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Prakash Tamang J, Kharnaior P, Pariyar P. Whole genome sequencing of the poly-γ-glutamic acid-producing novel Bacillus subtilis Tamang strain, isolated from spontaneously fermented kinema. Food Res Int 2024; 190:114655. [PMID: 38945588 DOI: 10.1016/j.foodres.2024.114655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Kinema, a traditional fermented soybean food from the Himalayas, is well-liked for its sticky texture and flavourful umami taste. Among 175 bacterial strains from spontaneously fermented kinema samples, Bacillus subtilis Tamang strain stood out for its high stickiness and viscosity. The strain's Poly-γ-glutamic acid (γ-PGA) contains various groups of glutamic acid and has a molecular weight of 660 kDa. It demonstrates the ability to solubilize iron, preserve ferritin in Caco-2 cells, and exhibit antibacterial properties. The genome of B. subtilis Tamang is devoid of plasmid elements but does feature nine insert elements. Noteworthy is the presence of unique secondary metabolites with potential antimicrobial effects, such as amyloliquecidin GF610, bogorol A, and thermoactinoamide A. A total of 132 carbohydrate-active enzymes (CAZy) were identified, hinting at possible prebiotic characteristics. The genome analysis revealed genes responsible for γ-PGA production via the capBCA complex. Furthermore, genes associated with fibrinolytic activity, taste enhancement, biopeptides, immunomodulators, and vitamins like B12 and K2 were found, along with probiotics and various health benefits. The genetic material for L-asparaginase production, known for its anti-cancer properties, was also detected, as well as CRISPR-Cas systems. The absence of virulence factors and antimicrobial resistance genes confirms the safety of consuming B. subtilis Tamang as a food-grade bacterium.
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Affiliation(s)
- Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Science Building, Gangtok 737102, Sikkim, India.
| | - Pynhunlang Kharnaior
- Department of Microbiology, School of Life Sciences, Sikkim University, Science Building, Gangtok 737102, Sikkim, India
| | - Priyambada Pariyar
- Department of Microbiology, School of Life Sciences, Sikkim University, Science Building, Gangtok 737102, Sikkim, India
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Juby S, Soumya P, Jayachandran K, Radhakrishnan EK. Morphological, Metabolomic and Genomic Evidences on Drought Stress Protective Functioning of the Endophyte Bacillus safensis Ni7. Curr Microbiol 2024; 81:209. [PMID: 38834921 DOI: 10.1007/s00284-024-03720-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
The metabolomic and genomic characterization of an endophytic Bacillus safensis Ni7 was carried out in this study. This strain has previously been isolated from the xerophytic plant Nerium indicum L. and reported to enhance the drought tolerance in Capsicum annuum L. seedlings. The effects of drought stress on the morphology, biofilm production, and metabolite production of B. safensis Ni7 are analyzed in the current study. From the results obtained, the organism was found to have multiple strategies such as aggregation and clumping, robust biofilm production, and increased production of surfactin homologues under the drought induced condition when compared to non-stressed condition. Further the whole genome sequencing (WGS) based analysis has demonstrated B. safensis Ni7 to have a genome size of 3,671,999 bp, N50 value of 3,527,239, and a mean G+C content of 41.58%. Interestingly the organism was observed to have the presence of various stress-responsive genes (13, 20U, 16U,160, 39, 17M, 18, 26, and ctc) and genes responsible for surfactin production (srfAA, srfAB, srfAC, and srfAD), biofilm production (epsD, epsE, epsF, epsG, epsH, epsI, epsK, epsL, epsM, epsN, and pel), chemotaxis (cheB_1, cheB_2, cheB_3, cheW_1, cheW_2 cheR, cheD, cheC, cheA, cheY, cheV, and cheB_4), flagella synthesis (flgG_1, flgG_2, flgG_3, flgC, and flgB) as supportive to the drought tolerance. Besides these, the genes responsible for plant growth promotion (PGP), including the genes for nitrogen (nasA, nasB, nasC, nasD, and nasE) and sulfur assimilation (cysL_1&L_2, cysI) and genes for phosphate solubilization (phoA, phoP_1& phoP_2, and phoR) could also be predicted. Along with the same, the genes for catalase, superoxide dismutase, protein homeostasis, cellular fitness, osmoprotectants production, and protein folding could also be predicted from its WGS data. Further pan-genome analysis with plant associated B. safensis strains available in the public databases revealed B. safensis Ni7 to have the presence of a total of 5391 gene clusters. Among these, 3207 genes were identified as core genes, 954 as shell genes and 1230 as cloud genes. This variation in gene content could be taken as an indication of evolution of strains of Bacillus safensis as per specific conditions and hence in the case of B. safensis Ni7 its role in habitat adaptation of plant is well expected. This diversity in endophytic bacterial genes may attribute its role to support the plant system to cope up with stress conditions. Overall, the study provides genomic evidence on Bacillus safensis Ni7 as a stress alleviating microbial partner in plants.
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Affiliation(s)
- Silju Juby
- School of Biosciences, Mahatma Gandhi University, Kottayam, India
| | - P Soumya
- School of Biosciences, Mahatma Gandhi University, Kottayam, India
| | - K Jayachandran
- School of Biosciences, Mahatma Gandhi University, Kottayam, India
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Akinsemolu AA, Onyeaka H, Odion S, Adebanjo I. Exploring Bacillus subtilis: Ecology, biotechnological applications, and future prospects. J Basic Microbiol 2024; 64:e2300614. [PMID: 38507723 DOI: 10.1002/jobm.202300614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/28/2024] [Accepted: 02/17/2024] [Indexed: 03/22/2024]
Abstract
From its early identification by Christian Gottfried Ehrenberg to its current prominence in scientific research, Bacillus subtilis (B. subtilis) has emerged as a foundational model organism in microbiology. This comprehensive review delves deep into its genetic, physiological, and biochemical intricacies, revealing a sophisticated cellular blueprint. With the incorporation of advanced techniques such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 and integrative computational methodologies, the potential applications of B. subtilis span diverse sectors. These encompass its significant contributions to biotechnology, agriculture, and medical fields and its potential for aiding environmental cleanup efforts. Yet, as we move forward, we must grapple with concerns related to safety, ethics, and the practical implementation of our lab findings in everyday scenarios. As our understanding of B. subtilis deepens, it is evident that its contributions will be central to pioneering sustainable solutions for global challenges in the years to come.
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Affiliation(s)
- Adenike A Akinsemolu
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
| | - Samuel Odion
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
- The Green Institute, Ondo, Ondo State, Nigeria
| | - Idris Adebanjo
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
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Canoy TS, Wiedenbein ES, Bredie WLP, Meyer AS, Wösten HAB, Nielsen DS. Solid-State Fermented Plant Foods as New Protein Sources. Annu Rev Food Sci Technol 2024; 15:189-210. [PMID: 38109492 DOI: 10.1146/annurev-food-060721-013526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The current animal-based production of protein-rich foods is unsustainable, especially in light of continued population growth. New alternative proteinaceous foods are therefore required. Solid-state fermented plant foods from Africa and Asia include several mold- and Bacillus-fermented foods such as tempeh, sufu, and natto. These fermentations improve the protein digestibility of the plant food materials while also creating unique textures, flavors, and taste sensations. Understanding the nature of these transformations is of crucial interest to inspire the development of new plant-protein foods. In this review, we describe the conversions taking place in the plant food matrix as a result of these solid-state fermentations. We also summarize how these (nonlactic) plant food fermentations can lead to desirable flavor properties, such as kokumi and umami sensations, and improve the protein quality by removing antinutritional factors and producing additional essential amino acids in these foods.
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Affiliation(s)
- Tessa S Canoy
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark; ,
| | | | - Wender L P Bredie
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark; ,
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
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Jiang C, Zhao G, Wang H, Zheng W, Zhang R, Wang L, Zheng Z. Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto. Gene 2024; 907:148264. [PMID: 38346457 DOI: 10.1016/j.gene.2024.148264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.
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Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Han Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Wenqian Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rui Zhang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Li Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
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Kharnaior P, Tamang JP. Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics. Int J Food Microbiol 2023; 407:110417. [PMID: 37774634 DOI: 10.1016/j.ijfoodmicro.2023.110417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/10/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Grep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPR-Cas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and peruñyaan with that of other fermented soybean foods of Asia revealed a distinct difference.
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Affiliation(s)
- Pynhunlang Kharnaior
- Department of Microbiology, Sikkim University, Science Building, Tadong 737102, Gangtok, Sikkim, India
| | - Jyoti Prakash Tamang
- Department of Microbiology, Sikkim University, Science Building, Tadong 737102, Gangtok, Sikkim, India.
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Kubo Y, Tanizaki Y, Hira D, Nakayama Y, Kadooka C, Oka T. Complete genome sequence of Bacillus subtilis subsp. natto NARUSE using PacBio sequencing. Microbiol Resour Announc 2023; 12:e0057823. [PMID: 37982649 PMCID: PMC10720478 DOI: 10.1128/mra.00578-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/19/2023] [Indexed: 11/21/2023] Open
Abstract
We report the complete genome sequence of Bacillus subtilis subsp. natto NARUSE, which has been traditionally employed for fermenting soybeans in Japan. The genome was sequenced using the PacBio system, yielding a sequence, yielding a sequence length of 4,148,793 nucleotides for the circular chromosome and 62,770 nucleotides for the plasmid.
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Affiliation(s)
- Yukie Kubo
- Kyushu Soy Food Co., Ltd., Kumamoto, Japan
- Marukin Foods Co., Ltd., Kumamoto, Japan
| | - Yoshiyuki Tanizaki
- Kyushu Soy Food Co., Ltd., Kumamoto, Japan
- Marukin Foods Co., Ltd., Kumamoto, Japan
| | - Daisuke Hira
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
| | - Yasumune Nakayama
- Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
- Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, Japan
| | - Takuji Oka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
- Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, Japan
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An F, Wu J, Feng Y, Pan G, Ma Y, Jiang J, Yang X, Xue R, Wu R, Zhao M. A systematic review on the flavor of soy-based fermented foods: Core fermentation microbiome, multisensory flavor substances, key enzymes, and metabolic pathways. Compr Rev Food Sci Food Saf 2023; 22:2773-2801. [PMID: 37082778 DOI: 10.1111/1541-4337.13162] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023]
Abstract
The characteristic flavor of fermented foods has an important impact on the purchasing decisions of consumers, and its production mechanisms are a concern for scientists worldwide. The perception of food flavor is a complex process involving olfaction, taste, vision, and oral touch, with various senses contributing to specific properties of the flavor. Soy-based fermented products are popular because of their unique flavors, especially in Asian countries, where they occupy an important place in the dietary structure. Microorganisms, known as the souls of fermented foods, can influence the sensory properties of soy-based fermented foods through various metabolic pathways, and are closely related to the formation of multisensory properties. Therefore, this review systematically summarizes the core microbiome and its interactions that play an active role in representative soy-based fermented foods, such as fermented soymilk, soy sauce, soybean paste, sufu, and douchi. The mechanism of action of the core microbial community on multisensory flavor quality is revealed here. Revealing the fermentation core microbiome and related enzymes provides important guidance for the development of flavor-enhancement strategies and related genetically engineered bacteria.
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Affiliation(s)
- Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, China
- Liaoning Provincial Engineering Research Center of Food Fermentation Technology, Shenyang, China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China
- Liaoning Provincial Engineering Research Center of Food Fermentation Technology, Shenyang, China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, China
| | - Yunzi Feng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Guoyang Pan
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Yuanyuan Ma
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Jinhui Jiang
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Xuemeng Yang
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Ruixia Xue
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China
- Liaoning Provincial Engineering Research Center of Food Fermentation Technology, Shenyang, China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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Lee G, Heo S, Kim T, Na HE, Lee JH, Jeong DW. Comparison of four multilocus sequence typing schemes and amino acid biosynthesis based on genomic analysis of Bacillus subtilis. PLoS One 2023; 18:e0282092. [PMID: 36809283 PMCID: PMC9943010 DOI: 10.1371/journal.pone.0282092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Bacillus subtilis, a valuable industrial microorganism used in starter cultures in soybean fermentation, is a species of bacteria with interspecies diversity. Here, four multilocus sequence typing (MLST) schemes developed to assess the diversity of B. subtilis or Bacillus spp. were applied and compared to confirm the interspecies diversity of B. subtilis. In addition, we analyzed correlations between amino acid biosynthesis genes and sequence types (STs); this is important because amino acids are key taste components in fermented foods. On applying the four MLST methods to 38 strains and the type strain of B. subtilis, 30 to 32 STs were identified. The discriminatory power was 0.362-0.964 for the genes used in the MLST methods; the larger the gene, the greater the number of alleles and polymorphic sites. All four MLST methods showed a correlation between STs and strains that do not possess the hutHUIG operon (which contains genes required for the production of glutamate from histidine). This correlation was verified using 168 further genome-sequence strains.
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Affiliation(s)
- Gawon Lee
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
| | - Sojeong Heo
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
| | - Tao Kim
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
| | - Hong-Eun Na
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, Republic of Korea
- * E-mail:
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A Genomic Analysis of Bacillus megaterium HT517 Reveals the Genetic Basis of Its Abilities to Promote Growth and Control Disease in Greenhouse Tomato. Int J Genomics 2022; 2022:2093029. [PMID: 36605453 PMCID: PMC9810399 DOI: 10.1155/2022/2093029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022] Open
Abstract
Bacillus megaterium is well known as a plant growth-promoting rhizobacterium, but the relevant molecular mechanisms remain unclear. This study aimed to elucidate the effects of B. megaterium HT517 on the growth and development of and the control of disease in greenhouse tomato and its mechanism of action. A pot experiment was conducted to determine the effect of B. megaterium on tomato growth, and this experiment included the HT517 group (3.2 × 108 cfu/pot) and the control group (inoculated with the same amount of sterilized suspension). An antagonistic experiment and a plate confrontation experiment were conducted to study the antagonistic effect of B. megaterium and Fusarium oxysporum f.sp. lycopersici. Liquid chromatography-mass spectrometry was used to determine the metabolite composition and metabolic pathway of HT517. PacBio+Illumina HiSeq sequencing was utilized for map sequencing of the samples. An in-depth analysis of the functional genes related to the secretion of these substances by functional bacteria was conducted. HT517 could secrete organic acids that solubilize phosphorus, promote root growth, secrete auxin, which that promotes early flowering and fruiting, and alkaloids, which control disease, and reduce the incidence of crown rot by 51.0%. The complete genome sequence indicated that the strain comprised one circular chromosome with a length of 5,510,339 bp (including four plasmids in the genome), and the GC content accounted for 37.95%. Seven genes (pyk, aceB, pyc, ackA, gltA, buk, and aroK) related to phosphate solubilization, five genes (trpA, trpB, trpS, TDO2, and idi) related to growth promotion, eight genes (hpaB, pheS, pheT, ileS, pepA, iucD, paaG, and kamA) related to disease control, and one gene cluster of synthetic surfactin were identified in this research. The identification of molecular biological mechanisms for extracellular secretion by the HT517 strain clarified that its organic acids solubilized phosphorus, that auxin promoted growth, and that alkaloids controlled tomato diseases.
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Wang Y, Zhao Q, Sun Z, Li Y, He H, Zhang Y, Yang X, Wang D, Dong B, Zhou H, Zhao M, Zheng H. Whole-genome analysis revealed the growth-promoting mechanism of endophytic bacterial strain Q2H1 in potato plants. Front Microbiol 2022; 13:1035901. [PMID: 36532474 PMCID: PMC9751815 DOI: 10.3389/fmicb.2022.1035901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/03/2022] [Indexed: 01/09/2024] Open
Abstract
INTRODUCTION Endophytes are non-pathogenic inhabitants of healthy plant tissues and have been found to promote plant growth and health. The endophytic bacterial strain Q2H1 was isolated from the roots of the potato and was identified to exhibit growth-promoting effects in potato plants. METHODS Whole-genome sequencing was performed to reveal the mechanism underlying its growth-promoting effect. The obtained sequencing data of approximately 5.65 MB encompassed 5,533 coding sequences. Of note, nine secondary metabolite gene clusters, including siderophore gene clusters, closely associated with plant growth promotion (PGP) were predicted by antiSMASH software. Comparative genomic analysis revealed that Q2H1 belongs to the genus Peribacillus. By gene function annotation, those genes related to plant growth-promoting activities, including indole-3-acetic acid (IAA) synthesis in tryptophan metabolism, siderophore biosynthetic activity, phosphate solubilization, nitrogen fixation, and related genes, were summarized. IAA (14.4 μg/ml) was presumptively produced by Q2H1 using the Salkowski colorimetric method. A total of five genes, namely, phoU, pstB, pstA1, pstC, and pstS, were annotated for phosphate solubilization, which is associated with the ability of the Q2H1 strain to solubilize phosphate under in vitro conditions. RESULTS It is revealed that genes in the Q2H1 genome associated with nitrogen fixation belonged to three groups, namely, nitrogen fixation (nifU, sufU, salA, and nifS), nitrogen metabolism (nirA, nrtB, and nasA), and glutamate synthesis (glnA, gltB, gltD, and gudB), supported by evidence that Q2H1 grew on medium without nitrogen. We have also identified a siderophore gene cluster located on the chromosome of Q2H1, including seven genes (viz., rbsR, rhbf, rhbE, rhbD, rhbC, rhbA, ddc, and an unknown gene). In the in vitro assay, a prominent brown circle around the colony was produced on the chrome azurol S medium at 48 and 72 h post-inoculation, indicating that the siderophore gene cluster in Q2H1 harbored the ability to produce siderophores. CONCLUSION In summary, these findings implied that identifying strain-specific genes for their metabolic pathways in bacterial endophytes may reveal a variety of significant functions of plant growth-promoting mechanisms.
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Affiliation(s)
- Yuhu Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Qianqian Zhao
- Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhenqi Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yahui Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongtao He
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuanyu Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Dong Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Baozhu Dong
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongli Zheng
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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Tokano M, Tarumoto N, Imai K, Sakai J, Maeda T, Kawamura T, Seo K, Takahashi K, Yamamoto T, Maesaki S. A Case of Bacterial Meningitis Caused by Bacillus subtilis var. natto. Intern Med 2022. [PMID: 36418098 PMCID: PMC10372276 DOI: 10.2169/internalmedicine.0768-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A 67-year-old woman with a 2-day history of a fever, headache and disturbed consciousness was admitted to our hospital. Bacillus subtilis was isolated from both the cerebrospinal fluid and blood. She was cured by the administration of vancomycin. Next-generation sequencing identified the strain as B. subtilis var. natto, the same strain found in natto, which this patient ate daily. We suspected that some of the B. subtilis that caused the infection may have actually been B. subtilis var. natto.
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Affiliation(s)
- Mieko Tokano
- Department of Infectious Disease and Infection Control, Saitama Medical University, Japan
- Departments of Allergy and Immunology, Faculty of Medicine, Saitama Medical University, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Japan
| | - Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Japan
| | - Takuya Maeda
- Department of Clinical Laboratory, Saitama Medical University, Japan
| | - Toru Kawamura
- Department of Clinical Laboratory, Saitama Medical University, Japan
| | - Kazuhide Seo
- Department of Neurology, Faculty of Medicine, Saitama Medical University, Japan
| | - Kazushi Takahashi
- Department of Neurology, Faculty of Medicine, Saitama Medical University, Japan
| | - Toshimasa Yamamoto
- Department of Neurology, Faculty of Medicine, Saitama Medical University, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Japan
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13
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Owusu-Kwarteng J, Agyei D, Akabanda F, Atuna RA, Amagloh FK. Plant-Based Alkaline Fermented Foods as Sustainable Sources of Nutrients and Health-Promoting Bioactive Compounds. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.885328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Traditional food fermentation is a practice that precedes human history. Acidic products such as yogurts and sourdoughs or alcoholic beverages produced through lactic acid or yeast fermentations, respectively, are widely described and documented. However, a relatively less popular group of fermented products known as alkaline fermented foods are common traditional products in Africa and Asia. These products are so called “alkaline” because the pH tends to increase during fermentation due to the formation of ammonia resulting from protein degradation by Bacillus species. Plant-based alkaline fermented foods (AFFs) are generally produced from legumes including soybean, non-soybean leguminous seeds, and other non-legume plant raw materials. Alkaline fermented food products such as natto, douchi, kinema, doenjang, chongkukjang, thua nao, meitauza, yandou, dawadawa/iru, ugba, kawal, okpehe, otiru, oso, ogiri, bikalga, maari/tayohounta, ntoba mbodi, cabuk, and owoh are produced at small industrial scale or household levels and widely consumed in Asia and Africa where they provide essential nutrients and health-promoting bioactive compounds for the population. Alkaline food fermentation is important for sustainable food security as it contributes to traditional dietary diversity, significantly reduces antinutritional components in raw plant materials thereby improving digestibility, improves health via the production of vitamins, and may confer probiotic and post-biotic effects onto consumers. In this review, we present currently available scientific information on plant-based AFFs and their role as sustainable sources of nutrients and bioactive compounds for improved health. Finally, we provide perspectives on research needs required to harness the full potential of AFFs in contributing to nutrition and health.
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Chu D, Ilyas N, Peng L, Wang X, Wang D, Xu Z, Gao Q, Tan X, Zhang C, Li Y, Yuan Y. Genomic insights on fighting bacterial wilt by a novel Bacillus amyloliquefaciens strain Cas02. Microb Biotechnol 2022; 15:1152-1167. [PMID: 34570959 PMCID: PMC8966013 DOI: 10.1111/1751-7915.13925] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 11/28/2022] Open
Abstract
Bacterial wilt, caused by the Ralstonia solanacearum, can infect several economically important crops. However, the management strategies available to control this disease are limited. Plant growth-promoting rhizobacteria (PGPR) have been considered promising biocontrol agents. In this study, Bacillus amyloliquefaciens strain Cas02 was isolated from the rhizosphere soil of healthy tobacco plants and evaluated for its effect on plant growth promotion and bacterial wilt suppression. Strain Cas02 exhibited several growth-promoting-related features including siderophore production, cellulase activity, protease activity, ammonia production and catalase activity. Moreover, strain Cas02 showed a significant inhibitory growth effect on R. solanacearum, and its active substances were separated and identified to be macrolactin A and macrolactin W by HPLC-DAD-ESI-MS/MS. Both greenhouse and field experiments demonstrated a good performance of Cas02 in plant growth promotion and bacterial wilt suppression. To explore the underlying genetic mechanisms, complete genome sequencing was performed and the gene clusters responsible for antibacterial metabolites expression were identified. Overall, these findings suggest that the strain Cas02 could be a potential biocontrol agent in bacterial wilt management and a source of antimicrobial compounds for further exploitation.
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Affiliation(s)
- Depeng Chu
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Naila Ilyas
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Lijuan Peng
- Yunnan Tobacco Quality Supervision and Test StationKunming650106China
| | - Xiaoqiang Wang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Dongkun Wang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Zongchang Xu
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Qiang Gao
- Yishui Agricultural Technology Demonstration ParkLinyi276400China
| | - Xiaolei Tan
- Yishui Agricultural Technology Demonstration ParkLinyi276400China
| | - Chengsheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Yiqiang Li
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Yuan Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
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15
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Tamang JP, Kharnaior P, Pariyar P, Thapa N, Lar N, Win KS, Mar A, Nyo N. Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar. PLoS One 2021; 16:e0260777. [PMID: 34919575 PMCID: PMC8682898 DOI: 10.1371/journal.pone.0260777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/09/2021] [Indexed: 11/19/2022] Open
Abstract
Pe poke is a naturally fermented sticky soybean food of Myanmar. The present study was aimed to profile the whole microbial community structure and their predictive gene functionality of pe poke samples prepared in different fermentation periods viz. 3 day (3ds), 4 days (4ds), 5 days (5ds) and sun-dried sample (Sds). The pH of samples was 7.6 to 8.7, microbial load was 2.1-3.9 x 108 cfu/g with dynamic viscosity of 4.0±1.0 to 8.0±1.0cP. Metataxonomic profile of pe poke samples showed different domains viz. bacteria (99.08%), viruses (0.65%), eukaryota (0.08%), archaea (0.03%) and unclassified sequences (0.16%). Firmicutes (63.78%) was the most abundant phylum followed by Proteobacteria (29.54%) and Bacteroidetes (5.44%). Bacillus thermoamylovorans was significantly abundant in 3ds and 4ds (p<0.05); Ignatzschineria larvae was significantly abundant in 5ds (p<0.05), whereas, Bacillus subtilis was significantly abundant in Sds (p <0.05). A total of 172 species of Bacillus was detected. In minor abundance, the existence of bacteriophages, archaea, and eukaryotes were also detected. Alpha diversity analysis showed the highest Simpson's diversity index in Sds comparable to other samples. Similarly, a non-parametric Shannon's diversity index was also highest in Sds. Good's coverage of 0.99 was observed in all samples. Beta diversity analysis using PCoA showed no significant clustering. Several species were shared between samples and many species were unique to each sample. In KEGG database, a total number of 33 super-pathways and 173 metabolic sub-pathways were annotated from the metagenomic Open Reading Frames. Predictive functional features of pe poke metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including various essential amino acids, different vitamins, and enzymes. Spearman's correlation was inferred between the abundant species and functional features.
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Affiliation(s)
- Jyoti Prakash Tamang
- Department of Microbiology, DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Pynhunlang Kharnaior
- Department of Microbiology, DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Priyambada Pariyar
- Department of Microbiology, DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Namrata Thapa
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Sikkim University, Tadong, Sikkim, India
| | - Ni Lar
- Department of Industrial Chemistry, University of Mandalay, Mandalay, Myanmar
| | - Khin Si Win
- Department of Industrial Chemistry, University of Mandalay, Mandalay, Myanmar
| | - Ae Mar
- Department of Industrial Chemistry, University of Mandalay, Mandalay, Myanmar
| | - Nyo Nyo
- Department of Geography, University of Mandalay, Mandalay, Myanmar
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Kłosowski G, Mikulski D, Pielech-Przybylska K. Pyrazines Biosynthesis by Bacillus Strains Isolated from Natto Fermented Soybean. Biomolecules 2021; 11:1736. [PMID: 34827734 PMCID: PMC8615529 DOI: 10.3390/biom11111736] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
Pyrazines are organic compounds with a varied, intense aroma of roasted nuts, occasionally with hints of baked potatoes, almonds, and others. As a result, they are used in the food industry as food flavorings. Biosynthesis of pyrazines using microorganisms in environmentally friendly conditions is an alternative to chemical synthesis. However, screening is required to isolate efficient producer strains for efficient biosynthesis of this compound. The study's goal was to assess the ability of Bacillus subtilis cultures isolated from natto (fermented soybeans) to biosynthesize a broad range of alkylpyrazines. B. subtilis isolated cultures were found to be capable of producing 2-methylpyrazine, 2,3-dimethylpyrazine, 2,5-dimethylpyrazine, 2,6-dimethylpyrazine, 2,3,5-trimethylpyrazine, and 2,3,5,6-tetramethylpyrazine. As a result of the screening, two cultures of B. subtilis capable of producing alkylpyrazines were isolated. At a total concentration of 3261 µg/L, the BcP4 strain primarily produced 2-methylpyrazine (690 µg/L), 2,3-dimethylpyrazine (680 µg/L), and 2,6-dimethylpyrazine (1891 µg/L). At a total concentration of 558 mg/L, the BcP21 strain produced 2,5-dimethylpyrazine (4.5 mg/L), 2,3,5-trimethylpyrazine (52.6 mg/L), and 2,3,5,6-tetramethylpyrazine (501.1 mg/L). The results show that different B. subtilis strains are predisposed to produce different alkylpyrazines.
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Affiliation(s)
- Grzegorz Kłosowski
- Department of Biotechnology, Faculty of Biological Sciences, Kazimierz Wielki University, 85-671 Bydgoszcz, Poland;
| | - Dawid Mikulski
- Department of Biotechnology, Faculty of Biological Sciences, Kazimierz Wielki University, 85-671 Bydgoszcz, Poland;
| | - Katarzyna Pielech-Przybylska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-530 Lodz, Poland;
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Gopikrishna T, Suresh Kumar HK, Perumal K, Elangovan E. Impact of Bacillus in fermented soybean foods on human health. ANN MICROBIOL 2021; 71:30. [PMID: 34305497 PMCID: PMC8285709 DOI: 10.1186/s13213-021-01641-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Fermented soybean foods (FSF) is popularly consumed in the South-East Asian countries. Bacillus species, a predominant microorganism present in these foods, have demonstrated beneficial and deleterious impacts on human health. These microorganisms produce bioactive compounds during fermentation that have beneficial impacts in improving human health. However, the health risks associated with FSF, food pathogens, biogenic amines (BAs) production, and late-onset anaphylaxis, remain a concern. The purpose of this review is to present an in-depth analysis of positive and negative impacts as a result of consumption of FSF along with the measures to alleviate health risks for human consumption. METHODS This review was composed by scrutinizing contemporary literature of peer-reviewed publications related to Bacillus and FSF. Based on the results from academic journals, this review paper was categorized into FSF, role of Bacillus species in these foods, process of fermentation, beneficial, and adverse influence of these foods along with methods to improve food safety. Special emphasis was given to the potential benefits of bioactive compounds released during fermentation of soybean by Bacillus species. RESULTS The nutritional and functional properties of FSF are well-appreciated, due to the release of peptides and mucilage, which have shown health benefits: in managing cardiac disease, gastric disease, cancer, allergies, hepatic disease, obesity, immune disorders, and especially microbial infections due to the presence of probiotic property, which is a potential alternative to antibiotics. Efficient interventions were established to mitigate pitfalls like the techniques to reduce BAs and food pathogens and by using a defined starter culture to improve the safety and quality of these foods. CONCLUSION Despite some of the detrimental effects produced by these foods, potential health benefits have been observed. Therefore, soybean foods fermented by Bacillus can be a promising food by integrating effective measures for maintaining safety and quality for human consumption. Further, in vivo analysis on the activity and dietary interventions of bioactive compounds among animal models and human volunteers are yet to be achieved which is essential to commercialize them for safe consumption by humans, especially immunocompromised patients.
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Affiliation(s)
- Trishala Gopikrishna
- Department of Biotechnology, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University, Chennai, India
| | - Harini Keerthana Suresh Kumar
- Department of Biotechnology, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University, Chennai, India
| | - Kumar Perumal
- Department of Biotechnology, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University, Chennai, India
| | - Elavarashi Elangovan
- Department of Biotechnology, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University, Chennai, India
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18
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Ruiz Sella SRB, Bueno T, de Oliveira AAB, Karp SG, Soccol CR. Bacillus subtilis natto as a potential probiotic in animal nutrition. Crit Rev Biotechnol 2021; 41:355-369. [PMID: 33563053 DOI: 10.1080/07388551.2020.1858019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The growing global demand for animal products and processed meat has created a challenge for the livestock sector to enhance animal productivity without compromising product quality. The restriction of antibiotics in animal feeds as growth promoters makes the use of probiotics a natural and safe alternative to obtain functional foods that provide animal health and quality and to maintain food safety for consumers. To incorporate these additives into the diet, detailed studies are required, in which in vitro and in vivo assays are used to prove the efficacy and to ensure the safety of probiotic candidate strains. Studies on the use of Bacillus subtilis natto as a spore-forming probiotic bacterium in animal nutrition have shown no hazardous effects and have demonstrated the effectiveness of its use as a probiotic, mainly due to its proven antimicrobial, anti-inflammatory, antioxidant, enzymatic, and immunomodulatory activity. This review summarizes the recent scientific background on the probiotic effects of B. subtilis natto in animal nutrition. It focuses on its safety assessment, host-associated efficacy, and industrial requirements.
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Affiliation(s)
- Sandra R B Ruiz Sella
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.,Departament of Research and Development, Production and Research Centre of Immunobiological Products, Secretaria de Estado da Saúde, Piraquara, Brazil
| | - Tarcila Bueno
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.,Biotechnology Coordination, Federal Institute of Paraná, Curitiba, Brazil
| | - Angelo A B de Oliveira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Susan Grace Karp
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
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19
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Heo J, Kim JS, Hong SB, Park BY, Kim SJ, Kwon SW. Genetic marker gene, recQ, differentiating Bacillus subtilis and the closely related Bacillus species. FEMS Microbiol Lett 2020; 366:5571089. [PMID: 31675066 DOI: 10.1093/femsle/fnz172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
RecQ, which encodes a DNA helicase, was selected in searching for a marker gene of Bacillus subtilis and related species via genome mining. RecQ gene sequence similarity of type strains among Bacillus species used in this study ranged from 66.2% to 96.6%, whereas orthologous average nucleotide identity ranged from 72.6% to 95.8%. According to the phylogenetic tree based on recQ sequences, each type strain of all Bacillus species or subspecies used in this study was placed in a unique taxonomic position. Four B. subtilis subspecies, Bacillus tequilensis and Bacillus vallismortis were grouped in one cluster (cluster A). Strains of B. subtilis subsp. subtilis were classified into A1 cluster, and divided into subgroups. Isolates from Natto, Japanese fermented bean food, were classified into one subgroup, whereas those from Cheonggukjang, Korean fermented bean food, were divided into several subgroups within A1. Type strains of Bacillus halotolerans and Bacillus mojavensis were grouped into another cluster (cluster B), related to cluster A. Bacillus siamensis, Bacillus velezensis and Bacillus amyloliquefaciens were grouped into an independent cluster (cluster E). Sequencing of recQ was useful for the classification or differentiation of B. subtilis and closely related species. Therefore, recQ gene can be applied to the classification of these taxa.
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Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Byeong-Yong Park
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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20
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Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture. Funct Integr Genomics 2020; 20:575-589. [PMID: 32198678 DOI: 10.1007/s10142-020-00736-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/17/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022]
Abstract
Bacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using Velvet 1.2.10, resulting in a whole genome of 4.09 Mb with 4332 genes. Genes involved in the production of indoles, siderophores, lipopeptides, volatile compounds, phytase, bacilibactin, and nitrogenase were predicted by gene annotation or by metabolic pathway prediction by RAST. These potential traits were determined using in vitro biochemical tests, finding that B. subtilis EA-CB0575 produces two families of lipopeptides (surfactin and fengycin), solubilizes phosphate, fixes nitrogen, and produces indole and siderophores compounds. Finally, strain EA-CB0575 increased 34.60% the total dry weight (TDW) of tomato plants with respect to non-inoculated plants at greenhouse level. These results suggest that the identification of strain-specific genes and predicted metabolic pathways might explain the strain potential to promote plant growth by several mechanisms of action, accelerating the development of plant biostimulants for sustainable agricultural.
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21
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Hong LTT, Hachiya T, Hase S, Shiwa Y, Yoshikawa H, Sakakibara Y, Nguyen SLT, Kimura K. Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene. J Biosci Bioeng 2019; 128:690-696. [PMID: 31272833 DOI: 10.1016/j.jbiosc.2019.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/21/2019] [Accepted: 05/27/2019] [Indexed: 02/06/2023]
Abstract
Poly-γ-glutamic acid (γPGA) production by Bacillus subtilis is regulated by the quorum sensing system where DegQ transmits the cell density signal to a DNA-binding protein DegU. A mutation suppressing the γPGA-negative phenotype of degQ gene knock-out mutant (ΔdegQ) was identified through whole genome sequencing. The mutation conferred an amino acid substitution of Ser103 to phenylalanine (S103F) in yabJ that belongs to the highly conserved YjgF/YER057c/UK114 family. Genetic experiments including LacZ-fusion assay of γPGA synthetic operon confirmed that the suppressor mutation (yabJS103F) was responsible for the recovery of γPGA production. The yabJ itself was not essential for the γPGA production and the mutant allele enabled γPGA production of the ΔdegQ strain even in the presence of wild type yabJ. Thus, yabJS103F was a dominant positive allele. degU-lacZ fusion gene was hyper-expressed in cells carrying the yabJS103F, but disruption of yabJ did not affect the transcription level of the degU-lacZ. These observations suggested that YabJ acquired a function to stimulate expression of degU by the S103F mutation which is involved in the regulation of γPGA synthesis.
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Affiliation(s)
- Le Thi Thu Hong
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Tsuyoshi Hachiya
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sumitaka Hase
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan; Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Yasubumi Sakakibara
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sy Le Thanh Nguyen
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Keitarou Kimura
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan.
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22
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Kimura 木村 啓太郎 K, Yokoyama 横山 智 S. Trends in the application of Bacillus in fermented foods. Curr Opin Biotechnol 2019; 56:36-42. [PMID: 30227296 DOI: 10.1016/j.copbio.2018.09.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/17/2018] [Accepted: 09/02/2018] [Indexed: 01/05/2023]
Abstract
Bacillus species such as Bacillus subtilis and Bacillus amyloliquefaciens are widely used to produce fermented foods from soybeans and locust beans in Asian and West African countries, respectively. Genomic information for B. subtilis strains isolated from Asian Bacillus-fermented foods (BFFs) has been gathered, and the chemical components of fermented products were defined with metabolomic approaches, facilitating the development of new starter strains and the evaluation of health claims. On the other hand, although advanced studies have been performed for some commercially produced BFFs, home-manufactured products still remain to be characterized in rural areas. In West Africa, the microbial flora of BFFs was examined in detail, leading to the isolation of candidates of the starter that produced bacteriocin against Bacillus cereus contaminating the products. These studies may provide a choice of Bacillus strains in food application and increase opportunities for further usage of Bacillus in foods.
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Affiliation(s)
- Keitarou Kimura 木村 啓太郎
- Applied Microbiology Unit, Food Research Institute, National Agriculture and Food Research Institute (NFRI/NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
| | - Satoshi Yokoyama 横山 智
- Department of Geography, Graduate School of Environmental Studies, Nagoya University, Furo-cho Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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23
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Bóka B, Manczinger L, Kocsubé S, Shine K, Alharbi NS, Khaled JM, Münsterkötter M, Vágvölgyi C, Kredics L. Genome analysis of a Bacillus subtilis strain reveals genetic mutations determining biocontrol properties. World J Microbiol Biotechnol 2019; 35:52. [PMID: 30868269 PMCID: PMC6435635 DOI: 10.1007/s11274-019-2625-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/01/2019] [Indexed: 11/03/2022]
Abstract
Several Bacillus strains are used as biocontrol agents, as they frequently have strong antagonistic effects against microbial plant pathogens. Bacillus strain SZMC 6179J, isolated from tomato rhizosphere, was previously shown to have excellent in vitro antagonistic properties against the most important fungal pathogens of tomato (Alternaria solani, Botrytis cinerea, Phytophthora infestans and Sclerotinia sclerotiorum) as well as several Fusarium species. Taxonomic investigations revealed that it is a member of the B. subtilis subsp. subtilis group and very closely related with the reference type strain B. subtilis subsp. subtilis 168. The sequenced genome of strain SZMC 6179J contains the genes responsible for the synthesis of the extracellular antibiotics surfactin, fengycin and bacilysin. Compared to strain 168, a prophage-like region is missing from the genome of SZMC 6179J, while there are 106 single nucleotide polymorphisms and 23 deletion-insertion polymorphisms. The high biocontrol potential of strain SZMC 6179J may results from a single base deletion in the sfp gene encoding the transcription factor of the surfactin and fengycin operons. Hypermutated regions reflecting short-time evolutionary processes could be detected in SZMC 6179J. The deletion-insertion polymorphism in the sfp gene and the detected hypermutations can be suggested as genetic determinants of biocontrol features in B. subtilis.
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Affiliation(s)
- Bettina Bóka
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - László Manczinger
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Kadaikunnan Shine
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Martin Münsterkötter
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky u. 4, Sopron, 9401, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.
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Rahimi T, Niazi A, Deihimi T, Taghavi SM, Ayatollahi S, Ebrahimie E. Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil. Funct Integr Genomics 2018; 18:533-543. [PMID: 29730772 DOI: 10.1007/s10142-018-0604-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/18/2018] [Accepted: 03/19/2018] [Indexed: 01/22/2023]
Abstract
One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison and analysis of orthologous genes carried out between B. subtilis MJ01, reference strain B. subtilis subsp. subtilis str. 168, and close relative spizizenii TU-B-10 by microscope platform and various bioinformatics tools. More than 88% of 4269 predicted coding sequences in MJ01 had at least one similar sequence in genome of reference strain and spizizenii TU-B-10. Despite this high similarity, some differences were detected among encoding sequences of non-ribosome protein and bacteriocins in MJ01 and spizizenii TU-B-10. MJ01 has unique nucleotide sequences and a novel predicted lasso-peptide bacteriocin; it also has not any similar nucleotide sequence in non-redundant nucleotide data base.
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Affiliation(s)
- Touraj Rahimi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran.
| | | | | | - Shahab Ayatollahi
- School of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Esmaeil Ebrahimie
- Institute of Biotechnology, Shiraz University, Shiraz, Iran. .,School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia. .,Adelaide Medicine School, The University of Adelaide, Adelaide, SA, Australia. .,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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Zeng W, Chen G, Guo Y, Zhang B, Dong M, Wu Y, Wang J, Che Z, Liang Z. Production of poly-γ-glutamic acid by a thermotolerant glutamate-independent strain and comparative analysis of the glutamate dependent difference. AMB Express 2017; 7:213. [PMID: 29177886 PMCID: PMC5701898 DOI: 10.1186/s13568-017-0512-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/11/2017] [Indexed: 01/28/2023] Open
Abstract
Poly-γ-glutamic acid (γ-PGA) is a promising microbial polymer with wide applications in industry, agriculture and medicine. In this study, a novel glutamate-independent γ-PGA producing strain with thermotolerant characteristics was isolated and identified as Bacillus subtilis GXG-5, then its product was also characterized. The fermentation process was optimized by single-factor tests, and results showed that high temperature (50 °C) was especially suitable for the γ-PGA production by GXG-5. The γ-PGA yield reached 19.50 ± 0.75 g/L with substrate conversion efficiency of 78% at 50 °C in 10 L fermentor. Comparison of GXG-5 and GXA-28 (glutamate-dependent strain) under respective optimal fermentation conditions, the γ-PGA yield of GXG-5 was 19.0% higher than that of GXA-28, and GXG-5 was also superior to GXA-28 in the availability of carbon sources and substrates. Furthermore, the glutamate dependent difference between GXA-28 and GXG-5 was analyzed by genomic sequencing, results indicated that genes related to the glutamate dependent difference mainly involved in carbohydrate transport and metabolism and amino acid metabolism, and 13 genes related to γ-PGA synthesis were mutated in GXG-5. This study provided a potential glutamate-independent strain to replace glutamate-dependent strain for γ-PGA production, and shared novel information for understanding the glutamate dependent difference at the genomic level.
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Sushma C, Anand AP, Veeranki VD. Enhanced production of glutaminase free L-asparaginase II by Bacillus subtilis WB800N through media optimization. KOREAN J CHEM ENG 2017. [DOI: 10.1007/s11814-017-0211-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Batista-García RA, Sutton T, Jackson SA, Tovar-Herrera OE, Balcázar-López E, Sánchez-Carbente MDR, Sánchez-Reyes A, Dobson ADW, Folch-Mallol JL. Characterization of lignocellulolytic activities from fungi isolated from the deep-sea sponge Stelletta normani. PLoS One 2017; 12:e0173750. [PMID: 28339473 PMCID: PMC5365110 DOI: 10.1371/journal.pone.0173750] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/24/2017] [Indexed: 12/03/2022] Open
Abstract
Extreme habitats have usually been regarded as a source of microorganisms that possess robust proteins that help enable them to survive in such harsh conditions. The deep sea can be considered an extreme habitat due to low temperatures (<5°C) and high pressure, however marine sponges survive in these habitats. While bacteria derived from deep-sea marine sponges have been studied, much less information is available on fungal biodiversity associated with these sponges. Following screening of fourteen fungi isolated from the deep-sea sponge Stelletta normani sampled at a depth of 751 metres, three halotolerant strains (TS2, TS11 and TS12) were identified which displayed high CMCase and xylanase activities. Molecular based taxonomic approaches identified these strains as Cadophora sp. TS2, Emericellopsis sp. TS11 and Pseudogymnoascus sp. TS 12. These three fungi displayed psychrotolerance and halotolerant growth on CMC and xylan as sole carbon sources, with optimal growth rates at 20°C. They produced CMCase and xylanase activities, which displayed optimal temperature and pH values of between 50-70°C and pH 5-8 respectively, together with good thermostability and halotolerance. In solid-state fermentations TS2, TS11 and TS12 produced CMCases, xylanases and peroxidase/phenol oxidases when grown on corn stover and wheat straw. This is the first time that CMCase, xylanase and peroxidase/phenol oxidase activities have been reported in these three fungal genera isolated from a marine sponge. Given the biochemical characteristics of these ligninolytic enzymes it is likely that they may prove useful in future biomass conversion strategies involving lignocellulosic materials.
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Affiliation(s)
- Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Thomas Sutton
- School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Omar Eduardo Tovar-Herrera
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, Mexico
| | - Edgar Balcázar-López
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | | | - Ayixon Sánchez-Reyes
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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Akashi M, Harada S, Moki S, Okouji Y, Takahashi K, Kada S, Yamagami K, Sekine Y, Watanabe S, Chibazakura T, Yoshikawa H. Transposition of insertion sequence IS256Bsu1 in Bacillus subtilis 168 is strictly dependent on recA. Genes Genet Syst 2017; 92:59-71. [PMID: 28344191 DOI: 10.1266/ggs.16-00071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We developed an insertion sequence transposition detection system called the "jumping cat assay" and applied it to the Bacillus subtilis chromosome using IS256Bsu1 derived from B. subtilis natto. The high frequency of transposition enabled us to explore host factors; combining the assay and genetic analyses revealed that recA is essential for the transposition of IS256Bsu1. Detailed analyses using various domain mutants of recA demonstrated that this essentiality is not related to the function of recA in homologous recombination. Instead, the ATP binding and hydrolysis function seemed to be crucial for IS transposition. To elucidate the role of recA, we focused on the muB gene of the enterobacteriophage Mu. Based on information from the NCBI Conserved Domain Database, both MuB and RecA belong to the P-loop dNTPase superfamily. Further experiments revealed that muB complements the transposition-defective phenotype of a recA deletant, although it could not rescue UV sensitivity. These results suggest that recA shares a common function with muB that helps the transposition of IS256Bsu1 in B. subtilis.
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Affiliation(s)
| | - Shota Harada
- Department of Bioscience, Tokyo University of Agriculture
| | - Syunsuke Moki
- Department of Bioscience, Tokyo University of Agriculture
| | - Yuki Okouji
- Department of Bioscience, Tokyo University of Agriculture
| | | | - Shigeki Kada
- Central Research Institute, Mitsukan Group Co., Ltd
| | | | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo (St Paul's) University
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