Lecture 8: human microbiome Flashcards
(35 cards)
There are several reasons why bacteria can reside in our gut and why there able to grow there, especially in our colon. Name these reasons.
- Suitable temperature
- Nutrients in high concentrations due to resorption of water in the colon.
- Food/nutrients resides in the colon for 24-48 hours → optimal uptake
- high pH
- Microbes are inhibited by their own metabolites → the colon resorpes these metabolite, so growth is not inhibited.
Bacteria in the gut are (in general) beneficial for our body. Name reasons why bacteria are beneficial.
- Humans lack enzymes for degradation of fibers and carbohydrates. Bacteria break down our food for us (and for themselves).
- Colonization resistance → due to the colonization of bacteria in the gut, other pathogens can’t colonize. Bacteria are thus tolerated, so that pathogens can’t.
- Humans can’t produce vitamin K, bacteria do.
- Brain-gut axis
- Bacteria educate our adaptive immune system (→ 1000 days from the moment of conception)
Fill in:
In earlier days, it was thought that there were … (1) times more bacteria than human cells. Now we know the ratio of human and bacterial cells in our body is … : … (2).
In earlier days, it was thought that there were 10 times more bacteria than human cells. Now we know the ratio of human and bacterial cells in our body is 1 : 1.
But while the ratio of bacterial to human cells is 1 : 1, bacteria are much more efficient compared to human cells. Why could you consider bacteria to be more efficient?
Humans have up to 20.000-25.000 genes and bacteria have about 3.3 million genes. 2% of human genes are protein encoding, while in bacteria almost all genes are protein encoding.
What’s the definition of the following:
- The microbiota
- The metagenome
- The microbiome
- Microbiota → the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space.
- Metagenome → the collection of genes that are encoded by the members of a microbiota.
- Microbiome → the entire habitat, including the microorganisms, their genomes and the surrounding environmental conditions.
In earlier days, microbiome research was based on culturing bacteria and using radiation probes. What development resulted in advancement of microbiome research?
The development of DNA sequencing technology, e.g. Sanger dideoxy sequencing and later the developent of Next-Generation Sequencing techniques like Illumina.
How can microbiota be identified?
Microbiota have conserved and variable regions in their genome. Microbiota with the same conserved regions are closely related and thus share the same genus. By looking at the variable regions of these same genus bacteria, you can identify the microbe at species level. This can only be done when there’s a database with known/identified microbiota.
Name two techniques that can be used to identify microbiota (in regard to the conserved and variable regions).
- Metagenomic sequencing → sequencing of variable regions with the use of 16s rRNA.
- Tagged PCR → using primers that bind to variable regions
What’s a limitation of DNA sequencing (e.g. tagged PCR or 16s rRNA sequencing) that isn’t a limitation in culturing bacteria?
With DNA sequencing, there’s no clue to whether the sequenced DNA originates from dead or live bacteria. In culture, you can bypass this by selective culturing with the use of e.g. antibiotics.
What’s another limitation of identification of bacteria by DNA/RNA sequencing?
DNA/RNA sequencing has a certain resolution, where in some cases a bacteria can only be identified on species or genus level.
Only knowing that the bacteria that is found is identified in the E. coli genus, isn’t enough. Only the strain will tell you whether the strain is harmfull or harmless. For example, E. coli strain K12 is commensal while E. coli strain O157:H7 is pathogenic.
What can be identified with 16s rRNA sequencing?
- Species
- Relative abundance of species within a sample.
Total microbiome DNA sequence is more demanding since you need a database to compare results with. But it generates lots of information about microbes. What can be identified with total microbiome DNA sequencing?
- Species
- Relative abundance of species within sample
- Genes
- Variants
- Polymorphisms
- Functional information
What is the definition of Operational Taxonomic Unit (OTU)?
In metagenomics, OTU is used to classify bacteria based on sequence similarity of the 16s marker gene. An OTU consists of a group of bacteria whose 16S marker gene shows a sequence identity of 97 percent and above. It is used to classify bacteria at the genus level.
What is seen here?
The surface of the colon, with epithelial cells in blue, mucus in black and bacteria in green. Bacteria reside on the shedding surface of epithelial cells. This prevents bacteria from colonizing for a long time and overgrowing and they also use the shedding and mucus as metabolites.
Why is it extremely difficult to cultivate gut microbes?
Because the gut is anaerobic and only obligate anaerobic microbes can grow there. To cultivate these microbes, they have to live anaerobically in vitro.
What microbe is responsible for stomach ulcers?
H. pylori
What bacteria dominate the gut?
Firmicutes and bacteriodes
What’s an enterotype?
Here, an organism is classified bases on the bacteriological composition of their gut microbiota.
It was previously thought that there are 3 different enterotypes in humans. What enterotypes are these?
- Enterotype with abundance of Bacteroides
- Enterotype with abundance of Prevotella
- Enterotype with abundance of Ruminococcus
Why isn’t it entirely true that there are 3 different enterotypes for humans?
Because in humans it’s more a continuous flow of different bacteria. For example, diet can be a major influence on the gut microbiota; if you eat a lot of carbohydrates (like in South-Asia or US), the gut is dominated by Prevotella. While in the Netherlands the gut is dominated by Bacteroides, due to our milk consumption.
Besides diet throughout our life, what else is important in determining what bacteria dominates our gut?
The way babies are born (ceasarian or natural childbirth), are fed (breast or bottle fed) or when they eat solid food.
What component in breast milk is important for the development of certain bacteria, like the bifidobacteria? And what do they do to solve this issue in babies that are bottle fed?
Oligosaccharides are important for the development of certain bacteria. Because of this, oligosaccharides are often added to milk formulas.
There are four postulates (Koch’s postulates) that determine whether a microbe is a pathogen. Name these postulates.
- Micro-organisms must be found in abundance in all organisms suffering from disease, but should not be found in healthy organisms.
- Micro-organism must be isolated from a diseased organism and grown in pure culture.
- Cultured micro-organism should cause disease when introduced in a healthy organism.
- Micro-organism must be resiolated from the inoculated, diseased (experimental) host and identified as being identifical to the original specific causative agent.
What is the role of gut microbiota in obesity in mouse models (compared to healthy mice)?
- Eubiosis (optimal balance of microbiota in the gut) in mice ensures an efficient way to gain energy from food (efficient energy metabolism). Mice stay lean with eubiosis.
- When the gut of mice is in dysbiosis, the mice will lack a hormone that inhibits the sensation of hunger. With this, more energy is obtained from the same diet and mice will get obese (inefficient energy metabolism).
