1
|
Lee J, Kim EJ, Park GS, Kim J, Kim TE, Lee YJ, Park J, Kang J, Koo JW, Choi TY. Lactobacillus reuteri ATG-F4 Alleviates Chronic Stress-induced Anhedonia by Modulating the Prefrontal Serotonergic System. Exp Neurobiol 2023; 32:313-327. [PMID: 37927130 PMCID: PMC10628864 DOI: 10.5607/en23028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/02/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023] Open
Abstract
Mental health is influenced by the gut-brain axis; for example, gut dysbiosis has been observed in patients with major depressive disorder (MDD). Gut microbial changes by fecal microbiota transplantation or probiotics treatment reportedly modulates depressive symptoms. However, it remains unclear how gut dysbiosis contributes to mental dysfunction, and how correction of the gut microbiota alleviates neuropsychiatric disorders. Our previous study showed that chronic consumption of Lactobacillus reuteri ATG-F4 (F4) induced neurometabolic alterations in healthy mice. Here, we investigated whether F4 exerted therapeutic effects on depressive-like behavior by influencing the central nervous system. Using chronic unpredictable stress (CUS) to induce anhedonia, a key symptom of MDD, we found that chronic F4 consumption alleviated CUS-induced anhedonic behaviors, accompanied by biochemical changes in the gut, serum, and brain. Serum and brain metabolite concentrations involved in tryptophan metabolism were regulated by CUS and F4. F4 consumption reduced the elevated levels of serotonin (5-HT) in the brain observed in the CUS group. Additionally, the increased expression of Htr1a, a subtype of the 5-HT receptor, in the medial prefrontal cortex (mPFC) of stressed mice was restored to levels observed in stress-naïve mice following F4 supplementation. We further demonstrated the role of Htr1a using AAV-shRNA to downregulate Htr1a in the mPFC of CUS mice, effectively reversing CUS-induced anhedonic behavior. Together, our findings suggest F4 as a potential therapeutic approach for relieving some depressive symptoms and highlight the involvement of the tryptophan metabolism in mitigating CUS-induced depressive-like behaviors through the action of this bacterium.
Collapse
|
2
|
Lee YS, Park GS, Ko SH, Yang WK, Seo HJ, Kim SH, Jeong N, Kang J. Lactobacillus paracasei ATG-E1 improves particulate matter 10 plus diesel exhaust particles (PM 10D)-induced airway inflammation by regulating immune responses. Front Microbiol 2023; 14:1145546. [PMID: 37180255 PMCID: PMC10174254 DOI: 10.3389/fmicb.2023.1145546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
Particulate matter (PM) exposure can adversely affect respiratory function. Probiotics can alleviate the inflammatory responses in respiratory diseases. We examined the protective effects of Lactobacillus paracasei ATG-E1 isolated from the feces of a newborn baby against airway inflammation in a PM10 plus diesel exhaust particle (DEP) (PM10D)-induced airway inflammation model. BALB/c mice were exposed to PM10D by intranasal injection three times at 3-day intervals for 12 days, and L. paracasei ATG-E1 was administered orally for 12 days. Analysis of immune cell population and expression of various inflammatory mediators and gut barrier-related genes were determined in bronchoalveolar lavage fluid (BALF), lung, peyer's patch, and small intestine. A histological analysis of the lungs was performed. In addition, the in vitro safety and their safety in genomic analyses were examined. L. paracasei ATG-E1 was found to be safe in vitro and by genomic analysis. L. paracasei ATG-E1 suppressed neutrophil infiltration and the number of CD4+, CD4+CD69+, CD62L-CD44+high, CD21/35+B220+, and Gr-1+CD11b+ cells, as well as the expression of inflammatory mediators, including chemokine (C-X-C motif) ligand (CXCL)-1, macrophage inflammatory protein (MIP)-2, interleukin (IL)-17a, tumor necrosis factor (TNF)-α, and IL-6 in BALF and lungs in PM10D-induced airway inflammation. It protected against histopathological damage in the lungs of mice with PM10D-induced airway inflammation. L. paracasei ATG-E1 concomitantly increased the expression levels of the gut barrier function-related genes occludin, claudin-1, and IL-10 in the small intestine, with an increased number of CD4+ and CD4+CD25+ immune cells in the peyer's patch. L. paracasei ATG-E1 suppressed immune activation and airway inflammatory responses in the airways and lungs by restoring the lung damage by PM10D. It also regulated intestinal immunity and ameliorated the gut barrier function in the ileum. These results indicate the potential of L. paracasei ATG-E1 as an protective and therapeutic agent against airway inflammation and respiratory diseases.
Collapse
|
3
|
Kim SH, Singh D, Son SY, Lee S, Suh DH, Lee NR, Park GS, Kang J, Lee CH. Characterization and temporal dynamics of the intra- and extracellular environments of Lactiplantibacillus plantarum using multi-platform metabolomics. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
4
|
Lee YS, Lee D, Park GS, Ko SH, Park J, Lee YK, Kang J. Lactobacillus plantarum HAC01 ameliorates type 2 diabetes in high-fat diet and streptozotocin-induced diabetic mice in association with modulating the gut microbiota. Food Funct 2021; 12:6363-6373. [PMID: 34105563 DOI: 10.1039/d1fo00698c] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a serious metabolic disorder that occurs worldwide; however, this condition can be managed with probiotics. We assessed the potential therapeutic effects of Lactobacillus plantarum HAC01 on hyperglycemia and T2DM and determined their potential mechanisms using mice with high-fat diet (HFD) and streptozotocin (STZ)-induced diabetes. The diabetic model was established with an HFD and 50 mg kg-1 STZ. L. plantarum HAC01 was then administered for 10 weeks. Body weight, food and water intake, biochemical parameters, and homeostasis model assessment for insulin resistance (HOMA-IR) were measured. Oral glucose tolerance test and histological analysis were performed, and the glucose metabolism-related gene expression and signaling pathways in the liver were determined. Fecal microbiota and serum short-chain fatty acids (SCFAs) were also analyzed. L. plantarum HAC01 significantly lowered blood glucose and HbA1c levels and improved glucose tolerance and HOMA-IR. Additionally, it increased the insulin-positive β-cell area in islets and decreased the mRNA expression levels of phosphoenolpyruvate carboxykinase and glucose 6-phosphatase, which are associated with gluconeogenesis. L. plantarum HAC01 also increased the phosphorylation of AMPK and Akt, which are involved in glucose metabolism in the liver. Notably, L. plantarum HAC01 increased the Akkermansiaceae family and increased SCFAs in serum. L. plantarum HAC01 could alleviate hyperglycemia and T2DM by regulating glucose metabolism in the liver, protecting the islet β-cell mass, and restoring the gut microbiota and SCFAs. L. plantarum HAC01 may thus be an effective therapeutic agent for T2DM.
Collapse
|
5
|
Park B, Bang CH, Lee C, Han JH, Choi W, Kim J, Park GS, Rhie JW, Lee JH, Kim C. 3D wide-field multispectral photoacoustic imaging of human melanomas in vivo: a pilot study. J Eur Acad Dermatol Venereol 2020; 35:669-676. [PMID: 33037671 DOI: 10.1111/jdv.16985] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND The Breslow depth is an important parameter to determine the excision margin and prognosis of melanoma. However, it is difficult to accurately determine the actual Breslow depth before surgery using the existing ocular micrometer and biopsy technique. OBJECTIVES To evaluate the use of 3D wide-field multispectral photoacoustic imaging to non-invasively measure depth and outline the boundary of melanomas for optimal surgical margin selection. METHODS Six melanoma patients were examined in vivo using the 3D multispectral photoacoustic imaging system. For five cases of melanomas (one in situ, three nodular, and one acral lentiginous type melanoma), the spectrally unmixed photoacoustic depths were calculated and compared against histopathological depths. RESULTS Spectrally unmixed photoacoustic depths and histopathological depths match well within a mean absolute error of 0.36 mm. In particular, the measured minimum and maximum depths in the in situ and nodular type of melanoma were 0.6 and 9.1 mm, respectively. In the 3D photoacoustic image of one metastatic melanoma, feeding vessels were visualized in the melanoma, suggesting the neovascularization around the tumour. CONCLUSIONS The 3D multispectral photoacoustic imaging not only provides well-measured depth and sizes of various types of melanomas, it also visualizes the metastatic type of melanoma. Obtaining accurate depth and boundary information of melanoma before surgery would play a useful role in the complete excision of melanoma during surgery.
Collapse
|
6
|
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: 0.8] [Reference Citation Analysis] [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.
Collapse
|
7
|
Beck BR, Park GS, Jeong DY, Lee YH, Im S, Song WH, Kang J. Multidisciplinary and Comparative Investigations of Potential Psychobiotic Effects of Lactobacillus Strains Isolated From Newborns and Their Impact on Gut Microbiota and Ileal Transcriptome in a Healthy Murine Model. Front Cell Infect Microbiol 2019; 9:269. [PMID: 31404163 PMCID: PMC6677118 DOI: 10.3389/fcimb.2019.00269] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Psychobiotics are probiotic microorganisms that may exert positive influence on the psychological status of the host. Studies have revealed immunological and microbiological correlations of gut microbiota and the gut-brain axis, and have investigated psychobiotics based on the findings of the gut-brain axis. Considering their mode of actions, the present study sets anti-inflammatory effect, neurotransmitter modulation, and gut microbiota modulation as three essential criteria to evaluate Lactobacillus casei ATG-F1 (F1), L. reuteri ATG-F3 (F3), and L. reuteri ATG-F4 (F4) isolated from newborns as psychobiotics candidates in a healthy mouse model and compares the results with a non-treated control group and an ampicillin-induced gut dysbiosis (Amp) group as a negative control. The F3 and F4 strains showed anti-inflammatory effects in vitro in RAW264.7 murine macrophages, and the level of anti-inflammatory cytokine interleukin (IL)-10 increased in ileums of mice orally administered with the F4 strain. Serum dopamine level significantly increased only in the F4-treated group as compared with the control group. Serum serotonin level was unaffected in Lactobacillus-treated groups, while a significant decrease in serum serotonin level was observed in the Amp group. Bacteroidetes population increased in fecal samples of the F4-treated group as compared with the control, and Bacteroidales S24-7 and Prevotellaceae population significantly increased at family level in fecal samples from the F4-treated group as compared with the control. In contrast, the Amp group showed an increase in the level of Proteobacteria and a decrease in the level of Bacteroidetes as compared with the control group. Transcriptome analysis revealed a distinctive clustering in ileums from the F4-treated group as compared to other experimental groups. In addition, the circadian rhythm pathway showed maximum enrichment in ileums of Lactobacillus-treated mice, and the F4-treated group showed the highest fold changes in circadian rhythm-related genes (Dbp, Per1, Per2, and Per3). Conclusively, L. reuteri ATG-F4 is suggested as a potential psychobiotics through demonstrations of anti-inflammatory effects, serum dopamine modulation, and gut microbiota modulation in a healthy murine model in the present study. Moreover, we carefully suggest gut circadian rhythm modulation as another important criterion of psychobiotics, which may have an important role in the gut-brain axis.
Collapse
|
8
|
Beck BR, Park GS, Lee YH, Im S, Jeong DY, Kang J. Whole Genome Analysis of Lactobacillus plantarum Strains Isolated From Kimchi and Determination of Probiotic Properties to Treat Mucosal Infections by Candida albicans and Gardnerella vaginalis. Front Microbiol 2019; 10:433. [PMID: 30894844 PMCID: PMC6414439 DOI: 10.3389/fmicb.2019.00433] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Three Lactobacillus plantarum strains ATG-K2, ATG-K6, and ATG-K8 were isolated from Kimchi, a Korean traditional fermented food, and their probiotic potentials were examined. All three strains were free of antibiotic resistance, hemolysis, and biogenic amine production and therefore assumed to be safe, as supported by whole genome analyses. These strains demonstrated several basic probiotic functions including a wide range of antibacterial activity, bile salt hydrolase activity, hydrogen peroxide production, and heat resistance at 70°C for 60 s. Further studies of antimicrobial activities against Candida albicans and Gardnerella vaginalis revealed growth inhibitory effects from culture supernatants, coaggregation effects, and killing effects of the three probiotic strains, with better efficacy toward C. albicans. In vitro treatment of bacterial lysates of the probiotic strains to the RAW264.7 murine macrophage cell line resulted in innate immunity enhancement via IL-6 and TNF-α production without lipopolysaccharide (LPS) treatment and anti-inflammatory effects via significantly increased production of IL-10 when co-treated with LPS. However, the degree of probiotic effect was different for each strain as the highest TNF-α and the lowest IL-10 production by the RAW264.7 cell were observed in the K8 lysate treated group compared to the K2 and K6 lysate treated groups, which may be related to genomic differences such as chromosome size (K2: 3,034,884 bp, K6: 3,205,672 bp, K8: 3,221,272 bp), plasmid numbers (K2: 3, K6 and K8: 1), or total gene numbers (K2: 3,114, K6: 3,178, K8: 3,186). Although more correlative inspections to connect genomic information and biological functions are needed, genomic analyses of the three strains revealed distinct genomic compositions of each strain. Also, this finding suggests genome level analysis may be required to accurately identify microorganisms. Nevertheless, L. plantarum ATG-K2, ATG-K6, and ATG-K8 demonstrated their potential as probiotics for mucosal health improvement in both microbial and immunological contexts.
Collapse
|
9
|
Kim J, Kim YH, Park B, Seo HM, Bang CH, Park GS, Park YM, Rhie JW, Lee JH, Kim C. Multispectral ex vivo photoacoustic imaging of cutaneous melanoma for better selection of the excision margin. Br J Dermatol 2018; 179:780-782. [PMID: 29663310 DOI: 10.1111/bjd.16677] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
10
|
Park YJ, Jung BK, Hong SJ, Park GS, Ibal JC, Pham H, Shin JH. Expression and Characterization of Calcium- and Zinc-Tolerant Xylose Isomerase from Anoxybacillus kamchatkensis G10. J Microbiol Biotechnol 2018; 28:606-612. [DOI: 10.4014/jmb.1712.12021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
11
|
Park YJ, Park CE, Jung BK, Ibal JC, Jung Y, Hong SJ, Park GS, Lee SH, Sook Ko H, Shin JH. The first complete mitochondrial genome sequence of the leucosiid crab Pyrhila pisum (Arthropoda, Decapoda, Leucosiidae). Mitochondrial DNA B Resour 2017; 2:885-886. [PMID: 33474023 PMCID: PMC7799897 DOI: 10.1080/23802359.2017.1407717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pyrhila pisum is known as leucosiid crab. So far, there is no study about whole mitochondrial genome in Leucosiidae family. Here, we report first the complete sequence of the mitochondrial genome from P. pisum, which is composed of 15,516 base pair encoding 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and A + T-rich region. The nucleotide composition of P. pisum was G + C: 25.5%, A + T: 74.5%, with a strong AT bias. In phylogenetic analysis using whole mitogenome, it was figured out that P. pisum was closely related to Sesarma neglectum but their family is different.
Collapse
|
12
|
Park YJ, Park CE, Hong SJ, Jung BK, Ibal JC, Park GS, Shin JH. The complete mitochondrial genome sequence of the greater wax moth Galleria mellonella (Insecta, Lepidoptera, Pyralidae): sequence and phylogenetic analysis comparison based on whole mitogenome. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:714-715. [PMID: 33473956 PMCID: PMC7800018 DOI: 10.1080/23802359.2017.1390418] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The larva of Galleria mellonella is widely used as a model organism for in vivo toxicology and pathogenicity testing. Here, we report complete sequence of the mitochondrial genome (mitogenome) from G. mellonella, which is comprised of 15,320 base pairs encoding 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and an A + T rich region. The overall base composition was G + C: 19.6%, A + T: 80.4%, with an apparent AT bias. Phylogenetic analysis using whole mitogenome revealed that G. mellonella was closely related to Corcyra cephalonica, which is in the same Pyralidae family.
Collapse
|
13
|
Shabani E, Ouma BJ, Idro R, Bangirana P, Opoka RO, Park GS, Conroy AL, John CC. Elevated cerebrospinal fluid tumour necrosis factor is associated with acute and long-term neurocognitive impairment in cerebral malaria. Parasite Immunol 2017; 39. [PMID: 28453871 DOI: 10.1111/pim.12438] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 04/24/2017] [Indexed: 12/25/2022]
Abstract
Systemic tumour necrosis factor-α (TNF-α) may contribute to the pathogenesis of cerebral malaria (CM) by promoting endothelial activation and parasite sequestration. However, less is known about the role of central nervous system (CNS) TNF-α in CM. We assessed plasma (n=249) and cerebrospinal fluid (CSF) (n=167) TNF-α levels in Ugandan children with CM, plasma TNF-α in Ugandan community control children (n=198) and CSF TNF-α in North American control children who had recovered from leukaemia (n=13). Plasma and CSF TNF-α were measured by magnetic bead assay. We compared plasma and CSF TNF-α levels in children with CM to mortality, acute and chronic neurologic deficits and long-term neurocognitive impairment. Plasma and CSF TNF-α levels were higher in CM than control children (P<.0001 for both). CSF TNF-α levels were higher in children who had neurologic deficits at discharge or 6-month follow-up (P≤.05 for both). Elevated CSF but not plasma TNF-α was associated with longer coma duration (Spearman's rho .18, P=.02) and deficits in overall cognition in children 5 years and older (β coefficient -.74, 95% CI -1.35 to -0.13, P=.02). The study findings suggest that CNS TNF-α may be involved in the development of acute and chronic neurologic and cognitive sequelae in children with CM.
Collapse
|
14
|
Park GS, Hong SJ, Jung BK, Park S, Jin H, Lee SJ, Shin JH, Lee HS. Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1. Braz J Microbiol 2017; 48:395-396. [PMID: 28256390 PMCID: PMC5498416 DOI: 10.1016/j.bjm.2016.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/18/2016] [Indexed: 11/11/2022] Open
Abstract
Pediococcus acidilactici strain S1, a lactic acid-fermenting bacterium, was isolated from makgeolli—a Korean traditional fermented alcoholic beverage. Here we report the 1,980,172 bp (G + C content, 42%) genome sequence of Pediococcus acidilactici strain S1 with 1,525 protein-coding sequences (CDS), of which 47% could be assigned to recognized functional genes. The genome sequence of the strain S1 might provide insights into the genetic basis of the lactic acid bacterium with alcohol-tolerant.
Collapse
|
15
|
Khan AR, Park GS, Asaf S, Hong SJ, Jung BK, Shin JH. Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants. PLoS One 2017; 12:e0171534. [PMID: 28187139 PMCID: PMC5302809 DOI: 10.1371/journal.pone.0171534] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 01/22/2017] [Indexed: 11/28/2022] Open
Abstract
Serratia marcescens RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator Solanum nigrum. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of S. marcescens RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant S. marcescens and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants.
Collapse
|
16
|
Khan AR, Ullah I, Waqas M, Park GS, Khan AL, Hong SJ, Ullah R, Jung BK, Park CE, Ur-Rehman S, Lee IJ, Shin JH. Host plant growth promotion and cadmium detoxification in Solanum nigrum, mediated by endophytic fungi. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 136:180-188. [PMID: 27931714 DOI: 10.1016/j.ecoenv.2016.03.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 05/13/2023]
Abstract
Current investigation conducted to evaluate the associated fungal endophyte interactions of a Cd hyper-accumulator Solanum nigrum Korean ecotype under varying concentrations of Cd. Two indole-3-acetic acid (IAA) producing fungal strains, RSF-4L and RSF-6L, isolated from the leaves of S. nigrum, were initially screened for Cd tolerance and accumulation potential. In terms of dry biomass production, the strain RSF-6L showed higher tolerance and accumulation capacity for Cd toxicity in comparison to RSF-4L. Therefore, RSF-6L was applied in vivo to S. nigrum and grown for six weeks under Cd concentrations of 0, 10, and 30mgKg-1 of dry sand. The effect of fungal inoculation assessed by plant physiological responses, endogenous biochemical regulations, and Cd profile in different tissues. Significant increase were observed in plant growth attributes such as shoot length, root length, dry biomass, leaf area, and chlorophyll contents in inoculated RSF-6L plants in comparison to non-inoculated plants with or without Cd contamination. RSF-6L inoculation decreased uptake of Cd in roots and above ground parts, as evidenced by a low bio-concentration factor (BCF) and improved tolerance index (TI). However, Cd concentration in the leaves remained the same for inoculated and non-inoculated plants under Cd spiking. Fungal inoculation protected the host plants, as evidenced by low peroxidase (POD) and polyphenol peroxidase (PPO) activities and high catalase (CAT) activity. Application of appropriate fungal inoculation that can improve tolerance mechanisms of hyper-accumulators and reduce Cd uptake can be recommended for phyto-stabilisation/immobilisation of heavy metals in crop fields.
Collapse
|
17
|
Khan AL, Al-Harrasi A, Asaf S, Park CE, Park GS, Khan AR, Lee IJ, Al-Rawahi A, Shin JH. The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman. PLoS One 2017; 12:e0169794. [PMID: 28085925 PMCID: PMC5235384 DOI: 10.1371/journal.pone.0169794] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/21/2016] [Indexed: 01/17/2023] Open
Abstract
Boswellia sacra (Burseraceae), a keystone endemic species, is famous for the production of fragrant oleo-gum resin. However, the genetic make-up especially the genomic information about chloroplast is still unknown. Here, we described for the first time the chloroplast (cp) genome of B. sacra. The complete cp sequence revealed a circular genome of 160,543 bp size with 37.61% GC content. The cp genome is a typical quadripartite chloroplast structure with inverted repeats (IRs 26,763 bp) separated by small single copy (SSC; 18,962 bp) and large single copy (LSC; 88,055 bp) regions. De novo assembly and annotation showed the presence of 114 unique genes with 83 protein-coding regions. The phylogenetic analysis revealed that the B. sacra cp genome is closely related to the cp genome of Azadirachta indica and Citrus sinensis, while most of the syntenic differences were found in the non-coding regions. The pairwise distance among 76 shared genes of B. sacra and A. indica was highest for atpA, rpl2, rps12 and ycf1. The cp genome of B. sacra reveals a novel genome, which could be used for further studied to understand its diversity, taxonomy and phylogeny.
Collapse
|
18
|
Park GS, Hong SJ, Park S, Jin H, Lee SJ, Shin JH, Lee HS. Draft genome sequence of alcohol-tolerant bacteria Pediococcus acidilactici strain K3. Braz J Microbiol 2017; 48:1-2. [PMID: 28043774 PMCID: PMC5220627 DOI: 10.1016/j.bjm.2016.07.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/12/2015] [Indexed: 12/03/2022] Open
Abstract
Pediococcus acidilactici strain K3 is an alcohol-tolerant lactic acid bacterium isolated from nuruk, which is a traditional Korean fermentation starter for makgeolli brewing. Draft genome of this strain was approximately 1,991,399 bp (G+C content, 42.1%) with 1525 protein-coding sequences (CDS), of which 44% were assigned to recognized functional genes. This draft genome sequence data of the strain K3 will provide insights into the genetic basis of its alcohol-tolerance.
Collapse
|
19
|
Jung BK, Khan AR, Hong SJ, Park GS, Park YJ, Park CE, Jeon HJ, Lee SE, Shin JH. Genomic and phenotypic analyses of Serratia fonticola strain GS2: a rhizobacterium isolated from sesame rhizosphere that promotes plant growth and produces N-acyl homoserine lactone. J Biotechnol 2016; 241:158-162. [PMID: 27923736 DOI: 10.1016/j.jbiotec.2016.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/16/2022]
Abstract
The genus Serratia incorporates many agriculturally important species. Serratia fonticola strain GS2, isolated from a sesame rhizosphere, can produce N-acyl homoserine lactone quorum sensing signal molecules and indole-3-acetic acid (IAA). Here we report the complete genome sequence and phenotypic characteristics based on genomic information of this bacterium. The complete genome sequence of S. fonticola strain GS2 consists of a chromosome of 6.1 Mbp and two plasmids of 132 kbp and 94 kbp. The genome clusters for IAA and N-acyl homoserine lactone biosynthesis were identified in the genome. Subsequently, the Salkowski test and gas chromatography-mass spectrometry (GC-MS) analysis also revealed that the strain GS2 produces indolic compounds (27.1μgmL-1) and IAA (6.7μgmL-1) in its culture broth. HPLC analysis confirmed that the strain GS2 produced the quorum sensing signal molecules N-hexanoyl-L-homoserine lactone and N-octanoyl-L-homoserine lactone. This new information on the genome sequence and phenotype features will inform future ecological studies related to plant-microbe interactions.
Collapse
|
20
|
Kwak Y, Park GS, Shin JH. High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium. Stand Genomic Sci 2016; 11:51. [PMID: 27555890 PMCID: PMC4994261 DOI: 10.1186/s40793-016-0173-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas lutea OK2(T) (=LMG 21974(T), CECT 5822(T)) is the type strain of the species and was isolated from the rhizosphere of grass growing in Spain in 2003 based on its phosphate-solubilizing capacity. In order to identify the functional significance of phosphate solubilization in Pseudomonas Plant growth promoting rhizobacteria, we describe here the phenotypic characteristics of strain OK2(T) along with its high-quality draft genome sequence, its annotation, and analysis. The genome is comprised of 5,647,497 bp with 60.15 % G + C content. The sequence includes 4,846 protein-coding genes and 95 RNA genes.
Collapse
|
21
|
Hong SJ, Park CE, Park GS, Kim MC, Jung BK, Shin JH. Draft genome sequence of sulfur-reducing archaeon Thermococcus thioreducens DSM 14981 T. Braz J Microbiol 2016; 48:3-4. [PMID: 27328615 PMCID: PMC5220636 DOI: 10.1016/j.bjm.2016.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/06/2016] [Accepted: 04/25/2016] [Indexed: 11/29/2022] Open
Abstract
Thermococcus thioreducens DSM 14981T, a sulfur-reducing archaeon, was isolated from the rainbow hydrothermal vent site on the Mid-Atlantic Ridge. Herein, we report the draft genome sequence of T. thioreducens DSM 14981T; we obtained 41 contigs with a genome size of 2,052,483 bp and G + C content of 53.5%. This genome sequence will not only help understand how the archaeon adapts to the deep-sea hydrothermal environment but also aid the development of enzymes that are highly stable under extreme conditions for industrial applications.
Collapse
|
22
|
Lee SC, Choi HW, Nam E, Noh YH, Lee S, Lee YJ, Park GS, Shin JH, Yoon IJ, Kang SY, Lee C. Pathogenicity and genetic characteristics associated with cell adaptation of a virulent porcine reproductive and respiratory syndrome virus nsp2 DEL strain CA-2. Vet Microbiol 2016; 186:174-88. [PMID: 27016772 DOI: 10.1016/j.vetmic.2016.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/03/2016] [Accepted: 03/03/2016] [Indexed: 02/06/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is the most common and world-widespread viral pathogen of swine. We previously reported genomic sequences and pathogenicity of type 2 Korean PRRSV strains belonging to the virulent lineage 1 family, which contain remarkable amino acid deletions in nonstructural protein 2 (nsp2 DEL) compared to VR-2332. Here, a virulent type 2 Korean PRRSV nsp2 DEL strain, CA-2, was serially propagated in MARC-145 cells for up to 100 passages (CA-2-P100). As the passage number increased, the phenotypic characteristics of cell-adapted CA-2 strains were altered, in terms of higher viral titers and larger plaque sizes compared to the parental virus. Pro-inflammatory cytokine genes, including TNF-α, IL-8, MCP-1, and MCP-2, were found to be significantly down-regulated in PAM cells with the CA-2-P100 strain compared to its parental nsp2 DEL virus. Animal inoculation studies demonstrated that the virulence of CA-2-P100 was reduced significantly, with showing normal weight gain, body temperatures, and lung lesions comparable to the control group. Furthermore, high-passage CA-2-P100 showed declined and transient viremia kinetics, as well as delayed and low PRRSV-specific antibody responses in infected pigs. In addition, we determined whole genome sequences of low to high-passage derivatives of CA-2. The nsp2 DEL pattern was conserved for 100 passages, whereas no other deletions or insertions arose during the cell adaptation process. However, CA-2-P100 possessed 54 random nucleotide substitutions that resulted in 27 amino acid changes distributed throughout the genome, suggesting that these genetic drifts provide a possible molecular basis correlated with the cell-adapted features in vitro and the attenuated phenotype in vivo. Taken together, our data indicate that the cell-attenuated CA-2-P100 strain is a promising candidate for developing a safe and effective live PRRSV vaccine.
Collapse
|
23
|
Park GS, Khan AR, Kwak Y, Hong SJ, Jung B, Ullah I, Kim JG, Shin JH. An improved effective microorganism (EM) soil ball-making method for water quality restoration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:1100-1107. [PMID: 26498821 DOI: 10.1007/s11356-015-5617-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Soil balls containing the so-called effective microorganisms (EM) have been applied to improve water quality of small ponds, lakes, and streams worldwide. However, neither the physical conditions facilitating their proper application nor the diversity of microbial community in such soil balls have been investigated. In this study, the application of 0.75% of hardener to the soil balls exerted almost neutral pH (pH 7.3) which caused up to a fourfold increased hardness of the soil ball. Moreover, the 0.75% of hardener in the soil ball also improved the water quality due to a significant reduction in dissolved oxygen, total phosphorus, and total nitrogen contents. Metagenomic analysis of the microbial community in the soil ball with 0.75% hardener was compared with control (traditional soil ball) through next-generation sequencing. The traditional soil ball microbial community comprised 96.1% bacteria, 2.7% eukaryota, and 1% archaea, whereas the soil ball with 0.75% hardener comprised 71.4% bacteria, 27.9% eukaryota, and 0.2% viruses. Additionally, metagenomic profiles for both traditional and improved soil balls revealed that the various xenobiotic biodegradation, such as those for caprolactam, atrazine, xylene, toluene, styrene, bisphenol, and chlorocyclohexane might be responsible for organic waste cleanup.
Collapse
|
24
|
Khan AR, Park CE, Park GS, Seo YJ, So JH, Shin JH. The whole chloroplast genome sequence of black nightshade plant (Solanum nigrum). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:169-170. [PMID: 26709631 DOI: 10.3109/19401736.2015.1115494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, complete chloroplast genome of Solanum nigrum, a wild relative of potato and tomato being important for its medicinal features, was sequenced. The genome size is 154 671 bp in length, with 40% GC content. A pair of inverted repeats, IRa and IRSb, were separated by a large single-copy region and a small single-copy region of 82 315 bp and 33 411 bp, respectively. The genome harbored 73 protein-coding genes, 36 tRNA genes, and three rRNA genes. The evolutionary relationships in our phylogenetic analysis revealed that S. nigrum is closer to S. tuberosum when compared with those of known relatives' species belonging to Solanum genus.
Collapse
|
25
|
Park CE, Park GS, Kim MC, Kim KH, Park HC, Shin JH. The complete mitochondrial genome sequence of Kichulchoia multifasciata (Teleostei, Cypriniformes, Cobitidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:119-120. [PMID: 26709873 DOI: 10.3109/19401736.2015.1111350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Kichulchoia multifasciata (Teleostei, Cypriniformes, Cobitidae) is one of the loaches and is endemic to Korea. The complete mitochondrial genome sequence consisted of 16 569 base pairs (bp) encoding 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding region. The overall base composition of K. multifasciata was G + C: 42.5% and A + T: 57.5%, apparently with a slight AT bias. Phylogenetic analysis showed that K. multifasciata was closely related to Koreocobitis rotundicaudata.
Collapse
|