Monday, July 09, 2007

More on human guts

Yet another interesting open access gut microbe paper in PLoS Biology came out in June. This one describes patterns in the colonization of the intenstines of human infants. As mentioned in a previous post, we are born with a sterile intestinal tract and depend upon the ingestion of compatible microbes for the establishment of our gut community. This study used 16S rhibosomal DNA sequences to document changes in the structure and diversity of infant guts over the first year of life. As with the previous paper, Liza Gross wrote a nice summary article.

Some key points:

  • 14 babies were followed (including one set of twins) for one year. Early the communities were quite different but by the end of the first year they had acquired a composition similar to that of the adult human.
  • At one week of age, two babies delivered by cesarian had fewer total gut bacteria indicating that during natural child birth, the colonization begins during the birthing process.
  • While broadly similar to each other and to the adult community, each infant had a distinct profile that persisted over time.

This paragraph from the end of the Gross summary provides a good overview of the most interesting findings:
The idiosyncratic nature of the early stages of colonization suggests that a baby’s initial bacterial profile largely results from incidental microbial encounters. The fact that some of the early stool samples matched their mother’s breast milk or vaginal sample supports this interpretation. Shared environment may also explain the coincidental appearance of microbes in the twins. The researchers explain the tendency of these communities to eventually converge by hypothesizing that the human–microbe symbiosis has likely evolved under strong selection and that certain well-adapted microbes repeatedly “win” the battle over the opportunistic early colonizers.
Selections from the final paragraph describes some of the future directions the work will take:
By comparing the surprising range of microbial profiles found in these healthy babies to the microbiota of infants born prematurely or with health problems, future studies can explore how diet, delivery method, or other factors might spell the difference between health and disease.
and that the approach used in the study will allow us to explore questions about
the environmental and genetic factors that shape and personalize the amazing “alien” ecosystem that lives within us.


marek said...

10,500 DNA probes - blows my mind :-) It takes me several hours to design one...
What might be the cost for the array? I assume one array slide does one sample - am I correct?

Also how good representative is the stool sample for human gut? Well, fistulating babies might be an issue :-)

10,500 probes, still blows my mind....

Andrew Staroscik said...

I am sure your custom designed probes are far superior to theirs. Note that they had ~1300 control probes, ~6000 group specific and ~3100 species specific. The quality of the probes varied and the actual analysis used only 6400 of the initial set. I assume that includes the 1300 controls, meaning over 1/2 were not good enough to use. I bet the bulk of the species specific probes were discarded.

Look at the results they chose to present. Their best data is at the highest taxonomic levels.

I don't know about cost. The analysis of a sample once the slide is made costs ~$100. This does not include the design and manufacturing of the slides. So $200 - $300 per sample?

genetic viagra said...

Oh my that's terrible, I think humans can't play with the dna until they we're sure something like this It's going to work otherwise why to screw with others people life, I know there are very good scientist but in some cases... people who works in a place like this, it's just sad.
Thanks and good luck