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Mbaye B, Wasfy RM, Alou MT, Borentain P, Gerolami R, Dufour JC, Million M. A catalog of ethanol-producing microbes in humans. Future Microbiol 2024; 19:697-714. [PMID: 38700288 PMCID: PMC11259083 DOI: 10.2217/fmb-2023-0250] [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: 11/10/2023] [Accepted: 02/13/2024] [Indexed: 05/05/2024] Open
Abstract
Aim: Endogenous ethanol production emerges as a mechanism of nonalcoholic steatohepatitis, obesity, diabetes and auto-brewery syndrome. Methods: To identify ethanol-producing microbes in humans, we used the NCBI taxonomy browser and the PubMed database with an automatic query and manual verification. Results: 85 ethanol-producing microbes in human were identified. Saccharomyces cerevisiae, Candida and Pichia were the most represented fungi. Enterobacteriaceae was the most represented bacterial family with mainly Escherichia coli and Klebsiella pneumoniae. Species of the Lachnospiraceae and Clostridiaceae family, of the Lactobacillales order and of the Bifidobacterium genus were also identified. Conclusion: This catalog will help the study of ethanol-producing microbes in human in the pathophysiology, diagnosis, prevention and management of human diseases associated with endogenous ethanol production.
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Affiliation(s)
- Babacar Mbaye
- Aix Marseille Université, AP-HM, MEPHI, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Reham Magdy Wasfy
- Aix Marseille Université, AP-HM, MEPHI, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille Université, AP-HM, MEPHI, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Patrick Borentain
- Department of Hepatology, La Timone University Hospital, AP-HM, Marseille, France
| | - Rene Gerolami
- Aix Marseille Université, AP-HM, MEPHI, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Department of Hepatology, La Timone University Hospital, AP-HM, Marseille, France
| | - Jean-Charles Dufour
- INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, ISSPAM, Aix Marseille University, 13385 Marseille, France
- APHM, Hôpital de la Timone, Service Biostatistique et Technologies de l'Information et de la Communication, 13385 Marseille, France
| | - Matthieu Million
- Aix Marseille Université, AP-HM, MEPHI, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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Liu Y, Angelov A, Übelacker M, Baudrexl M, Ludwig C, Rühmann B, Sieber V, Liebl W. Proteomic analysis of Viscozyme L and its major enzyme components for pectic substrate degradation. Int J Biol Macromol 2024; 266:131309. [PMID: 38580019 DOI: 10.1016/j.ijbiomac.2024.131309] [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: 12/25/2023] [Revised: 02/14/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Enzymatic degradation of plant biomass requires the coordinated action of various enzymes. In this study, the production of reducing sugars from pectic substrates and sugar beet pulp (SBP) was investigated and compared using commercial enzyme preparations, including M2, pectinase (E1), Viscozyme L (V-L) and L-40. V-L, a cellulolytic enzyme mix produced by Aspergillus sp. was further evaluated as the most robust enzyme cocktail with the strongest SBP degradation ability in terms of the release of monosaccharides, methanol, and acetate from SBP. Mass-spectrometry-based proteomics analysis of V-L revealed 156 individual proteins. Of these, 101 proteins were annotated as containing a carbohydrate-active enzyme module. Notably, of the 50 most abundant proteins, ca. 44 % were predicted to be involved in pectin degradation. To reveal the role of individual putative key enzymes in pectic substrate decomposition, two abundant galacturonases (PglA and PglB), were heterologously expressed in Pichia pastoris and further characterized. PglA and PglB demonstrated maximum activity at 57 °C and 68 °C, respectively, and exhibited endo-type cleavage patterns towards polygalacturonic acid. Further studies along this line may lead to a better understanding of efficient SBP degradation and may help to design improved artificial enzyme mixtures with lower complexity for future application in biotechnology.
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Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Maria Übelacker
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany.
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Guo Y, Liu Y, Guan M, Tang H, Wang Z, Lin L, Pang H. Production of butanol from lignocellulosic biomass: recent advances, challenges, and prospects. RSC Adv 2022; 12:18848-18863. [PMID: 35873330 PMCID: PMC9240921 DOI: 10.1039/d1ra09396g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Due to energy and environmental concerns, biobutanol is gaining increasing attention as an alternative renewable fuel owing to its desirable fuel properties. Biobutanol production from lignocellulosic biomass through acetone-butanol-ethanol (ABE) fermentation has gained much interest globally due to its sustainable supply and non-competitiveness with food, but large-scale fermentative production suffers from low product titres and poor selectivity. This review presents recent developments in lignocellulosic butanol production, including pretreatment and hydrolysis of hemicellulose and cellulose during ABE fermentation. Challenges are discussed, including low concentrations of fermentation sugars, inhibitors, detoxification, and carbon catabolite repression. Some key process improvements are also summarised to guide further research and development towards more profitable and commercially viable butanol fermentation.
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Affiliation(s)
- Yuan Guo
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China +86-771-2503940 +86-771-2503973
| | - Yi Liu
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China +86-771-2503940 +86-771-2503973
| | - Mingdong Guan
- College of Life Science and Technology, Guangxi University Nanning 530004 China
| | - Hongchi Tang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China +86-771-2503940 +86-771-2503973
| | - Zilong Wang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China +86-771-2503940 +86-771-2503973
| | - Lihua Lin
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China +86-771-2503940 +86-771-2503973
| | - Hao Pang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China +86-771-2503940 +86-771-2503973
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Rettenmaier R, Thieme N, Streubel J, Di Bello L, Kowollik ML, Huang L, Maus I, Klingl A, Liebl W, Zverlov VV. Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter. Int J Syst Evol Microbiol 2021; 71. [PMID: 34731077 DOI: 10.1099/ijsem.0.005044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MD1T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7-8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1T are C14:0 DMA and C16:0. Strain MD1T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1T are Mobilitalea sibirica P3M-3T and Anaerotaenia torta FH052T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family Lachnospiraceae, for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1T=DSM 110715T=JCM 39125T) is proposed.
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Affiliation(s)
- Regina Rettenmaier
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Nils Thieme
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Johanna Streubel
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Luca Di Bello
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Marie-Louise Kowollik
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Andreas Klingl
- Ludwig-Maximilians-Universität Munich, Plant Development & Electron Microscopy, Biocenter LMU Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Wolfgang Liebl
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V Zverlov
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany.,Institute of Molecular Genetics, National Research Centre 'Kurchatov Institute', Kurchatov Sq 2, 123182 Moscow, Russia
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Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T. Processes (Basel) 2021. [DOI: 10.3390/pr9071196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.
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Draft Genome Sequence of Clostridium beijerinckii Strain mbf-VZ-132, Isolated from an Environmental Soil Sample. Microbiol Resour Announc 2021; 10:10/17/e00131-21. [PMID: 33927028 PMCID: PMC8086202 DOI: 10.1128/mra.00131-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium beijerinckii strain mbf-VZ-132 was isolated from soil in Freising-Weihenstephan (Bavaria, Germany). The 16S rRNA gene sequence showed a 99.9% sequence identity to Clostridium diolis DSM 15410, which was recently reclassified as C. beijerinckii. In this study, we present the draft genome sequence of C. beijerinckii mbf-VZ-132, based on PacBio sequencing. Clostridium beijerinckii strain mbf-VZ-132 was isolated from soil in Freising-Weihenstephan (Bavaria, Germany). The 16S rRNA gene sequence showed a 99.9% sequence identity to that of Clostridium diolis DSM 15410, which was recently reclassified as C. beijerinckii. In this study, we present the draft genome sequence of C. beijerinckii mbf-VZ-132 based on PacBio sequencing.
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