Pythium combination had adverse effects on Penicillium, Trichoderma, and Fusarium, and decrease the overall alpha diversity. However, these compositional changes gradually reverted to those observed in the control by the 12th week. The predicted ecological functions of fungal communities in all Pythium and mefenoxam treatments shifted, leading to a decrease in symbiotrophs and plant pathogen functional groups. Moreover, the community-level physiological profiling approach, utilizing 96-well Biolog FF microplates, showed discernible variations in the utilization of 95 diverse carbon sources among the treatments. Notably, arbutin, L-arabinose, Tween 80, and succinamic acid demonstrated a strong positive association with Mortierella. Our findings demonstrate that a single application of mefenoxam at its recommended rate triggers substantial taxonomic and functional shifts in the soil fungal community. Considering this impact, the conventional agricultural practice of repeated mefenoxam application is likely to exert considerable shifts on the soil ecosystem that may affect agricultural sustainability.
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Affiliation(s)
- Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA
| | - Emma W Gachomo
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA.
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Andargie YE, Lee G, Jeong M, Tagele SB, Shin JH. Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere. Front Plant Sci 2023; 14:1301698. [PMID: 38116158 PMCID: PMC10728675 DOI: 10.3389/fpls.2023.1301698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.
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Affiliation(s)
- Yohannes Ebabuye Andargie
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
- Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu, Republic of Korea
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3
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Bashizi T, Kim MJ, Lee G, Tagele SB, Shin JH. Whole-Genome Sequence of Pseudomonas frederiksbergensis Strain A6, Isolated from the Rhizosphere of Pepper (Capsicum annuum L.). Microbiol Resour Announc 2023:e0022923. [PMID: 37358423 DOI: 10.1128/mra.00229-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
This research presents the whole-genome sequence of Pseudomonas frederiksbergensis strain A6, which was isolated from the rhizosphere soil of pepper (Capsicum annuum L.). The genome of the strain is composed of a single chromosome with 6,711,706 bp, and the GC content is 58.7%.
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Affiliation(s)
- Tino Bashizi
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Min-Ji Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- NGS Core Facility, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- NGS Core Facility, Kyungpook National University, Daegu, Republic of Korea
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Kim RH, Tagele SB, Jeong M, Jung DR, Lee D, Park T, Tino BF, Lim K, Kim MA, Park YJ, Shin JH. Spinach (Spinacia oleracea) as green manure modifies the soil nutrients and microbiota structure for enhanced pepper productivity. Sci Rep 2023; 13:4140. [PMID: 36914667 PMCID: PMC10011398 DOI: 10.1038/s41598-023-31204-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Spinach has been suggested as a potential rotation crop for increasing crop yield by enhancing beneficial fungal microbes in continuous monocropping. However, no research on the use of spinach as a green manure has been reported. Thus, we tested the effects of spinach and Korean mustard cultivars (green and red mustards) (10 g pot -1) as green manure on soil chemical properties, pepper productivity, and soil microbiome of long-year pepper-monocropped soil. Spinach improved the soil nutrition (e.g., pH, SOM, TN, NH4+, and K), weed suppression, and pepper growth. Spinach had by far the highest fruit yield, over 100% pepper fruit yield increment over the mustard green manures and control. Our study showed that the major influencing factors to cause a shift in both bacterial and fungal community assemblies were soil pH, TC TN, and K. Following green manure amendment Bacillota, especially Clostridium, Bacillus and Sedimentibacter, were enriched, whereas Chloroflexi and Acidobacteriota were reduced. In addition, spinach highly reduced the abundance of Leotiomycetes and Fusarium but enriched Papiliotrema. FAPROTAX and FUNGuild analysis revealed that predicted functional profiles of bacterial and fungal communities in spinach-amended soil were changed. Spinach-treated soil was differentially abundant in function related to hydrocarbon degradation and functional guilds of symbiotrophs and ectomycorrhizal. This study contributes significantly to our understanding of how the soil fertility and soil microbiome alteration via spinach green manure application as a pre-plant soil treatment might help alleviate continuous cropping obstacles.
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Affiliation(s)
- Ryeong-Hui Kim
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.,NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Da-Ryung Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dokyung Lee
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - TaeHyung Park
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Bashizi Flory Tino
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyeongmo Lim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Min A Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yeong-Jun Park
- NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Tagele SB, Kim RH, Jeong M, Lim K, Jung DR, Lee D, Kim W, Shin JH. Soil amendment with cow dung modifies the soil nutrition and microbiota to reduce the ginseng replanting problem. Front Plant Sci 2023; 14:1072216. [PMID: 36760641 PMCID: PMC9902886 DOI: 10.3389/fpls.2023.1072216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO 3 - , total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus, Rhodanobacter, Streptomyces, and Chaetomium, while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.
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Affiliation(s)
- Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- NGS core facility, Kyungpook National University, Daegu, Republic of Korea
| | - Ryeong-Hui Kim
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kyeongmo Lim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Da-Ryung Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Dokyung Lee
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Wanro Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- NGS core facility, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
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Fentie EG, Jeong M, Emire SA, Demsash HD, Kim MA, Jeon HJ, Lee SE, Tagele SB, Park YJ, Shin JH. Microbiome dataset of spontaneously fermented Ethiopian honey wine, Tej. Data Brief 2022; 42:108022. [PMID: 35313500 PMCID: PMC8933813 DOI: 10.1016/j.dib.2022.108022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022] Open
Abstract
This dataset contains raw and analyzed microbial data for the samples of spontaneously fermented Ethiopian honey wine, Tej, collected from three locations of Ethiopia. It was generated using culture independent amplicon sequencing technique. To gain a better understanding of microbial community variance and similarity across Tej samples from the same and different locations, the raw sequenced data obtained from the Illumina Miseq sequencer was subjected to a bioinformatics analysis. Lower diversity and richness of both bacterial and fungal communities were observed for all of the Tej samples. Besides, samples collected from Debre Markos area showed a significant discriminating tax for both bacterial and fungal communities. In nutshell, this amplicon sequencing dataset provides a useful collection of data for modernizing this spontaneous fermentation into a directed inoculated fermentation. Detail discussion on microbiome of Tej samples is given in [1].
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Abstract
Biofumigation is used to control soil-borne plant diseases, and it has paramount importance to reduce the cost of chemical fumigants. Information about the field control efficacies and impacts of Brassica-based biofumigation (BBF) on soil bacterial and fungal microbiota is scattered in the literature. Therefore, this review summarizes and discusses the nature and the underlying causes of soil bacterial and fungal community dynamics in response to BBF. In addition, the major factors influencing the interaction between a biofumigant and soil microbiota are discussed. The pros and cons of BBF to soil microbiota and the subsequent impacts on sustainable farming practices are also highlighted.
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Affiliation(s)
- Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ryeong-Hui Kim
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
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Kim MJ, Tagele SB, Jo H, Kim MC, Jung Y, Park YJ, So JH, Kim HJ, Kim HJ, Lee DG, Kang S, Shin JH. Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor. Sci Rep 2021; 11:10138. [PMID: 33980951 PMCID: PMC8115508 DOI: 10.1038/s41598-021-89606-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/07/2021] [Indexed: 02/01/2023] Open
Abstract
The skin microbiome, especially the axillary microbiome, consists of odor-causing bacteria that decompose odorless sweat into malodor compounds, which contributes to the formation of body odor. Plant-derived products are a cheap source of bioactive compounds that are common ingredients in cosmetics. Microbial bioconversion of natural products is an ecofriendly and economical method for production of new or improved biologically active compounds. Therefore, in this study, we tested the potential of a Lactobacillus acidophilus KNU-02-mediated bioconverted product (BLC) of Lotus corniculatus seed to reduce axillary malodor and its effect on the associated axillary microbiota. A chemical profile analysis revealed that benzoic acid was the most abundant chemical compound in BLC, which increased following bioconversion. Moreover, BLC treatment was found to reduce the intensity of axillary malodor. We tested the axillary microbiome of 18 study participants, divided equally into BLC and placebo groups, and revealed through 16S rRNA gene sequencing that Staphylococcus, Corynebacterium, and Anaerococcus were the dominant taxa, and some of these taxa were significantly associated with axillary malodor. After one week of BLC treatment, the abundance of Corynebacterium and Anaerococcus, which are associated with well-known odor-related genes that produce volatile fatty acids, had significantly reduced. Likewise, the identified odor-related genes decreased after the application of BLC. BLC treatment enhanced the richness and network density of the axillary microbial community. The placebo group, on the other hand, showed no difference in the microbial richness, odor associated taxa, and predicted functional genes after a week. The results demonstrated that BLC has the potential to reduce the axillary malodor and the associated odor-causing bacteria, which makes BLC a viable deodorant material in cosmetic products.
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Affiliation(s)
- Min-Ji Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - HyungWoo Jo
- R&I Center, COSMAX BTI, Seongnam, 13486, Republic of Korea
| | - Min-Chul Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - YeonGyun Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yeong-Jun Park
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jai-Hyun So
- National Development Institute of Korean Medicine, 94, Hwarang-ro, Gyeongsan, Gyeongsangbuk-do, 38540, Republic of Korea
| | - Hae Jin Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Ho Jin Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Seongnam, 13486, Republic of Korea
| | - Seunghyun Kang
- R&I Center, COSMAX BTI, Seongnam, 13486, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Lee YH, Kang GU, Jeon SY, Tagele SB, Pham HQ, Kim MS, Ahmad S, Jung DR, Park YJ, Han HS, Shin JH, Chong GO. Vaginal Microbiome-Based Bacterial Signatures for Predicting the Severity of Cervical Intraepithelial Neoplasia. Diagnostics (Basel) 2020; 10:diagnostics10121013. [PMID: 33256024 PMCID: PMC7761147 DOI: 10.3390/diagnostics10121013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/15/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Although emerging evidence revealed that the gut microbiome served as a tool and as biomarkers for predicting and detecting specific cancer or illness, it is yet unknown if vaginal microbiome-derived bacterial markers can be used as a predictive model to predict the severity of CIN. In this study, we sequenced V3 region of 16S rRNA gene on vaginal swab samples from 66 participants (24 CIN 1−, 42 CIN 2+ patients) and investigated the taxonomic composition. The vaginal microbial diversity was not significantly different between the CIN 1− and CIN 2+ groups. However, we observed Lactobacillus amylovorus dominant type (16.7%), which does not belong to conventional community state type (CST). Moreover, a minimal set of 33 bacterial species was identified to maximally differentiate CIN 2+ from CIN 1− in a random forest model, which can distinguish CIN 2+ from CIN 1− (area under the curve (AUC) = 0.952). Among the 33 bacterial species, Lactobacillus iners was selected as the most impactful predictor in our model. This finding suggests that the random forest model is able to predict the severity of CIN and vaginal microbiome may play a role as biomarker.
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Affiliation(s)
- Yoon Hee Lee
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu 41404, Korea;
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea;
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea;
| | - Gi-Ung Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (G.-U.K.); (S.B.T.); (H.Q.P.); (M.-S.K.); (S.A.); (Y.-J.P.)
| | - Se Young Jeon
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea;
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea;
| | - Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (G.-U.K.); (S.B.T.); (H.Q.P.); (M.-S.K.); (S.A.); (Y.-J.P.)
| | - Huy Quang Pham
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (G.-U.K.); (S.B.T.); (H.Q.P.); (M.-S.K.); (S.A.); (Y.-J.P.)
| | - Min-Sueng Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (G.-U.K.); (S.B.T.); (H.Q.P.); (M.-S.K.); (S.A.); (Y.-J.P.)
| | - Sajjad Ahmad
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (G.-U.K.); (S.B.T.); (H.Q.P.); (M.-S.K.); (S.A.); (Y.-J.P.)
| | - Da-Ryung Jung
- Department of Biomedical Convergence Science & Technology, Kyungpook National University, Daegu 41566, Korea;
| | - Yeong-Jun Park
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (G.-U.K.); (S.B.T.); (H.Q.P.); (M.-S.K.); (S.A.); (Y.-J.P.)
| | - Hyung Soo Han
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea;
- Department of Physiology, School of Medicine, Kyungpook National University, Daegu 41405, Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (G.-U.K.); (S.B.T.); (H.Q.P.); (M.-S.K.); (S.A.); (Y.-J.P.)
- Department of Biomedical Convergence Science & Technology, Kyungpook National University, Daegu 41566, Korea;
- Correspondence: (J.-H.S.); (G.O.C.); Tel.: +82-53-950-5716 (J.-H.S.); +82-53-200-2028 (G.O.C.); Fax: +82-53-953-7233 (J.-H.S.); +82-53-200-2684 (G.O.C.)
| | - Gun Oh Chong
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu 41404, Korea;
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea;
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea;
- Correspondence: (J.-H.S.); (G.O.C.); Tel.: +82-53-950-5716 (J.-H.S.); +82-53-200-2028 (G.O.C.); Fax: +82-53-953-7233 (J.-H.S.); +82-53-200-2684 (G.O.C.)
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Jung BK, Ibal JC, Pham HQ, Kim MC, Park GS, Hong SJ, Jo HW, Park CE, Choi SD, Jung Y, Tagele SB, Shin JH. Quorum Sensing System Affects the Plant Growth Promotion Traits of Serratia fonticola GS2. Front Microbiol 2020; 11:536865. [PMID: 33329415 PMCID: PMC7720635 DOI: 10.3389/fmicb.2020.536865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 10/12/2020] [Indexed: 11/13/2022] Open
Abstract
Quorum sensing (QS) enables bacteria to organize gene expression programs, thereby coordinating collective behaviors. It involves the production, release, and population-wide detection of extracellular signaling molecules. The cellular processes regulated by QS in bacteria are diverse and may be used in mutualistic coordination or in response to changing environmental conditions. Here, we focused on the influence of the QS-dependent genes of our model bacterial strain Serratia fonticola GS2 on potential plant growth promoting (PGP) activities including indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and biofilm formation. Based on genomic and phenotypic experimental data we identified and investigated the function of QS genes in the genome of the model strain. Our gene deletion study confirmed the biological functionality of the QS auto-inducer (gloI) and receptor (gloR) on potential PGP activities of GS2. A transcriptomic approach was also undertaken to understand the role of QS genes in regulation of genes primarily involved in PGP activities (IAA, ACC deaminase activity, and biofilm formation). Both transcriptomic and phenotypic data revealed that the QS-deletion mutants had considerably less PGP activities, as compared to the wild type. In addition, in vivo plant experiments showed that plants treated with GS2 had significantly higher growth rates than plants treated with the QS-deletion mutants. Overall, our results showed how QS-dependent genes regulate the potential PGP activities of GS2. This information may be helpful in understanding the relationship between QS-dependent genes and the PGP activity of bacteria, which aid in the production of practical bio-fertilizers for plant growth promotion.
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Affiliation(s)
- Byung Kwon Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,CJ Blossom Park, Suwon-si, South Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Huy Quang Pham
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Min-Chul Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Gun-Seok Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,Atogen Co., Ltd., Daejeon, South Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,Yeongnam Regional Office, Animal and Plant Quarantine Agency, Busan, South Korea
| | - Hyung Woo Jo
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,R&I Center, COSMAX BTI, Seongnam, South Korea
| | - Chang Eon Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Seung-Dae Choi
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Yeongyun Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Setu Bazie Tagele
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
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Jung Y, Tagele SB, Son H, Ibal JC, Kerfahi D, Yun H, Lee B, Park CY, Kim ES, Kim SJ, Shin JH. Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change. Microorganisms 2020; 8:microorganisms8091265. [PMID: 32825401 PMCID: PMC7569816 DOI: 10.3390/microorganisms8091265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.
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Affiliation(s)
- YeonGyun Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Setu Bazie Tagele
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Department of Applied Plant Sciences, University of Gondar, Gondar 196, Ethiopia
| | - HyunWoo Son
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Dorsaf Kerfahi
- Department of Biological Sciences, Keimyung University, Daegu 42601, Korea;
| | - Hyunju Yun
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Bora Lee
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Clara Yongjoo Park
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea;
| | - Sang-Jun Kim
- Department of Natural Sciences, Republic of Korea Naval Academy, Changwon 51702, Korea;
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Correspondence: ; Tel.: +82-53-950-5716; Fax: +82-53-953-7233
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Tagele SB, Kim SW, Lee HG, Lee YS. Potential of Novel Sequence Type of Burkholderia cenocepacia for Biological Control of Root Rot of Maize ( Zea mays L.) Caused by Fusarium temperatum. Int J Mol Sci 2019; 20:E1005. [PMID: 30813526 PMCID: PMC6429479 DOI: 10.3390/ijms20051005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/13/2019] [Accepted: 02/17/2019] [Indexed: 11/25/2022] Open
Abstract
In this study, two Burkholderia strains, strain KNU17BI2 and strain KNU17BI3, were isolated from maize rhizospheric soil, South Korea. The 16S rRNA gene and multilocus sequence analysis and typing (MLSA-MLST) were used for the identification of the studied strains. Strain KNU17BI2, which belonged to Burkholderia cenocepacia, was of a novel sequence type (ST) designated ST-1538, while strain KNU17BI3 had a similar allelic profile with the seven loci of Burkholderia contaminans strain LMG 23361. The strains were evaluated in vitro for their specific plant growth promoting (PGP) traits, such as zinc solubilization, phosphate solubilization, ammonia production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole acetic acid (IAA) production, siderophore, and hydrolytic enzyme activity. Interestingly, the strains exhibited a positive effect on all of the tested parameters. The strains also showed broad-spectrum antifungal activity against economically important phytopathogens in the dual culture assay. Furthermore, the strains were evaluated under greenhouse conditions for their in vivo effect to promote plant growth and to suppress the root rot of maize that is caused by Fusarium temperatum on four Korean maize cultivars. The results of the greenhouse study revealed that both of the strains were promising to significantly suppress fusarium root rot and enhance plant growth promotion on the four maize cultivars. This study, for the first time, reported in vitro antifungal potential of B. cenocepacia of novel ST against economically important plant pathogens viz., F. temperatum, Fusarium graminearum, Fusarium moniliforme, Fusarium oxysporum f.sp. melonis, Fusarium subglutinans, Phytophthora drechsleri, and Stemphylium lycopersici. This is also the first report of zinc solubilization by B. cenocepacia. Moreover, the present research work reports, for the first time, about the potential of B. cenocepacia and B. contaminans to control the root rot of maize that is caused by F. temperatum. Therefore, we recommend further studies to precisely identify the bioactive chemical compounds behind such activities that would be novel sources of natural products for biological control and plant growth promotion of different crops.
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Affiliation(s)
- Setu Bazie Tagele
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon 24341, Korea.
| | - Sang Woo Kim
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon 24341, Korea.
| | - Hyun Gu Lee
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon 24341, Korea.
| | - Youn Su Lee
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon 24341, Korea.
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Tagele SB, Lee HG, Kim SW, Lee YS. Phenazine and 1-Undecene Producing Pseudomonas chlororaphis subsp. aurantiaca Strain KNU17Pc1 for Growth Promotion and Disease Suppression in Korean Maize Cultivars. J Microbiol Biotechnol 2019; 29:66-78. [DOI: 10.4014/jmb.1808.08026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Tagele SB, Adhikari M, Gurung SK, Lee HG, Kim SW, Kim HS, Ju HJ, Gwon BH, Kosol S, Lee HB, Lee YS. New Records of Aspergillus allahabadii and Penicillium sizovae from Crop Field Soil in Korea. Mycobiology 2018; 46:297-304. [PMID: 30637137 PMCID: PMC6322351 DOI: 10.1080/12298093.2018.1538069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/31/2018] [Accepted: 09/20/2018] [Indexed: 05/05/2023]
Abstract
Two new records of Trichocomaceae, namely Aspergillus allahabadii and Penicillium sizovae, were isolated in 2016 during a survey of fungal diversity in different crop fields locations in Gyeongnam, Korea. These species were identified based on morphological characters and phylogenetic analysis using internal transcribed spacer region and β-tubulin-encoding gene sequence data. A. allahabadii and P. sizovae have not yet been reported in Korea. Thus, this is the first report of these species in Korea, and their descriptions as well as details of their morphological characters are presented.
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Affiliation(s)
- Setu Bazie Tagele
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Mahesh Adhikari
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Sun Kumar Gurung
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Hyun Gu Lee
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Sang Woo Kim
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Hyun Seung Kim
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Han Jun Ju
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Byeong Heon Gwon
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - San Kosol
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology & Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Youn Su Lee
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon, Korea
- CONTACT Youn Su Lee Division of Biological Resources Sciences, Kangwon National University, Chuncheon-si, 24341, Gangwon-do, Chuncheon, Korea
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