Analysis of feces from more than a thousand years shows how our intestinal flora has changed over time – 05/12/2021 – Science

By analyzing stool samples over a thousand years old, a large group of scientists (from the United States, Mexico, Canada, Italy, Denmark and Germany) were able to reassemble the genome of microorganisms from the past that lived inside the human body. Map the diversity and show how our intestinal flora has changed over time.

The result, published on Wednesday (12) in the journal Nature, shows that the intestinal flora (or microbiota as it is more commonly called by scientists today) registered in Paleofezes is more similar to that of non-industrialized populations. One of the microbes “lost” by industrialization is Treponema succinifaciens.

There is still a large amount of enzymes in old feces that can digest chitin, a type of carbohydrate that is used by insects to build their exoskeleton and that is also found in mushrooms and other fungi. The finding is an indication of how people’s diet was in the past.

Another analysis compared enzymes that are produced by microbes and activated by carbohydrates. In the past and in non-industrialized populations, it is easier to find enzymes that can digest starch, likely due to a higher intake of complex carbohydrates (like whole grains and certain tubers).

The same consideration applies to antibiotic resistance genes in microbes – they are far more common in industrialized populations and denounce the abuse of these drugs in both humans and meat production.

One of the greatest challenges was to reconstruct the genetic information of these microbes. An intact bacterial genome can have hundreds of thousands of base pairs or genetic “letters” (humans have 3 billion pairs by comparison). The genetic material in the sample was so damaged that the pieces of DNA averaged 174 base pairs.

Another concern was to ensure that the DNA from the old samples was not contaminated with newer DNA, which could cloud the conclusions.

A total of eight samples of faeces between 1,000 and 2,000 years old that were found in caves in the southwestern United States and Mexico were used.

In the end, scientists were able to reconstruct 498 genomes of microbes, 181 of which originate from the intestine and of which 61 (39%) represent as yet unknown species. The next step was to compare these results with the microbiota of “industrialized” populations and those that are now isolated and “non-industrialized”, such as certain tribes in the Amazon or the Fiji Islands.

“An important concept emerging from our work is that if the theory of the disappearance of the human microbiome is correct, then reducing the burden of chronic diseases simply by eating well and exercising is not enough – we have to somehow re-sowing the microbiome a modern human with the species we lost, ”Aleksandar Kostic, lead author of the study and professor of microbiology at Harvard University, told Folha.

The pharmaceutical and biotechnology industries are already very interested in creating new therapies based on this knowledge. For example, an infection that is resistant to the bacterium Clostridium difficile can be treated with stool transplantation and with a high success rate. There is research into treatments for inflammatory bowel disease and also for combined therapies in oncology.

According to Emmanuel Dias-Neto, a researcher at ACCamargo Cancer Center and a student of the human microbiome who did not participate in the study.

One of the greatest difficulties is having the exact dimension of the healthy. “We still have no indication of what a healthy microbiota would be for the Brazilian. There is no way to do a test and say that the amount of any particular bacterium is low, ”he says.

In any case, it is already possible to do something for the health of your microbiota: diet is one of the factors that most influence this composition.

Eating fiber, complex carbohydrates (such as oats and yams, and whole grain bread), and fresh fruit has been linked to better gastrointestinal health and a lower risk of colon cancer. In turn, excessive meat consumption leads us in the opposite direction.

However, there are other factors that are more difficult to control, such as: B. pollution and the uptake of microplastics, even in water. Thus the recomposition of the microbiota would never be absolute.

Because many of these factors are detrimental to microorganisms, others tend to quickly occupy these niches. An example, as quoted by Dias-Neto, are the microbes that survive the consumption of alcohol and tobacco and end up colonizing the mouth of the individual. The same organisms produce carcinogenic substances such as acetaldehyde and are therefore harmful to health.

“If you possibly work with this older type of microbiome, you can get good results. If they could be reintroduced at some level, we could potentially see a decline in this chronic disease epidemic that has become so problematic and continues to grow worldwide, especially as you deal with obesity, type 2 diabetes, and allergic diseases in young children deal. Says Kostic.

“I’m particularly interested in developing these ideas in animal models like mice with type 1 or type 2 diabetes. A first step is to transfer a ‘western’ microbiome into these animals and then try to transplant a ‘traditional’ microbiome into them and observe the disease process and see if there are any unexpected effects and other important safety issues. “

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