Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

Abstract

In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone librarybased surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.

Signature Protein of the PVC Superphylum

“…Although this analysis cannot be used to quantitatively assess the abundance of PVC microbes in the different habitats, the observed ecological patterns are consistent with those of known members of the superphylum. For example, the relatively low number of metagenomic SPs branching with known members of the Chlamydiae phylum is consistent with the generally low abundance of chlamydial protein sequences detected in metagenomes in a recent study (47). An explanation for this could be the low abundance of members of the phylum Chlamydiae (which are typically associated with eukaryotic hosts) in environmental samples, which would result in a low coverage of chlamydial genomes in metagenomic data sets.…”

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

“…To evaluate the prevalence and abundance of miBC members in gut microbiota, other host-derived ecosystems and environmental samples, we used an integrated metagenomic platform developed in-house and used in previous work (www.imngs.org) 16,57. All 16S rRNA gene amplicon studies available in the SRA 58 were extracted and organized in samplespecific databases.…”

Simkania negevensis, an insight into the biology and clinical importance of a novel member of the Chlamydiales order

“…Three evolutionary clusters appear to exist: (i) the Chlamydiaceae/Clavichlamydiaceae cluster, which harbors the smallest genomes and seems to have branched the earliest, (ii) the Parachlamydiaceae/ Waddliaceae/Criblamydiaceae cluster and (iii) the Simkaniaceae/Rhabdochlamydiaceae cluster (Lagkouvardos et al, 2014). Indeed, Simkaniaceae share an 86-87% homology in the 16S rRNA encoding gene sequence with Rhabdochlamydiaceae (Kostanjsek et al, 2004) and only 82% homology with Chlamydiaceae (Kahane et al, 1995).…”