Posts Tagged ‘microbiome’

The Uniqueness of Your Microbiome

 :: Posted by American Biotechnologist on 04-24-2013

The microbiome is your body’s set of microbial communities; microbial cells outnumber human cells roughly ten to one. Through studying the microbiome, scientists are learning more the relationship between these microbes and human health and disease. In looking at the effect of diet on the composition of the gut microbiome, Dr. Nanette Steinle of the University of Maryland’s School of Medicine and Dr. Emmanuel Mongodin of the University of Maryland Institute of Genome Sciences wanted to determine if the Mediterranean diet would cause changes in an individual’s microbiome. This diet was selected because it has already been associated with reduced risk of cardiovascular disease.

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Death by Sterility

 :: Posted by American Biotechnologist on 06-21-2012

In a research study appearing in Cell, Harvard scientists have found that an individual’s microbiome is very species-specific and likely the result of a co-evolutionary process involving the host and its bacterial tenants. Bacteria are important for our survival and any disturbances to our “bacterial make-up” may be harmful to our health. I say our “bacterial make-up” because studies show that we are infested with bacteria and that there are 9-fold more bacteria than there are human cells in our bodies.

While it is well accepted that resident bacteria play an essential role in our optimal health, the current study looked to analyze whether our microbiome is custom made for each individual or whether any bacterial cohort will do.


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Not Just Anybody’s Feces

 :: Posted by American Biotechnologist on 06-02-2011

Perhaps this isn’t the most glamorous title for a post, and considering that I’ve posted twice before on this subject (see fecal pharma and more fecal findings!) it might be assumed that I have a fecal fixation. Let me assure you that despite everyone’s initial “yuck” factor reaction to these stories, they are quite fascinating and potentially life-changing.

As I’ve mentioned previously, our colon’s microbiome plays an essential role in the gut’s health and “happiness.” Disturbances to the tens of thousands of bacteria found in our bodies can have detrimental effects including the development of irritable bowel syndrome and ulcerative colitis. In order to restore gut homeostasis, a technique called fecal transplantation may be employed. Fecal transplantation involves collecting 200-300 grams of fecal matter from healthy donors, filtering out solid particulate, and reintroducing the remaining bacteria to the patient via a colonoscope, an enema or a naso-gastric tube.

A recent study out of the University of Chicago medical center looked at the attitudes and concerns raised by this approach. According to the study’s author, David Rubin, MD, associate professor of medicine at the University of Chicago:

Once patients get past the yuck factor they find the concept appealing. They perceive it as ‘natural,’ similar to probiotics. Patients with severe inflammatory bowel disease tend to develop a high tolerance for therapies that others might consider unorthodox.

Patients biggest concerns were that they were receiving transplants from healthy donors with healthy dietary habits. Furthermore, patients much preferred to receive the transplantation via colonoscopy or enema than through an oral NG route.

Here’s ABC News’ take on the subject:

Click here to read more on this story.

More Fecal Findings!

 :: Posted by American Biotechnologist on 07-15-2010

At the risk of developing a complex that all I talk about is fecal matter, for the second time this week I would like to bring your attention to another study that focuses on the gut and its microbial habitat. A couple of days ago I discussed the challenge of identifying the huge number of microbes found in our bodies and the impact that our microbiome has on our physical health (see fecal pharma post).

In today’s issue of Nature, Alejandro Reyes from Washington University’s school of medicine published a paper showing that although the fecal microbiome is relatively stable between related individuals, the fecal virome exhibits a greater degree of inter-person variability and a lesser degree of intra-person variability. These findings are quite surprising since one would expect bacteriophage expression to be heavily dependent on its microbial environment and therefore to follow a similar pattern to microbial expression. Instead, this study shows that although there were similar microbes in the feces of related individuals their fecal viral expression was quite different. The authors conclude “that a predatory viral-microbial dynamic, manifest in a number of other characterized environmental ecosystems, is notably absent in the very distal intestine.” In other words, our traditional understanding of the relationship between viruses and bacteria in the laboratory setting is challenged when studied in anin-vivo environment.

Below is a this week’s Nature podcast which contains an interview with the study’s principal author Jeffrey Gordon. Scroll over to 15:04 to hear the interview.

The Poo Virome

This study is especially interesting considering the findings of an Israeli group which was published in Molecular Systems Biology back in October 2009. In that study, the authors showed that bacteriophages are strongly tuned to match their unique hosts while viruses that infect humans resemble all mammalian hosts equally. This seems to support Reyes’ et al. initial hypothesis that since related individuals exhibit a high degree of similarity in their fecal microbial expression it would be expected that inter-personal fecal bacteriophage expression would be similar as well. As such, the Reyes paper has left us with more questions than answers regarding fecal viral expression.

The fecal pharma post demonstrated the importance of microbiome research in the context of human health. Based on Reyes’ findings, those involved in the Human Microbiome Project would be wise to incorporate virome analysis into their research as well.

Alejandro Reyes, Matthew Haynes, Nicole Hanson, Florent E. Angly, Andrew C. Heath, Forest Rohwer, & Jeffrey I. Gordon (2010). Viruses in the faecal microbiota of monozygotic twins and their mothers Nature, 466, 334-338 : 10.1038/nature09199

Fecal Pharma

 :: Posted by American Biotechnologist on 07-13-2010

I just read a fascinating story by science writer Carl Zimmer published in Monday’s New York Times science section. In the article, Carl touches upon the work of Dr. Alexander Khoruts who performed a fecal transplantation, essentially injecting a stool sample from a healthy person into the colon of a patient with C. difficile, to help clear up the patient’s chronic diarrhea. Gene analysis pre and post transplantation revealed that the patient’s condition was exacerbated by a deficiency in her gut flora which was corrected with the injection of bacteria normally found in a healthy human colon.

Zimmer continues on to describe the complexity of the microbiome and the enormous challenge involved in deciphering what microbes are present in normal tissue and how their presence or absence affects various biological processes. Findings from the ongoing Human Microbiome Project have thus far revealed that there are tens of thousands of microbial genes to be found in our bodies which far outnumber the the approximately 20,000 protein-coding genes found in the human genome. One of the biggest challenges for scientists involves separating the microbial genes (some of which can only be detected with amplification techniques) from the human genes in order to properly characterize the microbial genome found in a particular organ.

With so many bacteria dictating the difference between normal and diseased human physiology, one has to wonder whether humans exist as individual beings or whether we are really just the sum of our microbiological parts! In fact, the language used throughout Zimmer’s article seems to imply that the human body can actually be broken down into various microbiological ecosystems populated by a multitude of varying bacteria. Talk about a multicultural society. If only humans could learn to live in such a mixed environment!

Anyhow, I am not a philosopher, (as you can clearly tell), but I am blown away by the microbiome project and I welcome anybody involved in this valiant effort to write in and tell us a bit about your experiences.