New Paper in Nature Communications: Pangenomics reveals alternative environmental lifestyles among chlamydiae


Chlamydiae are strictly intracellular bacteria and have long been considered primarily as major pathogens of humans. Yet, the phylum Chlamydiae is highly diverse, the host range unmatched among known microbes, and its members are increasingly also found in the environment.

In this study, a team from the University of Vienna and the DOE Joint Genome Institute around Stephan Köstlbacher and Matthias Horn exploited the power of metagenomics to gain insights into yet uncharacterized environmental chlamydiae. They have drawn on the published Genomes from Earth’s Microbiomes and added novel metagenome assembled genomes and draft genome sequences to establish the most complete genome sequence data set available for the phylum to date. This allowed them (i) to almost double the known taxonomic diversity of the phylum Chlamydiae, (ii) to reveal that the accessory genome varies strongly, reflecting adaptation to various environments and diverse hosts, (iii) to discover niche-specific adaptations that indicate unexpected lifestyles of chlamydiae, including evidence for light driven ATP synthesis, (iv) to show that members of several chlamydial lineages have the genetic potential for anaerobic energy metabolism and molecular hydrogen production, and (v) to carry out genome-informed diversity surveys, revealing the presence of chlamydiae in various anaerobic environments and providing evidence for an ubiquitous occurrence of chlamydiae, sometimes at surprisingly high abundance.