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Analysis of Human Feces From Thousands of Years Ago Sheds Light on the Evolutionary History of the Human Microbiome

Humans, like other mammals, are occupied by trillions of microorganisms, including bacteria, viruses, and fungi. These microorganisms are collectively referred to as symbiotic flora. In a sense, "human" is a multi-element complex composed of the human body and symbiotic flora.
 More importantly, the intestinal flora in the body is not static. In the process of growing up, we experience different environments and meet different people, and the symbiotic flora in our body also changes continuously. A large number of intestinal microbiome studies have shown that the human symbiotic flora can affect our health, physique, personality and even thinking to a certain extent.
Recently, researchers from the Jocelyn Diabetes Center of Harvard Medical School analyzed ancient feces in North America and found that the human gut microbiome has changed significantly in the past 2000 years. These changes reflect the difference between the pre-industrial diet and the modern diet, as well as the increase in antibiotic resistance genes, or help explain the relationship between the composition of the gut microbiome and chronic diseases.
 The comparison between the industrialized and non-industrialized populations of today shows that the industrialized lifestyle is related to the decline in the diversity of the gut microbiome and the increase in the incidence of chronic diseases (such as obesity and autoimmune diseases). However, due to the difficulty of obtaining well-preserved DNA, the lack of gut microbial data before industrialization limits our understanding of the evolution of the gut microbiome over time.
The team reconstructed 498 microbial genomes from these samples, of which 181 showed strong evidence of ancient human gut origin. Among them, 61 genomes have not been described before, indicating that there are microbial species different from modern populations.
Researchers compared these genomes with samples from industrialized and non-industrialized populations of today and found that these ancient, pre-industrialized genomes are more like the gut microbiome of non-industrialized populations.
These ancient, non-industrialized samples contained a large number of genes related to starch metabolism, perhaps because they consumed more complex carbohydrates than the industrialized population today. Compared with these ancient samples, industrialized and non-industrialized modern samples contain more antibiotic resistance genes.
These findings shed light on the evolutionary history of the human microbiome, and may improve our understanding of how microbes promote health and disease. 

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