My microbes
In a nutshell :
- The gut metagenome is the collection of all the genomes of all the microbes in the
human intestinal tract : it is specific to each human, like a second genetic
signature - At least in healthy humans, this personal metagenome is stable over time
- The gut metagenome is very large and complex: scientists developed innovative,
state-of-the-art, computational tools to analyse it with a high resolution
We all have E.coli
bacteria in our gut but each of us carries a version that is genetically
slightly different. The same can be said of most gut microbes: our own gut
metagenome, that is the sum of all the genomes of all our gut microbes, appears
to be really specific to each of us, and to remain stable over time. For the
first time, researchers from the European Molecular Biology Laboratory (EMBL)
have studied this metagenome at such a high resolution that individual
mutations in the various strains could be analysed. Their findings, published
today in Nature, could have widespread consequences in medicine: gut
microbes are known to be essential for functions as vital as digesting food or
providing vitamins, but can also be involved in diseases if they carry certain
mutations.
The scientists analysed the gut metagenome
of 207 individuals from Europe and the USA, matching more than 7 billion
pieces of DNA (of 100 lettres each) to the genomes of our most abundant gut
microbial species. “This large scale analysis showed that, at least when
healthy, we carry a unique set of bacterial strains and their mutations in our
gut, over a long time,” explains Peer Bork who led the study at EMBL. “It is
like a second genetic signature, but one that probably does not come from our
parents but that we acquire from the environment in early childhood.”
When comparing the specific
mutations from the same individual over time, the researchers found that the
metagenome remains stable for at least one year, and probably much longer when
the individuals are healthy. Results also show that there is only little
geographic difference when comparing metagenomes of European with
North-American individuals. This indicates that gradual adaptation is possible.
For each individual,
approximately 6 billion DNA letters of their gut metagenome have been analysed,
many more than the 3.3 billion DNA letters of human DNA that we inherit from
each of our parents. These 6 billion DNA letters belong to hundreds of
microbes, each with thousands of different strains or variants: mapping each
DNA fragment of the metagenome to its right place, in the right bacterial
genome, is extremely complex. To achieve this breakthrough and carry the
analysis down to the single DNA letter, scientists had to develop various new
computational methods. In the current study more than 10 million mutations have
been detected in the 207 individuals.
All these detailed data is now
stored in public databases, such as dbSNP, freely available to the scientific
community. These findings could lead to the development of new approaches in
the identification of gut diseases, pathogens, or antibiotic resistance. On the
longer term, they may also open new avenues for personalised therapies.
Further information:
More
information on the research projects of the Bork group
Previous research on the gut microbiome by Peer Bork
My Microbes project - discover your gut type
Source Article
Genomic variation landscape of
the human gut microbiome
Siegfried Schloissnig,
Manimozhiyan Arumugam, Shinichi Sunagawa, Makedonka Mitreva, Julien Tap, Ana
Zhu, Alison Waller, Daniel R. Mende, Jens Roat Kultima, John Martin, Karthik
Kota, Shamil R. Sunyaev, George M. Weinstock and Peer Bork. Nature, Advanced online Publication: 5 December, 2012
Article Abstract
While large-scale efforts have
rapidly advanced the understanding and practical impact of human genomic
variation, the latter is largely unexplored in the human microbiome. We
therefore developed a framework for metagenomic variation analysis and applied
it to 252 fecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101
reference species, we detected 10.3 million single nucleotide polymorphisms
(SNPs), 107,991 short indels, and 1,051 structural variants. The average ratio
of non-synonymous to synonymous polymorphism rates of 0.11 was more variable
between gut microbial species than across human hosts. Subjects sampled at
varying time intervals exhibited individuality and temporal stability of SNP
variation patterns, despite considerable composition changes of their gut
microbiota. This implies that individual-specific strains are not easily
replaced and that an individual might have a unique metagenomic genotype, which
may be exploitable for personalized diet or drug intake.
Press Contact
Isabelle Kling,
Communications Officer
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
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Tel: |
+49 6221 387-8355 |
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E-mail: |
Lena Raditsch, Head of Communications
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
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Tel: |
+49 6221 387-8125 |
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E-mail: |
http://www.embl.de/aboutus/communication_outreach/media_relations/2012/121205_Heidelberg/
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