Developing a Method to Study the Impact of Microbial DNA on the Brain Related to Alzheimer’s Disease – Can Food Make a Change?
(2022) KNLM01 20221Food Technology and Nutrition (M.Sc.)
- Abstract
- Understanding the gut-brain-microbiota axis can help us provide a new tool to manage conditions such as Alzheimer’s. However, a major challenge is selectively amplifying the bacterial DNA which is present at a much lower level than the host DNA. In this thesis, we aim to develop a methodology to extract, purify and quantify the bacterial DNA in the brain tissue of mice. The methodology that can be used for further application studying gut-brain-microbiota axis, which in this case is comparison of the microbial DNA composition in mice with Alzheimer’s disease vs. healthy littermates fed with natural foods. A major hurdle to this approach is to identify the possible bacterial contamination during the extraction step and to eliminate the host... (More)
- Understanding the gut-brain-microbiota axis can help us provide a new tool to manage conditions such as Alzheimer’s. However, a major challenge is selectively amplifying the bacterial DNA which is present at a much lower level than the host DNA. In this thesis, we aim to develop a methodology to extract, purify and quantify the bacterial DNA in the brain tissue of mice. The methodology that can be used for further application studying gut-brain-microbiota axis, which in this case is comparison of the microbial DNA composition in mice with Alzheimer’s disease vs. healthy littermates fed with natural foods. A major hurdle to this approach is to identify the possible bacterial contamination during the extraction step and to eliminate the host DNA. Brain is a unique and challenging organ to study. The amount of lipids content is second abundance to adipose tissue among others and the solid blood-brain-barrier (BBB) delicately protects the central nerve system (CNS) from microbe’s invasion. The extreme low amount of microbial DNA compared to host DNA after the extraction complicate the efficiency to characterize the microbiota community in the brain tissue. Therefore, in this study we evaluated the bacterial DNA extraction efficiency from murine brain samples and a human saliva, using two commercially available kits (Qiagen DNeasy Blood & Tissue Kits and Promega Wizard® Genomic DNA Purification Kit). While the host DNA depletion was performed using NEBNext Microbiome DNA Enrichment kit. The purified and enriched DNA was further analyzed using gel electrophoresis and finally sequenced by next-generation sequencing targeting the V4 region of the 16S ribosomal RNA gene. The percentage of microbiome DNA component increased in Qiagen compared to Promega method with host DNA depletion. DNA extraction with host DNA depletion influences microbial community composition underlying the need for careful selection of DNA extraction kit and usage of microbiome DNA enrichment to improve recovery from a range of bacterial taxa. Overall, the bacterial community profile of brain tissue was not well characterized in this study which needed further investigation. (Less)
- Popular Abstract
- Apart from our 30 trillion cells which constitute our body, every individual cell harbors 39 trillion little mighty guys that are invisible to human’s naked eyes including bacteria, viruses, yeasts, protozoa, and fungi. They can contribute to our health, or they can sometimes be pathogenic and make us sick. They started to build their communities within our body once we were exposed to this world out of our mother’s womb and expanded their communities with time. Every person has their unique mighty guy composition. Their composition can vary depending on our genetics, where we live, what we eat, and what we do.
Majority of microorganisms reside in our gut forming gut flora which is significantly dependent on what we eat. Sometimes... (More) - Apart from our 30 trillion cells which constitute our body, every individual cell harbors 39 trillion little mighty guys that are invisible to human’s naked eyes including bacteria, viruses, yeasts, protozoa, and fungi. They can contribute to our health, or they can sometimes be pathogenic and make us sick. They started to build their communities within our body once we were exposed to this world out of our mother’s womb and expanded their communities with time. Every person has their unique mighty guy composition. Their composition can vary depending on our genetics, where we live, what we eat, and what we do.
Majority of microorganisms reside in our gut forming gut flora which is significantly dependent on what we eat. Sometimes bacteria or their compounds travel around our body including the brain, our bodies most secure place. They would usually be stopped by the gut-blood and blood-brain-barrier. Yet, some of them can break through the lines under specific circumstances. For instance, it has been shown that production of a specific protein by-product called amyloid-beta causing Alzheimer’s disease, which makes our beloved one lose their precious memories, has been linked to changes in gut microbiota composition and also a damage to the blood-brain-barrier that may allow bacteria to come to the brain.
Therefore, we want to find out what kind of bacteria can break the blood-brain-barriers. In order to achieve this, we set out to develop a method to study the presence of bacterial genetic material in murine brain. Through this approach we would be able to better understand the bacterial community in the brain, taking us closer to understanding this process in humans and how we can be more mindful about prevention of diseases like Alzheimer’s. (Less) - Popular Abstract (Swedish)
- Förutom de 30 biljoner celler som utgör vår kropp, hyser varje individ 39 biljoner små mäktiga mikroorganismer som är osynliga för människans blotta ögon inklusive bakterier, virus, jästsvampar, protozoer och svampar. De kan gynna vår hälsa, men också vara patogena för att göra oss sjuka. De började bygga sina samhällen i vår kropp när vi exponerade den för denna värld ur vår mammas mage och expanderade med tiden. Varje person har sin unika mäktiga bakteriekomposition. Deras sammansättning kan variera beroende på vår genetik, var vi bor, vad vi äter och vad vi gör.
Majoriteten av mikroorganismerna finns i vår tarmbildande tarmflora som är mycket beroende på vad vi äter. Ibland färdas bakterier eller deras föreningar runt vår kropp... (More) - Förutom de 30 biljoner celler som utgör vår kropp, hyser varje individ 39 biljoner små mäktiga mikroorganismer som är osynliga för människans blotta ögon inklusive bakterier, virus, jästsvampar, protozoer och svampar. De kan gynna vår hälsa, men också vara patogena för att göra oss sjuka. De började bygga sina samhällen i vår kropp när vi exponerade den för denna värld ur vår mammas mage och expanderade med tiden. Varje person har sin unika mäktiga bakteriekomposition. Deras sammansättning kan variera beroende på vår genetik, var vi bor, vad vi äter och vad vi gör.
Majoriteten av mikroorganismerna finns i vår tarmbildande tarmflora som är mycket beroende på vad vi äter. Ibland färdas bakterier eller deras föreningar runt vår kropp inklusive hjärnan, vår säkraste plats i kroppen. De skulle vanligtvis stoppas av tarm-blod- och blod-hjärnbarriären. Ändå kan vissa av dem bryta igenom linjerna under specifika omständigheter. Det har till exempel visat sig att produktionen av en specifik proteinbiprodukt som kallas amyloid-beta som orsakar Alzheimers sjukdom, som gör att vår älskade förlorar de värdefulla minnena, har kopplats till förändringar i tarmmikrobiotans sammansättning och även en skada på blodet -hjärnbarriär som kan tillåta bakterier att komma till hjärnan.
Därför vill vi ta reda på vilken typ av bakterier som kan bryta blod-hjärnbarriärerna. För att uppnå detta siktar vi på att utveckla en metod för att studera närvaron av bakteriellt genetiskt material i murin hjärna. Genom detta tillvägagångssätt skulle vi kunna bättre förstå bakteriesamhället i hjärnan, vilket tar oss närmare förståelsen av denna process hos människor och hur vi kan vara mer uppmärksamma på att förebygga sjukdomar som Alzheimers. (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9102312
- author
- Yang, Fuh-Tzu LU
- supervisor
- organization
- course
- KNLM01 20221
- year
- 2022
- type
- H2 - Master's Degree (Two Years)
- subject
- keywords
- DNA extraction, Microbiome DNA enrichment, Host DNA depletion, 16S rRNA sequencing, Alzheimer’s disease, Gut-brain axis, Microbiota, Microbial DNA, Black currant, Applied Nutrition and Food Chemistry
- language
- English
- id
- 9102312
- date added to LUP
- 2022-10-27 11:37:46
- date last changed
- 2022-10-27 11:37:46
@misc{9102312,
abstract = {{Understanding the gut-brain-microbiota axis can help us provide a new tool to manage conditions such as Alzheimer’s. However, a major challenge is selectively amplifying the bacterial DNA which is present at a much lower level than the host DNA. In this thesis, we aim to develop a methodology to extract, purify and quantify the bacterial DNA in the brain tissue of mice. The methodology that can be used for further application studying gut-brain-microbiota axis, which in this case is comparison of the microbial DNA composition in mice with Alzheimer’s disease vs. healthy littermates fed with natural foods. A major hurdle to this approach is to identify the possible bacterial contamination during the extraction step and to eliminate the host DNA. Brain is a unique and challenging organ to study. The amount of lipids content is second abundance to adipose tissue among others and the solid blood-brain-barrier (BBB) delicately protects the central nerve system (CNS) from microbe’s invasion. The extreme low amount of microbial DNA compared to host DNA after the extraction complicate the efficiency to characterize the microbiota community in the brain tissue. Therefore, in this study we evaluated the bacterial DNA extraction efficiency from murine brain samples and a human saliva, using two commercially available kits (Qiagen DNeasy Blood & Tissue Kits and Promega Wizard® Genomic DNA Purification Kit). While the host DNA depletion was performed using NEBNext Microbiome DNA Enrichment kit. The purified and enriched DNA was further analyzed using gel electrophoresis and finally sequenced by next-generation sequencing targeting the V4 region of the 16S ribosomal RNA gene. The percentage of microbiome DNA component increased in Qiagen compared to Promega method with host DNA depletion. DNA extraction with host DNA depletion influences microbial community composition underlying the need for careful selection of DNA extraction kit and usage of microbiome DNA enrichment to improve recovery from a range of bacterial taxa. Overall, the bacterial community profile of brain tissue was not well characterized in this study which needed further investigation.}},
author = {{Yang, Fuh-Tzu}},
language = {{eng}},
note = {{Student Paper}},
title = {{Developing a Method to Study the Impact of Microbial DNA on the Brain Related to Alzheimer’s Disease – Can Food Make a Change?}},
year = {{2022}},
}