From microbiome composition to functional engineering, one step at a time.

Autor:	Burz SD; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Causevic S; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Dal Co A; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Dmitrijeva M; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland., Engel P; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Garrido-Sanz D; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Greub G; Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland., Hapfelmeier S; Institute for Infectious Diseases, University of Bern, Bern, Switzerland., Hardt W-D; Institute of Microbiology, ETH Zürich, Zürich, Switzerland., Hatzimanikatis V; Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland., Heiman CM; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Herzog MK-M; Institute of Microbiology, ETH Zürich, Zürich, Switzerland., Hockenberry A; Swiss Federal Institute for Aquatic Research, Dübendorf, Switzerland., Keel C; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Keppler A; Institute of Microbiology, ETH Zürich, Zürich, Switzerland., Lee S-J; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland., Luneau J; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Malfertheiner L; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland., Mitri S; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Ngyuen B; Institute of Microbiology, ETH Zürich, Zürich, Switzerland., Oftadeh O; Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland., Pacheco AR; Institute of Microbiology, ETH Zürich, Zürich, Switzerland., Peaudecerf F; Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland., Resch G; Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland., Ruscheweyh H-J; Institute of Microbiology, ETH Zürich, Zürich, Switzerland., Sahin A; Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland., Sanders IR; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland., Slack E; Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland., Sunagawa S; Institute of Microbiology, ETH Zürich, Zürich, Switzerland., Tackmann J; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland., Tecon R; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Ugolini GS; Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland., Vacheron J; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., van der Meer JR; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Vayena E; Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland., Vonaesch P; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland., Vorholt JA; Institute of Microbiology, ETH Zürich, Zürich, Switzerland.
Jazyk:	angličtina
Zdroj:	Microbiology and molecular biology reviews : MMBR [Microbiol Mol Biol Rev] 2023 Dec 20; Vol. 87 (4), pp. e0006323. Date of Electronic Publication: 2023 Nov 10.
DOI:	10.1128/mmbr.00063-23
Abstrakt:	SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N + 1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies. Competing Interests: The authors declare no conflict of interest.
Databáze:	MEDLINE
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