Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf

Abstract

The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.

Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

“…A previous metagenome-based study revealed the presence of actinobacterial reads in different tissues of mammoth remains 35 . However, studying metagenome data always has the risk for misassembly of (damaged) DNA, which is not the case when isolates are grown up and then sequenced.…”

Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth

“…We also attempted to use metagenome analysis to see if we could retrace the bacterial genome sequences in the intestinal metagenome and not in the surrounding ice. Previous studies on a mammoth microbiome showed that it is extremely difficult to get data of sufficient quality to ascertain the origin of microbes (Ferrari et al, 2018), and indeed we ran into similar issues, and the approach was abandoned. Finally, it is relevant to note that there are no records of scientists at our institute having previously worked with strains of the genera Oerskovia , Sanguibacter or Saccharopolyspora , nor are these known as common contaminants, which minimises the chance of laboratory contamination.…”

Metagenomic analysis of coprolites from three Late Pleistocene megaherbivores from the Southwestern United States

“…Modern contamination of ancient samples is typified by higher concentrations of DNA than the background of highly degraded endogenous genetic material (low coverage and depth). Ancient DNA is also highly fragmented, with a characteristic pattern of nucleotide modifications (Pääbo 1989; Dabney, Meyer, and Pääbo 2013; Skoglund et al 2014), even in frozen (Ravin, Prokhortchouk, and Skryabin 2015; Mardanov et al 2012; Ferrari et al 2018; Van Geel et al 2011) or fully desiccated (Hofreiter et al 2000; Karpinski, Mead, and Poinar 2017; Poinar et al 2003; Delsuc et al 2019; Wood et al 2013) specimens that tend to encourage DNA preservation.…”

“…Initially, these began with amplicon-based methods (Tito et al 2012; Hofreiter et al 2000) and permafrost specimens (Hagelberg, Hofreiter, and Keyser 2015; Mardanov et al 2012; Ravin, Prokhortchouk, and Skryabin 2015). More recently, shotgun metagenomics has been used to analyze all the DNA present within ancient samples without relying on PCR amplification, avoiding the associated biases, and giving a more accurate insight into the relative abundances of community members (McLaren, Willis, and Callahan 2019; Ferrari et al 2018; Durazzi et al 2021). Although shotgun metagenomics has been performed on ancient packrat ( Neotoma sp.)…”