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Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy.

Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, University of California San Diego, San Diego, CA, United States of America.

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.

No MeSH data available.


Related in: MedlinePlus

Panel A shows the procrustes analyses of extant human gut, saliva and skin, coprolites that did not undergo natural mummification, and mummy’s microbiomes.Panel B shows the Bayesian Source-Tracker results of paleofeces, descending colon (DC), transverse colon (TC) and ascending colon (AC) using soil microbiomes as non-human sources.
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pone.0138135.g003: Panel A shows the procrustes analyses of extant human gut, saliva and skin, coprolites that did not undergo natural mummification, and mummy’s microbiomes.Panel B shows the Bayesian Source-Tracker results of paleofeces, descending colon (DC), transverse colon (TC) and ascending colon (AC) using soil microbiomes as non-human sources.

Mentions: A total of 7,103 to 3,027,316 reads, with an average length of 270 bp and a GC-content percent ranging from 45.9 to 51.4% (Table 1) were analyzed. Alpha rarefaction curves for each sample type (n = 1) are shown in S1 Fig. We plotted alpha diversity measures present in bacterial communities using PD whole tree (Fig 2A), chao1 (Fig 2B) and observed species (Fig 2C). All alpha diversity indices showed that the paleofeces and transverse colon had the highest diversity, while the descending and ascending colon had the lowest. We also visualized beta-diversity measures of the paleofeces, and descending, transverse and ascending colon using procrustes plots. For comparison, we included the 16S rRNA gene profiles from ten pre-Columbian coprolites that did not undergo natural mummification and have previously been characterized using 16S rRNA gene high-throughput sequencing [8], as well as extant gut, saliva and skin microbiomes. We found that the majority of the human, coprolites and mummy microbiomes clustered according to sample type (Fig 3A). The mummy microbiomes shared some resemblance with the skin microbiomes, consistent with the source of the mummy’s sample collection being mainly the colon tissue. SourceTracker analyses with these same microbiomes showed that the mummy’s samples did not match any of the extant or coprolite microbiomes. In order to eliminate the possibility of non-human sources contributing to the results, we also performed the SourceTracker analyses using 45 soil microbiomes available in the SourceTracker tutorial [29]. Approximately 90% of the paleofeces microbiome matched soil microbiomes, while the vast majority of the descending, transverse and ascending colon microbiomes had no significant matches to any of the microbiomes used to track possible sources of contamination (Fig 3B).


Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy.

Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ - PLoS ONE (2015)

Panel A shows the procrustes analyses of extant human gut, saliva and skin, coprolites that did not undergo natural mummification, and mummy’s microbiomes.Panel B shows the Bayesian Source-Tracker results of paleofeces, descending colon (DC), transverse colon (TC) and ascending colon (AC) using soil microbiomes as non-human sources.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4589460&req=5

pone.0138135.g003: Panel A shows the procrustes analyses of extant human gut, saliva and skin, coprolites that did not undergo natural mummification, and mummy’s microbiomes.Panel B shows the Bayesian Source-Tracker results of paleofeces, descending colon (DC), transverse colon (TC) and ascending colon (AC) using soil microbiomes as non-human sources.
Mentions: A total of 7,103 to 3,027,316 reads, with an average length of 270 bp and a GC-content percent ranging from 45.9 to 51.4% (Table 1) were analyzed. Alpha rarefaction curves for each sample type (n = 1) are shown in S1 Fig. We plotted alpha diversity measures present in bacterial communities using PD whole tree (Fig 2A), chao1 (Fig 2B) and observed species (Fig 2C). All alpha diversity indices showed that the paleofeces and transverse colon had the highest diversity, while the descending and ascending colon had the lowest. We also visualized beta-diversity measures of the paleofeces, and descending, transverse and ascending colon using procrustes plots. For comparison, we included the 16S rRNA gene profiles from ten pre-Columbian coprolites that did not undergo natural mummification and have previously been characterized using 16S rRNA gene high-throughput sequencing [8], as well as extant gut, saliva and skin microbiomes. We found that the majority of the human, coprolites and mummy microbiomes clustered according to sample type (Fig 3A). The mummy microbiomes shared some resemblance with the skin microbiomes, consistent with the source of the mummy’s sample collection being mainly the colon tissue. SourceTracker analyses with these same microbiomes showed that the mummy’s samples did not match any of the extant or coprolite microbiomes. In order to eliminate the possibility of non-human sources contributing to the results, we also performed the SourceTracker analyses using 45 soil microbiomes available in the SourceTracker tutorial [29]. Approximately 90% of the paleofeces microbiome matched soil microbiomes, while the vast majority of the descending, transverse and ascending colon microbiomes had no significant matches to any of the microbiomes used to track possible sources of contamination (Fig 3B).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, University of California San Diego, San Diego, CA, United States of America.

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.

No MeSH data available.


Related in: MedlinePlus