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CEGIIR Issue # 5, July 8, 2015 1. What is the “microbiome”? Issue #5, JULY 8, 2015 Questions? Comments? • The fifth session of the CEGIIR GI Lunch’N’Learn Series was held on July 8, 2015 at noon in Katz 7-003. • Today’s newsletter brief is a Q & A summary by Dr. Madsen from this session about “Demystifying the Microbiome”. For inquiries, suggestions or feedback, please email Melissa Silva/Kayla-Marie Smith at [email protected] The CEGIIR Lunch’N’Learn News The “microbiome” is a newer term used to refer to the entire collection of genes found in all microbes associated with a particular host. We used to refer to it as “microflora” but this is misleading, as it sounds like we are colonized by plants! The “microbiota” refers to all the microorganisms that live in a particular environment. The “metagenome” refers to the genetic material from a mixed community of organisms. The “metatranscriptome” is the sum total of all messenger RNA expressed by a group of interacting organisms. Just over 10 years ago, we had to culture bacteria to find out what was out there, but now we can use whole genome sequencing. New technologies 1
Transcript of The CEGIIR Lunch’N’Learn News - University of...
CEGIIR Issue # 5, July 8, 2015
1. What is the “microbiome”?
Issue #5, JULY 8, 2015
Questions? Comments?
• The fifth session of the CEGIIR GI Lunch’N’Learn Series was held on July 8, 2015 at noon in Katz 7-003.
• Today’s newsletter brief is a Q & A summary by Dr. Madsen from this session about “Demystifying the Microbiome”.
For inquiries, suggestions or feedback, please email Melissa
Silva/Kayla-Marie Smith at [email protected]
The CEGIIR Lunch’N’Learn News
The “microbiome” is a newer term used to refer to the entire collection of genes found in all microbes
associated with a particular host. We used to refer to it as “microflora” but this is misleading, as it sounds like
we are colonized by plants!
The “microbiota” refers to all the microorganisms that live in a particular environment.
The “metagenome” refers to the genetic material from a mixed community of organisms.
The “metatranscriptome” is the sum total of all messenger RNA expressed by a group of interacting
organisms.
Just over 10 years ago, we had to culture bacteria to find out what was out there, but now we can use whole
genome sequencing.
New technologies
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CEGIIR Issue #5, July 8, 2015
There are more than 50 known bacterial phyla. Generally there are only 6 phyla found in the gut
- Bacteroidetes - Firmicutes - Actinobacteria - Proteobacteria - Verrucomicrobia - Fusobacteria
10-100 trillion organisms >1000 different species Bacteria, fungi, virus
2. How many types of bacteria are there?
3. Different sites of the body have different organisms living there
“Tree of Life”
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CEGIIR Issue #5, July 8, 2015
When talking about bacterial phylum, there is HUGE
diversity within a phylum.
Even in order, there are very different organisms within
this level.
4. Domain – kingdom – phylum . . .
Bacteria are very different genetically from one another.
Even with up to 40% shared genes, just as we are different from nematodes, each bacteria is different than another.
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CEGIIR Issue #5, July 8, 2015
We do not know exactly what a “healthy microbiota” is. Microbes in
the gut do influence immune function. Proinflammatory bacteria promote
imbalanced immune responses. So we need to keep bacteria in a balanced setting to keep the immune system
balanced.
5. What is a healthy microbiota?
Host microbiota and health
Intestinal microbes drive immune functions and profile
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CEGIIR Issue #5, July 8, 2015
6. How do you analyze the microbiome?
Analyzing the Microbiome: a flow diagram
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CEGIIR Issue #5, July 8, 2015
If you sequence this area, it can tell you which bacteria it is. You can take primers from the PCR reaction to amplify different regions of interest. By picking primers based on what bacteria you are interested in, you can then identify the bacteria in your sample.
7. What is 16S RNA gene sequencing?
It is here that you have all the bacterial genomes in one sample. You take it all and cut it into little pieces, sequence all the pieces, put it all back together and read them through a database.
It is like taking a poem apart and then putting it back together to see what is there.
You will get a HUGE amount of data back, and it is a lot of work to put it all back together.
There is one ribosomal gene that all bacteria have. Additionally, there are conserved regions common to all bacteria, but there are variable regions within this one gene that are specific to each bacterium.
8. What is metagenomics?
16S rRNA (rDNA) – Sequence 1 gene
How to analyze microbiota: 16S rRNA sequencing
Metagenomics The challenge: piecing it back together
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CEGIIR Issue #5, July 8, 2015
9. What about the metabolomics? Bacteria work together to
produce metabolites that other bacteria need or use.
If you lose key bacteria, like in
diseased states, you can lose the ability to produce beneficial
metabolites. You can measure the metabolome to find out
what the bacteria in that person are producing.
For example, butyrate is a
beneficial metabolite. You need lactate and acetate produced
buy certain bacteria, and other bacteria make acetyl-coA.
10. What factors influence the gut ecology?
Integrated microbial metabolism necessary for health
Production of butyrate requires cooperation
Healthy gut ecology can be affected by:
o Predation o Competition o Parasitism o Mutualism o
This leads to a diseased state which results in the compromise of:
o Nutrient availability o pH o Gas & ion concentrations o Transit time o Mucus o Attachment factors o Antimicrobial factors o Immune responses
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CEGIIR Issue #5, July 8, 2015
Did you know?
Fast Facts
11. What is diversity and richness?
Sample richness is the total numbers that exist.
Alpha diversity is defined by looking at samples and
indicating that there are a number of different groups
more groups means most diversity (Shannon or Simpson diversity index)
Between sample-beta diversity is how many
sample groups are shared between three samples
(Bray-Curtis)
We currently think that high diversity equates healthy and
low diversity equates unhealthy. Disease states will reduce the
diversity within those samples, leading to an overgrowth of
some bacteria and reduction in others.
Low diversity is associated with human disease states
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CEGIIR Issue #5, July 8, 2015
12. Where does your microbiome come from?
The placenta. Yes, the placenta has a microbiome. But is the placenta a filtration device or an incubator? No one knows!
Delivery method – babies born via vaginal delivery pick up different microbiomes than those born by c-section. Breast feeding? Breast tissue and breast milk contain microbes. Perhaps to expose the baby to microbes they need to develop their gut microbiome?
Bifidobacterium (an actinobacteria) are high colonizers of the infant gut – they are important for the immune development, but decrease to LOW amounts in adults.
Breast tissue and breast milk contain microbes
Microbiome of the Placenta
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CEGIIR Issue #5, July 8, 2015
13. Scientists have changed their views . . .
In 2011 – we thought humans had 3 types of microbiome – based on sequencing of about 300 people. We thought that was the way you were born and develop.
In 2015 – we realize that diet is the main determinate of gut microbial composition. In this bar graph, all these people are healthy, but depending on their diet, their microbiome is different. It seems to be more of the function of the bacteria (metabolites) rather than the person.
In 2015 – we also have realized that there are some changes in microbiota over time in any person, but for the most part, there is stability.
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CEGIIR Issue #5, July 8, 2015
14. Microbiome & disease
Diet intervention? Diet trials have been unsuccessful, but perhaps because they are only modifying one component of the diet. In addition, the diet of a host is significant, and perhaps giving a supplement daily may not work, but by pulsing a specific nutrient to encourage growth of a certain bacteria may help.
What about yogurt or probiotics? Many probiotics are made to get through stomach acid – they are selected for that reason, rather than for their function. Therefore they may not work unless you have all the correct bacteria to produce the end results.
What about fecal microbial transplant (FMT)? FMT has been shown to be very beneficial to treat recurrent Clostridium Difficile infection. However, it has not been as successful in IBD patients. This may be because IBD patients have underlying genetic defects that drive towards a certain microbiome. Repeated FMT may be needed to affect the microbiome.
Did you know? You can find updated information
on the Canadian Microbiome Initiative at:
http://www.cihr-irsc.gc.ca/e/39951.html
You can find additional information on the human microbiome at:
http://www.cdhf.ca/en/staying-healthy-/details/id/38
In The Media “Say Hello to Your Little
Friends”
http://www.theglobeandmail.com/life/health-and-fitness/health/whats-in-
our-guts-making-sense-of-the-microbiome/article24822224/
Fast Facts:
• microbial cells outnumber host cells by factor of at least 10:1
• they encode approximately 100-fold more genetic information than the human genome
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CEGIIR Issue # 5, July 8, 2015
Lastly…
Special thanks to Dr. Vivian Huang for founding the CEGIIR Lunch’N’Learn series,
Brian Reuter, Melissa Silva, contributing scientists (you know who you are), and of
course, YOU, for all your participation in our fifth session.
Contributing author: Dr. Karen Madsen; Editor: Dr. Vivian Huang, Melissa Silva, Kayla-Marie Smith
Profiling Trainees section The following students are conducting research on the microbiome. Studying the microbiome is
extremely important for understanding the GI disease, for diagnosing GI disease, for managing GI disease, and for improving the health of patients with GI diseases. Thank you for your hard work
and good luck this summer!
Aiden Zalasky is an undergraduate student in Dr. Madsen’s lab. Aiden is studying dabrafenib and its effects on ulcerative colitis. His investigations support the hypothesis that inhibition of the BRAF kinase will help reduce the
inflammatory response in the MAPR pathway. The study of this may allow the discovery of linkages between different inflammatory pathways.
Robert Fedorak is an undergraduate student in Dr. Madsen’s lab. Robert is studying the effects of a diet high in refined sugars (sucrose) on colitis in mice. Robert is investigating the role of fecal microbial transplants and if they
modulate and improve this diet-induced increase in susceptibility of DSS-induced colitis in mice.
Ammar Hassanzadeh Keshteli is a graduate student in Dr. Madsen’s lab. Ammar is studying the role that a Western-type diet plays in the development of IBD in mice. His investigations support the hypothesis that following a healthy
diet reduces frequency of relapse in UC patients.
Proposed future topics to be discussed this summer:
• How to make abstracts and posters • Upper GI Diseases • Lab Techniques
Thank you for attending the fifth session of the CEGIIR GI Lunch’N’Learn series. We look forward to having you participate in future sessions and incorporating your feedback!
Next CEGIIR GI Lunch’N’Learn session:
When? July 22, 2015
Where? Katz 7-003, noon
What? “Pregnancy in IBD: How Maternal IBD and Treatment Can Affect the Baby”
Who? Dr. Vivian Huang
Cartoon of the Day
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CEGIIR Issue #5, July 8, 2015
References • The Human Microbiome
o http://academy.asm.org/images/stories/documents/FAQ_Human_Microbiome.pdf
• Microbiome
o Image used with permission from Dr. Karen Madsen
• New technologies o Image used with permission from Dr. Karen Madsen
• Tree of Life Diagram
o Image used with permission from Dr. Karen Madsen
• Different Sites of the Body Have Different Organisms o Image used with permission from Dr. Karen Madsen
• Bacterial Phylum
o Images used with permission from Dr. Karen Madsen
• Host Microbiota & Health o Image used with permission from Dr. Karen Madsen
• Intestinal microbes drive immune function & profile
o Image used with permission from Dr. Karen Madsen
• Analyzing the Microbiome: a flow diagram o Image used with permission from Dr. Karen Madsen
• 16S rRNA gene sequencing
o Images used with permission from Dr. Karen Madsen
• Metagenomics o Images used with permission from Dr. Karen Madsen
• Integrated microbial metabolism necessary for health
o Images used with permission from Dr. Karen Madsen
• Production of butyrate requires cooperation o Images used with permission from Dr. Karen Madsen
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CEGIIR Issue #5, July 8, 2015
References (continued) • What Factors Influence Gut Ecology
o Image used with permission from Dr. Karen Madsen
• Diversity & Richness o Images used with permission from Dr. Karen Madsen
• Where does your microbiome come from?
o Images used with permission from Dr. Karen Madsen
• Scientists have changed their views… o Images used with permission from Dr. Karen Madsen
• Microbiome & Disease
o Image used with permission from Dr. Karen Madsen
• Different Sites of the Body Have Different Organisms o Image used with permission from Dr. Karen Madsen
• Sidebar o http://www.cihr-irsc.gc.ca/e/39951.html o http://www.cdhf.ca/en/staying-healthy-/details/id/38 o http://www.bcgsc.ca/about/news/cihr_logo_big_e.gif/view
o Fast Facts
• http://www.cihr-irsc.gc.ca/e/39951.html
• Cartoon Of The Day o https://egtheory.wordpress.com/2014/12/12/microbiome/
• All other images and information reproduced with permission of Dr. Karen
Madsen
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