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Böer T, Bengelsdorf FR, Daniel R, Poehlein A. Complete genome sequences of Blautia hydrogenotrophica DSM 10507 T isolated from human feces and Blautia coccoides DSM 935 T isolated from mouse feces. Microbiol Resour Announc 2024; 13:e0001624. [PMID: 38477460 PMCID: PMC11008154 DOI: 10.1128/mra.00016-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
We report on the closed genome sequences of the acetogen Blautia hydrogenotrophica S5a33T (DSM 10507T) and of Blautia coccoides CLC-1T (DSM 935T). The B. hydrogenotrophica S5a33T genome harbors a chromosome (3,590,609 bp) and a plasmid (7,176 bp). The B. coccoides CLC-1T genome consists of a single chromosome (6,097,890 bp).
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Affiliation(s)
- Tim Böer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Frank R. Bengelsdorf
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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D'hoe K, Vet S, Faust K, Moens F, Falony G, Gonze D, Lloréns-Rico V, Gelens L, Danckaert J, De Vuyst L, Raes J. Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community. eLife 2018; 7:37090. [PMID: 30322445 PMCID: PMC6237439 DOI: 10.7554/elife.37090] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022] Open
Abstract
The composition of the human gut microbiome is well resolved, but predictive understanding of its dynamics is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and Blautia hydrogenotrophica S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono- and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate. We quantified with a mechanistic model how well tri-culture dynamics was predicted from mono-culture data. With the model as reference, we demonstrated that strains grown in co-culture behaved differently than those in mono-culture and confirmed their altered behavior at the transcriptional level. In addition, we showed with replicate tri-cultures and simulations that dominance in tri-culture sensitively depends on the initial conditions. Our work has important implications for gut microbial community modeling as well as for ecological interaction detection from batch cultures. Our gut is home to trillions of microorganisms, most of them bacteria, which have an important impact on our body. During healthy periods, these microorganisms help our digestion, protect our cells, and compete against disease-causing bacteria. But specific communities of gut bacteria are linked to many diseases. We already have a good knowledge of the bacterial composition present in a wide range of human guts, but how the different bacterial species within such communities affect each other, has so far been unclear. Future disease treatments may be able to steer ‘bad’ communities to healthier mixtures. For this to happen we need to know how species interact and how these interactions change the behavior of the whole community. To investigate this further, D'hoe, Vet, Faust et al. studied three common species of gut bacteria under controlled conditions in the laboratory. The different species were either grown alone, in pairs or together, and the number of bacteria and the concentration of nutrients were measured over time. The results showed that when grown alone or together, their behavior changed. D'hoe et al. then used a mathematical model to estimate the rates at which species multiplied and consumed nutrients. This model was able to predict the dynamics of each of the species grown alone. However, the data from bacteria grown in pairs was needed to predict the dynamics of bacteria grown as a group of three. Next, D'hoe et al. compared the activity of genes between bacteria grown alone or together, and discovered several differences. This suggests that bacterial species affect each other greatly, and community behavior cannot be predicted from knowledge of its members alone. Therefore, studying bacteria in isolation is not enough to understand the complex environments of our guts, which are inhabited not by three but hundreds of bacterial species. In future, interactions between bacteria will need to be studied to ultimately be able to shift the gut community into better shapes.
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Affiliation(s)
- Kevin D'hoe
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Vet
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium.,Unité de Chronobiologie Théorique, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
| | - Frédéric Moens
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Verónica Lloréns-Rico
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, KU Leuven, Leuven, Belgium
| | - Jan Danckaert
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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