Comprehensive coverage of human last meal components revealed by a forensic DNA metabarcoding approach

Abstract

Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. While the identification of food components of plant and animal origin has traditionally been conducted by macro- and microscopical approaches in case of incomplete digestion, molecular methods provide the potential to increase sensitivity and taxonomic resolution. In particular, DNA metabarcoding (PCR-amplification and next generation sequencing of complex DNA mixtures) has seen a rapid growth in the field of wildlife ecology to assess species’ diets from faecal and gastric samples. Despite clear advantages, molecular approaches have not yet been established in routine human forensics to investigate the last meal components of deceased persons. In this pilot study we applied for the first time a DNA metabarcoding approach to assess both plant and vertebrate components of 48 human stomach content samples taken during medicolegal autopsies. We obtained a final dataset with 34 vertebrate and 124 vegetal unique sequences, that were clustered to 9 and 33 operational taxonomic units (OTUs), respectively. Our results suggest that this approach can provide crucial information about circumstances preceding death, and open promising perspectives for biomedical dietary surveys based on digested food items found in the gastrointestinal tract.

Issues of under-representation in quantitative DNA metabarcoding weaken the inference about diet of the tundra vole Microtus oeconomus

“…As part of our feeding experiment, all samples were amplified with the g and h primers ( Taberlet et al, 2007 ), targeting a highly variable length region (10–220 bp) from the P6 loop of the chloroplast trnL (UAA) intron in vascular plants. This primer set is particularly suitable for the analysis of highly degraded DNA ( Clarke et al, 2020 ; Hollingsworth, Graham & Little, 2011 ; Särkinen et al, 2012 ; Schneider et al, 2021 ; Willerslev et al, 2014 ) due to its short amplicon size, highly variable gene region and conserved priming sites ( Deagle et al, 2014 ; Taberlet et al, 2012a ). The primer sequences are 5′-GGGCAATCCTGAGCCAA-3′and 5′-CCATTGAGTCTCTGCACCTATC-3′, respectively.…”

DNA metabarcoding captures dietary plant diversity in individuals and cohorts

“…In total, we detected 187 unique trnL sequence variants representing 146 taxa, including plants from 73% of major food crop families present in the reference database. This expands from two prior trnL metabarcoding studies conducted in humans that detected 47 unique plant taxa across 11 individuals' fecal samples 24 and 124 across 48 individuals' stomach contents 25 . The strength of positive correlations (Spearman ~0.3-0.6) between pMR and indices calculated from validated survey tools falls within a range that is a workable proxy in dietary research: for example, the use of a simplified survey specifically for dietary diversity measurement is supported by Pearson correlations to nutrient adequacy from a more complex tool ranging from r=0.3-0.6 2,4,49 .…”

“…Relying on the fact that nearly all foods are derived from once-living organisms whose tissues contain DNA, variable regions in food genomes serve as molecular “barcodes” that can be amplified and sequenced from stool. Such “DNA metabarcoding” methods have been widely applied to study the diets of wild animals 22,23 and in proof-of- concept work to human stool 24 and stomach contents 25 . However, they have not been applied at scale in the setting of nutrition research, nor have they been used to calculate within-sample diversity, a practice commonplace in ecosystem and animal studies (where within-sample diversity is termed “alpha diversity” and species counts are termed “richness”) 26 .…”

Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans

“…Both can be surveyed with omic-scale tools (“metabarcoding” or “FoodSeq” for DNA, and “metaproteomics” for protein). Dietary DNA has been used to study foods consumed by wild animals, deceased humans (>200 years ago 14 or recently 15 ), and free-living populations 16 . Interestingly, before DNA-based techniques took hold in the field, the earliest animal dietary studies relied on detection of protein from consumed prey tissues.…”