Ancient Metagenomics

The techniques in this section of the book can be used in a variety of stages of any ancient metagenomics projects, for screening for pathogens (what species should I target for downstream genomic mapping?), for differential abundance analysis (does the community make of this sample change between different cultural periods?), but also for reference-free assembly of genomes (can I recover the genome architecture of a variety of species in my sample?). It focuses on the concept of ‘many samples to many genomes’ using high-throughput techniques and algorithms and trying to analyse data at whole ‘community’ levels.

Taxonomic Profiling

TBC

Functional Profiling

The value of microbial taxonomy lies in the implied biochemical properties of a given taxon. Historically taxonomy was determined by growth characteristics and cell properties, and more recently through genomic and genetic similarity.

The genomic content of microbial taxa, specifically the presence or absence of genes, determine how those taxa interact with their environment, including all the biochemical processes they participate in, both internally and externally. Strains within any microbial species may have different genetic content and therefore may behave strikingly differently in the same environment, which cannot be determined through taxonomic profiling. Functionally profiling a microbial community, or determining all of the genes present independent of the species they are derived from, reveals the biochemical reactions and metabolic products the community may perform and produce, respectively.

This approach may provide insights to community activity and environmental interactions that are hidden when using taxonomic approaches alone. In this chapter we will perform functional profiling of metagenomic communities to assess their genetic content and inferred metabolic pathways.

De novo Assembly

De novo assembly of ancient metagenomic samples enables the recovery of the genetic information of organisms without requiring any prior knowledge about their genomes. Therefore, this approach is very well suited to study the biological diversity of species that have not been studied well or are simply not known yet.

In this chapter, we will show you how to prepare your sequencing data and subsequently de novo assemble them. Furthermore, we will then learn how we can actually evaluate what organisms we might have assembled and whether we obtained enough data to reconstruct a whole metagenome-assembled genome. We will particularly focus on the quality assessment of these reconstructed genomes and how we can ensure that we obtained high-quality genomes.