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Maresca E, Aulitto M, Contursi P. Harnessing the dual nature of Bacillus (Weizmannia) coagulans for sustainable production of biomaterials and development of functional food. Microb Biotechnol 2024; 17:e14449. [PMID: 38593329 PMCID: PMC11003712 DOI: 10.1111/1751-7915.14449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024] Open
Abstract
Bacillus coagulans, recently renamed Weizmannia coagulans, is a spore-forming bacterium that has garnered significant interest across various research fields, ranging from health to industrial applications. The probiotic properties of W. coagulans enhance intestinal digestion, by releasing prebiotic molecules including enzymes that facilitate the breakdown of not-digestible carbohydrates. Notably, some enzymes from W. coagulans extend beyond digestive functions, serving as valuable biotechnological tools and contributing to more sustainable and efficient manufacturing processes. Furthermore, the homofermentative thermophilic nature of W. coagulans renders it an exceptional candidate for fermenting foods and lignocellulosic residues into L-(+)-lactic acid. In this review, we provide an overview of the dual nature of W. coagulans, in functional foods and for the development of bio-based materials.
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Affiliation(s)
- Emanuela Maresca
- Department of BiologyUniversity of Naples “Federico II”NaplesItaly
| | - Martina Aulitto
- Department of BiologyUniversity of Naples “Federico II”NaplesItaly
- Institute for Polymers, Composites and Biomaterials—IPCB, National Research Council of Italy (CNR)PozzuoliItaly
| | - Patrizia Contursi
- Department of BiologyUniversity of Naples “Federico II”NaplesItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
- BAT Center—Interuniversity Center for Studies on Bioinspired Agro‐Environmental TechnologyUniversity of Naples “Federico II”PorticiItaly
- Task Force on Microbiome StudiesUniversity of Naples “Federico II”NaplesItaly
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2
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Zhao N, Huang X, Liu Z, Gao Y, Teng J, Yu T, Yan F. Probiotic characterization of Bacillus smithii: Research advances, concerns, and prospective trends. Compr Rev Food Sci Food Saf 2024; 23:e13308. [PMID: 38369927 DOI: 10.1111/1541-4337.13308] [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: 12/02/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Bacillus smithii is a thermophilic Bacillus that can be isolated from white wine, hot spring soil, high-temperature compost, and coffee grounds, with various biofunctions and wide applications. It is resistant to both gastric acid and high temperature, which makes it easier to perform probiotic effects than traditional commercial probiotics, so it can maintain good vitality during food processing and has great application prospects. This paper starts with the taxonomy and genetics and focuses on aspects, including genetic transformation, functional enzyme production, waste utilization, and application in the field of food science as a potential probiotic. According to available studies during the past 30 years, we considered that B. smithii is a novel class of microorganisms with a wide range of functional enzymes such as hydrolytic enzymes and hydrolases, as well as resistance to pathogenic bacteria. It is available in waste degradation, organic fertilizer production, the feed and chemical industries, the pharmaceutical sector, and food fortification. Moreover, B. smithii has great potentials for applications in the food industry, as it presents high resistance to the technological processes that guarantee its health benefits. It is also necessary to systematically evaluate the safety, flavor, and texture of B. smithii and explore its biological mechanism of action, which is of great value for further application in multiple fields, especially in food and medicine.
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Affiliation(s)
- Nan Zhao
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Xuedi Huang
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Zhongyang Liu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Yufang Gao
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Jialuo Teng
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Ting Yu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Fujie Yan
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
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3
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Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities. Cell Host Microbe 2022; 30:1630-1645.e25. [DOI: 10.1016/j.chom.2022.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/30/2022] [Accepted: 09/13/2022] [Indexed: 12/26/2022]
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4
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González-Tortuero E, Anthon C, Havgaard JH, Geissler AS, Breüner A, Hjort C, Gorodkin J, Seemann SE. The Bacillaceae-1 RNA motif comprises two distinct classes. Gene 2022; 841:146756. [PMID: 35905857 DOI: 10.1016/j.gene.2022.146756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/10/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis, we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches.
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Affiliation(s)
- Enrique González-Tortuero
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jakob H Havgaard
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Adrian S Geissler
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Stefan E Seemann
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
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A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications. Int J Mol Sci 2022; 23:ijms23063135. [PMID: 35328559 PMCID: PMC8954581 DOI: 10.3390/ijms23063135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 03/11/2022] [Indexed: 12/20/2022] Open
Abstract
The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain's genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.
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Assessing the safety and probiotic characteristics of Bacillus coagulans 13002 based on complete genome and phenotype analysis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Maity C, Gupta AK, Saroj DB, Biyani A, Bagkar P, Kulkarni J, Dixit Y. Impact of a Gastrointestinal Stable Probiotic Supplement Bacillus coagulans LBSC on Human Gut Microbiome Modulation. J Diet Suppl 2020; 18:577-596. [PMID: 32896190 DOI: 10.1080/19390211.2020.1814931] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bacillus coagulans LBSC showed stability in acidic pH, bile and simulated human gastrointenstinal juices. Under static gut model, when passed through oral, gastric and intestinal phases, B. coagulans LBSC was found to be stable as free viable spores and also with various foods such as milk and baby foods, as well as American and European diets. In human studies, modulation of gut microbiota by B. coagulans LBSC was comprehended by whole genome metagenome analysis of fecal samples obtained from pre- and post-treatment of irritable bowel syndrome (IBS) patients. B. coagulans LBSC treatment showed positive modulation in gut microbiota, especially up regulation of phyla such as Actinobacteria and Firmicutes, whereas down regulation of Bacteroids, Proteobacteria, Streptophyta and Verrucomicrobia. Simultaneously, it has altered various microbiota associated metabolic pathways to create the normalcy of gut microenvironment.
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Affiliation(s)
| | | | - Dina B Saroj
- Advanced Enzyme Technologies Ltd, Thane, Maharashtra, India
| | - Atul Biyani
- Advanced Enzyme Technologies Ltd, Thane, Maharashtra, India
| | - Pratik Bagkar
- Advanced Enzyme Technologies Ltd, Thane, Maharashtra, India
| | | | - Yogini Dixit
- Advanced Enzyme Technologies Ltd, Thane, Maharashtra, India
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8
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Chen Y, Sun Y, Liu Z, Dong F, Li Y, Wang Y. Genome-scale modeling for Bacillus coagulans to understand the metabolic characteristics. Biotechnol Bioeng 2020; 117:3545-3558. [PMID: 32648961 DOI: 10.1002/bit.27488] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/01/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Lactic acid is widely used in many industries, especially in the production of poly-lactic acid. Bacillus coagulans is a promising lactic acid producer in industrial fermentation due to its thermophilic property. In this study, we developed the first genome-scale metabolic model (GEM) of B. coagulans iBag597, together with an enzyme-constrained model ec-iBag597. We measured strain-specific biomass composition and integrated the data into a biomass equation. Then, we validated iBag597 against experimental data generated in this study, including amino acid requirements and carbon source utilization, showing that simulations were generally consistent with the experimental results. Subsequently, we carried out chemostats to investigate the effects of specific growth rate and culture pH on metabolism of B. coagulans. Meanwhile, we used iBag597 to estimate the intracellular metabolic fluxes for those conditions. The results showed that B. coagulans was capable of generating ATP via multiple pathways, and switched among them in response to various conditions. With ec-iBag597, we estimated the protein cost and protein efficiency for each ATP-producing pathway to investigate the switches. Our models pave the way for systems biology of B. coagulans, and our findings suggest that maintaining a proper growth rate and selecting an optimal pH are beneficial for lactate fermentation.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yan Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhihao Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Fengqing Dong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanyuan Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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9
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Multiplexed Non-barcoded Long-Read Sequencing and Assembling Genomes of Bacillus Strains in Error-Free Simulations. Curr Microbiol 2019; 77:79-84. [PMID: 31722044 DOI: 10.1007/s00284-019-01808-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/02/2019] [Indexed: 10/25/2022]
Abstract
The generation of genomic data from microorganisms has revolutionized our abilities to understand their biology, but it is still challenging to obtain complete genome sequences of microbes in an automated high-throughput and cost-effective manner. While the advent of second-generation sequencing technologies provided significantly higher throughput, their shorter lengths and more pronounced sequence-context bias led to a shift towards resequencing applications. Recently, single molecule real-time (SMRT) DNA sequencing has been used to generate sequencing reads that are much longer than other sequencing platforms, facilitating de novo genome assembly and genome finishing. Here we introduced a novel multiplex strategy to make full use of the capacity and characteristics of SMRT sequencing in microbe genome assembly. We used error-free simulations to evaluate the practicability of assembling SMRT genomic sequencing data from multiple microbes into finished genomes once at a time. Then we compared the influence of two key factors, including sequencing coverage and read length, on multiplex assembling. Our results showed that long-read genomic sequencing inherently provided the ability to assemble genomic sequencing data from multiple microbes into finished genomes due to its long length. This approach might be helpful for the various groups of microbial genome projects or metagenomics research.
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10
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Elucidating the Role and Regulation of a Lactate Permease as Lactate Transporter in Bacillus coagulans DSM1. Appl Environ Microbiol 2019; 85:AEM.00672-19. [PMID: 31101607 DOI: 10.1128/aem.00672-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/07/2019] [Indexed: 01/17/2023] Open
Abstract
A key feature of Bacillus coagulans is its ability to produce l-lactate via homofermentative metabolism. A putative lactate permease-encoding gene (lutP) and the gene encoding its regulator (lutR) were identified in one operon in B. coagulans strains. LutP orthologs are highly conserved and located adjacent to the gene cluster related to lactate utilization in most lactate-utilizing microorganisms. However, no lactate utilization genes were found adjacent to lutP in all sequenced B. coagulans strains. The stand-alone presence of lutP in l-lactate producers indicates that it may have functions in lactate production. In this study, B. coagulans DSM1 was used as a representative strain, and the critical roles of LutP and its regulation were described. Transport property assays showed that LutP was essential for lactate uptake. Its regulator LutR directly interacted with the lutP-lutR intergenic region, and lutP transcription was activated by l-lactate via regulation by LutR. A biolayer interferometry assay further confirmed that LutR bound to an 11-bp inverted repeat in the intergenic region, and lutP transcription began when the binding of LutR to the lutP upstream sequence was inhibited. We conclusively showed that lutP encodes a functional lactate permease in B. coagulans IMPORTANCE Lactate-utilizing strains require lactate permease (LutP) to transport lactate into cells. Bacillus coagulans LutP is a previously uncharacterized lactate permease with no lactate utilization genes situated either adjacent to or remotely from it. In this study, an active lactate permease in an l-lactate producer, B. coagulans DSM1, was identified. Lactate supplementation regulated the expression of lactate permease. This study presents physiological evidence of the presence of a lactate transporter in B. coagulans Our findings indicate a potential target for the engineering of strains in order to improve their fermentation characteristics.
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11
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Glaser R, Venus J. Model-based characterisation of growth performance and l -lactic acid production with high optical purity by thermophilic Bacillus coagulans in a lignin-supplemented mixed substrate medium. N Biotechnol 2017; 37:180-193. [DOI: 10.1016/j.nbt.2016.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/07/2016] [Accepted: 12/26/2016] [Indexed: 10/20/2022]
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12
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Detoxification of Sap from Felled Oil Palm Trunks for the Efficient Production of Lactic Acid. Appl Biochem Biotechnol 2017; 183:412-425. [DOI: 10.1007/s12010-017-2454-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/07/2017] [Indexed: 01/29/2023]
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13
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Joo JC, Khusnutdinova AN, Flick R, Kim T, Bornscheuer UT, Yakunin AF, Mahadevan R. Alkene hydrogenation activity of enoate reductases for an environmentally benign biosynthesis of adipic acid. Chem Sci 2017; 8:1406-1413. [PMID: 28616142 PMCID: PMC5460604 DOI: 10.1039/c6sc02842j] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/08/2016] [Indexed: 12/26/2022] Open
Abstract
Adipic acid, a precursor for Nylon-6,6 polymer, is one of the most important commodity chemicals, which is currently produced from petroleum. The biosynthesis of adipic acid from glucose still remains challenging due to the absence of biocatalysts required for the hydrogenation of unsaturated six-carbon dicarboxylic acids to adipic acid. Here, we demonstrate the first enzymatic hydrogenation of 2-hexenedioic acid and muconic acid to adipic acid using enoate reductases (ERs). ERs can hydrogenate 2-hexenedioic acid and muconic acid producing adipic acid with a high conversion rate and yield in vivo and in vitro. Purified ERs exhibit a broad substrate spectrum including aromatic and aliphatic 2-enoates and a significant oxygen tolerance. The discovery of the hydrogenation activity of ERs contributes to an understanding of the catalytic mechanism of these poorly characterized enzymes and enables the environmentally benign biosynthesis of adipic acid and other chemicals from renewable resources.
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Affiliation(s)
- Jeong Chan Joo
- Center for Bio-based Chemistry , Division of Convergence Chemistry , Korea Research Institute of Chemical Technology , 141 Gajeong-ro, Yuseong-gu , Daejeon 34114 , Republic of Korea .
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Taeho Kim
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Uwe T Bornscheuer
- Institute of Biochemistry , Department of Biotechnology & Enzyme Catalysis , Greifswald University , Felix-Hausdorff-Strasse 4 , 17487 Greifswald , Germany
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
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Contributory roles of two l-lactate dehydrogenases for l-lactic acid production in thermotolerant Bacillus coagulans. Sci Rep 2016; 6:37916. [PMID: 27885267 PMCID: PMC5122838 DOI: 10.1038/srep37916] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 11/04/2016] [Indexed: 02/06/2023] Open
Abstract
Thermotolerant Bacillus coagulans is considered to be a more promising producer for bio-chemicals, due to its capacity to withstand harsh conditions. Two L-lactate dehydrogenase (LDH) encoding genes (ldhL1 and ldhL2) and one D-LDH encoding gene (ldhD) were annotated from the B. coagulans DSM1 genome. Transcriptional analysis revealed that the expression of ldhL2 was undetectable while the ldhL1 transcription level was much higher than that of ldhD at all growth phases. Deletion of the ldhL2 gene revealed no difference in fermentation profile compared to the wild-type strain, while ldhL1 single deletion or ldhL1ldhL2 double deletion completely blocked L-lactic acid production. Complementation of ldhL1 in the above knockout strains restored fermentation profiles to those observed in the wild-type strain. This study demonstrates ldhL1 is crucial for L-lactic acid production and NADH balance in B. coagulans DSM1 and lays the fundamental for engineering the thermotolerant B. coagulans strain as a platform chemicals producer.
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15
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Bosma EF, Koehorst JJ, van Hijum SAFT, Renckens B, Vriesendorp B, van de Weijer AHP, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg R. Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). Stand Genomic Sci 2016; 11:52. [PMID: 27559429 PMCID: PMC4995803 DOI: 10.1186/s40793-016-0172-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 08/09/2016] [Indexed: 11/10/2022] Open
Abstract
Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. Being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. We determined the complete genomic sequence of the B. smithii type strain DSM 4216(T), which consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880 genes. Genome annotation via RAST was complemented by a protein domain analysis. Some unique features of B. smithii central metabolism in comparison to related organisms included the lack of a standard acetate production pathway with no apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes, while acetate was the second fermentation product.
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Affiliation(s)
- Elleke F. Bosma
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
- Present address: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, 2800 Denmark
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | | | - Bernadet Renckens
- CMBI, NCMLS, Geert-Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | | | | | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
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Systematic development and optimization of chemically defined medium supporting high cell density growth of Bacillus coagulans. Appl Microbiol Biotechnol 2016; 100:8121-34. [PMID: 27262567 DOI: 10.1007/s00253-016-7644-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 10/21/2022]
Abstract
With determined components and experimental reducibility, the chemically defined medium (CDM) and the minimal chemically defined medium (MCDM) are used in many metabolism and regulation studies. This research aimed to develop the chemically defined medium supporting high cell density growth of Bacillus coagulans, which is a promising producer of lactic acid and other bio-chemicals. In this study, a systematic methodology combining the experimental technique with flux balance analysis (FBA) was proposed to design and simplify a CDM. The single omission technique and single addition technique were employed to determine the essential and stimulatory compounds, before the optimization of their concentrations by the statistical method. In addition, to improve the growth rationally, in silico omission and addition were performed by FBA based on the construction of a medium-size metabolic model of B. coagulans 36D1. Thus, CDMs were developed to obtain considerable biomass production of at least five B. coagulans strains, in which two model strains B. coagulans 36D1 and ATCC 7050 were involved.
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Genome Sequence of Bacillus coagulans P38, an Efficient Polymer-Grade l-Lactate Producer from Cellulosic Substrates. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00495-15. [PMID: 25999580 PMCID: PMC4440960 DOI: 10.1128/genomea.00495-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacillus coagulans P38 is an efficient polymer-grade l-lactic acid producer from a cellulosic carbon source. Here, the draft 3.37-Mb genome sequence of this potential strain may provide useful information to further improve the strain performance for higher titers and, importantly, to understand the mechanism of its high tolerance for 2-furfural.
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Draft Genome Sequence of Bacillus coagulans GBI-30, 6086, a Widely Used Spore-Forming Probiotic Strain. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01080-14. [PMID: 25377698 PMCID: PMC4223449 DOI: 10.1128/genomea.01080-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacillus coagulans GBI-30, 6086 is a safe strain, already available on the market, and characterized by certified beneficial effects. The draft genome sequence presented here constitutes the first pillar toward the identification of the molecular mechanisms responsible for its positive features and safety.
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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: 33] [Impact Index Per Article: 3.3] [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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Corona-Hernandez RI, Álvarez-Parrilla E, Lizardi-Mendoza J, Islas-Rubio AR, de la Rosa LA, Wall-Medrano A. Structural Stability and Viability of Microencapsulated Probiotic Bacteria: A Review. Compr Rev Food Sci Food Saf 2013; 12:614-628. [DOI: 10.1111/1541-4337.12030] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 05/23/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rocío I. Corona-Hernandez
- Departamento de Ciencias Químico-Biológicas; Instituto de Ciencias Biomédicas; Universidad Autónoma de Ciudad Juárez. Anillo Envolvente del PRONAF y Estocolmo s/n; Ciudad Juárez 32310; Chihuahua; México
| | - Emilio Álvarez-Parrilla
- Departamento de Ciencias Químico-Biológicas; Instituto de Ciencias Biomédicas; Universidad Autónoma de Ciudad Juárez. Anillo Envolvente del PRONAF y Estocolmo s/n; Ciudad Juárez 32310; Chihuahua; México
| | - Jaime Lizardi-Mendoza
- Coordinación de Tecnología de Alimentos de Origen Animal; Centro de Investigación en Alimentación y Desarrollo, AC. Carretera a la Victoria km. 0.6, AP 1735; Hermosillo 83000; Sonora; México
| | - Alma R. Islas-Rubio
- Coordinación de Tecnología de Alimentos de Origen Vegetal; Centro de Investigación en Alimentación y Desarrollo, AC. Carretera a la Victoria km. 0.6, AP 1735; Hermosillo 83000; Sonora; México
| | - Laura. A. de la Rosa
- Departamento de Ciencias Químico-Biológicas; Instituto de Ciencias Biomédicas; Universidad Autónoma de Ciudad Juárez. Anillo Envolvente del PRONAF y Estocolmo s/n; Ciudad Juárez 32310; Chihuahua; México
| | - Abraham Wall-Medrano
- Departamento de Ciencias Químico-Biológicas; Instituto de Ciencias Biomédicas; Universidad Autónoma de Ciudad Juárez. Anillo Envolvente del PRONAF y Estocolmo s/n; Ciudad Juárez 32310; Chihuahua; México
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Sharma A, Satyanarayana T. Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology. GENOMICS INSIGHTS 2013. [PMID: 26217108 PMCID: PMC4510601 DOI: 10.4137/gei.s12732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.
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Affiliation(s)
- Archana Sharma
- Department of Microbiology, University of Delhi, South Campus, Benito Juarez Road, New Delhi, India
| | - T Satyanarayana
- Department of Microbiology, University of Delhi, South Campus, Benito Juarez Road, New Delhi, India
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22
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Kovács ÁT, Eckhardt TH, van Kranenburg R, Kuipers OP. Functional analysis of the ComK protein of Bacillus coagulans. PLoS One 2013; 8:e53471. [PMID: 23301076 PMCID: PMC3536758 DOI: 10.1371/journal.pone.0053471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/29/2012] [Indexed: 11/27/2022] Open
Abstract
The genes for DNA uptake and recombination in Bacilli are commonly regulated by the transcriptional factor ComK. We have identified a ComK homologue in Bacillus coagulans, an industrial relevant organism that is recalcitrant for transformation. Introduction of B. coagulans comK gene under its own promoter region into Bacillus subtilis comK strain results in low transcriptional induction of the late competence gene comGA, but lacking bistable expression. The promoter regions of B. coagulans comK and the comGA genes are recognized in B. subtilis and expression from these promoters is activated by B. subtilis ComK. Purified ComK protein of B. coagulans showed DNA-binding ability in gel retardation assays with B. subtilis- and B. coagulans-derived probes. These experiments suggest that the function of B. coagulans ComK is similar to that of ComK of B. subtilis. When its own comK is overexpressed in B. coagulans the comGA gene expression increases 40-fold, while the expression of another late competence gene, comC is not elevated and no reproducible DNA-uptake could be observed under these conditions. Our results demonstrate that B. coagulans ComK can recognize several B.subtilis comK-responsive elements, and vice versa, but indicate that the activation of the transcription of complete sets of genes coding for a putative DNA uptake apparatus in B. coagulans might differ from that of B. subtilis.
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Affiliation(s)
- Ákos T. Kovács
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Tom H. Eckhardt
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | | | - Oscar P. Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
- * E-mail:
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Yang Y, Ramelot TA, Cort JR, Garcia M, Yee A, Arrowsmith CH, Kennedy MA. Solution NMR structure of hypothetical protein CV_2116 encoded by a viral prophage element in Chromobacterium violaceum. Int J Mol Sci 2012; 13:7354-7364. [PMID: 22837698 PMCID: PMC3397530 DOI: 10.3390/ijms13067354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/25/2012] [Accepted: 06/04/2012] [Indexed: 11/16/2022] Open
Abstract
CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and 13C- and 15N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β-sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.
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Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA; E-Mails: (Y.Y.); (T.A.R.)
| | - Theresa A. Ramelot
- Department of Chemistry and Biochemistry and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA; E-Mails: (Y.Y.); (T.A.R.)
| | - John R. Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; E-Mail:
| | - Maite Garcia
- Campbell Family Cancer Research Institute, Ontario Cancer Institute and the Northeast Structural Genomics Consortium, University Health Network, Toronto, ON, M5G 2C4, Canada; E-Mails: (M.G.); (A.Y.); (C.H.A.)
| | - Adelinda Yee
- Campbell Family Cancer Research Institute, Ontario Cancer Institute and the Northeast Structural Genomics Consortium, University Health Network, Toronto, ON, M5G 2C4, Canada; E-Mails: (M.G.); (A.Y.); (C.H.A.)
| | - Cheryl H. Arrowsmith
- Campbell Family Cancer Research Institute, Ontario Cancer Institute and the Northeast Structural Genomics Consortium, University Health Network, Toronto, ON, M5G 2C4, Canada; E-Mails: (M.G.); (A.Y.); (C.H.A.)
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH 45056, USA; E-Mails: (Y.Y.); (T.A.R.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-513-529-8267; Fax: +1-513-529-5715
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