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Paper Review Number One:

Human gut microbiome adopts an alternative state following small bowel transplantation

Hartman et al., 2009

Analysis of Figures

Conclusion and References

Conclusions / Opinion:

In conclusion Hartman et al. gave convincing evidence to support their theory that ileostomy in SBT patients leads to a shift from anaerobic to facultative microbial population community in the small bowel.  I found their argument to be supported by strong evidenc, especailly through figures, and therefore found it to be convincing.  Personally, their introduction was clear and decisive.  The researchers outlined the importance behind the study and the necessary background information about intestional conditions, SBT and ileostomiess to understand the questions asked.  I found the inclusion of the possible genetic component to be over-emphasized and misleading, although it was later ruled out as a possible contributing factor to the fluctuations in bacterial populations over time.  I also thought that there needed to be more emphsis on the undistirbued versus disturbed donor small bowels used in the transplant pateints.  The authors mentioned that in early SBT the donor bowel was “cleaned” of presumably gut flora, but in later SBT the bowel was not “cleaned.”  Were the transplanted bowels in this study all “cleaned” or “not cleaned?” I feel as if this is an important distinction that was never clearly stated.  In additional praise, I must commend Hartman et al. for including such ethical considerations in their paper, such as the IRB and informed consent approval standards and the note that such ileostomy portals are normal monitoring devices for such SBT procedures.  The background information provided on the study and its participants was also informative. 

In the experimental procedures themselves, the researchers did a clear job of painting a bigger picture and then focusing in on the possible cause of a microbial community shift in the small bowel in SBT patients.  Figure one deviated from the textual explanation a little bit, especially concerning ileostomy type clinical factors, which were not represented in the figure.  I also thought the explanation behind the experimentation to determine if the ileostomy was at fault for the shift and not the SBT to be very clear.  Their description behind how they consistently received effluent samples from post-closure patients by inserting ileostomies recently before sampling to prevent any long term shift was a great distinction and shows that the researchers put time into minimizing variability in the study.  In human trials consistency is often difficult to maintain and these researchers did the best they could in every manner to maintain such conserved variables.  The evaluation of biopsy versus effluent sample bacterial populations was another example of the researchers' detailed look into varying factors that may skew their results, although their data and conclusions (figure 3) for this analysis were a little vague and I wished they spent more time justifying their conclusions.  I also thought that the metabolic avenue explored only touched on the surface of such a topic, which tended to add confusion, especially in the overlapping metabolic network diagram.  Thankfully, Hartman et al. were able to simplify their data in text format to get the point across of a change in metabolite between pre and post-closure microbial bowel environments as well.  Finally, I thought that the discussion and conclusion were forceful and flowed perfectly.  There were very few sentences I had to re-read multiple times throughout the whole paper and the researchers did a wonderful job of recognizing potential problems and circumstances that may skew their data.  They used controls properly, when needed, and they introduced only a few variables, which increased the statistical relevance of their data.  I also appreciated the fact that Hartman et al. acknowledged that their was more to learn about this topic and that they did not have all of the answers.  Overall, I though that this paper was well written and well experimentally thought out.  It provided an interesting insight into the small bowel and I look forward to possible explanations behind why the shift does not cause any significant changes in the human body and how such a shift can revert back.



References: Ileostomy. 2009. 19 Oct. 2009 <>.

Hartman et al. "Human gut microbiome adopts an alternative state following small bowel transplantation." Proceedings of the National Academy of Sciences 2009; 106(40): 17187–17192.

Wikipedia: Real-time polymerase chain reaction. 14 Oct. 2009. 19 Oct. 2009 <>.


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