An international team of scientists have produced a catalogue of genes from the micro-organisms that live in our gut (the gut microbiome), and it is the first published work from the MetaHIT (Metagenomics of the Human Intestinal Tract) project. “This gene catalogue contains virtually all of the prevalent gut microbial genes in our cohort, provides a broad view of the functions important for bacterial life in the gut and indicates that many bacterial species are shared by different individuals,” write Junjie Qin and colleagues.
The research, published last week in the journal Nature, pieces together a staggering 576.6 gigabases of gene sequence to assemble and characterise 3.3 million non-redundant microbial genes from faecal samples from124 European individuals. The results provide a vital clue to the microbial species which are prevalent, and surprisingly common between different individuals, in the human gut.
The human body hosts trillions of micro-organism, most of which live in our gut. These gut bacteria are hugely important for human life, not only do they help us to get vital energy from the food we eat but changes in the types of micro-organisms in the gut are thought to contribute to bowel disease and obesity.
The researchers used an Illumina Genome Analyser to deep sequence DNA from faecal samples from Danish and Spanish adults who were healthy, overweight and obese, or had inflammatory bowel disease. This approach is called metagenomics and directly analyses genetic material from environmental samples, which means that organisms can be studied in their natural habitat and allows otherwise difficult-to-culture micro-organisms to be studied.
Qin et al. generated almost 200 times more metagenomic sequence data from the gut than had been produced in previous studies. The scientists found that their gene set was 150 times bigger than the human gene complement and included most of the known human intestinal microbial genes. Furthermore, their analysis revealed that 99% of the genes they identified were bacterial and that a common core of bacterial species existed in each person— including members of the Bacteriodetes and the Firmicutes, which have already been shown to be abundant in the gut environment. Finally, they used their gene catalogue to uncover the bacterial functions which are important for life in this habitat, such as synthesis of short-chain fatty acids, vital amino acids and vitamins, and the breakdown of complex polysaccharides.
“We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively,” conclude the investigators who hope that their extensive catalogue of the human gut microbiome will enable future studies of the association between microbial genes and human phenotypes, disease and living habits from birth to old age.
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., Xie, Y., Tap, J., Lepage, P., Bertalan, M., Batto, J., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H., Yu, C., Li, S., Jian, M., Zhou, Y., Li, Y., Zhang, X., Li, S., Qin, N., Yang, H., Wang, J., Brunak, S., Doré, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Antolin, M., Artiguenave, F., Blottiere, H., Borruel, N., Bruls, T., Casellas, F., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Forte, M., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Jamet, A., Juste, C., Kaci, G., Kleerebezem, M., Knol, J., Kristensen, M., Layec, S., Le Roux, K., Leclerc, M., Maguin, E., Melo Minardi, R., Oozeer, R., Rescigno, M., Sanchez, N., Tims, S., Torrejon, T., Varela, E., de Vos, W., Winogradsky, Y., Zoetendal, E., Bork, P., Ehrlich, S., & Wang, J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing Nature, 464 (7285), 59-65 DOI: 10.1038/nature08821