The human microbiome consists of all bacteria that inhabit the human body in areas such as the skin, mouth, and intestines. Each person has his or her own unique microbiome composition. The microbiome is essential to the homeostasis of the human body, and serious problems can arise when the microbiome changes composition. The gut microbiome alone has been associated with conditions such as obesity, autoimmune diseases, diabetes, inflammatory bowel disease, and colitis. While not all changes to the human microbiome are life-threatening, they certainly affect quality of life. For this reason, the microbiome is a topic of extensive research all over the world.
The study of the human microbiome extends to all ages, and scientists are investigating how it develops and changes throughout an individual’s lifetime. Studying this topic has thus far proven difficult, as there are a multitude of environmental influences and experiences that are specific to each individual person. Scientists are now examining the microbiomes of people that are not alive today by sequencing ancient, fossilized human gut bacteria in order to track the evolution of bacteria. Through this technique, scientists are working to gain as much knowledge about bacteria as possible in hopes of one day utilizing the knowledge to prevent disease or predict future bacterial gene evolution.
The gut microbiome alone has been associated with conditions such as obesity, autoimmune diseases, diabetes, inflammatory bowel disease, and colitis.
In a recent article published by Plos One, titled “Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy,” T. M. Santiago-Rodriguez and colleagues‒ researchers in the United States, Italy, and Puerto Rico‒ studied the preserved microbiome of an 11th century female pre-Columbian Andean mummy from Cuzco, Peru. The mummy had been stored at the Museum of Anthropology and Ethnology at the University of Florence, Italy. The female was estimated to have died at an age of 18-23 years old, and was preserved bound in a basket of vegetal fibers. The head was completely skeletonized, but the rest of the body was mummified. The condition of the body, specifically an enlarged esophagus, distended colon, enlarged heart– all with characteristic colonies of Trypanosoma cruzi – indicated that the once-mummy may have exhibited Chagas’ disease before death. Chagas’ disease is caused by infection of T. cruzi, and is an endemic in South America.
The scientists found that more than 96% of the bacteria from each section of the colon belonged to the phylum Firmicutes.
Feces samples, along with colon tissue samples, were collected from the descending, transverse, and ascending colon, using sterile techniques to avoid contamination of the ancient preserves. DNA was extracted from the samples, and sequenced using a technique called 16S rRNA gene amplification. The sequence was then used to identify bacteria in the sample. The transverse colon, as well as feces collected from this location, had the most diversity in terms of microbial composition. The heightened diversity means that there were many different types of bacteria found in this location, as compared to the descending and ascending regions. The scientists found that more than 96% of the bacteria from each section of the colon belonged to the phylum Firmicutes. On the level of family (Remember: kingdom, phylum, class, order, family, genus, species), Clostridiceae and Turicibacteraceae were the most abundant. The researchers used BLASTn, a tool provided by the National Center for Biotechnology Information database that is used to compare similarity between DNA sequences of different organisms, to determine the identity of some of the species found. The best hits found in all three locations of the colon included Clostridium tetani, Clostridium sporogenes, Clostridium disporicum, Clostridium tertium, Clostridium bifermentans, and Clostridium difficile. Bacteria were not the only organisms found in the samples, however, and genes associated with archaea, fungi, viruses, and eukaryotes were also sequenced.
Aside from the identified Clostridiceae and Turicibacteraseae families, there were many unidentified sequences from the mummy samples. The researchers tested the unidentified sequences against that of modern T. cruzi, and found what they presumed was ancient T. cruzi, with 90% similarity. This finding suggested that Chagas’ disease was prevalent in the Americas before European colonization. Additionally, because the ancient T. cruzi genes were not 100% similar to the modern genes, the researchers hope to use ancient T. cruzi to gain a better understanding of the modern pathogen. The unidentified sequences were then compared to Human papillomavirus (HPV). Several homologous sequences (at almost 100% complementary) to HPV were identified, which was surprising because few studies have previously reported the presence of HPV in mummies. This finding suggests that HPV was introduced into the Americas long before European colonization.
The researchers were also interested in identifying sequences associated with antibiotic-resistance, being that it is a prominent issue today. Sequences corresponding with putative beta-lactamases (a protein), penicillin-binding proteins, resistance to antibiotics (such as fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin), and multi-drug transporters (which up-take drugs into cells), were found in all three areas of the colon. Vancomycin-resistance was specifically studied, and sequences homologous to vanA, vanB, vanH, vanT, vanY, vanR and vanS were discovered. Vancomycin resistance means that the body is resistant to the effects of the antibiotic vancomycin, which is used to treat many different bacterial infections. These findings are particularly interesting because antibiotics, especially vancomycin, were only introduced recently. The discovery of gene sequences similar to current vancomycin resistance genes suggests that our current resistance genes originated from secluded populations that existed hundreds of years before vancomycin was ever used for treatment.
The discovery of gene sequences similar to current vancomycin resistance genes suggests that our current resistance genes originated from secluded populations that existed hundreds of years before vancomycin was ever used for treatment.
The findings of this study open up many questions about the evolution of human microbiome. For instance, this study provides evidence counter to the hypothesis that T. cruzi and HPV were not present in the Americas prior to European colonization. Additionally, it raises significant confusion about our current understanding of antibiotic-resistance genes. While this study does not provide concrete conclusions to previous questions, it highlights areas of interest that are guaranteed to be the source of future research. It also provides scientists with templates of ancient genes of bacteria which are helpful in characterizing the evolution of genetic information. Understanding the evolution of genes may enable scientists predict future evolution of bacteria, viruses, and even human genes.
Santiago-Rodriguez, T., Fornaciari, G., Luciani, S., Dowd, S., Toranzos, G., Marota, I., & Cano, R. (2015). Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy. PLoS ONE PLOS ONE.