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Ancient microbiomes offer insight into modern diseases

Genomic analysis of human samples from dry caves has revealed significant differences between ancient and modern gut microbiomes.

Gut microbiome

Various studies have shown that industrial lifestyles correlate with lower diversity in the gut microbiome and increased risk of chronic diseases. These include obesity and autoimmune disorders. By examining our ancestral gut microbiome, we can gain important insights into aspects of human-microbiome symbioses that have been altered by present-day life. However, to-date, researchers know very little about the composition of such pre-industrial gut microbiomes.

An emerging approach is the reconstruction of metagenome-assembled genomes to recover high-quality genomes and previously undescribed species. Despite the potential of de novo assembly to uncover undescribed species, researchers have yet to apply this method to palaeofaeces due to the challenges posed by highly damaged DNA.

Reconstructing ancient microbiomes

In this study, published in Nature, researchers undertook a large-scale de novo assembly of microbial genomes from indigenous human palaeofaeces. The researchers obtained eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico. From this, they were able to reconstruct 498 medium- and high-quality microbial genomes. Out of the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% were previously undescribed. The authors explained that ancient cultures ate more diverse foods (compared to the western diet) that enabled them to support a wider collection of microbes.

When the team compared these samples to 789 present-day human gut microbiome samples from eight countries, the samples were more similar to non-industrialised than to industrialised gut microbiomes. Functional profiling the samples also revealed a lower abundance of antibiotic-resistance and an enrichment of mobile genetic elements relative to industrial gut microbiomes.

Aleksandar Kostic, senior author, explained:

“We think this could be a strategy for the microbes to adapt in an environment that shifts a lot more than the modern industrialised microbiome, where we eat the same things and live the same life more or less year-round.

Whereas in a more traditional environment, things change, and microbes need to adapt. They might use this much larger collection of transposases to grab and collect genes that will help them adapt to the different environments.”

The team also investigated the key human symbiont Methanobrevibacter smithii in ancient samples. They found that its evolution was consistent with a shared ancestral strain that experts have dated to when humans first migrated into North America.

The researchers hope to expand their research to many other ancient microbiome specimens, aiming to detect novel species and trying to predict their metabolic functions.

Image credit: By wildpixel –

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Ancient DNA / Microbiome