Vertebrate host phylogeny influences gut archaeal diversity

Nicholas D Youngblut,Chris Walzer,Sophie Maisch,Georg H Reischer,Silke Dauser,Gabrielle Stalder,Andreas H Farnleitner,Ruth E Ley

doi:10.1038/s41564-021-00980-2

Abstract

Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea–host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea–Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea–vertebrate associations.

Highlights

Used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut
Failure was not correlated with host taxonomy, diet, other host characteristics, the amount of sample collected, the concentration or quality of genomic DNA or the Bacteria:Archaea ratio, as determined via metagenome sequencing (Supplementary Figs. 2–4)
16S rRNA gene copy number, as measured via quantitative polymerase chain reaction with ‘universall’ 16S primers, was significantly higher in the successful samples, suggesting that low microbial biomass was a major cause of failure (Supplementary Fig. 3b)

Summary

Introduction

Used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. Using 16S rRNA gene amplicon sequencing with primers that target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. Next-generation sequencing (NGS) has greatly expanded our view of archaeal diversity, which consists of nearly 40 major clades, 8 of which are currently known to be host-associated[1,2]. Many of these clades consist of methanogens, which utilize bacterial fermentation products (namely hydrogen and carbon dioxide) for obtaining energy and are generally the most abundant Archaea in the mammalian gut[3,4]. Using dietary and host phylogenetic relationships, as well as previously characterized bacterial diversity, we uncover robust relationships between Archaea, host phylogeny, and to some extent, host diet

Methods

Results

Conclusion