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Wang Q, Zhang L, Zhang Y, Chen H, Song J, Lyu M, Chen R, Zhang L. Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7. Front Microbiol 2022; 13:1008648. [PMID: 36419435 PMCID: PMC9677121 DOI: 10.3389/fmicb.2022.1008648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.
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Affiliation(s)
- Qian Wang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lei Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yiju Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianghua Song
- College of Horticulture, Anhui Agricultural University, Hefei, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lixin Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lixin Zhang,
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Agrawal S, Tipre D, Dave S. Biodegradation of Sulphonated Triazo Acid Black 210 Dye by Thermohalotolerant Bacillus pumilus SRS83: Kinetic, Metabolite and Toxicity Analysis. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Safara S, Harighi B, Bahramnejad B, Ahmadi S. Antibacterial Activity of Endophytic Bacteria Against Sugar Beet Root Rot Agent by Volatile Organic Compound Production and Induction of Systemic Resistance. Front Microbiol 2022; 13:921762. [PMID: 35722285 PMCID: PMC9201493 DOI: 10.3389/fmicb.2022.921762] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
The volatile organic compounds (VOCs) produced by endophytic bacteria have a significant role in the control of phytopathogens. In this research, the VOCs produced by the endophytic bacteria Streptomyces sp. B86, Pantoea sp. Dez632, Pseudomonas sp. Bt851, and Stenotrophomonas sp. Sh622 isolated from healthy sugar beet (Beta vulgaris) and sea beet (Beta maritima) were evaluated for their effects on the virulence traits of Bacillus pumilus Isf19, the causal agent of harvested sugar beet root rot disease. The gas chromatographymass spectrometry (GC-MS) analysis revealed that B86, Dez632, Bt851, and Sh622 produced 15, 28, 30, and 20 VOCs, respectively, with high quality. All antagonistic endophytic bacteria produced VOCs that significantly reduced soft root symptoms and inhibited the growth of B. pumilus Isf19 at different levels. The VOCs produced by endophytic bacteria significantly reduced swarming, swimming, and twitching motility by B. pumilus Isf19, which are important to pathogenicity. Our results revealed that VOCs produced by Sh622 and Bt851 significantly reduced attachment of B. pumilus Isf19 cells to sugar beetroots, and also all endophytic bacteria tested significantly reduced chemotaxis motility of the pathogen toward root extract. The VOCs produced by Dez632 and Bt851 significantly upregulated the expression levels of defense genes related to soft rot resistance. Induction of PR1 and NBS-LRR2 genes in sugar beetroot slices suggests the involvement of SA and JA pathways, respectively, in the induction of resistance against pathogen attack. Based on our results, the antibacterial VOCs produced by endophytic bacteria investigated in this study can reduce soft rot incidence.
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Affiliation(s)
- Somayeh Safara
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Behrouz Harighi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Bahman Bahramnejad
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Slahadin Ahmadi
- Department of Medical Physiology and Pharmacology, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
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Morgado-Gamero WB, Parody A, Medina J, Rodriguez-Villamizar LA, Agudelo-Castañeda D. Multi-antibiotic resistant bacteria in landfill bioaerosols: Environmental conditions and biological risk assessment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118037. [PMID: 34482243 DOI: 10.1016/j.envpol.2021.118037] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/31/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Landfills, as well as other waste management facilities are well-known bioaerosols sources. These places may foment antibiotic-resistance in bacterial bioaerosol (A.R.B.) due to inadequate pharmaceutical waste disposal. This issue may foster the necessity of using last-generation antibiotics with extra costs in the health care system, and deaths. The aim of this study was to reveal the multi-antibiotic resistant bacterial bioaerosol emitted by a sanitary landfill and the surrounding area. We evaluated the influence of environmental conditions in the occurrence of A.R.B. and biological risk assessment. Antibiotic resistance found in the bacteria aerosols was compared with the AWaRE consumption classification. We used the BIOGAVAL method to assess the workers' occupational exposure to antibiotic-resistant bacterial bioaerosols in the landfill. This study confirmed the multi-antibiotic resistant in bacterial bioaerosol in a landfill and in the surrounding area. Obtained mean concentrations of bacterial bioaerosols, as well as antibiotic-resistant in bacterial bioaerosol (A.R.B.), were high, especially for fine particles that may be a threat for human health. Results suggest the possible risk of antibiotic-resistance interchange between pathogenic and non-pathogenic species in the landfill facilities, thus promoting antibiotic multi-resistance genes spreading into the environment.
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Affiliation(s)
- Wendy B Morgado-Gamero
- Department of Exact and Natural Sciences, Universidad de la Costa, Calle 58#55-66, Barranquilla, Colombia.
| | - Alexander Parody
- Engineering Faculty, Universidad Libre Barranquilla, Cra 46 No. 48-170, Barranquilla, Colombia.
| | - Jhorma Medina
- Department of Exact and Natural Sciences, Universidad de la Costa, Calle 58#55-66, Barranquilla, Colombia.
| | | | - Dayana Agudelo-Castañeda
- Department of Civil and Environmental Engineering, Universidad del Norte, Km 5 via Puerto, Colombia.
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Fusini F, Colò G, Massè A, Girardo M. Uncommon cervical pain due by Bacillus pumilus spondylodiscitis in an immunocompetent patient: a case report. ACTA BIO-MEDICA : ATENEI PARMENSIS 2021; 92:e2021136. [PMID: 34747374 PMCID: PMC10523035 DOI: 10.23750/abm.v92is1.10189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/20/2020] [Indexed: 11/23/2022]
Abstract
A fifty-three year-old military patient, presented with a 3 months neck pain and paraesthesia of upper right extremity after gastroscopy. Radiological examination demonstrated anuncertain degenerative/infective involvement of C6-C7 intervertebral disc. The patient underwent anterior debridement with C5-C6 disc excisional biopsy, with microbiological findings of Bacillus pumilus with high bacterial concentration. After biopsy, segment arthrodesis was achieved only with vertebral plate cruentation and 3 months of cervical collar. He completed a six-weeks course of intravenous antibiotics for the treatment of atypical spondylodiscitis. At one year of follow-up, he had no residual neck pain or neurological signs or symptoms.
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Affiliation(s)
- Federico Fusini
- Department of Orthopaedic and Traumatology, Orthopaedic and Trauma Center, University of Turin, via Zuretti 29, 10121, Turin.
| | - Gabriele Colò
- Department of Orthopaedics and Traumatology, Regional Center for Joint Arthroplasty, ASO Alessandria, via Venezia 16, 16121 Alessandria, Italy..
| | - Alessandro Massè
- Department of Orthopaedic and Traumatology, Orthopaedic and Trauma Centre, Città della Salute e della Scienza di Torino, University of Turin, via Zuretti 29, 10121, Turin, Italy..
| | - Massimo Girardo
- Spine Surgery Unit, Orthopaedic and Trauma Centre, Città della Salute e della Scienza di Torino, University of Turin, via Zuretti 29, 10121, Turin, Italy..
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Husni AAA, Ismail SI, Jaafar NM, Zulperi D. Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches. THE PLANT PATHOLOGY JOURNAL 2021; 37:243-257. [PMID: 34111914 PMCID: PMC8200583 DOI: 10.5423/ppj.oa.02.2021.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus, were found not to be grouped with B. pumilus. However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis, whereas Cluster B consisted of three isolates attributed to B. safensis. This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.
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Affiliation(s)
- Ainur Ainiah Azman Husni
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Noraini Md. Jaafar
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Dzarifah Zulperi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Laboratory of Sustainable Resources Management, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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Fu Y, Liang L, Deng S, Wu Y, Yuan Y, Gao M. Novel spore lytic enzyme from a Bacillus phage leading to spore killing. Enzyme Microb Technol 2020; 142:109698. [PMID: 33220860 DOI: 10.1016/j.enzmictec.2020.109698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/03/2023]
Abstract
Bacterial spores maintain metabolic dormancy and have high resistance to external pressure. Germination requires degradation of the spore cortex and the participation of germination-specific cortex-lytic enzymes (GSLEs). Previously reported GSLEs have been identified in bacteria and facilitate germination. In this study, we have characterized a novel spore lytic enzyme, Ply67, from Bacillus pumilus phage vB_BpuM_BpSp. Ply67 had a similar cortex-lytic activity to GSLEs but disrupted the inner membranes (IMs) of spores, leading to spore killing rather than germination. The amino acid sequence of the complete protein, Ply67FL, exhibited 40% homology to the GSLE SleB. Domain prediction showed that Ply67FL was composed of three domains: a signal peptide, N-terminal domain protein and C-terminal domain protein. Ply67FL rapidly caused E. coli cells lysis when it was expressed in E. coli. The protein containing the C-terminal domain protein, Ply67C, could kill B. pumilus spores. The protein containing the N-terminal domain protein, Ply67N, could combine with the decoated B. pumilus spores, indicating that N-terminal was the binding domain and C-terminal was the hydrolase domain. The protein lacking the signal peptide but containing the N-terminal and C-terminal domain proteins, Ply67, had activity against spores of various Bacillus species. The surface of spores treated with Ply67 shrank and the permeability barrier was disrupted, and the inner contents leaked out. Immunoelectron microscopic observation showed that Ply67 was mainly acted on the spore cortex. Overall, Ply67 is a novel spore lytic enzyme that differs from other GSLEs not only in amino acid sequence but also in activity against spores, and Ply67 might have the potential to kill spores of pathogenic Bacillus species, e.g., B. cereus and B. anthracis.
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Affiliation(s)
- Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Leiqin Liang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Sangsang Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Yihui Yuan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, PR China.
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Kilic T, Coleri Cihan A. Biofilm Formation of the Facultative Thermophile Bacillus pumilus D194A and Affects of Sanitation Agents on Its Biofilms. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Stanisavljević N, Soković Bajić S, Jovanović Ž, Matić I, Tolinački M, Popović D, Popović N, Terzić-Vidojević A, Golić N, Beškoski V, Samardžić J. Antioxidant and Antiproliferative Activity of Allium ursinum and Their Associated Microbiota During Simulated in vitro Digestion in the Presence of Food Matrix. Front Microbiol 2020; 11:601616. [PMID: 33335521 PMCID: PMC7736176 DOI: 10.3389/fmicb.2020.601616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/09/2020] [Indexed: 12/29/2022] Open
Abstract
In this study, for the first time, the comprehensive analysis of antiproliferative and antioxidant activities of ramson, followed by the analysis of its associated microbiota and health-promoting effects of lactic acid bacteria (LAB), was performed. Ramson (Allium ursinum) is recognized as a medicinal plant with a long history of use in traditional medicine due to its antimicrobial and antioxidant activity. In this study the influence of in vitro gastrointestinal digestion on the cytotoxic activity of A. ursinum extracts against human malignant cell lines was demonstrated. Seven sulfur compounds, the degradation products of thiosulfinates, including diallyl disulfide were shown to inhibit proliferation of malignant cells by inducing accumulation within G2/M phase as well as to induce apoptosis through activation of caspase-3 and mitochondrial signaling pathway. Further, the A. ursinum microbiota, particularly LAB with potential probiotic effects, was analyzed by culture-dependent method and culture-independent method [denaturing gradient gel electrophoresis (DGGE)]. The obtained results revealed that the most abundant genera were Streptococcus, Lactobacillus, and Bacillus. The Lactobacillus genus was mainly represented by L. fermentum. The pulsed-field gel electrophoresis (PFGE) analysis revealed the presence of two PFGE pulsotypes. The probiotic potential of the strain L. fermentum BGSR163 belonging to PFGE pulsotype 1 and the strain L. fermentum BGSR227 belonging to the PFGE pulsotype 2 was characterized. The results revealed that both strains are safe for human use, successfully survive the simulated gastrointestinal conditions, have potential to transiently colonize the gastrointestinal tract (GIT) and have a protective immunomodulatory effect, inducing the production of proinflammatory cytokine IL17 and regulatory cytokine IL10, while decreasing the production of proinflammatory cytokine IFN-γ. In conclusion, the results of this study suggest that consumption of A. ursinum might have health-promoting properties, including anticancer effects, while L. fermentum strains isolated from A. ursinum leaves could be used as probiotics for human consumption.
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Affiliation(s)
- Nemanja Stanisavljević
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- *Correspondence: Nemanja Stanisavljević,
| | - Svetlana Soković Bajić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Živko Jovanović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ivana Matić
- Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Maja Tolinački
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Dušanka Popović
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nikola Popović
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Amarela Terzić-Vidojević
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nataša Golić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Jelena Samardžić
- Laboratory for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Yuan Y, Yu Q, Yang S, Wen J, Guo Z, Wang X, Wang N. Ultrafast Recovery of Uranium from Seawater by Bacillus velezensis Strain UUS-1 with Innate Anti-Biofouling Activity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900961. [PMID: 31559134 PMCID: PMC6755527 DOI: 10.1002/advs.201900961] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/29/2019] [Indexed: 05/05/2023]
Abstract
Highly-efficient recovery of uranium from seawater is of great concern in the growing demand for nuclear energy. Bacteria are thought to be potential alternatives for uranium recovery. Herein, a Bacillus velezensis strain, UUS-1, with highly-efficient uranium immobilization capacity is isolated and is used in the recovery of uranium from seawater. The strain exhibits time-dependent uranium recovery capacity and only immobilizes uranium after growing for 12 h. The carboxyl group together with the amino group inside the bacterial cells, but not previously identified phosphate group, are essential for uranium immobilization. UUS-1 shows broad-spectrum antimicrobial activity by producing diverse antimicrobial metabolites, which endows the strain with innate resistance to the biofouling of marine microorganisms. Based on the dry weight of the initially used bacterial cultures, UUS-1 concentrates uranium by 6.26 × 105 times and reaches the high immobilization capacity of 9.46 ± 0.39 mg U g-1 bacterial cultures in real seawater within 48 h, which is the fastest uranium immobilization capacity observed from real seawater. Overall considering the ultrafast and highly-efficient uranium recovery capacity and the innate anti-biofouling activity, UUS-1 is a promising alternative for uranium recovery from seawater.
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Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikou570228P. R. China
| | - Qiuhan Yu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikou570228P. R. China
| | - Shuo Yang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikou570228P. R. China
| | - Jun Wen
- Institute of Nuclear Physics and ChemistryChina Academy of Engineering PhysicsMianyang621900P. R. China
| | - Zhanhu Guo
- Integrated Composites Laboratory (ICL)Department of Chemical and Biomolecular EngineeringUniversity of TennesseeKnoxvilleTN37996USA
- College of Chemical and Environmental EngineeringShandong University of Science and TechnologyQingdao266590P. R. China
| | - Xiaolin Wang
- Institute of Nuclear Physics and ChemistryChina Academy of Engineering PhysicsMianyang621900P. R. China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikou570228P. R. China
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Morgado-Gamero WB, Mendoza Hernandez M, Castillo Ramirez M, Medina-Altahona J, De La Hoz S, Posso Mendoza H, Parody A, Teixeira EC, Agudelo-Castañeda DM. Antibiotic Resistance of Airborne Viable Bacteria and Size Distribution in Neonatal Intensive Care Units. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E3340. [PMID: 31510047 PMCID: PMC6765827 DOI: 10.3390/ijerph16183340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/08/2019] [Accepted: 05/16/2019] [Indexed: 12/16/2022]
Abstract
Despite their significant impact on public health, antibiotic resistance and size distributions of airborne viable bacteria in indoor environments in neonatal intensive care units (NICU) remain understudied. Therefore, the objective of this study was to assess the antibiotic resistance of airborne viable bacteria for different sizes (0.65-7 µm) in private-style and public-style neonatal intensive care units (NICU). Airborne bacteria concentrations were assessed by a six-stage Andersen impactor, operating at 28.3 L/min. Public-style NICU revealed higher concentrations of airborne viable bacteria (53.00 to 214.37 CFU/m3) than private-style NICU (151.94-466.43), indicating a possible threat to health. In the public-style NICU, Staphylococcus was the highest bacterial genera identified in the present study, were Staphylococcus saprophyticus and Staphylococcus epidermidis predominated, especially in the second bronchi and alveoli size ranges. Alloiococcus otitidis, Bacillus subtiles, Bacillus thuringiensis, Kocuria rosea, and Pseudomonas pseudoalcaligene, were identified in the alveoli size range. In NICU#2, eight species were identified in the alveoli size range: Bacillus cereus, Bacillus subtilis, Bacillus thuringiensis, Eikenella corrodens, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus gordoni. Multi-drug-resistant organisms (MDROs) were found in both of the NICUs. Bacillus cereus strains were resistant to Ampicillin, Cefoxitin, Ceftaroline, and Penicillin G. Staphylococcus cohnii ssp. cohnii was resistant in parallel to ampicillin and G penicillin. Staphylococcus saprophyticus strains were resistant to Ampicillin, Penicillin G, Oxaxilin, and Erythromycin. Results may indicate a potential threat to human health due to the airborne bacteria concentration and their antibiotic resistance ability. The results may provide evidence for the need of interventions to reduce indoor airborne particle concentrations and their transfer to premature infants with underdeveloped immune systems, even though protocols for visitors and cleaning are well-established.
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Affiliation(s)
- Wendy Beatriz Morgado-Gamero
- Department of Exact and Natural Sciences, Universidad de la Costa, Calle 58#55-66, Barranquilla 080002, Colombia.
| | - Martha Mendoza Hernandez
- Department of Civil and Environmental Engineering, Universidad del Norte, Km 5 Vía Puerto Colombia, Barranquilla 081007, Colombia.
| | | | - Jhorma Medina-Altahona
- Department of Exact and Natural Sciences, Universidad de la Costa, Calle 58#55-66, Barranquilla 080002, Colombia
| | - Stephanie De La Hoz
- Department of Exact and Natural Sciences, Universidad de la Costa, Calle 58#55-66, Barranquilla 080002, Colombia.
| | - Heidy Posso Mendoza
- Department of Bacteriology, Universidad Metropolitana, Calle 76 No. 42-78, Barranquilla 080020, Colombia.
| | - Alexander Parody
- Engineering Faculty, Universidad Libre Barranquilla, Carrera 46 No. 48-170, Barranquilla 080002, Colombia.
| | - Elba C Teixeira
- Postgraduate Program in Remote Sensing, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre, RS 91501-970, Brazil.
| | - Dayana Milena Agudelo-Castañeda
- Department of Civil and Environmental Engineering, Universidad del Norte, Km 5 Vía Puerto Colombia, Barranquilla 081007, Colombia.
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Yuan Y, Peng Q, Zhang S, Liu T, Yang S, Yu Q, Wu Y, Gao M. Phage Reduce Stability for Regaining Infectivity during Antagonistic Coevolution with Host Bacterium. Viruses 2019; 11:v11020118. [PMID: 30699954 PMCID: PMC6410104 DOI: 10.3390/v11020118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/15/2019] [Accepted: 01/28/2019] [Indexed: 12/19/2022] Open
Abstract
The coevolution between phage and host bacterium is an important force that drives the evolution of the microbial community, yet the coevolution mechanisms have still not been well analyzed. Here, by analyzing the interaction between a Bacillus phage vB_BthS_BMBphi and its host bacterium, the coevolution mechanisms of the first-generation phage-resistant bacterial mutants and regained-infectivity phage mutants were studied. The phage-resistant bacterial mutants showed several conserved mutations as a potential reason for acquiring phage resistance, including the mutation in flagellum synthesis protein FlhA and cell wall polysaccharide synthesis protein DltC. All the phage-resistant bacterial mutants showed a deleted first transmembrane domain of the flagellum synthesis protein FlhA. Meanwhile, the regain-infectivity phage mutants all contained mutations in three baseplate-associated phage tail proteins by one nucleotide, respectively. A polymorphism analysis of the three mutant nucleotides in the wild-type phage revealed that the mutations existed before the interaction of the phage and the bacterium, while the wild-type phage could not infect the phage-resistant bacterial mutants, which might be because the synchronized mutations of the three nucleotides were essential for regaining infectivity. This study for the first time revealed that the synergism mutation of three phage baseplate-associated proteins were essential for the phages’ regained infectivity. Although the phage mutants regained infectivity, their storage stability was decreased and the infectivity against the phage-resistant bacterial mutants was reduced, suggesting the phage realized the continuation of the species by way of “dying to survive”.
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Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Qin Peng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Shaowen Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Tingting Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Shuo Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Qiuhan Yu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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Yuan Y, Peng Q, Yang S, Zhang S, Fu Y, Wu Y, Gao M. Isolation of A Novel Bacillus thuringiensis Phage Representing A New Phage Lineage and Characterization of Its Endolysin. Viruses 2018; 10:v10110611. [PMID: 30404215 PMCID: PMC6266608 DOI: 10.3390/v10110611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 01/03/2023] Open
Abstract
Phages, the parasites of bacteria, are considered as a new kind of antimicrobial agent due to their ability to lyse pathogenic bacteria. Due to the increase of available phage isolates, the newly isolated phage showed increasing genomic similarities with previously isolated phages. In this study, the novel phage vB_BthS_BMBphi, infecting the Bacillus thuringiensis strain BMB171, is isolated and characterized together with its endolysin. This phage is the first tadpole-like phage infecting the Bacillus strains. Genomic analysis shows that the phage genome is dissimilar to all those of previously characterized phages, only exhibiting low similarities with partial regions of the B. thuringiensis prophages. Phylogenetic analysis revealed that the phage was distant from the other Bacillus phages in terms of evolution. The novel genome sequence, the distant evolutionary relationship, and the special virion morphology together suggest that the phage vB_BthS_BMBphi could be classified as a new phage lineage. The genome of the phage is found to contain a restriction modification system, which might endow the phage with immunity to the restriction modification system of the host bacterium. The function of the endolysin PlyBMB encoded by the phage vB_BthS_BMBphi was analyzed, and the endolysin could lyse all the tested Bacillus cereus group strains, suggesting that the endolysin might be used in controlling pathogenic B. cereus group strains. The findings of this study enrich the understanding of phage diversity and provide a resource for controlling the B. cereus group pathogenic bacteria.
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Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Qin Peng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Shuo Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Shaowen Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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Peng Q, Yuan Y. Characterization of a novel phage infecting the pathogenic multidrug-resistant Bacillus cereus and functional analysis of its endolysin. Appl Microbiol Biotechnol 2018; 102:7901-7912. [PMID: 30008020 DOI: 10.1007/s00253-018-9219-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/24/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023]
Abstract
Bacillus cereus is widely distributed food-borne pathogenic bacterium. Due to the harmness to human hearth and the generation of multidrug-resistant B. cereus, it is urgent to develop novel antimicrobial agents. Phage and phage endolysin were taken as novel antimicrobial substance for their specific lytic activity against pathogenic bacteria. In this study, a Myoviridae family phage, designated as vB_BceM-HSE3, infecting the pathogenic multidrug-resistant B. cereus strain was isolated and characterized along with its endolysin. Phage vB_BceM-HSE3 can specially infect the B. cereus group strains, including B. cereus, B. anthracis, and B. thuringiensis, and exhibits high temperature and pH tolerance, which endow it with high potential for been used in controlling pathogenic B. cereus group strains. Genomic analysis reveals that vB_BceM-HSE3 is a novel phage and only shows extremely low genome similarity with available phage genome. Functional analysis of endolysin PlyHSE3 encoding by vB_BceM-HSE3 shows that PlyHSE3 exhibits broader lytic spectrum than the phage and can lyse all the tested B. cereus group strains as well as the tested pathogenic strain of P. aeruginosa. PlyHSE3 also shows broad temperature and pH tolerance, and can efficiently lyse B. cereus strain at temperature at 4 °C and higher than 45 °C, which indicating that PlyHSE3 might can be used in controlling food-borne B. cereus during both the cold storage of food and the stage after the heat treatment of food. The findings of this study enrich our understanding of phage diversity as well as providing resources for developing phage therapy.
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Affiliation(s)
- Qin Peng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, People's Republic of China
| | - Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
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Adedeji BS, Ezeokoli OT, Ezekiel CN, Obadina AO, Somorin YM, Sulyok M, Adeleke RA, Warth B, Nwangburuka CC, Omemu AM, Oyewole OB, Krska R. Bacterial species and mycotoxin contamination associated with locust bean, melon and their fermented products in south-western Nigeria. Int J Food Microbiol 2017; 258:73-80. [DOI: 10.1016/j.ijfoodmicro.2017.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/06/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022]
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16
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Yuan Y, Gao M. Characteristics and complete genome analysis of a novel jumbo phage infecting pathogenic Bacillus pumilus causing ginger rhizome rot disease. Arch Virol 2016; 161:3597-3600. [PMID: 27619796 DOI: 10.1007/s00705-016-3053-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/05/2016] [Indexed: 01/22/2023]
Abstract
Tailed phages with genomes larger than 200 kbp are classified as jumbo phage and exhibit extremely high diversity. In this study, a novel jumbo phage, vB_BpuM_BpSp, infecting pathogenic Bacillus pumilus, the cause of ginger rhizome rot disease, was isolated. Notable features of phage vB_BpuM_BpSp are the large phage capsid of 137 nm and baseplate-attached curly tail fibers. The genome of the phage is 255,569 bp in size with G+C content of 25.9 %, and it shows low similarity to known biological entities. The phage genome contains 318 predicted coding sequences. Among these predicted coding sequences, 26 genes responsible for nucleotide metabolism were found, and seven structural genes could be identified. The findings of this study provide new understanding of the genetic diversity of phages.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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Stepanov VG, Tirumalai MR, Montazari S, Checinska A, Venkateswaran K, Fox GE. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation. PLoS One 2016; 11:e0157331. [PMID: 27351589 PMCID: PMC4924849 DOI: 10.1371/journal.pone.0157331] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
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Affiliation(s)
- Victor G. Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Aleksandra Checinska
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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Viaene T, Langendries S, Beirinckx S, Maes M, Goormachtig S. Streptomycesas a plant's best friend? FEMS Microbiol Ecol 2016; 92:fiw119. [DOI: 10.1093/femsec/fiw119] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2016] [Indexed: 11/14/2022] Open
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Genome Sequence of Bacillus pumilus Strain Bonn, Isolated from an Anthrax-Like Necrotic Skin Infection Site of a Child. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01741-15. [PMID: 26868410 PMCID: PMC4751334 DOI: 10.1128/genomea.01741-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Bacillus pumilus strain Bonn associated with human skin infection. B. pumilus Bonn was isolated from a carbuncle-like necrotic site, resembling cutaneous anthrax, on the back of the hand of a 10-year-old child.
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