An international team of scientists that catalogued the genes of microbes that live in our gut has established that at 3.3 million, they vastly outnumber the 23,000 or so genes in the human genome, and say they hope the catalogue will help us better understand how to keep a healthy balance in our gut flora as well as improve diagnosis and treatment of disease.

You can read a scientific paper about this in the 4 March online issue of Nature. The study was coordinated by Dr Dusko Ehrlich at the Institut National de la Recherche Agronomique, in France, and is the joint effort of scientists working on a European project called MetaHIT (Metagenomics of the Human Intestinal Tract) in collaboration with Dr Jun Wang and colleagues at the Beijing Genomics Institute at Shenzhen, China.

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Escherichia coli

Gut flora is essential to human health. Dubbed the “microbiome”, it comprises thousands of bacteria, fungi and other microbes that break down toxins, make vitamins and essential amino acids, and create a barrier against invaders.

To get a comprehensive picture of the diversity of genes present in gut flora, the researchers used a metagenomic approach, where you take samples from the environment you wish to study and then sequence the genes they contain. The challenge is how to do this quickly when you are dealing with millions of genes.

One of the research centres working on the MetaHIT project is the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. They told the press that this is the first time that a metagenomics study has used a high-throughput method called Illumina, which others thought would not be feasible.

The process involves taking lots and lots of short strips of DNA, assembling them into larger sections, and then comparing them to known sequences stored in reference databases and ruling out those known to belong to the human genome.

For this study the researchers used fecal samples from 124 Europeans. Some of the donors were healthy, others were obese or overweight and some had inflammatory bowel disease.

By estimating the average bacterial genome size, the researchers predicted that the 3.3 million gut flora genes they counted probably represent about a total of about 1,000 species of microbe living in the guts of all the participants.

Dr George Weinstock, a geneticist at Washington University in St Louis, US, told NatureNews that:

“This is the most powerful microscope that’s been used so far to describe microbial communities.”

The study has also revealed a number of clues about how bacteria manage to survive in the rather unhospitable environment of the human gut.

For most bacteria, the human gut is not a good place to be: it has low pH (very acidic) hardly any oxygen, and no light. The only way to thrive here is to evolve, and this study has unveiled some interesting clues about how they did this.

The researchers found that each individual bacterium needs certain genes to survive in the human gut, but there are also other genes that have to be present in some individual microbes, but not all, for the colony to survive.

This could explain another interesting discovery. The researchers found that while individual participants of the study had only about 160 of the 1,000 possible species, about 40 per cent of any one one participant’s gut flora species was also present in around 50 per cent of the other participants.

The researchers think one of the interesting questions that should be investigated next is whether these shared genes come from the same or from different bacteria among different humans.

They also hope that their gut flora gene catalogue will be used as a reference resource for investigating the genetic links between gut bacteria and particular diseases and lifestyle patterns such as diet.

Co-author Dr Peer Bork, senior scientist and joint group leader of the Structural and Computational Biology Unit at EMBL, told the media that:

“Knowing which combination of genes is necessary for the right balance of microbes to thrive within our gut may allow us to use stool samples, which are non-invasive, as a measure of health.”

“One day, we may even be able to treat certain health problems simply by eating a yoghurt with the right bacteria in it,” he added.

“A human gut microbial gene catalogue established by metagenomic sequencing.”
Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada, et al.
Nature, 464, 59- 65 (4 March 2010)

Sources: European Molecular Biology Laboratory, NatureNews.

Written by: Catharine Paddock, PhD