Genome-reconstruction for eukaryotes from complex natural microbial communities

Abstract

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.

Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake

“…To reconstruct environmental genomes, metagenomic quality-controlled reads from all samples were coassembled using Megahit (Li et al, 2015 ) software with a k-mer size of 31 and setting (see Supplementary Table 1 for additional summary statistics). EukRep (West et al, 2018 ) was used to remove any eukaryotic DNA from the contigs prior to the formation of an Anvio (v5) (Eren et al, 2015 ) contig database. The contig database was generated by removing contigs under 1000 bp, and gene prediction was performed in the Anvio environment.…”

Accurate and complete genomes from metagenomes

“…Then, eukaryote-specific gene predictions can be established and gene annotations used to estimate genome completeness. The k-merbased classifier, EukRep, was developed to accomplish this separation (West et al 2018). Although eukaryote genome recovery from metagenomes is increasingly reported (Quandt et al 2015;Mosier et al 2016;Olm et al 2019), to our knowledge, none have been extensively curated or completed.…”

Genetic and behavioral adaptation ofCandida parapsilosisto the microbiome of hospitalized infants revealed byin situgenomics, transcriptomics and proteomics

“…Samples of the Neonatal Intensive Care Unit (NICU) were taken from six patient rooms within the hospital housing the infants (Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA). Candida genomes were assembled from samples containing >2 Mbp of predicted eukaryotic DNA using a EukRep-based pipeline (West et al 2018; see the "Methods" section for details). Three of the Candida genomes ) and the bacterial component were analyzed previously (see the "Methods" section).…”

“…A co-assembly was then performed on the pooled reads for each infant with IDBA-UD in order to assemble sequences from low abundance organisms. The Eukaryotic porton of each sample assembly was predicted with EukRep (West et al 2018) and putative eukaryotic bins were generated by running CONCOCT (Alneberg et al 2014) with default settings on the output of EukRep. To reduce computational load, resulting eukaryotic bins shorter than 2.5 mbp in length were not included in further analyses.…”

“…The subsequent DNA sequences are assembled, and metagenome-assembled genomes (MAGs) are reconstructed. Much work of this type has focused on the bacterial members of the human microbiome; however, recently developed methods such as EukRep (West et al 2018) enable reconstruction of eukaryotic genomes from metagenomes with greater consistency, including genomes of Candida species . The availability of genomes enables evolutionary studies and the application of other 'omics' approaches, such as transcriptomics, proteomics, and metabolomics, making it possible to go beyond metabolic potential to study activity in situ.…”