title: Species-function relationships shape ecological properties of the human gut microbiome.
abstract: Despite recent progress, the organization and ecological properties of the intestinal microbial ecosystem remain under-investigated. Here, using a manually curated metabolic module framework for (meta-)genomic data analysis, we studied species-function relationships in gut microbial genomes and microbiomes. Half of gut-associated species were found to be generalists regarding overall substrate preference, but we observed significant genus-level metabolic diversification linked to bacterial life strategies. Within each genus, metabolic consistency varied significantly, being low in Firmicutes genera and higher in Bacteroides. Differentiation of fermentable substrate degradation potential contributed to metagenomic functional repertoire variation between individuals, with different enterotypes showing distinct saccharolytic/proteolytic/lipolytic profiles. Finally, we found that module-derived functional redundancy was reduced in the low-richness Bacteroides enterotype, potentially indicating a decreased resilience to perturbation, in line with its frequent association to dysbiosis. These results provide insights into the complex structure of gut microbiome-encoded metabolic properties and emphasize the importance of functional and ecological assessment of gut microbiome variation in clinical studies.
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.
authors: Sara
authors: 0000-0002-4616-7602
authors: S
authors: Vieira-Silva
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.
authors: Gwen
authors: G
authors: Falony
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.|Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
authors: Youssef
authors: 0000-0001-7655-5764
authors: Y
authors: Darzi
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.|Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
authors: Gipsi
authors: G
authors: Lima-Mendez
authors: VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.|Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
authors: Roberto
authors: R
authors: Garcia Yunta
authors: Niigata University Graduate School of Medical and Dental Sciences 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.
authors: Shujiro
authors: 0000-0002-7704-8104
authors: S
authors: Okuda
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.|Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
authors: Doris
authors: D
authors: Vandeputte
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.
authors: Mireia
authors: M
authors: Valles-Colomer
authors: VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.|Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
authors: Falk
authors: 0000-0002-0078-8948
authors: F
authors: Hildebrand
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.|Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
authors: Samuel
authors: S
authors: Chaffron
authors: Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.|VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.|Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
authors: Jeroen
authors: J
authors: Raes
mesh_terms: D017753:Ecosystem; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D056186:Metagenomics; D064307:Microbiota