Abstract
The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses.
Highlights
Studies on the human microbiome represent an opportunity to better understand microbe-host interactions, the membership and ecology of microbes, and its impact in health and disease
Oral bacterial diversity has been shown to differ in modern subjects compared to those from the Neolithic Era, possibly due to changes in dietary habits [10]; and pathogens associated with oral diseases have been identified in dental calculus [11]
We found that the majority of the human, coprolites and mummy microbiomes clustered according to sample type (Fig 3A)
Summary
Studies on the human microbiome represent an opportunity to better understand microbe-host interactions, the membership and ecology of microbes, and its impact in health and disease. The gut microbiome has been more extensively characterized compared to other human surfaces, and has been associated with several health conditions including obesity [1], colitis [2], autism [3], autoimmune diseases [4], cancer [5], diabetes [6] and inflammatory bowel disease [7]. Similar approaches have more recently been applied to characterize the microbial community structure of ancient samples [8,9,10,11]. This approach is augmenting our understanding of microbe-host interactions, and the evolution of commensal microorganisms and infectious diseases [9]. Ancient microbiomes have shown to act as reservoirs of putative antibiotic-resistance genes, indicating that antibiotic-resistance originates from ancient environments [11, 12]
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