The gut microbiome of a pre-Columbian Andean mummy looks much different than our own

A photo of the mummy whose microbiome was studied

The study of ancient humans’ microbiomes is a topic of growing interest, because it is believed that these microbiomes more closely resemble native or ‘natural’ microbiomes than the ones we have today.  There have been a few studies on humans’ microbiomes at different periods of history, and another data point was added to the list last week.  Researchers from Italy and California were able to measure the microbiome of a pre-Columbian human (11th century to be exact) that was mummified naturally after he died in the cold, harsh, and high elevations of the Andes Mountains in Chile.  The researchers published their findings in the journal PLoS ONE.

The researchers sequenced the bacteria that were in the mummy’s colon, as well as the mummy’s feces.  Strikingly, around 99% of the bacteria belonged to the Firmicutes genus, mainly dominated by Clostridia, and Turicibacter.  In addition, the human appeared to have many bacteria associated with modern day diseases.  For example the mummy’s microbiome contained Clostridium difficile (the cause of C. difficile infection), Trypansoma cruzi (the cause of Chagas’ disease), and many types of human papilloma virus (HPV).  Finally, the researchers noted that many genes associated with antibiotic resistance were found in the mummy’s microbiome, long before these antibiotics were introduced.

This paper revealed many fascinating aspects about our ancient microbiomes.  First, it is interesting to see that Firmicutes dominated our ancient flora, especially because Bacteroidetes, which are much more common in our guts today, are broadly associated with health.  Also, it appears that many of the pathogens that afflict all sorts of diseases today have prehistoric counterparts, and may have been more abundant, or even more tolerable long ago.  Finally, the revelation about antibiotic resistance genes show that the mutations that cause them appear common enough that they occurred naturally in thousand year old colons.

Different diets can affect C. diff infection and survival

We’ve covered the topic of Clostridium difficile infection extensively on this blog. We know that infection of this bacteria (CDI) can be nasty, sometimes even leading to death. A lot of research has been done to find ways to treat the effects of C. diff infection or to find out how the infection is acquired, but few papers have investigated dietary interventions to help treat CDI.  A new study published by PLoS One examined this, studying how different diets, and specifically how protein content of those diets, affected the severity of CDI.

          7-8 week old male mice were weighed and separated into five groups, each given a different diet. One group was fed a protein-deficient 2% protein diet, and a counterpart group was fed a 20% protein diet. Another group was given a Research Diets regional basic malnutrition diet, while its counterpart was fed a matched control. A fifth group was fed a traditional (corn, wheat, soybean) diet, and acted as the positive control. Mice were fed the diets 12-14 days before being given antibiotics and then infected by C. difficile.  After infection, the mice were housed individually to prevent being affected by other mice. Stool and colon samples were collected from the mice up to two weeks after infection, and the bacterial content was sequenced.

Mice on the 20% protein diet showed delayed onset disease with a 25% survival rate over 2 weeks. Mice on the 2% diet also showed delayed disease onset and had a survival rate of 57.1% over two weeks. A significant statistically difference in survival and weigh loss was seen between the traditional diet and both the 20% and 2% diets, however the survival difference between the 20% and 2% groups was not significant.

In another part of the study done by the researchers, they chose to examine the presence of four gut microbiota groups ( Firmicutes, Bacteroides, Enterobacteriaceae, and total bacteria), after antibiotics or no antibiotics. All aspect of the experiment were the same except for this one factor. In mice not given antibiotics, the total number of bacteria was greater in the colon of mice given traditional diet. In mice given antibiotics, traditional diet-fed mice had lower levels of Bacteroidetes but higher levels of Firmicutes and Enterobacteriaceae. The most significant finding the researchers may have made however, is that traditional diet-fed and antibiotic given mice had the highest levels of C. difficile and therefore C. difficile toxins.

In the end, it can be assumed that diet does influence rates of C. diff infection. The presence of antibiotics also alters the bacterial compositions of the colon, with lower protein diets seeming to protect against or prevent full potential C. difficile infection.