1
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Ingelman H, Heffernan JK, Harris A, Brown SD, Shaikh KM, Saqib AY, Pinheiro MJ, de Lima LA, Martinez KR, Gonzalez-Garcia RA, Hawkins G, Daleiden J, Tran L, Zeleznik H, Jensen RO, Reynoso V, Schindel H, Jänes J, Simpson SD, Köpke M, Marcellin E, Valgepea K. Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness. N Biotechnol 2024; 83:S1871-6784(24)00023-2. [PMID: 38871051 DOI: 10.1016/j.nbt.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named "LAbrini", exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain "LAbrini" to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
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Affiliation(s)
- Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | - Asfand Yar Saqib
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Marina J Pinheiro
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Karen Rodriguez Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | - Ricardo A Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | | | | | | | | | - Jürgen Jänes
- Institute of Molecular Systems Biology, ETH Zürich, 8049 Zürich, Switzerland
| | | | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia.
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2
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Mehdizadeh Gohari I, Edwards AN, McBride SM, McClane BA. The impact of orphan histidine kinases and phosphotransfer proteins on the regulation of clostridial sporulation initiation. mBio 2024; 15:e0224823. [PMID: 38477571 DOI: 10.1128/mbio.02248-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
Sporulation is an important feature of the clostridial life cycle, facilitating survival of these bacteria in harsh environments, contributing to disease transmission for pathogenic species, and sharing common early steps that are also involved in regulating industrially important solvent production by some non-pathogenic species. Initial genomics studies suggested that Clostridia lack the classical phosphorelay that phosphorylates Spo0A and initiates sporulation in Bacillus, leading to the hypothesis that sporulation in Clostridia universally begins when Spo0A is phosphorylated by orphan histidine kinases (OHKs). However, components of the classical Bacillus phosphorelay were recently identified in some Clostridia. Similar Bacillus phosphorelay components have not yet been found in the pathogenic Clostridia or the solventogenic Clostridia of industrial importance. For some of those Clostridia lacking a classical phosphorelay, the involvement of OHKs in sporulation initiation has received support from genetic studies demonstrating the involvement of several apparent OHKs in their sporulation. In addition, several clostridial OHKs directly phosphorylate Spo0A in vitro. Interestingly, there is considerable protein domain diversity among the sporulation-associated OHKs in Clostridia. Further adding to the emergent complexity of sporulation initiation in Clostridia, several candidate OHK phosphotransfer proteins that were OHK candidates were shown to function as phosphatases that reduce sporulation in some Clostridia. The mounting evidence indicates that no single pathway explains sporulation initiation in all Clostridia and supports the need for further study to fully understand the unexpected and biologically fascinating mechanistic diversity of this important process among these medically and industrially important bacteria.
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Affiliation(s)
- Iman Mehdizadeh Gohari
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Bruce A McClane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Kumar K, Barbora L, Moholkar VS. Genomic insights into clostridia in bioenergy production: Comparison of metabolic capabilities and evolutionary relationships. Biotechnol Bioeng 2024; 121:1298-1313. [PMID: 38047471 DOI: 10.1002/bit.28610] [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: 11/15/2022] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Bacteria from diverse genera, including Acetivibrio, Bacillus, Cellulosilyticum, Clostridium, Desulfotomaculum, Lachnoclostridium, Moorella, Ruminiclostridium, and Thermoanaerobacterium, have attracted significant attention due to their versatile metabolic capabilities encompassing acetogenic, cellulolytic, and C1-metabolic properties, and acetone-butanol-ethanol fermentation. Despite their biotechnological significance, a comprehensive understanding of clostridial physiology and evolution has remained elusive. This study reports an extensive comparative genomic analysis of 48 fully sequenced bacterial genomes from these genera. Our investigation, encompassing pan-genomic analysis, central carbon metabolism comparison, exploration of general genome features, and in-depth scrutiny of Cluster of Orthologous Groups genes, has established a holistic whole-genome-based phylogenetic framework. We have classified these strains into acetogenic, butanol-producing, cellulolytic, CO2-fixating, chemo(litho/organo)trophic, and heterotrophic categories, often exhibiting overlaps. Key outcomes include the identification of misclassified species and the revelation of insights into metabolic features, energy conservation, substrate utilization, stress responses, and regulatory mechanisms. These findings can provide guidance for the development of efficient microbial systems for sustainable bioenergy production. Furthermore, by addressing fundamental questions regarding genetic relationships, conserved genomic features, pivotal enzymes, and essential genes, this study has also contributed to our comprehension of clostridial biology, evolution, and their shared metabolic potential.
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Affiliation(s)
- Karan Kumar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Lepakshi Barbora
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Vijayanand S Moholkar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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4
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Oehlenschläger K, Volkmar M, Stiefelmaier J, Langsdorf A, Holtmann D, Tippkötter N, Ulber R. New insights into the influence of pre-culture on robust solvent production of C. acetobutylicum. Appl Microbiol Biotechnol 2024; 108:143. [PMID: 38231267 PMCID: PMC10794392 DOI: 10.1007/s00253-023-12981-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
Clostridia are known for their solvent production, especially the production of butanol. Concerning the projected depletion of fossil fuels, this is of great interest. The cultivation of clostridia is known to be challenging, and it is difficult to achieve reproducible results and robust processes. However, existing publications usually concentrate on the cultivation conditions of the main culture. In this paper, the influence of cryo-conservation and pre-culture on growth and solvent production in the resulting main cultivation are examined. A protocol was developed that leads to reproducible cultivations of Clostridium acetobutylicum. Detailed investigation of the cell conservation in cryo-cultures ensured reliable cell growth in the pre-culture. Moreover, a reason for the acid crash in the main culture was found, based on the cultivation conditions of the pre-culture. The critical parameter to avoid the acid crash and accomplish the shift to the solventogenesis of clostridia is the metabolic phase in which the cells of the pre-culture were at the time of inoculation of the main culture; this depends on the cultivation time of the pre-culture. Using cells from the exponential growth phase to inoculate the main culture leads to an acid crash. To achieve the solventogenic phase with butanol production, the inoculum should consist of older cells which are in the stationary growth phase. Considering these parameters, which affect the entire cultivation process, reproducible results and reliable solvent production are ensured. KEY POINTS: • Both cryo- and pre-culture strongly impact the cultivation of C. acetobutylicum • Cultivation conditions of the pre-culture are a reason for the acid crash • Inoculum from cells in stationary growth phase ensures shift to solventogenesis.
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Affiliation(s)
- Katharina Oehlenschläger
- Institute of Bioprocess Engineering, University of Kaiserslautern-Landau, Gottlieb-Daimler-Straße 49, 67663, Kaiserslautern, Germany
| | - Marianne Volkmar
- Institute of Bioprocess Engineering, University of Kaiserslautern-Landau, Gottlieb-Daimler-Straße 49, 67663, Kaiserslautern, Germany
| | - Judith Stiefelmaier
- Institute of Bioprocess Engineering, University of Kaiserslautern-Landau, Gottlieb-Daimler-Straße 49, 67663, Kaiserslautern, Germany
| | - Alexander Langsdorf
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstraße 14, 35390, Giessen, Germany
| | - Dirk Holtmann
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Nils Tippkötter
- Institute of Bioprocess Engineering and Downstream Processing, University of Applied Sciences Aachen, Heinrich-Mußmann-Straße 1, 52428, Jülich, Germany
| | - Roland Ulber
- Institute of Bioprocess Engineering, University of Kaiserslautern-Landau, Gottlieb-Daimler-Straße 49, 67663, Kaiserslautern, Germany.
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Sadr S, Zargar B, Perez J, Aucoin MG, Ingalls B. Heterologous expression of NoxA confers aerotolerance in Clostridium sporogenes. Biotechnol J 2024; 19:e2300161. [PMID: 37818934 DOI: 10.1002/biot.202300161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/06/2023] [Accepted: 10/05/2023] [Indexed: 10/13/2023]
Abstract
Clostridium is a genus of gram-positive obligate anaerobic bacteria. Some species of Clostridium, including Clostridium sporogenes, may be of use in bacteria-mediated cancer therapy. Spores of Clostridium are inert in healthy normoxic tissue but germinate when in the hypoxic regions of solid tumors, causing tumor regression. However, such treatments fail to completely eradicate tumors partly because of higher oxygen levels at the tumor's outer rim. In this study, we demonstrate that a degree of aerotolerance can be introduced to C. sporogenes by transfer of the noxA gene from Clostridium aminovalericum. NoxA is a water-forming NADH oxidase enzyme, and so has no detrimental effect on cell viability. In addition to its potential in cancer treatment, the noxA-expressing strain described here could be used to alleviate challenges related to oxygen sensitivity of C. sporogenes in biomanufacturing.
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Affiliation(s)
- Sara Sadr
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | | | | | - Marc G Aucoin
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Brian Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada
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6
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Furuya K, Kiyoshi K, Punjuy C, Yoshida N, Maruyama R, Yasuda T, Watanabe K, Kadokura T, Nakayama S. Effect of spo0A, sigE, sigG, and sigK disruption on butanol production and spore formation in Clostridium saccharoperbutylacetonicum strain N1-4 (ATCC13564). J Biosci Bioeng 2023; 136:198-204. [PMID: 37487916 DOI: 10.1016/j.jbiosc.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: 02/22/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
Clostridium saccharoperbutylacetonicum strain N1-4 (ATCC13564) is a butanol-producing strain suitable for application to butanol production from cellulosic materials by co-culture with cellulolytic and thermophilic species, such as Hungateiclostridium thermocellum (synonym: Clostridium thermocellum). The optimal temperature for butanol production by strain N1-4 is 30 °C, and the strain is sensitive to a high culture temperature of 37 °C. Given that spore formation is observed at high frequency when strain N1-4 is cultivated at 37 °C, we assumed in a previous study that the initiation of sporulation is related to a decrease in butanol production. Therefore, to investigate the relationship between butanol production and spore formation, we generated strain N1-4 isolates in which genes related to spore formation were disrupted. The sporulation-related gene disruptants of spo0A, sigE, sigG, and sigK lost the ability to produce heat-resistant spores, irrespective of the culture temperature. Among the gene disruptants produced, only the spo0A disruptant lost butanol-producing ability when cultivated at 30 °C. Interestingly, the sigE disruptant maintained butanol productivity similar to that observed at 30 °C, even when cultivated at 37 °C. In addition, the sigE disruptant successfully produced butanol from Avicel cellulose by co-culture with H. thermocellum at a fermentation temperature of 37 °C.
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Affiliation(s)
- Kazuhiko Furuya
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Keiji Kiyoshi
- Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Chaophaya Punjuy
- Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Naoto Yoshida
- Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Risa Maruyama
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Tatsuki Yasuda
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kota Watanabe
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Toshimori Kadokura
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shunichi Nakayama
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
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7
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Guerrero M. GG. Sporulation, Structure Assembly, and Germination in the Soil Bacterium Bacillus thuringiensis: Survival and Success in the Environment and the Insect Host. MICROBIOLOGY RESEARCH 2023. [DOI: 10.3390/microbiolres14020035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Bacillus thuringiensis (Bt) is a rod-shaped, Gram-positive soil bacterium that belongs to the phylum Firmicutes and the genus Bacillus. It is a spore-forming bacterium. During sporulation, it produces a wide range of crystalline proteins that are toxic to different orders of insects. Sporulation, structure assembly, and germination are essential stages in the cell cycle of B. thuringiensis. The majority of studies on these issues have focused on the model organism Bacillus subtilis, followed by Bacillus cereus and Bacillus anthracis. The machinery for sporulation and germination extrapolated to B. thuringiensis. However, in the light of recent findings concerning the role of the sporulation proteins (SPoVS), the germination receptors (Gr), and the cortical enzymes in Bt, the theory strengthened that conservation in sporulation, structure assembly, and germination programs drive the survival and success of B. thuringiensis in the environment and the insect host. In the present minireview, the latter pinpointed and reviewed.
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Affiliation(s)
- Gloria G. Guerrero M.
- Unidad Académica de Ciencias Biológicas, Laboratorio de Immunobiología, Universidad Autónoma de Zacatecas, Av. Preparatoria S/N, Col. Agronomicas, Zacatecas 98066, Mexico
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8
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Humphreys JR, Debebe BJ, Diggle SP, Winzer K. Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity. Front Microbiol 2023; 13:1075609. [PMID: 36704551 PMCID: PMC9871927 DOI: 10.3389/fmicb.2022.1075609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when grown continuously. This phenomenon sees cells lose their ability to produce solvents and spores, posing a significant problem for industrial applications. To investigate the mechanistic and evolutionary basis of degeneration we combined comparative genomics, ultra-deep sequencing, and concepts of sociomicrobiology using Clostridium beijerinckii NCIMB 8052 as our model organism. These approaches revealed spo0A, the master regulator gene involved in spore and solvent formation, to be key to the degeneration process in this strain. Comparative genomics of 71 degenerate variants revealed four distinct hotspot regions that contained considerably more mutations than the rest of the genome. These included spo0A as well as genes suspected to regulate its expression and activity. Ultra-deep sequencing of populations during the subculturing process showed transient increases in mutations we believe linked to the spo0A network, however, these were ultimately dominated by mutations in the master regulator itself. Through frequency-dependent fitness assays, we found that spo0A mutants gained a fitness advantage, relative to the wild type, presumably allowing for propagation throughout the culture. Combined, our data provides new insights into the phenomenon of clostridial strain degeneration and the C. beijerinckii NCIMB 8052 solvent and spore regulation network.
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Affiliation(s)
- Jonathan R. Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United Kingdom
| | - Bisrat J. Debebe
- DeepSeq, Centre for Genetics and Genomics, The University of Nottingham, Nottingham, United Kingdom
| | - Stephen P. Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United Kingdom,*Correspondence: Klaus Winzer, ✉
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9
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Benito-Vaquerizo S, Nouse N, Schaap PJ, Hugenholtz J, Brul S, López-Contreras AM, Martins dos Santos VAP, Suarez-Diez M. Model-driven approach for the production of butyrate from CO 2/H 2 by a novel co-culture of C. autoethanogenum and C. beijerinckii. Front Microbiol 2022; 13:1064013. [PMID: 36620068 PMCID: PMC9815533 DOI: 10.3389/fmicb.2022.1064013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO2/H2 gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Niels Nouse
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,UNLOCK Large Scale Infrastructure for Microbial Communities, Wageningen University and Research and Delft University of Technology, Wageningen, Netherlands
| | - Jeroen Hugenholtz
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Ana M. López-Contreras
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, Netherlands
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,*Correspondence: Maria Suarez-Diez ✉
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10
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Cao Q, Zhang W, Lian T, Wang S, Yin F, Zhou T, Wei X, Dong H. Revealing mechanism of micro-aeration for enhancing volatile fatty acids production from swine manure. BIORESOURCE TECHNOLOGY 2022; 365:128140. [PMID: 36252761 DOI: 10.1016/j.biortech.2022.128140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Micro-aeration is considered a new strategy for improving volatile fatty acids (VFAs) production of agricultural waste. This study investigated the effect and mechanism of micro-aeration of air and oxygen (O2) on VFAs production from swine manure. The results showed that Air-micro-aeration had the most significant improvement effect, with the highest VFAs of 8.21 g/L, which was increased by 22.4%. Moreover, the mixing effects of different micro-aeration were limited, and the microbial communities significantly varied. Firmicutes and Bacteroidota were the dominant hydrolytic and acidogenic bacteria, and Air-micro-aeration preferentially promoted electron transfer activity and energy generation. Methanosarcina, Methanocorpusculum, and Methanobrevibacter can adapt to environmental changes according to their different oxygen tolerance, and the consumption and conversion of VFAs by methanogens were slow under Air-micro-aeration condition. This study revealed mechanism of micro-aeration for improving VFAs production from swine manure, providing a theoretical basis for micro-aeration regulation optimization.
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Affiliation(s)
- Qitao Cao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wanqin Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Tianjing Lian
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, PR China
| | - Shunli Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Fubin Yin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Tanlong Zhou
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoman Wei
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Hongmin Dong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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11
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Chang WL, Hou W, Xu M, Yang ST. High-rate continuous n-butanol production by Clostridium acetobutylicum from glucose and butyric acid in a single-pass fibrous bed bioreactor. Biotechnol Bioeng 2022; 119:3474-3486. [PMID: 36059064 DOI: 10.1002/bit.28223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Abstract
Biobutanol produced in acetone-butanol-ethanol (ABE) fermentation at batch mode cannot compete with chemically derived butanol because of the low reactor productivity. Continuous fermentation can dramatically enhance productivity and lower capital and operating costs but are rarely used in industrial fermentation because of increased risks in culture degeneration, cell washout, and contamination. In this study, cells of the asporogenous Clostridium acetobutylicum ATCC55025 were immobilized in a single-pass fibrous-bed bioreactor (FBB) for continuous production of butanol from glucose and butyrate at various dilution rates. Butyric acid in the feed medium helped maintaining cells in the solventogenic phase for stable continuous butanol production. At the dilution rate of 1.88 h-1 , butanol was produced at 9.55 g/L with a yield of 0.24 g/g and productivity of 16.8 g/L/h, which was the highest productivity ever achieved for biobutanol fermentation and an 80-fold improvement over the conventional ABE fermentation. The extremely high productivity was attributed to the high density of viable cells (~100 g/L at >70% viability) immobilized in the fibrous matrix, which also enabled the cells to better tolerate butanol and butyric acid. The FBB was stable for continuous operation for an extended period of over one month. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wei-Lun Chang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA
| | - Wenjie Hou
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA.,College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mengmeng Xu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210, USA
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Liu L, Ao D, Cai X, Huang P, Cai N, Lin S, Wu B. Early gut microbiota in very low and extremely low birth weight preterm infants with feeding intolerance: a prospective case-control study. J Microbiol 2022; 60:1021-1031. [PMID: 35984614 PMCID: PMC9390111 DOI: 10.1007/s12275-022-2180-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Ling Liu
- Jinan University, Guangzhou, Guangdong, 510000, China
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Dang Ao
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Xiangsheng Cai
- University of the Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518000, China
| | - Peiyi Huang
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Nali Cai
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Shaozhu Lin
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524000, China
| | - Benqing Wu
- Jinan University, Guangzhou, Guangdong, 510000, China.
- University of the Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518000, China.
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Chai R, Tai Z, Zhu Y, Chai C, Chen Z, Zhu Q. Symbiotic microorganisms: prospects for treating atopic dermatitis. Expert Opin Biol Ther 2022; 22:911-927. [PMID: 35695265 DOI: 10.1080/14712598.2022.2089560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Atopic dermatitis (AD) is a common chronic recurrent inflammatory skin disease. The pathogenesis is unclear but may be related to genetic, immune, and environmental factors and abnormal skin barrier function. Symbiotic microorganisms in the gut and on the skin are associated with AD occurrence. AREAS COVERED We discuss the metabolism and distribution of intestinal and skin flora and review their relationship with AD, summarizing the recent applications of intestinal and skin flora in AD treatment, and discussing the prospect of research on these two human microbiota systems and their influence on AD treatment. The PubMed database was searched to identify relevant publications from 1949 to 2020 for the bibliometric analysis of atopic dermatitis and symbiotic microorganisms. EXPERT OPINION Many studies have suggested a potential contribution of microbes in the intestine and on the skin to AD. Bacteria living on the skin can aggravate AD by secreting numerous virulence factors. Moreover, the metabolism of intestinal flora can influence AD occurrence and development via the circulatory system. Current evidence suggests that by regulating intestinal and skin flora, AD can be treated and prevented.
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Affiliation(s)
- Rongrong Chai
- Department of Pharmacy, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai P.R. China
| | - Zongguang Tai
- Department of Pharmacy, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai P.R. China.,Department of Pharmacy, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Yunjie Zhu
- RnD-I, Zifo RnD Solution, Shanghai, P.R. China
| | - Chaochao Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing P.R. China
| | - Zhongjian Chen
- Department of Pharmacy, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai P.R. China
| | - Quangang Zhu
- Department of Pharmacy, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai P.R. China
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Doyle DA, Smith PR, Lawson PA, Tanner RS. Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An acid/alcohol-producing, Gram-stain-positive, obligately anaerobic, rod-shaped, non-motile, non-spore forming acetogen, designated as strain P21T, was isolated from old hay after enrichment with CO as the substrate. Spores not observed even after prolonged incubation (30 days). Phylogenetic analysis of the 16S rRNA gene sequence of strain P21T showed it was closely related to
Clostridium carboxidivorans
DSM 15243T (97.9%),
Clostridium scatologenes
DSM 757T (97.7 %) and
Clostridium drakei
DSM 12750T (97.7 %). The genome is 5.6 Mb and the G+C content is 29.4 mol%. Average nucleotide identity between strain P21T,
C. carboxidivorans
,
C. scatologenes
and
C. drakei
was 87.1, 86.4, 86.4 %, respectively. Strain P21T grew on CO:CO2, H2:CO2, l-arabinose, ribose, xylose, fructose, galactose, glucose, lactose, mannose, cellobiose, sucrose, cellulose, starch, pyruvate, choline, glutamate, histidine, serine, threonine and casamino acids. End products of metabolism were acetate, butyrate, caproate, ethanol and hexanol. Dominant cellular fatty acids (>10 %) were C16 : 0 (41.5 %), C16 : 1 ω7c/C16 : 1 ω6c (10.0 %), and a summed feature containing cyclo C17 : 1/C18 : 0 (17.3 %). Based on the phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain P21T represents a new species in the genus
Clostridium
, for which the name Clostridium muellerianum sp. nov. is proposed. The type strain is P21T (=DSM 111390T=NCIMB 15261T).
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Affiliation(s)
- D. Annie Doyle
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Parker R. Smith
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Ralph S. Tanner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
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The Measurement, Application and Effect of Oxygen in Microbial Fermentations: Focusing on Methane and Carboxylate Production. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8040138] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Oxygen is considered detrimental to anaerobic fermentation processes by many practitioners. However, deliberate oxygen sparging has been used successfully for decades to remove H2S in anaerobic digestion (AD) systems. Moreover, microaeration techniques during AD have shown that small doses of oxygen may enhance process performance and promote the in situ degradation of recalcitrant compounds. However, existing oxygen dosing techniques are imprecise, which has led to inconsistent results between studies. At the same time, real-time oxygen fluxes cannot be reliably quantified due to the complexity of most bioreactor systems. Thus, there is a pressing need for robust monitoring and process control in applications where oxygen serves as an operating parameter or an experimental variable. This review summarizes and evaluates the available methodologies for oxygen measurement and dosing as they pertain to anaerobic microbiomes. The historical use of (micro-)aeration in anaerobic digestion and its potential role in other anaerobic fermentation processes are critiqued in detail. This critique also provides insights into the effects of oxygen on these microbiomes. Our assessment suggests that oxygen dosing, when implemented in a controlled and quantifiable manner, could serve as an effective tool for bioprocess engineers to further manipulate anaerobic microbiomes for either bioenergy or biochemical production.
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ACETONE-BUTYL FERMENTATION PECULIARITIES OF THE BUTANOL STRAINS -PRODUCER. BIOTECHNOLOGIA ACTA 2022. [DOI: 10.15407/biotech15.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The aim of this review was to generalize and analyze the features of acetone-butyl fermentation as a type of butyric acid fermentation in the process of obtaining butanol as an alternative biofuel. Methods. The methods of analysis and generalization of analytical information and literature sources were used in the review. The results were obtained using the following methods such as microbiological (morphological properties of strains), chromatographic (determination of solvent concentration), spectrophotometric (determination of bacterial concentration), and molecular genetic (phylogenetic analysis of strains). Results. The process of acetone-butyl fermentation was analyzed, the main producer strains were considered, the features of the relationship between alcohol formation and sporulation were described, the possibility of butanol obtaining from synthesis gas was shown, and the features of the industrial production of butanol were considered. Conclusions. The features of the mechanism of acetone-butyl fermentation (the relationships between alcohol formation and sporulation, the duration of the acid-forming and alcohol-forming stages during batch fermentation depending on the change in the concentration of H2, CO, partial pressure, organic acids and mineral additives) and obtaining an enrichment culture during the production of butanol as an alternative fuel were shown. The possibility of using synthesis gas as a substrate for reducing atmospheric emissions during the fermentation process was shown. The direction of increasing the productivity of butanol-producing strains to create a competitive industrial biofuel technology was proposed.
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Patakova P, Branska B, Vasylkivska M, Jureckova K, Musilova J, Provaznik I, Sedlar K. Transcriptomic studies of solventogenic clostridia, Clostridium acetobutylicum and Clostridium beijerinckii. Biotechnol Adv 2021; 58:107889. [PMID: 34929313 DOI: 10.1016/j.biotechadv.2021.107889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022]
Abstract
Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.
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Affiliation(s)
- Petra Patakova
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic.
| | - Barbora Branska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | - Maryna Vasylkivska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | | | - Jana Musilova
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Ivo Provaznik
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Karel Sedlar
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
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