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Rozwalak P, Barylski J, Wijesekara Y, Dutilh BE, Zielezinski A. Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces. Nat Commun 2024; 15:495. [PMID: 38263397 PMCID: PMC10805732 DOI: 10.1038/s41467-023-44370-0] [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: 06/13/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.
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Affiliation(s)
- Piotr Rozwalak
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
| | - Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland.
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Botin T, Ramirez-Chamorro L, Vidic J, Langella P, Martin-Verstraete I, Chatel JM, Auger S. The Tolerance of Gut Commensal Faecalibacterium to Oxidative Stress Is Strain Dependent and Relies on Detoxifying Enzymes. Appl Environ Microbiol 2023; 89:e0060623. [PMID: 37382539 PMCID: PMC10370306 DOI: 10.1128/aem.00606-23] [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: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Obligate anaerobic bacteria in genus Faecalibacterium are among the most dominant taxa in the colon of healthy individuals and contribute to intestinal homeostasis. A decline in the abundance of this genus is associated with the occurrence of various gastrointestinal disorders, including inflammatory bowel diseases. In the colon, these diseases are accompanied by an imbalance between the generation and elimination of reactive oxygen species (ROS), and oxidative stress is closely linked to disruptions in anaerobiosis. In this work, we explored the impact of oxidative stress on several strains of faecalibacteria. An in silico analysis of complete genomes of faecalibacteria revealed the presence of genes encoding O2- and/or ROS-detoxifying enzymes, including flavodiiron proteins, rubrerythrins, reverse rubrerythrins, superoxide reductases, and alkyl peroxidase. However, the presence and the number of these detoxification systems varied greatly among faecalibacteria. These results were confirmed by O2 stress survival tests, in which we found that strains differed widely in their sensitivity. We showed the protective role of cysteine, which limited the production of extracellular O2•- and improved the survival of Faecalibacterium longum L2-6 under high O2 tension. In the strain F. longum L2-6, we observed that the expression of genes encoding detoxifying enzymes was upregulated in the response to O2 or H2O2 stress but with different patterns of regulation. Based on these results, we propose a first model of the gene regulatory network involved in the response to oxidative stress in F. longum L2-6. IMPORTANCE Commensal bacteria in the genus Faecalibacterium have been proposed for use as next-generation probiotics, but efforts to cultivate and exploit the potential of these strains have been limited by their sensitivity to O2. More broadly, little is known about how commensal and health-associated bacterial species in the human microbiome respond to the oxidative stress that occurs as a result of inflammation in the colon. In this work, we provide insights regarding the genes that encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria, which may facilitate future advances in work with these important bacteria.
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Affiliation(s)
- Tatiana Botin
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Luis Ramirez-Chamorro
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Jasmina Vidic
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogénèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
| | - Jean-Marc Chatel
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Sandrine Auger
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
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