1
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Yang L, Cai J, Qian H, Li Y, Zhang H, Qi X, Wang L, Cao G. Effect of cyclodextrin glucosyltransferase extracted from Bacillus xiaoxiensis on wheat dough and bread properties. Front Nutr 2022; 9:1026678. [PMID: 36386911 PMCID: PMC9664062 DOI: 10.3389/fnut.2022.1026678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/04/2022] [Indexed: 11/25/2022] Open
Abstract
In this study, the cyclodextrin glucosyltransferase (CGTase) was extracted from Bacillus xiaoxiensis. CGTase had negative effects on dough viscoelastic properties and gluten strength but had positive effects on bread baking qualities and anti-staling properties. Adding an appropriate amount of CGTase (less than 0.3 U/g) could improve the specific volume, crumb texture, crust color, moisture content, and crumb hardness of bread. The bread crumb with 0.4 U/g CGTase (based on flour weight) had the lowest retrogradation enthalpy of 0.53 ± 0.10 J/g and the lowest relative crystallinity of 16.1%, which indicated the alleviating effect of amylopectin crystallization. Moreover, CGTase reduced the moisture from forming crystal lattices and limited starch molecule migration. The T2 transverse relaxation results showed that the increase of immobilized water content in the bread with CGTase was lower than the control after 5 days of storage, which implied the water-holding capacity of the bread was enhanced and provided information on the inhibition of water migration. Hence, the CGTase could be a potential bread improver.
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Affiliation(s)
- Lianzhan Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jinxin Cai
- Lingquegu Biotechnology Co., Ltd., Quanzhou, China
| | - Haifeng Qian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hui Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiguang Qi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Li Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China,*Correspondence: Li Wang,
| | - Guoliang Cao
- Jiangsu Daddy Sweety Food Technology Co., Ltd., Wuxi, China,Guoliang Cao,
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2
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Liu ZX, Chen JH, Yang LL, Feng YZ, Deng LY, He JW, Tang SK, Chen YG. Halomonas faecis sp. nov., a halophilic bacterium isolated from human faeces. Extremophiles 2022; 26:20. [PMID: 35716203 DOI: 10.1007/s00792-022-01269-w] [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: 04/07/2022] [Accepted: 05/12/2022] [Indexed: 02/05/2023]
Abstract
A novel moderately halophilic, Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-sporulating, non-motile rod, designated strain JSM 104105 T, was isolated from human faeces. Strain JSM 104105 T was able to grow with 0.5-18% (w/v) NaCl (optimum 4-9%), at pH 6-10.5 (optimum pH 7-8) and at 10-40 °C (optimum 30 °C) in complex media. The major cellular fatty acids were C18:1ω7c, C16:0, C16:1ω7c and/or C16:1ω6c, C19:0 cyclo ω8c and C12:0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid and three unidentified phospholipids. The predominant respiratory quinone was Q-9 and the genomic DNA G + C content was 64.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 104105 T should be assigned to the genus Halomonas, and was most closely related to Halomonas gudaonensis SL014B-69 T (99.0% sequence similarity), followed by Halomonas azerbaijanica TBZ202T (98.6%) and Halomonas lysinitropha 3(2)T (97.3%). The whole genomic analysis showed that strain JSM 104105 T constituted a different taxon separated from the recognized Halomonas species. Combined data from phenotypic and genotypic studies demonstrated that strain JSM 104105 T represents a new species of the genus Halomonas, for which the name Halomonas faecis sp. nov. is proposed. The type strain is JSM 104105 T (= CCTCC AB 2014160 T = CGMCC 1.12945 T = KCTC 42146 T).
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Affiliation(s)
- Zhu-Xiang Liu
- College of Biology and Environmental Sciences, Jishou University, No.120, South Renmin Road, Jishou, 416000, China
| | - Jin-Hua Chen
- College of Biology and Environmental Sciences, Jishou University, No.120, South Renmin Road, Jishou, 416000, China.
| | - Ling-Ling Yang
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
| | - Yu-Zhou Feng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610065, China
| | - Li-Ying Deng
- College of Biology and Environmental Sciences, Jishou University, No.120, South Renmin Road, Jishou, 416000, China
| | - Jian-Wu He
- College of Biology and Environmental Sciences, Jishou University, No.120, South Renmin Road, Jishou, 416000, China
| | - Shu-Kun Tang
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
| | - Yi-Guang Chen
- College of Biology and Environmental Sciences, Jishou University, No.120, South Renmin Road, Jishou, 416000, China.
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3
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Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Corrigendum: Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera. Front Microbiol 2022; 13:871596. [PMID: 35401476 PMCID: PMC8988803 DOI: 10.3389/fmicb.2022.871596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
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4
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Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera. Front Microbiol 2021; 12:722369. [PMID: 34707580 PMCID: PMC8543038 DOI: 10.3389/fmicb.2021.722369] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199T) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, and iso-C17:0. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199T. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199T belonged to the family Bacillaceae and exhibited a distinctive position among the members of the genus Alkalihalobacillus (Ahb.). Strain MEB199T shared the highest 16S rRNA gene sequence similarity with Alkalihalobacillus alkalinitrilicus ANL-iso4T (98.36%), whereas with type species Ahb. alcalophilus DSM 485T, it is 94.91%, indicating that strain MEB199T is distinctly related to the genus Alkalihalobacillus. The G + C content of genomic DNA was 36.47 mol%. The digital DNA-DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199T and Ahb. alkalinitrilicus ANL-iso4T confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus Alkalihalobacillus ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus Alkalihalobacillus separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus Alkalihalobacillus. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus Alkalihalobacillus into seven new genera for which the names Alkalihalobacterium gen. nov., Halalkalibacterium gen. nov., Halalkalibacter gen. nov., Shouchella gen. nov., Pseudalkalibacillus gen. nov., Alkalicoccobacillus gen. nov., and Alkalihalophilus gen. nov. are proposed and provide an emended description of Alkalihalobacillus sensu stricto. Also, we propose the Ahb. okuhidensis as a heterotypic synonym of Alkalihalobacillus halodurans. Based on the polyphasic taxonomic analysis, strain MEB199T represents a novel species of newly proposed genus for which the name Alkalihalobacterium elongatum gen. nov. sp. nov. is proposed. The type strain is MEB199T (= MCC 2982T, = JCM 33704T, = NBRC 114256T, = CGMCC 1.17254T).
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Affiliation(s)
- Amaraja Joshi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Sonia Thite
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Prachi Karodi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Neetha Joseph
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
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5
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Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406-438. [PMID: 31617837 DOI: 10.1099/ijsem.0.003775] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.
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Affiliation(s)
- Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
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6
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Wu QL, Chen JH, Deng LY, Liu ZX, He JW, Liu ZX, Yang LL, Tang SK, Chen YG. Sediminibacillus terrae sp. nov., a moderate halophile isolated from non-saline farm soil. Int J Syst Evol Microbiol 2019; 70:1139-1144. [PMID: 31751198 DOI: 10.1099/ijsem.0.003892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, moderately halophilic, strictly aerobic, endospore-forming, rod-shaped bacterium, strain JSM 102062T, was isolated from a non-saline farm soil sample collected from Dehang Canyon in Hunan, PR China. Growth occurred with 0.5-20 % (w/v) NaCl (optimum 4-7 %) at pH 5.5-11.0 (optimum pH 8.0) and at 20-50 °C (optimum 30-35 °C). Contained cell-wall peptidoglycan based on meso-diaminopimelic acid and possessed menaquinone-7 (MK-7) as the major respiratory isoprenoid quinone. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, five unidentified phospholipids and an unidentified glycolipid. The DNA G+C content was 44.1 mol%. Phylogeny based on 16S rRNA gene sequences indicated that strain JSM 102062T belonged to the genus Sediminibacillus, sharing high 16S rRNA gene sequence similarities to Sediminibacillus halophilus EN8dT (99.4 %) and Sediminibacillus albus NHBX5T (98.3 %). The whole genomic analysis showed that strain JSM 102062T constituted a different taxon separated from the recognized Sediminibacillus species. Combined data from phenotypic and genotypic studies demonstrated that strain JSM 102062T represents a noval species of the genus Sediminibacillus, for which the name Sediminibacillus terrae sp. nov. is proposed; the type strain is JSM 102062T (=CCTCC AB 2014166T = CGMCC 1.12957T=DSM 28949T=KCTC 33541T).
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Affiliation(s)
- Qiu-Lei Wu
- National & Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Jin-Hua Chen
- National & Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Li-Ying Deng
- National & Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Zhi-Xiong Liu
- National & Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Jian-Wu He
- National & Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Zhu-Xiang Liu
- National & Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
| | - Ling-Ling Yang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yi-Guang Chen
- National & Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, PR China
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7
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Fredsgaard C, Moore DB, Chen F, Clark BC, Schneegurt MA. Prevalence of sucretolerant bacteria in common soils and their isolation and characterization. Antonie Van Leeuwenhoek 2017; 110:995-1005. [PMID: 28409237 PMCID: PMC5511755 DOI: 10.1007/s10482-017-0873-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
Sucretolerant microbes grow in the presence of sugar concentrations high enough to substantially lower water activities. Natural habitats high in sugars are mainly limited to dried fruit, floral nectar, honey, sugarcane, and associated soils. Organisms that tolerate extremes of solute concentration, high enough to lower water activities, might not be expected in common oligoosmotic soils. We report on the isolation of sucretolerant bacteria from common soils using media supplemented with 50% sucrose (a w 0.91) and their physiological characterization and identification by 16S rRNA gene phylogeny. Fifteen of these sucretolerant isolates from common soils were related to four Bacillus spp. A Lysinibacillus and a Microbacterium (actinomycete) also were collected. All grew at 50% sucrose and 13 grew at 60% sucrose. Most probable number counts were used to determine the abundance of sucretolerant microbes in several common soil types, including agricultural, managed turf, and native prairie. Microbial abundance (with fungicides) was about 105 and 103 cells g-1 soil in media containing 50 or 70% sucrose, respectively. The abundances of sucretolerant bacteria in common soils mirror those of halotolerant bacteria that grow at 10 and 20% NaCl. However, there is not a correlation between halotolerance and sucretolerance in our isolates, nor can predictions be made based on taxonomy. Specific solute effects may be at work, rather than biological responses to a single physicochemical parameter such as a w. The occurrence of spore-forming sucretolerant bacteria in common soils has relevance to forward planetary protection and astrobiology. Extraterrestrial habitable regions are defined in part by tolerance to high solute concentrations and osmotolerant soil microbes may contaminate spacecraft.
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Affiliation(s)
- Casper Fredsgaard
- Department of Biological Sciences, Wichita State University, 1845 Fairmount, Wichita, KS, 67260, USA
| | - Donald B Moore
- Department of Biological Sciences, Wichita State University, 1845 Fairmount, Wichita, KS, 67260, USA
| | - Fei Chen
- Planetary Protection Group, Jet Propulsion Laboratory, NASA, Pasadena, CA, USA
| | | | - Mark A Schneegurt
- Department of Biological Sciences, Wichita State University, 1845 Fairmount, Wichita, KS, 67260, USA.
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8
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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9
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Barbosa TM, Phelan RW, Leong D, Morrissey JP, Adams C, Dobson ADW, O’Gara F. A novel erythromycin resistance plasmid from Bacillus sp. strain HS24, isolated from the marine sponge Haliclona simulans. PLoS One 2014; 9:e115583. [PMID: 25548909 PMCID: PMC4280177 DOI: 10.1371/journal.pone.0115583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/01/2014] [Indexed: 11/19/2022] Open
Abstract
A better understanding of the origin and natural reservoirs of resistance determinants is fundamental to efficiently tackle antibiotic resistance. This paper reports the identification of a novel 5.8 kb erythromycin resistance plasmid, from Bacillus sp. HS24 isolated from the marine sponge Haliclona simulans. pBHS24B has a mosaic structure and carries the erythromycin resistance gene erm(T). This is the first report of an erythromycin resistance plasmid from a sponge associated bacteria and of the Erm(T) determinant in the genus Bacillus.
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Affiliation(s)
| | - Robert W. Phelan
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
| | - Dara Leong
- Department of Microbiology, University College Cork, Cork, Ireland
| | - John P. Morrissey
- Department of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Claire Adams
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- Department of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Fergal O’Gara
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
- Curtin University, School of Biomedical Sciences, Perth WA 6845, Australia
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10
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Bacillus lonarensis sp. nov., an alkalitolerant bacterium isolated from a soda lake. Arch Microbiol 2014; 197:27-34. [DOI: 10.1007/s00203-014-1040-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/30/2014] [Accepted: 09/25/2014] [Indexed: 11/27/2022]
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Liu B, Liu GH, Sengonca C, Schumann P, Wang MK, Tang JY, Chen MC. Bacillus cihuensis sp. nov., isolated from rhizosphere soil of a plant in the Cihu area of Taiwan. Antonie van Leeuwenhoek 2014; 106:1147-55. [DOI: 10.1007/s10482-014-0284-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 09/11/2014] [Indexed: 11/25/2022]
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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13
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Zhao F, Feng YZ, Chen RR, Zhang HY, Wang JH, Lin XG. Bacillus fengqiuensis sp. nov., isolated from a typical sandy loam soil under long-term fertilization. Int J Syst Evol Microbiol 2014; 64:2849-2856. [PMID: 24871777 DOI: 10.1099/ijs.0.063081-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, endospore-forming, moderately alkaliphilic bacterium, strain NPK15(T), was isolated from a typical sandy loam soil under long-term NPK fertilization in northern China and was subjected to a polyphasic taxonomic study. The diamino acid of the cell-wall peptidoglycan of strain NPK15(T) was found to be meso-diaminopimelic acid and the cell-wall sugars were xylose, glucose and traces of mannose. The only respiratory quinone found in strain NPK15(T) was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0), C(16 : 0) and C(16 : 1)ω6c/C(16 : 1)ω7c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis of the strain based on its 16S rRNA gene sequence showed that it was related most closely to 'Bacillus thaonhiensis' KACC 17216 (99.59%), B. songklensis KCTC 13881(T) (99.52%) and B. abyssalis CCTCC AB 2012074(T) (99.00%). DNA-DNA hybridization results indicated that the strain was distinct from other species of the genus Bacillus, the degree of relatedness being 35.4% with B. abyssalis CCTCC AB 2012074(T), 39.7% with B. songklensis KCTC 13881(T) and 51.2% with 'B. thaonhiensis' KACC 17216. The DNA G+C content of strain NPK15(T) was 45.5 mol%. Phenotypic, chemotaxonomic and molecular analyses identified strain NPK15(T) as a member of a novel species of the genus Bacillus, for which the name Bacillus fengqiuensis sp. nov. is proposed. The type strain is NPK15(T) ( = DSM 26745(T) = CCTCC AB 2013156(T)).
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Affiliation(s)
- Fei Zhao
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - You-Zhi Feng
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Rui-Rui Chen
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Hua-Yong Zhang
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Jun-Hua Wang
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xian-Gui Lin
- Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University & Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
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Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00211-14. [PMID: 24652985 PMCID: PMC3961732 DOI: 10.1128/genomea.00211-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus strains JCM 19045, JCM 19046, and JCM 19047 are alkaliphiles that produce β-cyclodextrin from starch. They are related to Bacillus xiaoxiensis and Bacillus lehensis. The genome information for these three strains will be useful for studies of the physiological role of cyclodextrin and cyclodextrin production.
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Lei Z, Qiu P, Ye R, Tian J, Liu Y, Wang L, Tang SK, Li WJ, Tian Y. Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. J GEN APPL MICROBIOL 2014. [DOI: 10.2323/jgam.60.101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013; 10:996-998. [PMID: 23955772 DOI: 10.1007/978-3-319-44409-3_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 07/15/2013] [Indexed: 05/20/2023]
Abstract
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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Liu YJ, Long LJ, Huang XF, You ZQ, Wang FZ, Li J, Kim CJ, Tian XP, Zhang S. Bacillus oceani sp. nov., a new slightly halophilic bacterium, isolated from a deep sea sediment environment. Antonie van Leeuwenhoek 2013; 104:829-36. [PMID: 23934481 DOI: 10.1007/s10482-013-9995-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
Abstract
A strictly aerobic, Gram-stain positive, slightly halophilic strain, designated SCSIO 04524(T), was isolated from a deep sea sediment sample collected from the northern South China Sea at a depth of 3415 m. The isolate slightly embedded into the medium after 72 h incubation at 30 °C. Growth was found to occur on media with 0-10 % NaCl but extremely weak growth occurred without supplying NaCl. The predominant menaquinone was determined to be MK-7. The major cellular fatty acid identified was iso-C15:0. The diagnostic polar lipids were determined to be diphosphatidylglycerol, phosphatidyl methylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content was determined to be 38 mol%. 16S rRNA gene sequences analysis showed that this strain had the highest similarities with Bacillus carboniphilus JCM 9731(T) (94.7 %) and Bacillus endophyticus 2DT(T) (94.3 %). Phylogenetic analysis revealed that strain SCSIO 04524(T) formed a distinct lineage with Bacillus chungangensis CAU 348(T) and B. carboniphilus JCM 9731(T). Physiological characteristics including utilization of sole nitrogen and carbon sources, and chemotaxonomic properties of cellular fatty acids and polar lipids could readily distinguish strain SCSIO 04524(T) from its most closely related species. Based on this polyphasic taxonomic data, a new species, Bacillus oceani sp. nov., is proposed, with the type strain SCSIO 04524(T) (=DSM 26213(T) = KCTC 33077(T)).
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Affiliation(s)
- Yu-Juan Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, CAS, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
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Chen QH, Chen JH, Ruan Y, Zhang YQ, Tang SK, Liu ZX, Li WJ, Chen YG. Sphingomonas hunanensis sp. nov., isolated from forest soil. Antonie van Leeuwenhoek 2011; 99:753-60. [DOI: 10.1007/s10482-011-9549-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
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