First let’s get the introduction out of the way! I’m
Rose, a college student at Alverno College. This semester I am diving into the
wonderful world of microbes. Part of the course requires a blogging assignment.
This assignment entails learning about a fascinating microbiology topic with
the use of the magical World Wide Web. Next I am to blog all about this topic
and share how and where it’s being discussed online. So what better topic then
the Human Microbiome Project. Hopefully you are interested enough at
this point to keep on reading (and if not give it a few more minutes I promise
if your into science this is a great topic). Enjoy!
Friday, March 14, 2014
Introduction to the Human Microbiome Project
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| Image source: http://commonfund.nih.gov |
Facing stereotypes, it’s something that many have dealt
with directly or indirectly and it is realized that even when given accurate information
some have tremendous difficulty eradicating these ingrained beliefs. One widespread stereotype is the concepts on
bacteria. From a young age many have been trained to avoid bacteria to prevent
illness by measures including hygienic practices, consuming food properly
handled and cooked, drinking clean water, and avoiding others with visible illness.
While it is extremely important to take the appropriate measures to maintain
health and avoid disease, in recent times major discoveries have revealed that
the majority or bacteria and microorganisms are harmless and can even be
beneficial. In 2007 hundreds in the scientific community set out to map the microbial
make-up of healthy individuals (National Institutes of Health [NIH], 2012).
This project was named the Human Microbiome Project (HMP) and the findings from
this project have truly changed the fundamental understandings of the
relationship microorganisms have with humans!
Methods
To understand this project it is of some importance to
understand the methods and certain terms, so I’ll briefly go over this. Firstly
HMP had to define what a healthy individual was. In this project a healthy
individual was free from disease and furthermore had to refrain from the use of
antibiotics or medicines that would interfere with their normal flora (The
Human Microbiome Project Consortium, 2012). In all there was 242 participants
from the western population, 129 males and 113 females. Males had specimens
collected from 15 body sites, which included nasal, oral, skin, and lower
intestine. Females had specimens collected from the same 15 sites as the males
with the addition of 3 specimens collected from 3 areas within the vagina.
Participants had specimens collected several times over a period of time to
insure that the microbial data on each participant was an accurate representation
of their healthy and normal microbiome. In all there was 4,788 specimens
collected and analyzed (NIH, 2012). Now to the real scientific stuff; how did
they identify the different microbial species within the specimens?? Some microorganisms
can be grown by means of cultures and various testing performed to identify
them, but it was realized very early on in the history of microbiology that
MANY microorganisms just don’t culture. The conditions needed for most
microorganisms to grow are just too specific to be replicated in a lab environment
(Case, Funke, Tortora, 2013). So the project utilized computer technology that
was able to sort through the samples using DNA sequencing. This allowed
scientist to separate the human DNA from microbial, due to the differences in
ribosomes between microorganisms and humans. It was 16s rRNA that was used to
identify the different species of bacteria in the samples. From here this DNA
was studied to reveal the metabolic capabilities of the microbial communities
within different body sites (NIH, 2012).
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| Image source: http://genome.cshlp.org |
This diagram shows the process used in the project to identify the microorganisms in the samples, metagenomics refers to the genetic material that was within the samples.
Intial Findings
Bacterial Distribution by Body Site |
| Image source: http://genome.cshlp.org
In 2012 multiple reports were published sharing the
exciting results of this 5 year study. One of the first facts that astounded
many was the enormous amount of species identified. It was previously estimated
that at most there was a few hundred species inhabiting the human body, but the
HMP found more than 10,000 microbial species. The project believes they have
identified about 81%-99% of all the microbes in human body. What was one of the
most important findings of the study was the realization that peoples normal
microbial communities vary from one another. A microbe that would be consider a
pathogen in one person can exist within another as part of a microbial community
and cause no harm. This has raised questions that the medical community is
eager to explore including how and why a microbe becomes deadly. This is significant
because once these questions are addressed the views on how microbes actually
cause disease will be completely changed. Furthermore, the project has shown
that there is strong correlation between the shifts in the normal microbial
communities and the occurrence of disease and the physiological state of a
person (NIH, 2012).
Beyond these microbial communities simply coexisting in
our bodies and the occasional illness that can come from a few of the species,
there has been an array of new findings that illustrate just how essential
these microorganisms are to human survival. They
perform such tasks as digesting foods and excreting vital nutrients that the
body can absorb (30% of the nutrition we digest comes from food that bacteria
digests within us), they produce vitamins that the body uses, and provide
anti-inflammatories that are a major role in the immune system response
(Birren, 2010). They perform such tasks as digesting foods and
excreting vital nutrients that the body can absorb, they produce vitamins that
the body uses, and provide anti-inflammatories that are a major role in the
immune system response. Many of these tasks are enabled by the protein coding
genes within the microbes. A human has approximately 22,000 protein coding
genes that carry out various tasks within the body, while the human microbiome
contains 8 million protein coding genes that enable them to take on such major
roles in the bodily functions of humans. From these initial results microbial
communities are being extensively studied and compelling evidence is mounting that
these communities are effecting human life much more than could have ever been
imagined.
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MIND CONTROL?!?!?
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| Image source: http://www.wbur.org
Are you really in control of your behavior, emotions, and
thoughts?? Well of course! But there has been recent developments in various
studies stemming from HMP that are looking into the possibility of this. In a
study by Dr. Emeran Mayer there are strong indications that bacteria from our
gut may be influencing us and possibly even playing a role with the development
of the human brain. Dr. Mayer began testing this hypothesis of his by
performing brain scans on participants and examining the species of bacteria that
was living in their gut. It appears from this information that connections to
certain regions in people’s brains develop differently depending on what
bacteria is in their gut. Another research team has been experimenting with
mice to see if changing the mix of microbes within their gut will result in
changes of behavior. In one test the researchers replaced microbes from the gut
from mice that were anxious with microbes from fearless mice. The amazing
result was that these previously anxious mice now appear to be freed from their
timid ways. This study also tested what changes could be observed when the
microbial communities within the mice guts were changed through diet, probiotics,
and antibiotics. Astoundingly they recorded major changes in behavior and when
they looked further into what was happening found that after modifying the
bacteria in the guts of the mice there was noticeable changes in the chemicals
that effect the brain in areas such as mood, emotion, and memory. So how
exactly would bacteria in the gut even effect the brain? The vagus nerve
happens to connect the gut and the brain in order for communications of the
cells in the gut to signal the brain for various purposes. The bacteria is suspected
of also sending signals to the brain. Another break-through study found a correlation
on gut bacteria and autism behaviors in mice, and once given certain probiotics
the behaviors were all of a sudden non-existent. These researchers and many in
the medical field are eager to see what scale relations are between the
microbial communities with in humans and brain functions, and are excited with
the implications it could have for treatment of psychiatric treatments. Some
early testing of the introduction of certain probiotics to people with diagnosed
psychiatric disorders is showing promising signs.
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Meet your microbes
In this video is Bruce Birren, who is the director of the
Genome Sequencing Center for Infectious Diseases and the co-director of the
Genome Sequencing and Analysis Program at the Broad Institute of MIT and Harvard,
gives an amazing lecture explaining HMP and some interesting findings coming from
this project. The lecture is about an hour long so in case you just don’t have
the time to view it I will go over a few of the highlights.
- · Clostridium Difficile infection has become a major issue in the hospitals, due to the amount of antibiotics and other medicines patients are given for treatment. While these medicines are essential they also have the adverse effect of killing of bacteria in the body that aids the body, especially in the gut. Without this bacteria here other bacteria can inhabit the gut, like C. difficile, and cause major illness. This particular illness can be treated, but many times it is likely to become recurrent. With research coming from HMP a new treatment, fecal transplant, has arose that is helping cure the most severe cases. Yes this treatment is as bizarre as it sounds! A specimen of stool from a healthy person is collected and the microbes from this sample are then injected into the ill person’s gut so that these microbes can recolonize their gut. It is an astounding breakthrough for medicine! Treatments like this are not only cost effective, but unlike so many medicines these days it is natural with no side effects.
- · Research has shown that people with varying inflammatory diseases, like ulcerative colitis and Crohn’s disease, also have very distinct microbial communities when compared to healthy individuals and one another. This implies that there is a chance that a relationship exists between certain make-ups of microbial communities and disease. If this turns out to be the case, these chronic diseases that often have no cure can be treated effectively by reestablishing new microbial communities within them, just like is seen in the fecal transplants.
- · Correlations have been observed between a person’s weight and the bacteria in their gut. In a lean individual the gut contains a lesser amount of firmicutes and more bacteroidetes, while an obese individual’s gut contains more firmicutes and less bacteroidetes. When the obese individual dieted for a year changes in the amount of these bacteria were seen every few months. By the end of the year these obese people microbes now looked like those of the lean people, containing less firmicutes and more bacteroidetes. This information could lead to new and effective ways of aiding obese people reach healthy weights with the use of bacteria.
For
more mind blowing information watch the video!!
Look who's talking...
HMP has been a hot topic since it began in 2007. Just a
simple google search brings up articles, videos, tweets and more! So here is a
little insight to what’s out there…
10 Ways the Human Microbiome Project Could Change the Future of Science and Medicine http://t.co/gWu4J5J4ql #microbiome
— Andrea Graziano (@digitag) December 18, 2013
The linked article on this tweet discusses the ways in
which medical world could be changed by the HMP. Some interesting thoughts
revolve around the way in which treatments could be tailored to the individual,
how your bacterial make-up could become part of your medical identity just like
your weight, height, and blood type, and the evolution in the way we view
bacteria (losing the war mentality towards them).
Here is a few more interesting tweets on this topic…
Do gut microbes contribute to preterm birth? New study in #PLOSONE: Meconium #Microbiome Analysis Identifies... http://t.co/nkwWXvVMnP
— Meghan Azad (@MeghanAzad) March 14, 2014
The human body is teeming with bacteria and fungi – and business opportunities for the biotech industry: http://t.co/47j2b7EMLm
— Knowledge @ Wharton (@knowledgwharton) March 9, 2014
Facebook even has few pages on HMP (here's one)!
https://www.facebook.com
This link is to a reddit post where one of the scientists that work on HMP and other projects answers peoples questions on all kinds of things related to his work!!
http://www.reddit.com
Mind-altering microbes: how the microbiome affects brain and behavior
More on how the human brain is effected by microbes!!!
References
Case,
Funke, & Tortora. (2013). Microbiology:
An introduction (11 ed.). Glenview, IL: Pearson Education, Inc.
Stein,
R. (2013, November 18). Gut bacteria might guide the workings of our minds.
Retrieved from http://www.wbur.org/npr/244526773/gut-bacteria-might-guide-the-workings-of-our-minds
National
Institutes of Health. (2012, June 13). NIH human microbiome project defines
normal bacterial makeup of the body. NIH
News. Retrieved from http://www.genome.gov/27549144
The
Human Microbiome Project Consortium. (2012). Structure, function, and diversity
of the human microbiome. Nature, 486, 207-214.
doi: 10.1038/nature11234
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