title: Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence.
abstract: Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM.
authors.affiliation: Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
authors.forename: Lucie
authors.initials: L
authors.lastname: Kropáčková
authors.affiliation: Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Těšický
authors.affiliation: Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.|Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Albrecht
authors.affiliation: Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Kubovčiak
authors.affiliation: Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Čížková
authors.affiliation: Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.|Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
authors.forename: Oldřich
authors.initials: O
authors.lastname: Tomášek
authors.affiliation: Montpellier-SupAgro, UMR CBGP, Montferrier-sur-Lez, France.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Martin
authors.affiliation: Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
authors.forename: Lukáš
authors.initials: L
authors.lastname: Bobek
authors.affiliation: Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
authors.forename: Tereza
authors.initials: T
authors.lastname: Králová
authors.affiliation: Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Procházka
authors.affiliation: Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
authors.forename: Jakub
authors.identifier: http://orcid.org/0000-0001-9375-9814
authors.initials: J
authors.lastname: Kreisinger
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification*; D018153:Czech Republic; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D046109:Passeriformes / Q000145:classification / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: birds; cophylogeny; metagenomics; microbiome; neutral/adaptive evolution