How many genes in the human microbiome?

US scientists have begun the daunting task of trying to work out how many genes there are in the human microbiome.

Even when you consider just the gut and the mouth (in itself, a unique research double) the numbers are potentially overwhelming.

Microbiologists and bioinformaticians from Harvard Medical School and Joslin Diabetes Centre gathered all publicly available sequencing data on human oral and gut microbiomes and analyzed the DNA from around 3500 samples – 1400 from mouths and 2100 from guts.

In all, there were nearly 46 million bacterial genes – 24 million in the oral microbiome and 22 million in the gut.

That leads the team to suggest that there may be more genes in the collective human microbiome than there are stars in the observable universe (we’re talking trillions) – and that at least half of them may be unique to each individual.

“Ours is a gateway study, the first step on a what will likely be a long journey toward understanding how differences in gene content drive microbial behaviour and modify disease risk,” says Harvard’s Braden Tierney, first author of a paper published in the journal Cell Host & Microbe, with admirable understatement.

Most research to date has focused on mapping the types of bacteria that inhabit our bodies in an effort to determine whether and how the presence of a given bacterial species might affect disease risk, the researchers say. 

In contrast, their work looks at the genes that make up the various microbial species and strains.{%recommended 7962%}

Given that genetic content varies greatly between the same microbes, understanding how and whether individual microbial genes affect disease risk is important.

“Just like no two siblings are genetically identical, no two bacterial strains are genetically identical either,” says co-senior author Chirag Patel, also from Harvard. 

“Two members of the same bacterial strain could have markedly different genetic makeup, so information about bacterial species alone could mask critical differences that arise from genetic variation.”

More than half of the 23 million bacterial genes in the study occurred only once, rendering them unique to the individual. The researchers call them “singletons”, and they appeared to perform different functions to the other genes.

Commonly shared genes, appeared to be involved in more or less basic functions critical to a microbe’s day-to-day survival, such the consumption and breakdown of enzymes, energy conversion and metabolism. 

Unique genes, by contrast, tended to carry out more specialised functions, such as gaining resistance against antibiotics and other pressures and helping to build a microbe’s protective cell wall, which shields it from external assaults.

This finding, the researchers say, suggests singleton genes are key parts of a microbe’s evolutionary survival kit.

“If a microbe needs to become resistant to an antibiotic because of exposure to drugs or suddenly faces a new selective pressure, the singleton genes may be the wellspring of genetic diversity the microbe can pull from to adapt,” Tierney says.