Review
- Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis
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Anyeseu Park, Chanhee Lee, Jeong Yoon Lee
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J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024
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DOI: https://doi.org/10.1007/s12275-024-00112-5
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Abstract
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Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.
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- In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef
Journal Articles
- Effects of Feather Hydrolysates Generated by Probiotic Bacillus licheniformis WHU on Gut Microbiota of Broiler and Common carp
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Kamin Ke, Yingjie Sun, Tingting He, Wenbo Liu, Yijiao Wen, Siyuan Liu, Qin Wang, Xiaowei Gao
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J. Microbiol. 2024;62(6):473-487. Published online February 29, 2024
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DOI: https://doi.org/10.1007/s12275-024-00118-z
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76
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Abstract
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Due to the ever-increasing demand for meat, it has become necessary to identify cheap and sustainable sources of protein for animal feed. Feathers are the major byproduct of poultry industry, which are rich in hard-to-degrade keratin protein.
Previously we found that intact feathers can be digested into free amino acids, short peptides, and nano-/micro-keratin particles by the strain Bacillus licheniformis WHU in water, and the resulting feather hydrolysates exhibit prebiotic effects on mice. To explore the potential utilization of feather hydrolysate in the feed industry, we investigated its effects on the gut microbiota of broilers and fish. Our results suggest that feather hydrolysates significantly decrease and increase the diversity of gut microbial communities in broilers and fish, respectively. The composition of the gut microbiota was markedly altered in both of the animals. The abundance of bacteria with potentially pathogenic phenotypes in the gut microbial community of the fish significantly decreased. Staphylococcus spp., Pseudomonas spp., Neisseria spp., Achromobacter spp. were significantly inhibited by the feather hydrolysates. In addition, feather hydrolysates significantly improved proteolytic activity in the guts of broilers and fish. In fish, the expression levels of ZO-1 and TGF-α significantly improved after administration of feather hydrolysates. The results presented here suggest that feather hydrolysates generated by B. licheniformis WHU could be an alternative protein source in aquaculture and could exert beneficial effects on fish.
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- Keratinous bioresources: their generation, microbial degradation, and value enhancement for biotechnological applications
Vijan Lal Vikash, Numbi Ramudu Kamini, Ganesan Ponesakki, Suresh Kumar Anandasadagopan
World Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef
- The inability of Bacillus licheniformis perR mutant to grow is mainly due to the lack of PerR-mediated fur repression
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Jung-Hoon Kim , Yoon-Mo Yang , Chang-Jun Ji , Su-Hyun Ryu , Young-Bin Won , Shin-Yeong Ju , Yumi Kwon , Yeh-Eun Lee , Hwan Youn , Jin-Won Lee
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J. Microbiol. 2017;55(6):457-463. Published online April 22, 2017
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DOI: https://doi.org/10.1007/s12275-017-7051-x
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81
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Abstract
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PerR, a member of Fur family protein, is a metal-dependent H2O2 sensing transcription factor that regulates genes in-volved in peroxide stress response. Industrially important bac-terium Bacillus licheniformis contains three PerR-like pro-teins (PerRBL, PerR2, and PerR3) compared to its close rela-tive Bacillus subtilis. Interestingly, unlike other bacteria in-cluding B. subtilis, no authentic perRBL null mutant could be established for B. licheniformis. Thus, we constructed a con-ditional perRBL mutant using a xylose-inducible promoter, and investigated the genes under the control of PerRBL. PerRBL regulon genes include katA, mrgA, ahpC, pfeT, hemA, fur, and perR as observed for PerRBS. However, there is some variation in the expression levels of fur and hemA genes be-tween B. subtilis and B. licheniformis in the derepressed state. Furthermore, katA, mrgA, and ahpC are strongly induced, whereas the others are only weakly or not induced by H2O2 treatment. In contrast to the B. subtilis perR null mutant which frequently gives rise to large colony phenotype mainly due to the loss of katA, the suppressors of B. licheniformis perR mutant, which can form colonies on LB agar, were all cata-lase-positive. Instead, many of the suppressors showed in-creased levels of siderophore production, suggesting that the suppressor mutation is linked to the fur gene. Consistent with this, perR fur double mutant could grow on LB agar without Fe supplementation, whereas perR katA double mutant could only grow on LB agar with Fe supplementation. Taken toge-ther, our data suggest that in B. licheniformis, despite the si-milarity in PerRBL and PerRBS regulon genes, perR is an essen-tial gene required for growth and that the inability of perR null mutant to grow is mainly due to elevated expression of Fur.
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Citations
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Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from
Bacillus thuringiensis
Lu Liu, Dehua Luo, Yongji Zhang, Dingqi Liu, Kang Yin, Qing Tang, Shan-Ho Chou, Jin He, Beile Gao
Microbiology Spectrum.2024;[Epub] CrossRef - Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs
Caroline H. Steingard, John D. Helmann, Tina M. Henkin
Journal of Bacteriology.2023;[Epub] CrossRef - Divergent Effects of Peptidoglycan Carboxypeptidase DacA on Intrinsic β-Lactam and Vancomycin Resistance
Si Hyoung Park, Umji Choi, Su-Hyun Ryu, Han Byeol Lee, Jin-Won Lee, Chang-Ro Lee, Krisztina M. Papp-Wallace
Microbiology Spectrum.2022;[Epub] CrossRef - Microbial Redox Regulator-Enabled Pulldown for Rapid Analysis of Plasma Low-Molecular-Weight Biothiols
Jin Oh Lee, Yoon-Mo Yang, Jae-Hoon Choi, Tae-Wuk Kim, Jin-Won Lee, Young-Pil Kim
Analytical Chemistry.2019; 91(15): 10064. CrossRef - Redox Sensing by Fe2+in Bacterial Fur Family Metalloregulators
Azul Pinochet-Barros, John D. Helmann
Antioxidants & Redox Signaling.2018; 29(18): 1858. CrossRef
Research Support, Non-U.S. Gov'ts
- NOTE] Isolation and Characterization of Histamine-Producing Bacteria from Fermented Fish Products
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Jin Seok Moon , So-Young Kim , Kyung-Ju Cho , Seung-Joon Yang , Gun-Mook Yoon , Hyun-Ju Eom , Nam Soo Han
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J. Microbiol. 2013;51(6):881-885. Published online December 19, 2013
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DOI: https://doi.org/10.1007/s12275-013-3333-0
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51
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Abstract
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Histamine is mainly produced by microorganisms that are
found in fermented foods, and is frequently involved in food
poisoning. Two histamine-producing bacteria were isolated
from fermented fish products, anchovy sauce, and sand lance
sauce by using a histidine decarboxylating medium. The
species were identified as Bacillus licheniformis A7 and B.
coagulans SL5. Multiplex PCR analysis showed the presence
of the conserved histidine decarboxylase (hdc) gene in the
chromosome of these bacteria. B. licheniformis A7 and B.
coagulans SL5 produced the maximum amount of histamine
(22.3±3.5 and 15.1±1.5 mg/L, respectively). As such, they
were determined to be potential histamine-producing bacteria
among the tested cultures.
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- Low salt and biogenic amines fermented fish sauce (Mahyaveh) as potential functional food and ingredient
Hoda Ghayoomi, Mohammad Bagher Habibi Najafi, Mohammad Reza Edalatian Dovom, Amir Pourfarzad
LWT.2023; 182: 114801. CrossRef - Histamine-degrading halophilic bacteria from traditional fish sauce: Characterization of Virgibacillus campisalis TT8.5 for histamine reduction
Thi Thu Hang Tran, Thi Phuong Anh Nguyen, Thi Diu Pham, Thi Hong Nguyen, Thi Lam Doan Nguyen, Thi Thanh Thuy Nguyen, Thi Lan Huong Tran, Trung Khoa Giang, Thi Thu Hien Bui, Bien-Cuong Do, Tien-Thanh Nguyen, Dietmar Haltrich, Hoang Anh Nguyen
Journal of Biotechnology.2023; 366: 46. CrossRef - Detection, Identification, and Inactivation of Histamine-forming Bacteria in Seafood: A Mini-review
Daniel Lance Nevado, Sophia Delos Santos, Gelian Bastian, Jimson Deyta, El-jay Managuelod, Jamil Allen Fortaleza, Rener De Jesus
Journal of Food Protection.2023; 86(3): 100049. CrossRef - Influence of polyamine production and proteolytic activities of co-cultivated bacteria on histamine production by Morganiella morganii
Suma Devivilla, Manjusha Lekshmi, Fathima Salam, Sanath Kumar H, Rajendran Kooloth Valappil, Sibnarayan Dam Roy, Binaya Bhusan Nayak
The Journal of General and Applied Microbiology.2022; 68(5): 213. CrossRef - Isolation and Identification of Aroma-producing Yeast from Mackerel Fermentation Broth and Its Fermentation Characteristics
Yu Wu, Xiao’e Chen, Xubo Fang, Lili Ji, Fang Tian, Hui Yu, Yan Chen
Journal of Aquatic Food Product Technology.2021; 30(10): 1264. CrossRef - Effect of fermentation by Aspergillus oryzae on the biochemical and sensory properties of anchovy (Engraulis japonicus) fish sauce
Jianan Sun, Xiaohang Yu, Bohuan Fang, Lei Ma, Changhu Xue, Zhaohui Zhang, Xiangzhao Mao
International Journal of Food Science & Technology.2016; 51(1): 133. CrossRef - Characterization of Tryptamine-Producing Bacteria Isolated from Commercial Salted and Fermented Sand Lance Ammodytes personatus Sauces
In-Seon Um, Tae-Ok Kim, Hee-Dai Kim, Kwon-Sam Park
Korean Journal of Fisheries and Aquatic Sciences.2016; 49(6): 792. CrossRef - Relationship between chemical characteristics and bacterial community of a Korean salted-fermented anchovy sauce, Myeolchi-Aekjeot
Hae-Won Lee, Yun-Jeong Choi, In Min Hwang, Sung Wook Hong, Mi-Ai Lee
LWT.2016; 73: 251. CrossRef - Isolation and Characterization of Putrescine-producing Bacteria in Commercially Available Sauces Made from Salted and Fermented Sand Lance Ammodytes personatus
In-Seon Um, Tae-Ok Kim, Kwon-Sam Park
Korean Journal of Fisheries and Aquatic Sciences.2016; 49(5): 573. CrossRef
- Detailed Modes of Action and Biochemical Characterization of endo-Arabinanase from Bacillus licheniformis DSM13
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Jung-Mi Park , Myoung-Uoon Jang , Jung-Hyun Kang , Min-Jeong Kim , So-Won Lee , Yeong Bok Song , Chul-Soo Shin , Nam Soo Han , Tae-Jip Kim
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J. Microbiol. 2012;50(6):1041-1046. Published online December 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-2489-3
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43
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Abstract
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An endo-arabinanase (BLABNase) gene from Bacillus licheniformis DSM13 was cloned and expressed in Escherichia coli, and the biochemical properties of its encoded enzyme were characterized. The BLABNase gene consists of a single
open reading frame of 987 nucleotides that encodes 328 amino acids with a predicted molecular mass of about 36 kDa. BLABNase exhibited the highest activity against debranched α-(1,5)-arabinan in 50 mM sodium acetate buffer (pH 6.0) at 55°C. Enzymatic characterization revealed that BLABNase hydrolyzes debranched or linear arabinans with a much higher activity than branched arabinan from sugar
beet. Enzymatic hydrolysis pattern analyses demonstrated BLABNase to be a typical endo-(1,5)-α-L-arabinanase (EC 3.2.1.99) that randomly cleaves the internal α-(1,5)-linked L-arabinofuranosyl residues of a branchless arabinan backbone to release arabinotriose mainly, although a small amount of arabino-oligosaccharide intermediates is also liberated. Our results indicated that BLABNase acts preferentially along with the oligosaccharides longer than arabinopentaose,
thus enabling the enzymatic production of various arabinooligosaccharides.
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- Functional Characterization of Endo- and Exo-Hydrolase Genes in Arabinan Degradation Gene Cluster of Bifidobacterium longum subsp. suis
Yewon Kang, Chang-Yun Choi, Jihun Kang, Ye-Rin Ju, Hye Bin Kim, Nam Soo Han, Tae-Jip Kim
International Journal of Molecular Sciences.2024; 25(6): 3175. CrossRef - Thermophilic Hemicellulases Secreted by Microbial Consortia Selected from an Anaerobic Digester
Luca Bombardi, Marco Orlando, Martina Aulitto, Salvatore Fusco
International Journal of Molecular Sciences.2024; 25(18): 9887. CrossRef - GH43 endo-arabinanase from Bacillus licheniformis: Structure, activity and unexpected synergistic effect on cellulose enzymatic hydrolysis
Erick Giancarlo S. Farro, Ana Elisa T. Leite, Isabela A. Silva, Jefferson G. Filgueiras, Eduardo R. de Azevedo, Igor Polikarpov, Alessandro S. Nascimento
International Journal of Biological Macromolecules.2018; 117: 7. CrossRef - Novel approaches for biotechnological production and application of L-arabinose
Csaba Fehér
Journal of Carbohydrate Chemistry.2018; 37(5): 251. CrossRef - Exploiting sp2‐Hybridisation in the Development of Potent 1,5‐α‐l‐Arabinanase Inhibitors
Travis Coyle, Aleksandra W. Debowski, Annabelle Varrot, Keith A. Stubbs
ChemBioChem.2017; 18(11): 974. CrossRef - An Acid-Adapted Endo-α-1,5-l-arabinanase for Pectin Releasing
Chong Lang, Rujian Yang, Ying Yang, Bei Gao, Li Zhao, Wei Wei, Hualei Wang, Shingo Matsukawa, Jingli Xie, Dongzhi Wei
Applied Biochemistry and Biotechnology.2016; 180(5): 900. CrossRef - In vitro digestion and fermentation properties of linear sugar-beet arabinan and its oligosaccharides
Jin Seok Moon, So Yeon Shin, Hye Sun Choi, Wooha Joo, Seung Kee Cho, Ling Li, Jung-Hyun Kang, Tae-Jip Kim, Nam Soo Han
Carbohydrate Polymers.2015; 131: 50. CrossRef - Increased biomass saccharification by supplementation of a commercial enzyme cocktail with endo-arabinanase from Bacillus licheniformis
Carla Botelho Machado, Ana Paula Citadini, Rosana Goldbeck, Evandro Antônio de Lima, Fernanda Lopes Figueiredo, Tony Márcio da Silva, Zaira Bruna Hoffmam, Amanda Silva de Sousa, Fábio Márcio Squina, Maria de Lourdes Teixeira de Moraes Poliz, Roberto Rulle
Biotechnology Letters.2015; 37(7): 1455. CrossRef - Biochemical Characterization of a Novel Endo-1,5-α-l-arabinanase fromRhizomucor miehei
Zhou Chen, Yu Liu, Qiaojuan Yan, Shaoqing Yang, Zhengqiang Jiang
Journal of Agricultural and Food Chemistry.2015; 63(4): 1226. CrossRef
- Identification of a New Bacillus licheniformis Strain Producing a Bacteriocin-Like Substance
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Yaoqi Guo , Zhanqiao Yu , Jianhua Xie , Rijun Zhang
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J. Microbiol. 2012;50(3):452-458. Published online June 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-2051-3
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62
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Abstract
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The emergence of antibiotic resistance has spurred a great number of studies for development of new antimicrobials in the past decade. The purpose of this study was to screen environmental samples for Bacillus strains producing potent antimicrobial agents. A new strain, which showed strong antimicrobial activity against Staphylococcus aureus and Salmonella enterica ser. Pullorum, was isolated from soil and designated as B116. This new isolate was identified as Bacillus licheniformis by morphological, biochemical and genetic analyses. The production of bacteriocin-like substance (BLS) started at early exponential phase and achieved highest level at early stationary phase. The BLS was precipitated by ammonium sulfate and its molecular mass was determined as ~4 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Culture supernatant of the new isolate exhibited antimicrobial activity against both Gram-positive and Gram-negative bacteria, including Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes, Micrococcus luteus, Escherichia coli, and Salmonella spp. The BLS was resistant to heat, acid and alkaline treatment. Activity of the BLS was totally lost after digestion by pronase and partially lost after digestion by papain and lipase. The new isolate and relevant BLS are potentially useful in food and feed applications.
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Journal Article
- Chitinase Production by Bacillus thuringiensis and Bacillus licheniformis: Their Potential in Antifungal Biocontrol
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Eman Zakaria Gomaa
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J. Microbiol. 2012;50(1):103-111. Published online February 27, 2012
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DOI: https://doi.org/10.1007/s12275-012-1343-y
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55
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Abstract
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Thirty bacterial strains were isolated from the rhizosphere
of plants collected from Egypt and screened for production
of chitinase enzymes. Bacillus thuringiensis NM101-19 and
Bacillus licheniformis NM120-17 had the highest chitinolytic
activities amongst those investigated. The production
of chitinase by B. thuringiensis and B. licheniformis was optimized
using colloidal chitin medium amended with 1.5%
colloidal chitin, with casein as a nitrogen source, at 30°C after
five days of incubation. An enhancement of chitinase production
by the two species was observed by addition of sugar
substances and dried fungal mats to the colloidal chitin
media. The optimal conditions for chitinase activity by B.
thuringiensis and B. licheniformis were at 40°C, pH 7.0 and
pH 8.0, respectively. Na+, Mg2+, Cu2+, and Ca2+ caused enhancement
of enzyme activities whereas they were markedly
inhibited by Zn2+, Hg2+, and Ag+. In vitro, B. thuringiensis
and B. licheniformis chitinases had potential for cell wall lysis
of many phytopathogenic fungi tested. The addition of B.
thuringiensis chitinase was more effective than that of B. licheniformis
in increasing the germination of soybean seeds
infected with various phytopathogenic fungi.
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Research Support, Non-U.S. Gov't
- Evaluation of Antagonistic Activities of Bacillus subtilis and Bacillus licheniformis Against Wood-Staining Fungi: In Vitro and In Vivo Experiments
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Natarajan Velmurugan , Mi Sook Choi , Sang-Sub Han , Yang-Soo Lee
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J. Microbiol. 2009;47(4):385-392. Published online September 9, 2009
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DOI: https://doi.org/10.1007/s12275-009-0018-9
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Abstract
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The antifungal activity of bacterial strains Bacillus subtilis EF 617317 and B. licheniformis EF 617325 was demonstrated against sapstaining fungal cultures Ophiostoma flexuosum, O. tetropii, O. polonicum, and O. ips in both in vitro and in vivo conditions. The crude active supernatant fractions of 7 days old B. subtilis and B. licheniformis cultures inhibited the growth of sapstaining fungi in laboratory experiments. Thermostability and pH stability of crude supernatants were determined by series of experiments. FT-IR analysis was performed to confirm the surface structural groups of lipoproteins present in the crude active supernatant. Partial purification of lipopeptides present in the crude supernatant was done by using Cellulose anion exchange chromatography and followed by Sephadex gel filtration chromatography. Partially purified compounds significantly inhibited the sapstaining fungal growth by in vitro analysis. The lipopeptides responsible for antifungal activity were identified by electrospray ionization mass spectrometry after partial purification by ion exchange and gel filtration chromatography. Four major ion peaks were identified as m/z 1023, 1038, 1060, and 1081 in B. licheniformis and 3 major ion peaks were identified as m/z 1036, 1058, and 1090 in B. subtilis. In conclusion, the partially purified lipopeptides may belong to surfactin and iturin family. In vivo analysis for antifungal activity of lipopeptides on wood was conducted in laboratory. In addition, the potential of extracts for fungal inhibition on surface and internal part of wood samples were analyzed by scanning electron microscopy.