1
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Snyder AB, Martin N, Wiedmann M. Microbial food spoilage: impact, causative agents and control strategies. Nat Rev Microbiol 2024:10.1038/s41579-024-01037-x. [PMID: 38570695 DOI: 10.1038/s41579-024-01037-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Microbial food spoilage is a major contributor to food waste and, hence, to the negative environmental sustainability impacts of food production and processing. Globally, it is estimated that 15-20% of food is wasted, with waste, by definition, occurring after primary production and harvesting (for example, in households and food service establishments). Although the causative agents of food spoilage are diverse, many microorganisms are major contributors across different types of foods. For example, the genus Pseudomonas causes spoilage in various raw and ready-to-eat foods. Aerobic sporeformers (for example, members of the genera Bacillus, Paenibacillus and Alicyclobacillus) cause spoilage across various foods and beverages, whereas anaerobic sporeformers (for example, Clostridiales) cause spoilage in a range of products that present low-oxygen environments. Fungi are also important spoilage microorganisms, including in products that are not susceptible to bacterial spoilage due to their low water activity or low pH. Strategies that can reduce spoilage include improved control of spoilage microorganisms in raw material and environmental sources as well as application of microbicidal or microbiostatic strategies (for example, to products and packaging). Emerging tools (for example, systems models and improved genomic tools) represent an opportunity for rational design of systems, processes and products that minimize microbial food spoilage.
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Affiliation(s)
| | - Nicole Martin
- Department of Food Science, Cornell University, Ithaca, NY, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, USA.
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2
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Nagel OG, Gasparotti ML, Machado SI, Althaus RL. Similarities of Geobacillus bacteria based on their profiles of antimicrobial susceptibility in milk samples. Rev Argent Microbiol 2024; 56:102-111. [PMID: 37704517 DOI: 10.1016/j.ram.2023.07.003] [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: 12/28/2022] [Revised: 05/29/2023] [Accepted: 07/03/2023] [Indexed: 09/15/2023] Open
Abstract
The genus Geobacillus is composed of thermophilic bacteria that exhibit diverse biotechnological potentialities. Specifically, Geobacillus stearothermophilus is included as a test bacterium in commercial microbiological inhibition methods, although it exhibits limited sensitivity to aminoglycosides, macrolides, and quinolones. Therefore, this article evaluates the antibiotic susceptibility profiles of five test bacteria (G. stearothermophilus subsp. calidolactis C953, Geobacillus thermocatenulatus LMG 19007, Geobacillus thermoleovorans LMG 9823, Geobacillus kaustophilus DSM 7263 and Geobacillus vulcani 13174). For that purpose, the minimum inhibitory concentrations (MICs) of 21 antibiotics were determined in milk samples for five test bacteria using the radial diffusion microbiological inhibition method. Subsequently, the similarities between bacteria and antibiotics were analyzed using cluster analysis. The dendrogram of this multivariate analysis shows an association between a group formed by G. thermocatenulatus and G. stearothermophilus and another by G. thermoleovorans, G. kaustophilus and G. vulcani. Finally, future microbiological methods could be developed in microtiter plates using G. thermocatenulatus as test bacterium, as it exhibits similar sensitivities to G. stearothermophilus. Conversely, G. vulcani, G. thermoleovorans and G. kaustophilus show higher MICs than G. thermocatenulatus.
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Affiliation(s)
- Orlando G Nagel
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina
| | - Maria L Gasparotti
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina
| | - Selva I Machado
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina
| | - Rafael L Althaus
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina.
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3
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Bidart GN, Gharabli H, Welner DH. Functional characterization of the phosphotransferase system in Parageobacillus thermoglucosidasius. Sci Rep 2023; 13:7131. [PMID: 37130962 PMCID: PMC10154347 DOI: 10.1038/s41598-023-33918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium characterized by rapid growth, low nutrient requirements, and amenability to genetic manipulation. These characteristics along with its ability to ferment a broad range of carbohydrates make P. thermoglucosidasius a potential workhorse in whole-cell biocatalysis. The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates and sugar derivatives in bacteria, making it important for their physiological characterization. In this study, the role of PTS elements on the catabolism of PTS and non-PTS substrates was investigated for P. thermoglucosidasius DSM 2542. Knockout of the common enzyme I, part of all PTSs, showed that arbutin, cellobiose, fructose, glucose, glycerol, mannitol, mannose, N-acetylglucosamine, N-acetylmuramic acid, sorbitol, salicin, sucrose, and trehalose were PTS-dependent on translocation and coupled to phosphorylation. The role of each putative PTS was investigated and six PTS-deletion variants could not grow on arbutin, mannitol, N-acetylglucosamine, sorbitol, and trehalose as the main carbon source, or showed diminished growth on N-acetylmuramic acid. We concluded that PTS is a pivotal factor in the sugar metabolism of P. thermoglucosidasius and established six PTS variants important for the translocation of specific carbohydrates. This study lays the groundwork for engineering efforts with P. thermoglucosidasius towards efficient utilization of diverse carbon substrates for whole-cell biocatalysis.
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Affiliation(s)
- Gonzalo N Bidart
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Hani Gharabli
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Ditte Hededam Welner
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark.
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4
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Li X, Zhang W, Zhong XR, Han HX, Dong B. Genome sequencing analysis of a novel thermophilic strain Geobacillus sp. CX412. Front Microbiol 2022; 13:1035311. [DOI: 10.3389/fmicb.2022.1035311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
The thermophilic spore-forming strain Geobacillus sp. CX412 was isolated from hot spring soil in Tengchong City, Yunnan Province, China. We sequenced the complete genome of Geobacillus sp. CX412 using PacBio SMRT Sequencing. Genome-scale phylogenetic analysis and average nucleotide identity (ANI) results indicated that Geobacillus sp. CX412 is a novel species in the genus Geobacillus. The metabolic potential of Geobacillus sp. CX412 based on COG, KEGG, and CAZymes analysis demonstrated that Geobacillus sp. CX412 was a highly adaptable strain with an unusually high number of 73 annotated transposons in the genome, which is relatively rare in Geobacillus. Compared with the near-derived strains, it was found that Geobacillus sp. CX412 has the unique β-lactam resistance and more active metabolism (more than 50.5–100.1%). Additionally, its genome encodes glycoside hydrolases and other genes related to lignocellulose breakdown, suggesting that Geobacillus sp. CX412 has a considerable biomass degradation potential. Thus, Geobacillus sp. CX412 is a new thermophilic bacterial species that add to the increasing repertoire of known lignocellulose degraders.
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5
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Viegas MF, Neves RPP, Ramos MJ, Fernandes PA. QM/MM Study of the Reaction Mechanism of Thermophilic Glucuronoyl Esterase for Biomass Treatment. Chemphyschem 2022; 23:e202200269. [PMID: 35925549 DOI: 10.1002/cphc.202200269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/23/2022] [Indexed: 11/06/2022]
Abstract
Hydrolysis of lignocellulosic biomass, composed of a lignin-carbohydrate-complex (LCC) matrix, is critical for producing bioethanol from glucose. However, current methods for LCC processing require costly and polluting processes. The fungal Thermothelomyces thermophila glucuronoyl esterase (TtGE) is a promising thermophilic enzyme that hydrolyses LCC ester bonds. This study describes the TtGE catalytic mechanism using QM/MM methods. Two nearly-degenerate rate-determining transition states were found, with barriers of 16 and 17 kcal ⋅ mol-1 , both with a zwitterionic nature that results from a proton interplay from His346 to either the Ser213-hydroxyl or the lignin leaving group and the rehybridisation of the ester moiety of the substrate to an alkoxide. An oxyanion hole, characteristic of esterases, was provided by the conserved Arg214 through its backbone and sidechain. Our work further suggests that a mutation of Glu267 to a non-negative residue will decrease the energetic barrier in ca. -5 kcal ⋅ mol-1 , improving the catalytic rate of TtGE.
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Affiliation(s)
- Matilde F Viegas
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Rui P P Neves
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria J Ramos
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro A Fernandes
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
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6
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Belaouni HA, Compant S, Antonielli L, Nikolic B, Zitouni A, Sessitsch A. In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region. Appl Microbiol Biotechnol 2022; 106:3113-3137. [PMID: 35435457 DOI: 10.1007/s00253-022-11907-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 11/02/2022]
Abstract
Endophytic strains belonging to the Bacillus cereus group were isolated from the halophytes Atriplex halimus L. (Amaranthaceae) and Tamarix aphylla L. (Tamaricaceae) from costal and continental regions in Algeria. Based on their salt tolerance (up to 5%), the strains were tested for their ability to alleviate salt stress in tomato and wheat. Bacillus sp. strain BH32 showed the highest potential to reduce salinity stress (up to + 50% and + 58% of dry weight improvement, in tomato and wheat, respectively, compared to the control). To determine putative mechanisms involved in salt tolerance and plant growth promotion, the whole genome of Bacillus sp. BH32 was sequenced, annotated, and used for comparative genomics against the genomes of closely related strains. The pangenome of Bacillus sp. BH32 and its closest relative was further analyzed. The phylogenomic analyses confirmed its taxonomic position, a member of the Bacillus cereus group, with intergenomic distances (GBDP analysis) pinpointing to a new taxon (digital DNA-DNA hybridization, dDDH < 70%). Genome mining unveiled several genes involved in stress tolerance, production of anti-oxidants and genes involved in plant growth promotion as well as in the production of secondary metabolites. KEY POINTS : • Bacillus sp. BH32 and other bacterial endophytes were isolated from halophytes, to be tested on tomato and wheat and to limit salt stress adverse effects. • The strain with the highest potential was then studied at the genomic level to highlight numerous genes linked to plant growth promotion and stress tolerance. • Pangenome approaches suggest that the strain belongs to a new taxon within the Bacillus cereus group.
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Affiliation(s)
- Hadj Ahmed Belaouni
- Laboratoire de Biologie Des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria.
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
| | - Branislav Nikolic
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
| | - Abdelghani Zitouni
- Laboratoire de Biologie Des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
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7
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Abstract
Synthetic biology applications rely on a well-characterized set of microbial strains, with an established toolbox of molecular biology methods for their genetic manipulation. Since there are no thermophiles with such attributes, most biotechnology and synthetic biology studies use organisms that grow in the mesophilic temperature range. As a result, thermophiles, a heterogenous group of microbes that thrive at high (>50 °C) temperatures, are largely overlooked, with respect to their biotechnological potential, even though they share several favorable traits. Thermophilic bacteria tend to grow at higher rates compared to their mesophilic counterparts, while their growth has lower cooling requirements and is less prone to contamination. Over the last few years, there has been renewed interest in developing tools and methods for thermophile bioengineering. In this perspective, we explain why it is a good idea to invest time and effort into developing a thermophilic synthetic biology direction, which is the state of the art, and why we think that the implementation of a thermophilic synthetic biology platform—a thermochassis—will take synthetic biology to the extremes.
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Aliyu H, de Maayer P, Neumann A. Not All That Glitters Is Gold: The Paradox of CO-dependent Hydrogenogenesis in Parageobacillus thermoglucosidasius. Front Microbiol 2021; 12:784652. [PMID: 34956151 PMCID: PMC8696081 DOI: 10.3389/fmicb.2021.784652] [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: 09/28/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
The thermophilic bacterium Parageobacillus thermoglucosidasius has recently gained interest due to its ability to catalyze the water gas shift reaction, where the oxidation of carbon monoxide (CO) is linked to the evolution of hydrogen (H2) gas. This phenotype is largely predictable based on the presence of a genomic region coding for a carbon monoxide dehydrogenase (CODH—Coo) and hydrogen evolving hydrogenase (Phc). In this work, seven previously uncharacterized strains were cultivated under 50% CO and 50% air atmosphere. Despite the presence of the coo—phc genes in all seven strains, only one strain, Kp1013, oxidizes CO and yields H2. The genomes of the H2 producing strains contain unique genomic regions that code for proteins involved in nickel transport and the detoxification of catechol, a by-product of a siderophore-mediated iron acquisition system. Combined, the presence of these genomic regions could potentially drive biological water gas shift (WGS) reaction in P. thermoglucosidasius.
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Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2 - Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Pieter de Maayer
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Anke Neumann
- Institute of Process Engineering in Life Science 2 - Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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9
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Carbon Monoxide Induced Metabolic Shift in the Carboxydotrophic Parageobacillus thermoglucosidasius DSM 6285. Microorganisms 2021; 9:microorganisms9051090. [PMID: 34069472 PMCID: PMC8159138 DOI: 10.3390/microorganisms9051090] [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: 03/22/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022] Open
Abstract
Parageobacillus thermoglucosidasius is known to catalyse the biological water gas shift (WGS) reaction, a pathway that serves as a source of alternative energy and carbon to a wide variety of bacteria. Despite increasing interest in this bacterium due to its ability to produce biological hydrogen through carbon monoxide (CO) oxidation, there are no data on the effect of toxic CO gas on its physiology. Due to its general requirement of O2, the organism is often grown aerobically to generate biomass. Here, we show that carbon monoxide (CO) induces metabolic changes linked to distortion of redox balance, evidenced by increased accumulation of organic acids such as acetate and lactate. This suggests that P. thermoglucosidasius survives by expressing several alternative pathways, including conversion of pyruvate to lactate, which balances reducing equivalents (oxidation of NADH to NAD+), and acetyl-CoA to acetate, which directly generates energy, while CO is binding terminal oxidases. The data also revealed clearly that P. thermoglucosidasius gained energy and grew during the WGS reaction. Combined, the data provide critical information essential for further development of the biotechnological potential of P. thermoglucosidasius.
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Krska D, Larsbrink J. Investigation of a thermostable multi-domain xylanase-glucuronoyl esterase enzyme from Caldicellulosiruptor kristjanssonii incorporating multiple carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:68. [PMID: 32308737 PMCID: PMC7151638 DOI: 10.1186/s13068-020-01709-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/02/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Efficient degradation of lignocellulosic biomass has become a major bottleneck in industrial processes which attempt to use biomass as a carbon source for the production of biofuels and materials. To make the most effective use of the source material, both the hemicellulosic as well as cellulosic parts of the biomass should be targeted, and as such both hemicellulases and cellulases are important enzymes in biorefinery processes. Using thermostable versions of these enzymes can also prove beneficial in biomass degradation, as they can be expected to act faster than mesophilic enzymes and the process can also be improved by lower viscosities at higher temperatures, as well as prevent the introduction of microbial contamination. RESULTS This study presents the investigation of the thermostable, dual-function xylanase-glucuronoyl esterase enzyme CkXyn10C-GE15A from the hyperthermophilic bacterium Caldicellulosiruptor kristjanssonii. Biochemical characterization of the enzyme was performed, including assays for establishing the melting points for the different protein domains, activity assays for the two catalytic domains, as well as binding assays for the multiple carbohydrate-binding domains present in CkXyn10C-GE15A. Although the enzyme domains are naturally linked together, when added separately to biomass, the expected boosting of the xylanase action was not seen. This lack of intramolecular synergy might suggest, together with previous data, that increased xylose release is not the main beneficial trait given by glucuronoyl esterases. CONCLUSIONS Due to its thermostability, CkXyn10C-GE15A is a promising candidate for industrial processes, with both catalytic domains exhibiting melting temperatures over 70 °C. Of particular interest is the glucuronoyl esterase domain, as it represents the first studied thermostable enzyme displaying this activity.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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Bashir Z, Sheng L, Anil A, Lali A, Minton NP, Zhang Y. Engineering Geobacillus thermoglucosidasius for direct utilisation of holocellulose from wheat straw. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:199. [PMID: 31452680 PMCID: PMC6701081 DOI: 10.1186/s13068-019-1540-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/06/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND A consolidated bioprocessing (CBP), where lignocellulose is converted into the desired product(s) in a single fermentative step without the addition of expensive degradative enzymes, represents the ideal solution of renewable routes to chemicals and fuels. Members of the genus Geobacillus are able to grow at elevated temperatures and are able to utilise a wide range of oligosaccharides derived from lignocellulose. This makes them ideally suited to the development of CBP. RESULTS In this study, we engineered Geobacillus thermoglucosidasius NCIMB 11955 to utilise lignocellulosic biomass, in the form of nitric acid/ammonia treated wheat straw to which expensive hydrolytic enzymes had not been added. Two different strains, BZ9 and BZ10, were generated by integrating the cglT (β-1,4-glucosidase) gene from Thermoanaerobacter brockii into the genome, and localising genes encoding different cellulolytic enzymes on autonomous plasmids. The plasmid of strain BZ10 carried a synthetic cellulosomal operon comprising the celA (Endoglucanase A) gene from Clostridium thermocellum and cel6B (Exoglucanase) from Thermobifida fusca; whereas, strain BZ9 contained a plasmid encoding the celA (multidomain cellulase) gene from Caldicellulosiruptor bescii. All of the genes were successfully expressed, and their encoded products secreted in a functionally active form, as evidenced by their detection in culture supernatants by Western blotting and enzymatic assay. In the case of the C. bescii CelA enzyme, this is one of the first times that the heterologous production of this multi-functional enzyme has been achieved in a heterologous host. Both strains (BZ9 and BZ10) exhibited improved growth on pre-treated wheat straw, achieving a higher final OD600 and producing greater numbers of viable cells. To demonstrate that cellulosic ethanol can be produced directly from lignocellulosic biomass by a single organism, we established our consortium of hydrolytic enzymes in a previously engineered ethanologenic G. thermoglucosidasius strain, LS242. We observed approximately twofold and 1.6-fold increase in ethanol production in the recombinant G. thermoglucosidasius equivalent to BZ9 and BZ10, respectively, compared to G. thermoglucosidasius LS242 strain at 24 h of growth. CONCLUSION We engineered G. thermoglucosidasius to utilise a real-world lignocellulosic biomass substrate and demonstrated that cellulosic ethanol can be produced directly from lignocellulosic biomass in one step. Direct conversion of biomass into desired products represents a new paradigm for CBP, offering the potential for carbon neutral, cost-effective production of sustainable chemicals and fuels.
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Affiliation(s)
- Zeenat Bashir
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Lili Sheng
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Annamma Anil
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parikh Marg, Mumbai, 400019 India
| | - Arvind Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parikh Marg, Mumbai, 400019 India
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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12
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Singh DN, Sood U, Singh AK, Gupta V, Shakarad M, Rawat CD, Lal R. Genome Sequencing Revealed the Biotechnological Potential of an Obligate Thermophile Geobacillus thermoleovorans Strain RL Isolated from Hot Water Spring. Indian J Microbiol 2019; 59:351-355. [PMID: 31388213 DOI: 10.1007/s12088-019-00809-x] [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: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 01/11/2023] Open
Abstract
In the present study, we report the draft genome sequence of an obligate thermophile Geobacillus thermoleovorans strain RL isolated from Manikaran hot water spring located atop the Himalayan ranges, India. Strain RL grew optimally at 70 °C but not below 45 °C. The draft genome (3.39 Mb) obtained by Illumina sequencing contains 138 contigs with an average G + C content of 52.30%. RAST annotation showed that amino acid metabolism pathways were most dominant followed by carbohydrate metabolism. Genome-wide analysis using NCBI's Prokaryotic Genome Annotation Pipeline revealed that strain RL encodes for a cocktail of industrially important hydrolytic enzymes glycoside hydrolase, α-and β-glucosidase, xylanase, amylase, neopullulanase, pullulanase and lipases required for white biotechnology. In addition, the presence of genes encoding green biocatalyst multicopper polyphenol oxidase (laccase) and an anticancer enzyme l-glutaminase reflects the significance of strain RL in gray and red biotechnology, respectively. Strain RL is a thermophilic multi-enzyme encoding bacterium which could be the source for the recombinant production of biotechnologically significant enzymes. In, addition whole cells of strain RL may be used in bioremediation studies.
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Affiliation(s)
| | - Utkarsh Sood
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | - Amit Kumar Singh
- 3Department of Biotechnology, Jamia Millia Islamia, New Delhi, Delhi 110025 India
| | - Vipin Gupta
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | | | - Charu Dogra Rawat
- 4Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
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13
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Gilman J, Singleton C, Tennant RK, James P, Howard TP, Lux T, Parker DA, Love J. Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications. ACS Synth Biol 2019; 8:1175-1186. [PMID: 30995831 DOI: 10.1021/acssynbio.9b00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space.
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Affiliation(s)
- James Gilman
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Chloe Singleton
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Richard K. Tennant
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Paul James
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Thomas P. Howard
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-upon-Tyne NE1 7RU, U.K
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich 85764, Germany
| | - David A. Parker
- Biodomain, Shell Technology Center Houston, 3333 Highway 6 South, Houston, Texas 77082-3101, United States
| | - John Love
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
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14
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Current Status of the Degradation of Aliphatic and Aromatic Petroleum Hydrocarbons by Thermophilic Microbes and Future Perspectives. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15122782. [PMID: 30544637 PMCID: PMC6313336 DOI: 10.3390/ijerph15122782] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 01/10/2023]
Abstract
Contamination of the environment by petroleum products is a growing concern worldwide, and strategies to remove these contaminants have been evaluated. One of these strategies is biodegradation, which consists of the use of microorganisms. Biodegradation is significantly improved by increasing the temperature of the medium, thus, the use of thermophiles, microbes that thrive in high-temperature environments, will render this process more efficient. For instance, various thermophilic enzymes have been used in industrial biotechnology because of their unique catalytic properties. Biodegradation has been extensively studied in the context of mesophilic microbes, and the mechanisms of biodegradation of aliphatic and aromatic petroleum hydrocarbons have been elucidated. However, in comparison, little work has been carried out on the biodegradation of petroleum hydrocarbons by thermophiles. In this paper, a detailed review of the degradation of petroleum hydrocarbons (both aliphatic and aromatic) by thermophiles was carried out. This work has identified the characteristics of thermophiles, and unraveled specific catabolic pathways of petroleum products that are only found with thermophiles. Gaps that limit our understanding of the activity of these microbes have also been highlighted, and, finally, different strategies that can be used to improve the efficiency of degradation of petroleum hydrocarbons by thermophiles were proposed.
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15
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Lebre PH, Aliyu H, De Maayer P, Cowan DA. In silico characterization of the global Geobacillus and Parageobacillus secretome. Microb Cell Fact 2018; 17:156. [PMID: 30285747 PMCID: PMC6171300 DOI: 10.1186/s12934-018-1005-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera within the phylum Firmicutes. These taxa have long been of biotechnological interest due to their ability to secrete thermostable enzymes and other biomolecules that have direct applications in various industrial and clinical fields. Despite the commercial and industrial interest in these microorganisms, the full scope of the secreted protein, i.e. the secretome, of Geobacillus and Parageobacillus species remains largely unexplored, with most studies focusing on single enzymes. A genome-wide exploration of the global secretome can provide a platform for understanding the extracellular functional “protein cloud” and the roles that secreted proteins play in the survival and adaptation of these biotechnologically relevant organisms. Results In the present study, the global secretion profile of 64 Geobacillus and Parageobacillus strains, comprising 772 distinct proteins, was predicted using comparative genomic approaches. Thirty-one of these proteins are shared across all strains used in this study and function in cell-wall/membrane biogenesis as well as transport and metabolism of carbohydrates, amino acids and inorganic ions. An analysis of the clustering patterns of the secretomes of the 64 strains according to shared functional orthology revealed a correlation between the secreted profiles of different strains and their phylogeny, with Geobacillus and Parageobacillus species forming two distinct functional clades. Conclusions The in silico characterization of the global secretome revealed a metabolically diverse set of secreted proteins, which include proteases, glycoside hydrolases, nutrient binding proteins and toxins. Electronic supplementary material The online version of this article (10.1186/s12934-018-1005-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Habibu Aliyu
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Pieter De Maayer
- School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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16
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Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications. Curr Microbiol 2017; 75:49-56. [PMID: 28900693 PMCID: PMC5765199 DOI: 10.1007/s00284-017-1349-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/28/2017] [Indexed: 01/12/2023]
Abstract
In attempt to obtain a thermophilic host for the conversion of lignocellulose derived substrates into lactic acid, Geobacillus thermodenitrificans T12 was isolated from a compost heap. It was selected from over 500 isolates as a genetically tractable hemicellulolytic lactic acid producer, requiring little nutrients. The strain is able to ferment glucose and xylose simultaneously and can produce lactic acid from xylan, making it a potential host for biotechnological applications. The genome of strain T12 consists of a 3.64 Mb chromosome and two plasmids of 59 and 56 kb. It has a total of 3.676 genes with an average genomic GC content of 48.7%. The T12 genome encodes a denitrification pathway, allowing for anaerobic respiration. The identity and localization of the responsible genes are similar to those of the denitrification pathways found in strain NG80-2. The hemicellulose utilization (HUS) locus was identified based on sequence homology against G. stearothermophilus T-6. It appeared that T12 has all the genes that are present in strain T-6 except for the arabinan degradation cluster. Instead, the HUS locus of strain T12 contains genes for both an inositol and a pectate degradation pathway. Strain T12 has complete pathways for the synthesis of purine and pyrimidine, all 20 amino acids and several vitamins except D-biotin. The host-defense systems present comprise a Type II and a Type III restriction-modification system, as well as a CRISPR-Cas Type II system. It is concluded that G. thermodenitrificans T12 is a potentially interesting candidate for industrial applications.
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17
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Burgess SA, Flint SH, Lindsay D, Cox MP, Biggs PJ. Insights into the Geobacillus stearothermophilus species based on phylogenomic principles. BMC Microbiol 2017; 17:140. [PMID: 28651524 PMCID: PMC5485677 DOI: 10.1186/s12866-017-1047-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/13/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise lactose, but the ability of dairy strains of G. stearothermophilus to use lactose has now been well established. RESULTS This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative lac operon in four dairy strains. CONCLUSIONS The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative lac operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach.
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Affiliation(s)
- S A Burgess
- School of Food and Nutrition, Massey University, Palmerston North, New Zealand.
- Infectious Disease Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
| | - S H Flint
- School of Food and Nutrition, Massey University, Palmerston North, New Zealand
| | - D Lindsay
- Fonterra Research Institute, Palmerston North, New Zealand
| | - M P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - P J Biggs
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
- Infectious Disease Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
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18
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Pogrebnyakov I, Jendresen CB, Nielsen AT. Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. PLoS One 2017; 12:e0171313. [PMID: 28152017 PMCID: PMC5289569 DOI: 10.1371/journal.pone.0171313] [Citation(s) in RCA: 17] [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: 11/11/2016] [Accepted: 01/19/2017] [Indexed: 11/20/2022] Open
Abstract
Species of genus Geobacillus are thermophilic bacteria and play an ever increasing role as hosts for biotechnological applications both in academia and industry. Here we screened a number of Geobacillus strains to determine which industrially relevant carbon sources they can utilize. One of the strains, G. thermoglucosidasius C56-YS93, was then chosen to develop a toolbox for controlled gene expression over a wide range of levels. It includes a library of semi-synthetic constitutive promoters (76-fold difference in expression levels) and an inducible promoter from the xylA gene. A library of synthetic in silico designed ribosome binding sites was also created for further tuning of translation. The PxylA was further used to successfully express native and heterologous xylanases in G. thermoglucosidasius. This toolbox enables fine-tuning of gene expression in Geobacillus species for metabolic engineering approaches in production of biochemicals and heterologous proteins.
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Affiliation(s)
- Ivan Pogrebnyakov
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian Bille Jendresen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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Brumm PJ, Gowda K, Robb FT, Mead DA. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. Front Microbiol 2016; 7:1979. [PMID: 28066333 PMCID: PMC5167688 DOI: 10.3389/fmicb.2016.01979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.
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Affiliation(s)
- Phillip J. Brumm
- C5-6 Technologies LLCFitchburg, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
| | - Krishne Gowda
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Frank T. Robb
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of MarylandBaltimore, MD, USA
| | - David A. Mead
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Varigen Biosciences CorporationMadison, WI, USA
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20
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Warda AK, Siezen RJ, Boekhorst J, Wells-Bennik MHJ, de Jong A, Kuipers OP, Nierop Groot MN, Abee T. Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PLoS One 2016; 11:e0156796. [PMID: 27272929 PMCID: PMC4896439 DOI: 10.1371/journal.pone.0156796] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022] Open
Abstract
We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.
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Affiliation(s)
- Alicja K. Warda
- TI Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, Wageningen, The Netherlands
| | - Roland J. Siezen
- TI Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, RadboudUMC, Nijmegen, The Netherlands
- Microbial Bioinformatics, Ede, The Netherlands
| | - Jos Boekhorst
- TI Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, RadboudUMC, Nijmegen, The Netherlands
- NIZO Food Research B.V., Ede, The Netherlands
| | | | - Anne de Jong
- TI Food and Nutrition, Wageningen, The Netherlands
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Oscar P. Kuipers
- TI Food and Nutrition, Wageningen, The Netherlands
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Masja N. Nierop Groot
- TI Food and Nutrition, Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, Wageningen, The Netherlands
| | - Tjakko Abee
- TI Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
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21
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Behera SS, Ray RC. Solid state fermentation for production of microbial cellulases: Recent advances and improvement strategies. Int J Biol Macromol 2016; 86:656-69. [DOI: 10.1016/j.ijbiomac.2015.10.090] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/23/2022]
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22
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Brumm PJ, Land ML, Mead DA. Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost. Stand Genomic Sci 2016; 11:33. [PMID: 27123157 PMCID: PMC4847372 DOI: 10.1186/s40793-016-0153-y] [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: 08/06/2015] [Accepted: 04/19/2016] [Indexed: 11/10/2022] Open
Abstract
Geobacillus sp. WCH70 was one of several thermophilic organisms isolated from hot composts in the Middleton, WI area. Comparison of 16 S rRNA sequences showed the strain may be a new species, and is most closely related to G. galactosidasius and G. toebii. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2009 (CP001638). The genome of Geobacillus species WCH70 consists of one circular chromosome of 3,893,306 bp with an average G + C content of 43 %, and two circular plasmids of 33,899 and 10,287 bp with an average G + C content of 40 %. Among sequenced organisms, Geobacillus sp. WCH70 shares highest Average Nucleotide Identity (86 %) with G. thermoglucosidasius strains, as well as similar genome organization. Geobacillus sp. WCH70 appears to be a highly adaptable organism, with an exceptionally high 125 annotated transposons in the genome. The organism also possesses four predicted restriction-modification systems not found in other Geobacillus species.
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Affiliation(s)
- Phillip J. Brumm
- />C5-6 Technologies LLC, Fitchburg, Wisconsin USA
- />Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin USA
| | - Miriam L. Land
- />Oak Ridge National Laboratory, Oak Ridge, Tennessee USA
| | - David A. Mead
- />Lucigen Corporation, Middleton, Wisconsin USA
- />Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin USA
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Comparative genome analyses of novel Mangrovimonas -like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes. Mar Genomics 2016; 25:115-121. [DOI: 10.1016/j.margen.2015.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/09/2015] [Accepted: 12/16/2015] [Indexed: 11/22/2022]
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24
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Draft Genome Sequence of Thermophilic Geobacillus sp. Strain Sah69, Isolated from Saharan Soil, Southeast Algeria. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01447-15. [PMID: 26679578 PMCID: PMC4683223 DOI: 10.1128/genomea.01447-15] [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
Geobacillus spp. are potential sources of novel enzymes, such as those involved in the degradation of recalcitrant polymers. Here, we report a Geobacillus genome that may help reveal genomic differences between this strain and publicly available representatives of the same genus from diverse niches.
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