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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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2
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Ishikawa K, Hasegawa R, Furukawa K, Kawai F, Uehara Y, Ohkusu K, Mori N. Recurrent Bacillus subtilis Var. Natto Bacteremia and Review of the Literature on Bacillus subtilis: The First Case Report. AMERICAN JOURNAL OF CASE REPORTS 2024; 25:e942553. [PMID: 38332578 PMCID: PMC10862081 DOI: 10.12659/ajcr.942553] [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: 09/14/2023] [Revised: 12/30/2023] [Accepted: 12/22/2023] [Indexed: 02/10/2024]
Abstract
BACKGROUND Fermented foods, such as yogurt, are often considered healthy; however, there have been numerous reported cases of bacteremia associated with their consumption. In this report, we present a case of Bacillus subtilis var. natto (B. subtilis var. natto) bacteremia related to the consumption of natto, a traditional Japanese food made from fermented soybeans. We also conducted a literature review on B. subtilis bacteremia. CASE REPORT We report the case of a 41-year-old woman who presented with fever, had a medical history of congenital liver fibrosis, and experienced recurrent B. subtilis var. natto bacteremia along with acute cholangitis. Although she discontinued eating natto, she developed pyogenic thrombophlebitis due to B. subtilis var. natto. We successfully treated her with meropenem and an anti-coagulant. To investigate the management and prognosis of B. subtilis var. natto bacteremia, we conducted a literature review of B. subtilis intra-abdominal infection. We identified 17 papers describing 30 cases of B. subtilis intra-abdominal infection, 4 cases of which were caused by B. subtilis var. natto; the median age of the patients was 71 years (range, 15-96 years), 14 patients (47%) were female, and 3 patients (10%) died. From our findings, our case was the only one of recurrent B. subtilis var. natto infection. Even after patients discontinue eating natto, they should be carefully monitored. CONCLUSIONS Due to advancements in PCR identification techniques, case reports of infections caused by B. subtilis var. natto are increasing.
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Affiliation(s)
- Kazuhiro Ishikawa
- Department of Infectious Diseases, St Luke’s International Hospital, Tokyo, Japan
| | - Ryo Hasegawa
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Keitaro Furukawa
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan
| | - Fujimi Kawai
- Library Department of Academic Resources, St. Luke’s International University, Tokyo, Japan
| | - Yuki Uehara
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kiyofumi Ohkusu
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan
| | - Nobuyoshi Mori
- Department of Infectious Diseases, St Luke’s International Hospital, Tokyo, Japan
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Ma W, Guan X, Miao Y, Zhang L. Whole Genome Resequencing Revealed the Effect of Helicase yqhH Gene on Regulating Bacillus thuringiensis LLP29 against Ultraviolet Radiation Stress. Int J Mol Sci 2023; 24:ijms24065810. [PMID: 36982883 PMCID: PMC10054049 DOI: 10.3390/ijms24065810] [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: 01/27/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Bacillus thuringiensis (Bt) is a widely used microbial pesticide. However, its duration of effectiveness is greatly shortened due to the irradiation of ultraviolet rays, which seriously hinders the application of Bt preparations. Therefore, it is of great importance to study the resistance mechanism of Bt to UV at the molecular level to improve the UV-resistance of Bt strains. In order to know the functional genes in the UV resistance, the genome of UV-induced mutant Bt LLP29-M19 was re-sequenced and compared with the original strain Bt LLP29. It was shown that there were 1318 SNPs, 31 InDels, and 206 SV between the mutant strain and the original strain Bt LLP29 after UV irradiation, which were then analyzed for gene annotation. Additionally, a mutated gene named yqhH, a member of helicase superfamily II, was detected as an important candidate. Then, yqhH was expressed and purified successfully. Through the result of the enzymatic activity in vitro, yqhH was found to have ATP hydrolase and helicase activities. In order to further verify its function, the yqhH gene was knocked out and complemented by homologous recombinant gene knockout technology. The survival rate of the knockout mutant strain Bt LLP29-ΔyqhH was significantly lower than that of the original strain Bt LLP29 and the back-complemented strain Bt LLP29-ΔyqhH-R after treated with UV. Meanwhile, the total helicase activity was not significantly different on whether Bt carried yqhH or not. All of these greatly enrich important molecular mechanisms of Bt when it is in UV stress.
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Affiliation(s)
- Weibo Ma
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiong Guan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Miao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lingling Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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4
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Effects of Bacillus subtilis Natto Strains on Antiviral Responses in Resiquimod-Stimulated Human M1-Phenotype Macrophages. Foods 2023; 12:foods12020313. [PMID: 36673407 PMCID: PMC9858497 DOI: 10.3390/foods12020313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Bacillus subtilis natto is used in the production of natto, a traditional fermented soy food, and has beneficial immunomodulatory effects in humans. Single-stranded RNA (ssRNA) viruses, including influenza and coronavirus, often cause global pandemics. We proposed a human cell culture model mimicking ssRNA viral infection and investigated the ability of B. subtilis natto to induce antiviral effects in the model. The gene expressions were analyzed using quantitative real-time reverse transcription PCR. M1-phenotype macrophages derived from THP-1 cells strongly express the Toll-like receptor 8 (76.2-hold), CD80 (64.2-hold), and CCR7 (45.7-hold) mRNA compared to M0 macrophages. One µg/mL of resiquimod (RSQ)-stimulation induced the expression of IRF3 (1.9-hold), CXCL10 (14.5-hold), IFNβ1 (3.5-hold), ISG20 (4.4-hold), and MxA (1.7-hold) mRNA in the M1-phenotype macrophages. Based on these results, the RSQ-stimulated M1-phenotype macrophages were used as a cell culture model mimicking ssRNA viral infection. Moreover, the B. subtilis natto XF36 strain induced the expression of genes associated with antiviral activities (IFNβ1, IFNλ1, ISG20, and RNase L) and anti-inflammatory activities (IL-10) in the cell culture model. Thus, it is suggested that the XF36 suppresses viral infections and excessive inflammation by inducing the expression of genes involved in antiviral and anti-inflammatory activities.
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Tomofuji Y, Kishikawa T, Maeda Y, Ogawa K, Otake-Kasamoto Y, Kawabata S, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Takagaki M, Oyama N, Todo K, Yamamoto K, Sonehara K, Yagita M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Shinzaki S, Nakamura S, Iijima H, Inohara H, Kishima H, Takehara T, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases. CELL GENOMICS 2022; 2:100219. [PMID: 36778050 PMCID: PMC9903723 DOI: 10.1016/j.xgen.2022.100219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/27/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022]
Abstract
We reconstructed 19,084 prokaryotic and 31,395 viral genomes from 787 Japanese gut metagenomes as Japanese metagenome-assembled genomes (JMAG) and Japanese Virus Database (JVD), which are large microbial genome datasets for a single population. Population-specific enrichment of the Bacillus subtilis and β-porphyranase among the JMAG could derive from the Japanese traditional food natto (fermented soybeans) and nori (laver), respectively. Dairy-related Enterococcus_B lactis and Streptococcus thermophilus were nominally associated with the East Asian-specific missense variant rs671:G>A in ALDH2, which was associated with dairy consumption. Of the species-level viral genome clusters in the JVD, 62.9% were novel. The β crAss-like phage composition was low among the Japanese but relatively high among African and Oceanian peoples. Evaluations of the association between crAss-like phages and diseases showed significant disease-specific associations. Our large catalog of virus-host pairs identified the positive correlation between the abundance of the viruses and their hosts.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Corresponding author
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kotaro Ogawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Yuriko Otake-Kasamoto
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Makoto Kinoshita
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Naoki Oyama
- Department of Stroke Medicine, Kawasaki Medical School, Kurashiki 701-0192, Japan
| | - Kenichi Todo
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Department of Pediatrics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan
| | - Mayu Yagita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Akiko Hosokawa
- Department of Neurology, Suita Municipal Hospital, Suita 564-8567, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shinichiro Shinzaki
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Hideki Iijima
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Tetsuo Takehara
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan,Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan,Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan,Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Corresponding author
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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: 2.0] [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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7
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Afzaal M, Saeed F, Islam F, Ateeq H, Asghar A, Shah YA, Ofoedu CE, Chacha JS. Nutritional Health Perspective of Natto: A Critical Review. Biochem Res Int 2022; 2022:5863887. [PMID: 36312453 PMCID: PMC9616652 DOI: 10.1155/2022/5863887] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/25/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Natto, a traditional soy food fermented by Bacillus subtilis, is made by steaming or cooking soaked soybean seeds, inoculating them with the bacteria, and then letting them sit for an incubation period. Natto soya has grown popular because of its nutritional importance and health advantages. As a result, farmers have more opportunities, thanks to the natto soybean market. For the natto soybean market to remain stable and grow, improved soybean cultivars with enhanced natto quality traits are essential. Natto's high-quality attributes are influenced by the bacteria strain, processing parameters, and soybean variety. Natto has a specific flavor and aroma with a slimy, sticky consistency. Natto possesses various therapeutic potentials and contains a range of essential nutrients and bioactive compounds, i.e., nattokinase, soybean isoflavone, γ-polyglutamic acid, vitamin K2, and biogenic amines. Bacterial species, processing conditions, and cultivars of soybean determine the quality characteristics of natto. Natto food is higher in menaquinone-7 and contains 100 times more menaquinone-7 than most cheeses. The present review highlights the production technology, microbiology, nutritional composition, and therapeutic potentials of natto.
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Affiliation(s)
- Muhammad Afzaal
- Department of Food Science, Government College University, Faisalabad, Pakistan
| | - Farhan Saeed
- Department of Food Science, Government College University, Faisalabad, Pakistan
| | - Fakhar Islam
- Department of Food Science, Government College University, Faisalabad, Pakistan
| | - Huda Ateeq
- Department of Food Science, Government College University, Faisalabad, Pakistan
| | - Aasma Asghar
- Department of Home Economics, Government College University, Faisalabad, Pakistan
| | - Yasir Abbas Shah
- Department of Food Science, Government College University, Faisalabad, Pakistan
| | - Chigozie E. Ofoedu
- Department of Food Science and Technology, School of Engineering and Engineering Technology, Federal University of Technology, Owerri, Imo State, Nigeria
| | - James S. Chacha
- Department of Food Science and Agroprocessing, Sokoine University of Agriculture, P.O. Box 3006, Chuo Kikuu, Morogoro, Tanzania
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Itaya M, Sato M, Watanabe S, Kataoka M. Effective plasmid delivery to a plasmid-free Bacillus natto strain by a conjugational transfer system. J Biochem 2022; 172:313-319. [PMID: 36047835 DOI: 10.1093/jb/mvac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
In this study, a Bacillus natto strain named NEST141 was constructed. The strain carries no plasmids and is an authentic proline auxotroph-a feature that confers effective selection conditions for plasmids transferred from a donor, such as B. subtilis 168, via a pLS20-based conjugational transfer system. We have provided a standard effective protocol for the delivery of plasmids larger than 50 kilobase pairs. These results indicate that the B. natto NEST141 strain can become a standard model, like B. subtilis 168, for extensive genetic engineering with diverse applications.
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Affiliation(s)
- Mitsuhiro Itaya
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano-shi, Nagano 380-8553, Japan.,Institute for Advanced Biosciences, Keio University, Nipponkoku, Tsuruoka, Yamagata 997-0017, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Tsuruoka, Yamagata 997-0017, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masakazu Kataoka
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano-shi, Nagano 380-8553, Japan
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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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Lin YC, Wu CY, Huang HT, Lu MK, Hu WS, Lee KT. Bacillus subtilis natto Derivatives Inhibit Enterococcal Biofilm Formation via Restructuring of the Cell Envelope. Front Microbiol 2021; 12:785351. [PMID: 34956152 PMCID: PMC8695906 DOI: 10.3389/fmicb.2021.785351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 01/15/2023] Open
Abstract
Enterococcus faecalis is considered a leading cause of hospital-acquired infections. Treatment of these infections has become a major challenge for clinicians because some E. faecalis strains are resistant to multiple clinically used antibiotics. Moreover, the presence of E. faecalis biofilms can make infections with E. faecalis more difficult to eradicate with current antibiotic therapies. Thus, our aim in this study was to investigate the effects of probiotic derivatives against E. faecalis biofilm formation. Bacillus subtilis natto is a probiotic strain isolated from Japanese fermented soybean foods, and its culture fluid potently inhibited adherence to Caco-2 cell monolayers, aggregation, and biofilm production without inhibiting the growth of E. faecalis. An apparent decrease in the thickness of E. faecalis biofilms was observed through confocal laser scanning microscopy. In addition, exopolysaccharide synthesis in E. faecalis biofilms was reduced by B. subtilis natto culture fluid treatment. Carbohydrate composition analysis also showed that carbohydrates in the E. faecalis cell envelope were restructured. Furthermore, transcriptome sequencing revealed that the culture fluid of B. subtilis natto downregulated the transcription of genes involved in the WalK/WalR two-component system, peptidoglycan biosynthesis and membrane glycolipid biosynthesis, which are all crucial for E. faecalis cell envelope synthesis and biofilm formation. Collectively, our work shows that some derivatives present in the culture fluid of B. subtilis natto may be useful for controlling E. faecalis biofilms.
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Affiliation(s)
- Yu-Chieh Lin
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chun-Yi Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Hung-Tse Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan.,Ministry of Health and Welfare, National Research Institute of Chinese Medicine, Taipei, Taiwan
| | - Mei-Kuang Lu
- Ministry of Health and Welfare, National Research Institute of Chinese Medicine, Taipei, Taiwan.,Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, United States
| | - Kung-Ta Lee
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
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11
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Thapa P, Thapa A, Khadka S, Sapkota S, Panta OP, Sharma S, Karki TB, Poudel P. Screening and characterization of potent poly glutamic acid producing Bacillus sp. isolated from Kinema, water and soil samples. Heliyon 2021; 7:e07715. [PMID: 34401591 PMCID: PMC8358410 DOI: 10.1016/j.heliyon.2021.e07715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/18/2021] [Accepted: 08/02/2021] [Indexed: 12/30/2022] Open
Abstract
Microbially produced gamma poly glutamic acid (γ-PGA) is a commercially important biopolymer with many applications in foods and various other substances and are abundantly used in different parts of the world. With an aim to study the potent γ-PGA producing Bacillus species, a total of 47 different samples (Kinema, soil, and water) were randomly collected from different locations across the country, and Bacillus sp. were selectively isolated, screened, and characterized by performing physiological, biochemical, morphological, and 16S rRNA gene sequencing. The microbial production of γ-PGA was assayed with the selected isolates on the PGA medium and the metabolite obtained was recovered by ethanol precipitation method and further characterized by thin-layer chromatography (TLC). Thermotolerance (25-60 °C), pH tolerance (4-9), and NaCl tolerance (1-9%) tests were performed to optimize the bacterial growth and γ-PGA production and its viscosity were measured by Ostwald's viscometer. Out of 145 randomly selected colonies, 63 isolates were Gram-positive, rods, and endospore producers and were presumptively confirmed as genus Bacillus. Higher growth of γ-PGA producers were reported in 22 isolates and was found at optimum conditions such as temperature (30-37 °C), pH (6.5-7), incubation time (3 days), and NaCl concentration (3%) and γ-PGA thus produced was further verified by TLC with the retention factor (RF) value 0.27. The potent isolates were closely similar to Bacillus subtilis subsp. stercoris, Bacillus cereus, Bacillus paranthracis, and Bacillus licheniformis etc. Based on the findings of the study, B. licheniformis is the most potent γ-PGA producing Bacillus sp. which can further be used for the commercial production of γ-PGA. To the best of our knowledge, there is yet no published research from Nepal showing the production of the γ-PGA although microbially produced γ-PGA are the major constituents in some popular foods in particular communities of the country.
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Affiliation(s)
- Punam Thapa
- Department of Microbiology, National College (NIST), Tribhuvan University, P.O. Box: 8659, Khusibu, Naya Bazar, Kathmandu, Nepal
| | - Alina Thapa
- State Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sujan Khadka
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sanjeep Sapkota
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Om Prakash Panta
- Department of Microbiology, National College (NIST), Tribhuvan University, P.O. Box: 8659, Khusibu, Naya Bazar, Kathmandu, Nepal
| | - Suprina Sharma
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, 44601, Nepal
| | - Tika Bahadur Karki
- Department of Microbiology, National College (NIST), Tribhuvan University, P.O. Box: 8659, Khusibu, Naya Bazar, Kathmandu, Nepal
| | - Pramod Poudel
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, 44618, Nepal
- Research Division, University Grants Commission (UGC), P.O. Box: 10796, Sanothimi, Bhaktapur, Nepal
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12
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Lin YC, Chen EHL, Chen RPY, Dunny GM, Hu WS, Lee KT. Probiotic Bacillus Affects Enterococcus faecalis Antibiotic Resistance Transfer by Interfering with Pheromone Signaling Cascades. Appl Environ Microbiol 2021; 87:e0044221. [PMID: 33893118 PMCID: PMC8316027 DOI: 10.1128/aem.00442-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/16/2021] [Indexed: 01/02/2023] Open
Abstract
Enterococcus faecalis, a member of the commensal flora in the human gastrointestinal tract, has become a threatening nosocomial pathogen because it has developed resistance to many known antibiotics. More concerningly, resistance gene-carrying E. faecalis cells may transfer antibiotic resistance to resistance-free E. faecalis cells through their unique quorum sensing-mediated plasmid transfer system. Therefore, we investigated the role of probiotic bacteria in the transfer frequency of the antibiotic resistance plasmid pCF10 in E. faecalis populations to mitigate the spread of antibiotic resistance. Bacillus subtilis subsp. natto is a probiotic strain isolated from Japanese fermented soybean foods, and its culture fluid potently inhibited pCF10 transfer by suppressing peptide pheromone activity from chromosomally encoded CF10 (cCF10) without inhibiting E. faecalis growth. The inhibitory effect was attributed to at least one 30- to 50-kDa extracellular protease present in B. subtilis subsp. natto. Nattokinase of B. subtilis subsp. natto was involved in the inhibition of pCF10 transfer and cleaved cCF10 (LVTLVFV) into LVTL plus VFV fragments. Moreover, the cleavage product LVTL (L peptide) interfered with the conjugative transfer of pCF10. In addition to cCF10, faecalis-cAM373 and gordonii-cAM373, which are mating inducers of vancomycin-resistant E. faecalis, were also cleaved by nattokinase, indicating that B. subtilis subsp. natto can likely interfere with vancomycin resistance transfer in E. faecalis. Our work shows the feasibility of applying fermentation products of B. subtilis subsp. natto and L peptide to mitigate E. faecalis antibiotic resistance transfer. IMPORTANCE Enterococcus faecalis is considered a leading cause of hospital-acquired infections. Treatment of these infections has become a major challenge for clinicians because some E. faecalis strains are resistant to multiple clinically used antibiotics. Moreover, antibiotic resistance genes can undergo efficient intra- and interspecies transfer via E. faecalis peptide pheromone-mediated plasmid transfer systems. Therefore, this study provided the first experimental demonstration that probiotics are a feasible approach for interfering with conjugative plasmid transfer between E. faecalis strains to stop the transfer of antibiotic resistance. We found that the extracellular protease(s) of Bacillus subtilis subsp. natto cleaved peptide pheromones without affecting the growth of E. faecalis, thereby reducing the frequency of conjugative plasmid transfer. In addition, a specific cleaved pheromone fragment interfered with conjugative plasmid transfer. These findings provide a potential probiotic-based method for interfering with the transfer of antibiotic resistance between E. faecalis strains.
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Affiliation(s)
- Yu-Chieh Lin
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Eric H.-L. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Rita P.-Y. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kung-Ta Lee
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
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13
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Steinke K, Mohite OS, Weber T, Kovács ÁT. Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex. mSystems 2021; 6:e00057-21. [PMID: 33688015 PMCID: PMC8546965 DOI: 10.1128/msystems.00057-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/19/2021] [Indexed: 12/20/2022] Open
Abstract
Microbes produce a plethora of secondary (or specialized) metabolites that, although not essential for primary metabolism, benefit them to survive in the environment, communicate, and influence cell differentiation. Biosynthetic gene clusters (BGCs), responsible for the production of these secondary metabolites, are readily identifiable on bacterial genome sequences. Understanding the phylogeny and distribution of BGCs helps us to predict the natural product synthesis ability of new isolates. Here, we examined 310 genomes from the Bacillus subtilis group, determined the inter- and intraspecies patterns of absence/presence for all BGCs, and assigned them to defined gene cluster families (GCFs). This allowed us to establish patterns in the distribution of both known and unknown products. Further, we analyzed variations in the BGC structures of particular families encoding natural products, such as plipastatin, fengycin, iturin, mycosubtilin, and bacillomycin. Our detailed analysis revealed multiple GCFs that are species or clade specific and a few others that are scattered within or between species, which will guide exploration of the chemodiversity within the B. subtilis group. Surprisingly, we discovered that partial deletion of BGCs and frameshift mutations in selected biosynthetic genes are conserved within phylogenetically related isolates, although isolated from around the globe. Our results highlight the importance of detailed genomic analysis of BGCs and the remarkable phylogenetically conserved erosion of secondary metabolite biosynthetic potential in the B. subtilis group.IMPORTANCE Members of the B. subtilis species complex are commonly recognized producers of secondary metabolites, among those, the production of antifungals, which makes them promising biocontrol strains. While there are studies examining the distribution of well-known secondary metabolites in Bacilli, intraspecies clade-specific distribution has not been systematically reported for the B. subtilis group. Here, we report the complete biosynthetic potential within the B. subtilis group to explore the distribution of the biosynthetic gene clusters and to reveal an exhaustive phylogenetic conservation of secondary metabolite production within Bacillus that supports the chemodiversity within this species complex. We identify that certain gene clusters acquired deletions of genes and particular frameshift mutations, rendering them inactive for secondary metabolite biosynthesis, a conserved genetic trait within phylogenetically conserved clades of certain species. The overview guides the assignment of the secondary metabolite production potential of newly isolated Bacillus strains based on genome sequence and phylogenetic relatedness.
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Affiliation(s)
- Kat Steinke
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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14
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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: 37] [Impact Index Per Article: 12.3] [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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15
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Kada S, Sekine Y, Yoshikawa H. Stabilization of <i>γ</i>-PGA Production by a <i>recA </i>Mutant in <i>Bacillus subtilis</i>. J JPN SOC FOOD SCI 2021. [DOI: 10.3136/nskkk.68.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Shigeki Kada
- Central Research Institute, Mizkan Holdings Co., Ltd
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University
| | - Hirofumi Yoshikawa
- Department of Bioscience, Graduate School of Agricultural Science, Tokyo University of Agriculture
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16
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Abstract
Fermentation processes in foods often lead to changes in nutritional and biochemical quality relative to the starting ingredients. Fermented foods comprise very complex ecosystems consisting of enzymes from raw ingredients that interact with the fermenting microorganisms’ metabolic activities. Fermenting microorganisms provide a unique approach towards food stability via physical and biochemical changes in fermented foods. These fermented foods can benefit consumers compared to simple foods in terms of antioxidants, production of peptides, organoleptic and probiotic properties, and antimicrobial activity. It also helps in the levels of anti-nutrients and toxins level. The quality and quantity of microbial communities in fermented foods vary based on the manufacturing process and storage conditions/durability. This review contributes to current research on biochemical changes during the fermentation of foods. The focus will be on the changes in the biochemical compounds that determine the characteristics of final fermented food products from original food resources.
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17
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Sugiura H, Nagase A, Oiki S, Mikami B, Watanabe D, Hashimoto W. Bacterial inducible expression of plant cell wall-binding protein YesO through conflict between Glycine max and saprophytic Bacillus subtilis. Sci Rep 2020; 10:18691. [PMID: 33122638 PMCID: PMC7596534 DOI: 10.1038/s41598-020-75359-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/07/2020] [Indexed: 01/22/2023] Open
Abstract
Saprophytic bacteria and plants compete for limited nutrient sources. Bacillus subtilis grows well on steamed soybeans Glycine max to produce the fermented food, natto. Here we focus on bacterial responses in conflict between B. subtilis and G. max. B. subtilis cells maintained high growth rates specifically on non-germinating, dead soybean seeds. On the other hand, viable soybean seeds with germinating capability attenuated the initial growth of B. subtilis. Thus, B. subtilis cells may trigger saprophytic growth in response to the physiological status of G. max. Scanning electron microscope observation indicated that B. subtilis cells on steamed soybeans undergo morphological changes to form apertures, demonstrating cell remodeling during saprophytic growth. Further, transcriptomic analysis of B. subtilis revealed upregulation of the gene cluster, yesOPQR, in colonies growing on steamed soybeans. Recombinant YesO protein, a putative, solute-binding protein for the ATP-binding cassette transporter system, exhibited an affinity for pectin-derived oligosaccharide from plant cell wall. The crystal structure of YesO, in complex with the pectin oligosaccharide, was determined at 1.58 Å resolution. This study expands our knowledge of defensive and offensive strategies in interspecies competition, which may be promising targets for crop protection and fermented food production.
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Affiliation(s)
- Haruka Sugiura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ayumi Nagase
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Sayoko Oiki
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Daisuke Watanabe
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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18
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Schönbichler A, Díaz-Moreno SM, Srivastava V, McKee LS. Exploring the Potential for Fungal Antagonism and Cell Wall Attack by Bacillus subtilis natto. Front Microbiol 2020; 11:521. [PMID: 32296406 PMCID: PMC7136451 DOI: 10.3389/fmicb.2020.00521] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
To develop more ecologically sustainable agricultural practices requires that we reduce our reliance on synthetic chemical pesticides for crop protection. This will likely involve optimized biocontrol approaches - the use of beneficial soil microbes to attack potential plant pathogens to protect plants from diseases. Many bacterial species, including strains of Bacillus subtilis, have been explored for their biocontrol properties, as they can control the growth of harmful fungi, often by disrupting the fungal cell wall. A strain that is not often considered for this particular application is Bacillus subtilis natto, primarily known for fermenting soybeans via cell wall degradation in the Japanese probiotic dish "natto." Because deconstruction of the fungal cell wall is considered an important biocontrol trait, we were motivated to explore the possible anti-fungal properties of the B. subtilis natto strain. We show that B. subtilis natto can use complex fungal material as a carbon source for growth, and can effectively deconstruct fungal cell walls. We found degradation of fungal cell wall proteins, and showed that growth on a mix of peptides was very strong. We also found that intact fungal cell walls can induce the secretion of chitinases and proteases. Surprisingly, we could show that chitin, the bulk component of the fungal cell wall, does not permit successful growth of the natto strain or induce the secretion of chitinolytic enzymes, although these were produced during exposure to proteins or to complex fungal material. We have further shown that protease secretion is likely a constitutively enabled mechanism for nutrient scavenging by B. subtilis natto, as well as a potent tool for the degradation of fungal cell walls. Overall, our data highlight B. subtilis natto as a promising candidate for biocontrol products, with relevant behaviors that can be optimized by altering growth conditions. Whereas it is common for bacterial biocontrol products to be supplied with chitin or chitosan as a priming polysaccharide, our data indicate that this is not a useful approach with this particular bacterium, which should instead be supplied with either glucose or attenuated fungal material.
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Affiliation(s)
- Anna Schönbichler
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Sara M Díaz-Moreno
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lauren Sara McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Center, Stockholm, Sweden
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19
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Rahman MS, Gulshan MA, Matsumura S, Ikawa Y. Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:715-729. [PMID: 32039645 DOI: 10.1080/15257770.2019.1687909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The modular structure of bacterial ribonuclease P (RNase P) ribozymes, which recognize tertiary structures of precursor tRNAs (pre-tRNAs) to cleave their 5' leader sequence, can be dissected physically into the two structured domain RNAs (S-domain and C-domain). Separately prepared S-domain RNA and C-domain RNA assemble to form bimolecular forms of RNase P ribozymes. We analyzed the effects of polyethylene glycols (PEGs) on pre-tRNA cleavage catalyzed by bimolecular RNase P ribozymes to examine the effects of molecular crowding on the reaction. PEG molecular crowders significantly enhanced the activities of bimolecular RNase P ribozymes, some of which were hardly active without PEGs.
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Affiliation(s)
- Md Sohanur Rahman
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Mst Ara Gulshan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
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20
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Tamang JP, Cotter PD, Endo A, Han NS, Kort R, Liu SQ, Mayo B, Westerik N, Hutkins R. Fermented foods in a global age: East meets West. Compr Rev Food Sci Food Saf 2020; 19:184-217. [PMID: 33319517 DOI: 10.1111/1541-4337.12520] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]
Abstract
Fermented foods and alcoholic beverages have long been an important part of the human diet in nearly every culture on every continent. These foods are often well-preserved and serve as stable and significant sources of proteins, vitamins, minerals, and other nutrients. Despite these common features, however, many differences exist with respect to substrates and products and the types of microbes involved in the manufacture of fermented foods and beverages produced globally. In this review, we describe these differences and consider the influence of geography and industrialization on fermented foods manufacture. Whereas fermented foods produced in Europe, North America, Australia, and New Zealand usually depend on defined starter cultures, those made in Asia and Africa often rely on spontaneous fermentation. Likewise, in developing countries, fermented foods are not often commercially produced on an industrial scale. Although many fermented products rely on autochthonous microbes present in the raw material, for other products, the introduction of starter culture technology has led to greater consistency, safety, and quality. The diversity and function of microbes present in a wide range of fermented foods can now be examined in detail using molecular and other omic approaches. The nutritional value of fermented foods is now well-appreciated, especially in resource-poor regions where yoghurt and other fermented foods can improve public health and provide opportunities for economic development. Manufacturers of fermented foods, whether small or large, should follow Good Manufacturing Practices and have sustainable development goals. Ultimately, preferences for fermented foods and beverages depend on dietary habits of consumers, as well as regional agricultural conditions and availability of resources.
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Affiliation(s)
- Jyoti Prakash Tamang
- DAICENTER and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Paul D Cotter
- Food Biosciences, Principal Research Officer, Teagasc Food Research Centre, Moorepark, Fermoy and APC Microbiome Ireland, Cork, Ireland
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Tokyo, Japan
| | - Nam Soo Han
- Department of Food Science and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Remco Kort
- Department of Molecular Cell Biology, VU University Amsterdam, The Netherlands.,Yoba for Life foundation, Amsterdam, The Netherlands
| | - Shao Quan Liu
- Food Science and Technology Programme, National University of Singapore
| | - Baltasar Mayo
- Department of Microbiology and Chemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Nieke Westerik
- Department of Molecular Cell Biology, VU University Amsterdam, The Netherlands.,Yoba for Life foundation, Amsterdam, The Netherlands
| | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska
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21
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Vitamin K as a Diet Supplement with Impact in Human Health: Current Evidence in Age-Related Diseases. Nutrients 2020; 12:nu12010138. [PMID: 31947821 PMCID: PMC7019739 DOI: 10.3390/nu12010138] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/24/2019] [Accepted: 12/31/2019] [Indexed: 12/12/2022] Open
Abstract
Vitamin K health benefits have been recently widely shown to extend beyond blood homeostasis and implicated in chronic low-grade inflammatory diseases such as cardiovascular disease, osteoarthritis, dementia, cognitive impairment, mobility disability, and frailty. Novel and more efficient nutritional and therapeutic options are urgently needed to lower the burden and the associated health care costs of these age-related diseases. Naturally occurring vitamin K comprise the phylloquinone (vitamin K1), and a series of menaquinones broadly designated as vitamin K2 that differ in source, absorption rates, tissue distribution, bioavailability, and target activity. Although vitamin K1 and K2 sources are mainly dietary, consumer preference for diet supplements is growing, especially when derived from marine resources. The aim of this review is to update the reader regarding the specific contribution and effect of each K1 and K2 vitamers in human health, identify potential methods for its sustainable and cost-efficient production, and novel natural sources of vitamin K and formulations to improve absorption and bioavailability. This new information will contribute to foster the use of vitamin K as a health-promoting supplement, which meets the increasing consumer demand. Simultaneously, relevant information on the clinical context and direct health consequences of vitamin K deficiency focusing in aging and age-related diseases will be discussed.
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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: 7.0] [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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Caputo A, Fournier PE, Raoult D. Genome and pan-genome analysis to classify emerging bacteria. Biol Direct 2019; 14:5. [PMID: 30808378 PMCID: PMC6390601 DOI: 10.1186/s13062-019-0234-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. With the help of pan-genomic analyses, species can be redefined, and new species definitions generated. Results Genomics, coupled with culturomics, has led to the discovery of many novel bacterial species or genera, including Akkermansia muciniphila and Microvirga massiliensis. Using the genome to define species has been applied within the genus Klebsiella. A discontinuity or an abrupt break in the core/pan-genome ratio can uncover novel species. Conclusions Applying genomic and pan-genomic analyses to the reclassification of other bacterial species or genera will be important in the future of medical microbiology. The pan-genome is one of many new innovative tools in bacterial taxonomy. Reviewers This article was reviewed by William Martin, Eric Bapteste and James Mcinerney. Open peer review Reviewed by William Martin, Eric Bapteste and James Mcinerney.
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Affiliation(s)
- Aurélia Caputo
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
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24
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Itaya M, Nagasaku M, Shimada T, Ohtani N, Shiwa Y, Yoshikawa H, Kaneko S, Tomita M, Sato M. Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids. FEMS Microbiol Lett 2019; 366:5307882. [PMID: 30726909 DOI: 10.1093/femsle/fnz032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis (natto) is generally regarded as a safe bacterium and used as a host for the production of several materials. However, genetic engineering of B. subtilis (natto) is not well established because of poor DNA delivery methods and the lack of a standard strain for the aim. Here, we developed a genetic delivery tool in B. subtilis (natto) using the pLS20 conjugational plasmid (65 kbp). Transmission of pLS20 from B. subtilis 168 to wild-type B. subtilis (natto) did not occur via established mating protocols. We isolated B. subtilis (natto) mutants showing dramatically increased recipient activity. Whole-genome sequence analyses revealed three common alterations: mutations in the restriction endonuclease gene and in the methyl-accepting chemotaxis protein gene, and a 43-kbp deletion at the genome replication termination locus. A representative strain named NEST116 was generated as the first B. subtilis (natto) strain suitable for exploring pLS20-based genetic engineering.
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Affiliation(s)
- Mitsuhiro Itaya
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Mayumi Nagasaku
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Tomoe Shimada
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Naoto Ohtani
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shinya Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
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25
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Kubo Y, Sriyam S, Nakagawa R, Kimura K. A Survey of Phage Contamination in Natto-producing Factories and Development of Phage-resistant Bacillus subtilis (natto) Strains. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2018. [DOI: 10.3136/fstr.24.485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yuji Kubo
- Industrial Technology Institute of Ibaraki Prefecture
| | - Supawadee Sriyam
- Applied Microbiology Unit, Food Research Institute-National Agriculture and Food Research Organization (NFRI-NARO)
- Department of Agro-Industry, Faculty of Science and Agricultural Technology, Rajamangala University of Technology Lanna
| | | | - Keitarou Kimura
- Applied Microbiology Unit, Food Research Institute-National Agriculture and Food Research Organization (NFRI-NARO)
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26
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Whole genome sequencing and functional features of UMX-103: a new Bacillus strain with biosurfactant producing capability. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0550-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Willms IM, Hoppert M, Hertel R. Characterization of Bacillus Subtilis Viruses vB_BsuM-Goe2 and vB_BsuM-Goe3. Viruses 2017; 9:E146. [PMID: 28604650 PMCID: PMC5490822 DOI: 10.3390/v9060146] [Citation(s) in RCA: 21] [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: 03/27/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 12/25/2022] Open
Abstract
The Spounavirinae viruses are ubiquitous in nature and have an obligatory virulent lifestyle. They infect Firmicutes, a bacterial phylum containing an array of environmental non-pathogenic and pathogenic organisms. To expand the knowledge of this viral subfamily, new strains were isolated and investigated in this study. Here we present two new viruses, vB_BsuM-Goe2 and vB_BsuM-Goe3, isolated from raw sewage and infecting Bacillus species. Both were morphologically classified via transmission electron microscopy (TEM) as members of the Spounavirinae subfamily belonging to the Myoviridae family. Genomic sequencing and analyses allowed further affiliation of vB_BsuM-Goe2 to the SPO1-like virus group and vB_BsuM-Goe3 to the Bastille-like virus group. Experimentally determined adsorption constant, latency period, burst size and host range for both viruses revealed different survival strategies. Thus vB_BsuM-Goe2 seemed to rely on fewer host species compared to vB_BsuM-Goe3, but efficiently recruits those. Stability tests pointed out that both viruses are best preserved in LB-medium or TMK-buffer at 4 or 21 °C, whereas cryopreservation strongly reduced viability.
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Affiliation(s)
- Inka M Willms
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany.
| | - Michael Hoppert
- Department of General Microbiology, Institute of Microbiology and Genetics, University of Goettingen, 37077 Goettingen, Germany.
| | - Robert Hertel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany.
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28
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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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29
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Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B. Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB). Stand Genomic Sci 2016; 11:80. [PMID: 27777650 PMCID: PMC5062929 DOI: 10.1186/s40793-016-0199-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 10/04/2016] [Indexed: 11/18/2022] Open
Abstract
Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermodynamic equilibrium and of considerable importance in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding 3450 predicted protein-encoding genes, of which only 1472 (43 %) have been assigned tentative functions. The genome encodes further 44 tRNA genes and three rRNA genes (5S, 16S and 23S rRNA). This study presents assembling and annotation features as well as genomic traits related to ammonia tolerance and methanogenesis.
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Affiliation(s)
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07 Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, SE 750 07 Sweden
| | - Bettina Müller
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07 Sweden
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30
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Willms IM, Hertel R. Phage vB_BsuP-Goe1: the smallest identified lytic phage of Bacillus subtilis. FEMS Microbiol Lett 2016; 363:fnw208. [PMID: 27609230 DOI: 10.1093/femsle/fnw208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2016] [Indexed: 01/20/2023] Open
Abstract
Currently, interest in phage science is on the rise again as this subject remains largely unexplored, and its potential diversity mainly untapped. Here, we present phage vB_BsuP-Goe1, a new isolate that infects Bacillus subtilis The phage forms round plaques with a matt outline on agar plates containing a B. subtilis Δ6 lawn. Transmission electron microscopy and genomic analyses revealed that phage vB_BsuP-Goe1 belongs to the Podoviridae family as a new member of the Phi29likevirus genus. The phage genome comprises 18 379 bp that encode for one RNA gene and for 24 open reading frames. Phage vB_BsuP-Goe1 clusters with phage B103 and Nf within the Phi29likevirus genus and is currently the smallest member of this genus. Genome comparison with members of the Phi29likevirus genus reveals a conserved gene set coding for essential replication and morphogenesis functions while the genome extremities are more prone to gene and genome organisation variability.
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Affiliation(s)
- Inka Marie Willms
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Robert Hertel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
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31
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Chettri R, Bhutia MO, Tamang JP. Poly-γ-Glutamic Acid (PGA)-Producing Bacillus Species Isolated from Kinema, Indian Fermented Soybean Food. Front Microbiol 2016; 7:971. [PMID: 27446012 PMCID: PMC4914496 DOI: 10.3389/fmicb.2016.00971] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Kinema, an ethnic fermented, non-salted and sticky soybean food is consumed in the eastern part of India. The stickiness is one of the best qualities of good kinema preferred by consumers, which is due to the production of poly-γ-glutamic acid (PGA). Average load of Bacillus in kinema was 107 cfu/g and of lactic acid bacteria was 103 cfu/g. Bacillus spp. were screened for PGA-production and isolates of lactic acid bacteria were also tested for degradation of PGA. Only Bacillus produced PGA, none of lactic acid bacteria produced PGA. PGA-producing Bacillus spp. were identified by phenotypic characterization and also by 16S rRNA gene sequencing as Bacillus subtilis, B. licheniformis and B. sonorensis.
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Affiliation(s)
- Rajen Chettri
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok India
| | - Meera O Bhutia
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok India
| | - Jyoti P Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok India
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32
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Draft Genome Sequence of Bacillus subtilis subsp. natto Strain CGMCC 2108, a High Producer of Poly-γ-Glutamic Acid. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00426-16. [PMID: 27231363 PMCID: PMC4882944 DOI: 10.1128/genomea.00426-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the 4.1-Mb draft genome sequence of Bacillus subtilis subsp. natto strain CGMCC 2108, a high producer of poly-γ-glutamic acid (γ-PGA). This sequence will provide further help for the biosynthesis of γ-PGA and will greatly facilitate research efforts in metabolic engineering of B. subtilis subsp. natto strain CGMCC 2108.
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33
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Tamang JP, Shin DH, Jung SJ, Chae SW. Functional Properties of Microorganisms in Fermented Foods. Front Microbiol 2016; 7:578. [PMID: 27199913 PMCID: PMC4844621 DOI: 10.3389/fmicb.2016.00578] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/08/2016] [Indexed: 12/25/2022] Open
Abstract
Fermented foods have unique functional properties imparting some health benefits to consumers due to presence of functional microorganisms, which possess probiotics properties, antimicrobial, antioxidant, peptide production, etc. Health benefits of some global fermented foods are synthesis of nutrients, prevention of cardiovascular disease, prevention of cancer, gastrointestinal disorders, allergic reactions, diabetes, among others. The present paper is aimed to review the information on some functional properties of the microorganisms associated with fermented foods and beverages, and their health-promoting benefits to consumers.
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Affiliation(s)
- Jyoti P. Tamang
- Department of Microbiology, School of Life Sciences, Sikkim UniversityGangtok, India
| | - Dong-Hwa Shin
- Shindonghwa Food Research InstituteJeonju, South Korea
- Clinical Trial Center for Functional Foods, Chonbuk National University HospitalJeonju, South Korea
| | - Su-Jin Jung
- Clinical Trial Center for Functional Foods, Chonbuk National University HospitalJeonju, South Korea
| | - Soo-Wan Chae
- Clinical Trial Center for Functional Foods, Chonbuk National University HospitalJeonju, South Korea
- Division of Pharmacology, Chonbuk National University Medical SchoolJeonju, South Korea
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34
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Tamang JP, Watanabe K, Holzapfel WH. Review: Diversity of Microorganisms in Global Fermented Foods and Beverages. Front Microbiol 2016; 7:377. [PMID: 27047484 PMCID: PMC4805592 DOI: 10.3389/fmicb.2016.00377] [Citation(s) in RCA: 335] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/08/2016] [Indexed: 01/03/2023] Open
Abstract
Culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. Traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. Holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. The application of culture-independent technique has thrown new light on the diversity of a number of hitherto unknown and non-cultural microorganisms in naturally fermented foods. Functional bacterial groups ("phylotypes") may be reflected by their mRNA expression in a particular substrate and not by mere DNA-level detection. An attempt has been made to review the microbiology of some fermented foods and alcoholic beverages of the world.
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Affiliation(s)
- Jyoti P. Tamang
- Department of Microbiology, School of Life Sciences, Sikkim UniversityTadong, India
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan UniversityTaipei, Taiwan
| | - Wilhelm H. Holzapfel
- Advance Green Energy and Environment Institute, Handong Global UniversityPohang-si, South Korea
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35
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Kamada M, Hase S, Fujii K, Miyake M, Sato K, Kimura K, Sakakibara Y. Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods. PLoS One 2015; 10:e0141369. [PMID: 26505996 PMCID: PMC4624242 DOI: 10.1371/journal.pone.0141369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/06/2015] [Indexed: 12/22/2022] Open
Abstract
Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. subtilis strains and its relationship with the productivity of extracellular poly-γ-glutamic acid (γPGA), we sequenced the whole genome of eight B. subtilis stains isolated from non-salted fermented soybean foods in Southeast Asia. Assembled nucleotide sequences were compared with those of a natto (fermented soybean food) starter strain B. subtilis BEST195 and the laboratory standard strain B. subtilis 168 that is incapable of γPGA production. Detected variants were investigated in terms of insertion sequences, biotin synthesis, production of subtilisin NAT, and regulatory genes for γPGA synthesis, which were related to fermentation process. Comparing genome sequences, we found that the strains that produce γPGA have a deletion in a protein that constitutes the flagellar basal body, and this deletion was not found in the non-producing strains. We further identified diversity in variants of the bio operon, which is responsible for the biotin auxotrophism of the natto starter strains. Phylogenetic analysis using multilocus sequencing typing revealed that the B. subtilis strains isolated from the non-salted fermented soybeans were not clustered together, while the natto-fermenting strains were tightly clustered; this analysis also suggested that the strain isolated from "Tua Nao" of Thailand traces a different evolutionary process from other strains.
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Affiliation(s)
- Mayumi Kamada
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kazushi Fujii
- Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masato Miyake
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Keitarou Kimura
- Division of Applied Microbiology, National Food Research Institute, 2-1-12 12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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36
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Hayashi S, Usami S, Nakamura Y, Ozaki K, Okada M. Identification of a quorum sensing pheromone posttranslationally farnesylated at the internal tryptophan residue from Bacillus subtilis subsp. natto. Biosci Biotechnol Biochem 2015; 79:1567-9. [DOI: 10.1080/09168451.2015.1032884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
Bacillus subtilis subsp. natto produces poly-γ-glutamic acid under the control of quorum sensing. We identified ComXnatto pheromone as the quorum-sensing pheromone with an amino acid sequence of Lys-Trp-Pro-Pro-Ile-Glu and the tryptophan residue posttranslationally modified by a farnesyl group. ComXnatto pheromone is unique in the sense that the 5th tryptophan residue from the C-terminal is farnesylated.
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Affiliation(s)
- Shunsuke Hayashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Syohei Usami
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Yuta Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Koki Ozaki
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Masahiro Okada
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
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37
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Okada M, Nakamura Y, Hayashi S, Ozaki K, Usami S. Chemical structure and biological activity of a quorum sensing pheromone from Bacillus subtilis subsp. natto. Bioorg Med Chem Lett 2015; 25:4293-6. [PMID: 26276536 DOI: 10.1016/j.bmcl.2015.07.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/21/2015] [Accepted: 07/24/2015] [Indexed: 11/26/2022]
Abstract
Bacillus subtilis subsp. natto secrets a peptide pheromone, named ComXnatto pheromone, as an inducer for biofilm formation containing poly-γ-glutamic acid. Recently, the ComXnatto pheromone was identified to be a hexapeptide with an amino acid sequence of Lys-Trp-Pro-Pro-Ile-Glu, and the tryptophan residue was post-translationally modified with a farnesyl group. In order to determine the precise modification of the tryptophan residue, ComXnatto pheromone was synthesized using solid-phase peptide synthesis. Biological activity of the ComXnatto pheromone was then investigated. It was demonstrated that poly-γ-glutamic acid production were accelerated by ComXnatto pheromone at more than 1 nM in natto.
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Affiliation(s)
- Masahiro Okada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yuta Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Shunsuke Hayashi
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Koki Ozaki
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Syohei Usami
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
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Grau RR, de Oña P, Kunert M, Leñini C, Gallegos-Monterrosa R, Mhatre E, Vileta D, Donato V, Hölscher T, Boland W, Kuipers OP, Kovács ÁT. A Duo of Potassium-Responsive Histidine Kinases Govern the Multicellular Destiny of Bacillus subtilis. mBio 2015; 6:e00581. [PMID: 26152584 PMCID: PMC4495169 DOI: 10.1128/mbio.00581-15] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/01/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Multicellular biofilm formation and surface motility are bacterial behaviors considered mutually exclusive. However, the basic decision to move over or stay attached to a surface is poorly understood. Here, we discover that in Bacillus subtilis, the key root biofilm-controlling transcription factor Spo0A~Pi (phosphorylated Spo0A) governs the flagellum-independent mechanism of social sliding motility. A Spo0A-deficient strain was totally unable to slide and colonize plant roots, evidencing the important role that sliding might play in natural settings. Microarray experiments plus subsequent genetic characterization showed that the machineries of sliding and biofilm formation share the same main components (i.e., surfactin, the hydrophobin BslA, exopolysaccharide, and de novo-formed fatty acids). Sliding proficiency was transduced by the Spo0A-phosphorelay histidine kinases KinB and KinC. We discovered that potassium, a previously known inhibitor of KinC-dependent biofilm formation, is the specific sliding-activating signal through a thus-far-unnoticed cytosolic domain of KinB, which resembles the selectivity filter sequence of potassium channels. The differential expression of the Spo0A~Pi reporter abrB gene and the different levels of the constitutively active form of Spo0A, Sad67, in Δspo0A cells grown in optimized media that simultaneously stimulate motile and sessile behaviors uncover the spatiotemporal response of KinB and KinC to potassium and the gradual increase in Spo0A~Pi that orchestrates the sequential activation of sliding, followed by sessile biofilm formation and finally sporulation in the same population. Overall, these results provide insights into how multicellular behaviors formerly believed to be antagonistic are coordinately activated in benefit of the bacterium and its interaction with the host. IMPORTANCE Alternation between motile and sessile behaviors is central to bacterial adaptation, survival, and colonization. However, how is the collective decision to move over or stay attached to a surface controlled? Here, we use the model plant-beneficial bacterium Bacillus subtilis to answer this question. Remarkably, we discover that sessile biofilm formation and social sliding motility share the same structural components and the Spo0A regulatory network via sensor kinases, KinB and KinC. Potassium, an inhibitor of KinC-dependent biofilm formation, triggers sliding via a potassium-perceiving cytosolic domain of KinB that resembles the selectivity filter of potassium channels. The spatiotemporal response of these kinases to variable potassium levels and the gradual increase in Spo0A~Pi levels that orchestrates the activation of sliding before biofilm formation shed light on how multicellular behaviors formerly believed to be antagonistic work together to benefit the population fitness.
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Affiliation(s)
- Roberto R Grau
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Paula de Oña
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Maritta Kunert
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Cecilia Leñini
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Darío Vileta
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Verónica Donato
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Oscar P Kuipers
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
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Kinjo Y, Saitoh S, Tokuda G. An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches. Microbes Environ 2015; 30:208-20. [PMID: 26156552 PMCID: PMC4567559 DOI: 10.1264/jsme2.me14153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Whole-genome sequencing has emerged as one of the most effective means to elucidate the biological roles and molecular features of obligate intracellular symbionts (endosymbionts). However, the de novo assembly of an endosymbiont genome remains a challenge when host and/or mitochondrial DNA sequences are present in a dataset and hinder the assembly of the genome. By focusing on the traits of genome evolution in endosymbionts, we herein developed and investigated a genome-assembly strategy that consisted of two consecutive procedures: the selection of endosymbiont contigs from an output obtained from a de novo assembly performed using a TBLASTX search against a reference genome, named TBLASTX Contig Selection and Filtering (TCSF), and the iterative reassembling of the genome from reads mapped on the selected contigs, named Iterative Mapping and ReAssembling (IMRA), to merge the contigs. In order to validate this approach, we sequenced two strains of the cockroach endosymbiont Blattabacterium cuenoti and applied this strategy to the datasets. TCSF was determined to be highly accurate and sensitive in contig selection even when the genome of a distantly related free-living bacterium was used as a reference genome. Furthermore, the use of IMRA markedly improved sequence assemblies: the genomic sequence of an endosymbiont was almost completed from a dataset containing only 3% of the sequences of the endosymbiont’s genome. The efficiency of our strategy may facilitate further studies on endosymbionts.
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Affiliation(s)
- Yukihiro Kinjo
- Tropical Biosphere Research Center, University of the Ryukyus
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Chettri R, Tamang JP. Bacillus species isolated from tungrymbai and bekang, naturally fermented soybean foods of India. Int J Food Microbiol 2015; 197:72-6. [PMID: 25574846 DOI: 10.1016/j.ijfoodmicro.2014.12.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/02/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
Tungrymbai and bekang are naturally fermented soybean foods commonly consumed in Meghalaya and Mizoram states of India. A total of 39 samples of tungrymbai and 43 samples of bekang were collected from different villages and markets of Meghalaya and Mizoram, respectively and were analysed for microbial load. In both tungrymbai and bekang, the average population of Bacillus spp. was 8.2±0.1 log cfu/g. A total of 428 isolates of Bacillus were isolated from tungrymbai (211) and bekang (217) for detailed identification. On the basis of a combination of phenotypic and molecular characterisation using ARDRA, ITS-PCR and RAPD-PCR techniques, species of Bacillus isolated from tungrymbai were identified as Bacillus licheniformis (25.5%), Bacillus pumilus (19.5%) and Bacillus subtilis (55%), and species of Bacillus from bekang were Bacillus brevis (2%), Bacillus circulans (7.5%), Bacillus coagulans (6.5%), B. licheniformis (16.5%), B. pumilus (9.1%), Bacillus sphaericus (4.6%), B. subtilis (51.8%), and Lysinibacillus fusiformis (2%). The most dominant bacterium in both products was B. subtilis.
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Affiliation(s)
- Rajen Chettri
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Tadong 737102, Sikkim, India
| | - Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Tadong 737102, Sikkim, India.
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41
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Sim M, Kim J. Metagenome assembly through clustering of next-generation sequencing data using protein sequences. J Microbiol Methods 2015; 109:180-7. [PMID: 25572018 DOI: 10.1016/j.mimet.2015.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/03/2015] [Accepted: 01/03/2015] [Indexed: 11/16/2022]
Abstract
The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising.
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Affiliation(s)
- Mikang Sim
- Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Jaebum Kim
- Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
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Feng Z, Xu M, Zhai S, Chen H, Li AL, Lv XT, Deng HL. Application of Autochthonous Mixed Starter for Controlled Kedong Sufu Fermentation in Pilot Plant Tests. J Food Sci 2014; 80:M129-36. [DOI: 10.1111/1750-3841.12740] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/05/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Zhen Feng
- Key Laboratory of Dairy Science; Ministry of Education; College of Food Science; Northeast Agricultural Univ; 59 Mucai Rd. 150030 Harbin Heilongjiang China
| | - Miao Xu
- Key Laboratory of Dairy Science; Ministry of Education; College of Food Science; Northeast Agricultural Univ; 59 Mucai Rd. 150030 Harbin Heilongjiang China
| | - Shuang Zhai
- Key Laboratory of Dairy Science; Ministry of Education; College of Food Science; Northeast Agricultural Univ; 59 Mucai Rd. 150030 Harbin Heilongjiang China
| | - Hong Chen
- Key Laboratory of Dairy Science; Ministry of Education; College of Food Science; Northeast Agricultural Univ; 59 Mucai Rd. 150030 Harbin Heilongjiang China
| | - Ai-li Li
- Key Laboratory of Dairy Science; Ministry of Education; College of Food Science; Northeast Agricultural Univ; 59 Mucai Rd. 150030 Harbin Heilongjiang China
| | - Xin-tong Lv
- Key Laboratory of Dairy Science; Ministry of Education; College of Food Science; Northeast Agricultural Univ; 59 Mucai Rd. 150030 Harbin Heilongjiang China
| | - Hong-ling Deng
- Key Laboratory of Dairy Science; Ministry of Education; College of Food Science; Northeast Agricultural Univ; 59 Mucai Rd. 150030 Harbin Heilongjiang China
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Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MCJ. A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 2014; 15:1138. [PMID: 25523208 PMCID: PMC4377854 DOI: 10.1186/1471-2164-15-1138] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/04/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Highly parallel, 'second generation' sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population genomics. Most of these data are publically available as unassembled short-read sequence files that require extensive processing before they can be used for analysis. The provision of data in a uniform format, which can be easily assessed for quality, linked to provenance and phenotype and used for analysis, is therefore necessary. RESULTS The performance of de novo short-read assembly followed by automatic annotation using the pubMLST.org Neisseria database was assessed and evaluated for 108 diverse, representative, and well-characterised Neisseria meningitidis isolates. High-quality sequences were obtained for >99% of known meningococcal genes among the de novo assembled genomes and four resequenced genomes and less than 1% of reassembled genes had sequence discrepancies or misassembled sequences. A core genome of 1600 loci, present in at least 95% of the population, was determined using the Genome Comparator tool. Genealogical relationships compatible with, but at a higher resolution than, those identified by multilocus sequence typing were obtained with core genome comparisons and ribosomal protein gene analysis which revealed a genomic structure for a number of previously described phenotypes. This unified system for cataloguing Neisseria genetic variation in the genome was implemented and used for multiple analyses and the data are publically available in the PubMLST Neisseria database. CONCLUSIONS The de novo assembly, combined with automated gene-by-gene annotation, generates high quality draft genomes in which the majority of protein-encoding genes are present with high accuracy. The approach catalogues diversity efficiently, permits analyses of a single genome or multiple genome comparisons, and is a practical approach to interpreting WGS data for large bacterial population samples. The method generates novel insights into the biology of the meningococcus and improves our understanding of the whole population structure, not just disease causing lineages.
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Kamada M, Hase S, Sato K, Toyoda A, Fujiyama A, Sakakibara Y. Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads. PLoS One 2014; 9:e109999. [PMID: 25329997 PMCID: PMC4199626 DOI: 10.1371/journal.pone.0109999] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 09/04/2014] [Indexed: 01/24/2023] Open
Abstract
De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.
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Affiliation(s)
- Mayumi Kamada
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
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Chiu KC, Lin CJ, Shaw GC. Transcriptional regulation of the l-lactate permease gene lutP by the LutR repressor of Bacillus subtilis RO-NN-1. Microbiology (Reading) 2014; 160:2178-2189. [DOI: 10.1099/mic.0.079806-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bacillus subtilis lutABC operon encodes three iron–sulfur-containing proteins required for l-lactate utilization and involved in biofilm formation. The transcriptional regulator LutR of the GntR family negatively controls lutABC expression. The lutP gene, which is situated immediately upstream of lutR, encodes an l-lactate permease. Here, we show that lutP expression can be strongly induced by l-lactate and is subject to partial catabolite repression by glucose. Disruption of the lutR gene led to a strong derepression of lutP and no further induction by l-lactate, suggesting that the LutR repressor can also negatively control lutP expression. Electrophoretic mobility shift assay revealed a LutR-binding site located downstream of the promoter of lutA or lutP and containing a consensus inverted repeat sequence 5′-TCATC-N1-GATGA-3′. Reporter gene analysis showed that deletion of each LutR-binding site caused a strong derepression of lutA or lutP. These results indicated that these two LutR-binding sites can function as operators in vivo. Moreover, deletion analysis identified a DNA segment upstream of the lutP promoter to be important for lutP expression. In contrast to the truncated LutR of laboratory strains 168 and PY79, the full-length LutR of the undomesticated strain RO-NN-1, and probably many other B. subtilis strains, can directly and negatively regulate lutP transcription. The absence or presence of the N-terminal 21 aa of the full-length LutR, which encompass a small part of the predicted winged helix–turn–helix DNA-binding motif, may probably alter the DNA-binding specificity or affinity of LutR.
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Affiliation(s)
- Kuo-Chin Chiu
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, Taiwan, Republic of China
| | - Chen-Jyun Lin
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, Taiwan, Republic of China
| | - Gwo-Chyuan Shaw
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, Taiwan, Republic of China
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Card DC, Schield DR, Reyes-Velasco J, Fujita MK, Andrew AL, Oyler-McCance SJ, Fike JA, Tomback DF, Ruggiero RP, Castoe TA. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. PLoS One 2014; 9:e106649. [PMID: 25192061 PMCID: PMC4156343 DOI: 10.1371/journal.pone.0106649] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 08/07/2014] [Indexed: 12/04/2022] Open
Abstract
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
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Affiliation(s)
- Daren C. Card
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Drew R. Schield
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Jacobo Reyes-Velasco
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Matthew K. Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Audra L. Andrew
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Sara J. Oyler-McCance
- United States Geological Survey – Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Jennifer A. Fike
- United States Geological Survey – Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Diana F. Tomback
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - Robert P. Ruggiero
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Todd A. Castoe
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
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Zhang Y, Sun Y, Cole JR. A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PLoS Comput Biol 2014; 10:e1003737. [PMID: 25122209 PMCID: PMC4133164 DOI: 10.1371/journal.pcbi.1003737] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 06/05/2014] [Indexed: 11/21/2022] Open
Abstract
Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material. Next-generation sequencing (NGS) provides an efficient and affordable way to sequence the genomes or transcriptomes of a large amount of organisms. With fast accumulation of the sequencing data from various NGS projects, the bottleneck is to efficiently mine useful knowledge from the data. As NGS platforms usually generate short and fragmented sequences (reads), one key step to annotate NGS data is to assemble short reads into longer contigs, which are then used to recover functional elements such as protein-coding genes. Short read assembly remains one of the most difficult computational problems in genomics. In particular, the performance of existing assembly tools is not satisfactory on complicated NGS data sets. They cannot reliably separate genes of high similarity, recover under-represented genes, and incur high computational time and memory usage. Hence, we propose a targeted gene assembly tool, SAT-Assembler, to assemble genes of interest directly from NGS data with low memory usage and high accuracy. Our experimental results on a transcriptomic data set and two microbial community data sets showed that SAT-Assembler used less memory and recovered more target genes with better accuracy than existing tools.
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Affiliation(s)
- Yuan Zhang
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Yanni Sun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
| | - James R. Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
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Abstract
In this report, we present a draft sequence of Bacillus subtilis KATMIRA1933. Previous studies demonstrated probiotic properties of this strain partially attributed to production of an antibacterial compound, subtilosin. Comparative analysis of this strain’s genome with that of a commercial probiotic strain, B. subtilis Natto, is presented.
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49
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Su F, Xu P. Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals. Sci Rep 2014; 4:3926. [PMID: 24473268 PMCID: PMC3905273 DOI: 10.1038/srep03926] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/14/2014] [Indexed: 11/16/2022] Open
Abstract
Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species.
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Affiliation(s)
- Fei Su
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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Nagai T. A Defective Bacteriophage Produced by Bacillus subtilis MAFF 118147 and a Mutant Producing No Normal Particles of the Defective Bacteriophage. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2014. [DOI: 10.3136/fstr.20.1229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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