17: The Microbiome Flashcards
What is the difference between microbiota and the microbiome?
Microbiota: It is a number of communities of symbiotic microorganisms living in and on the human. Body that have co evolved with the human host and form part of the human landscape. Bacteria, archaea, viruses and micro eukaryotic.
Microbiome: (metagenome). The catalogue of genes that these microorganisms harbour. They provide to the host with a number of functions that humans cannot exert themselves aka digestion complex polysaccharides
What groups of microorganisms form the microbiota?
Bacteria, Archaea, Microeukaryotes (including fungi) and viruses (bacteriophages)
What is meant by the term commensal microbiota?
Cause no harm to the host (humans).
What four bacterial phyla dominate the commensal microbiota in humans?
Firmicutes, Bacteroidetes, Actinobacteria and proteobacteria
List four factors that may determine the differences in composition of the microbiota between individuals
- genetic makeup
- mode of delivery
- diet during infancy or in adulthood
- use of antibiotics and other therapeutics
List two technological developments that have allowed the advancement of the microbiota research and briefly explain why.
High throughput sequencing technologies
Next gen sequencing
PCR
What is meant by the term Operational Taxomic or OTU
Cluster of 16S rRNA sequence/reads that are similar. Each cluster represents a single genus/species of bacteria depending on the similarity threshold (95% / 98-99%)
Why do we use the 16S rRNA for profiling the composition of the microbiota?
- is a universal molecule (all microbiota have it)
- contains both variable and constant regions
- variable regions contain ‘fingerprints’ that serve to identify bacteria to species level. Detection specificity
- constant region allows for the use of universal primers
- molecular clock: it evolves at relative constant rates, which allows to infer phylogenetic relationships
Briefly explain the advantages/disadvantages of sequencing a fragment of the 16S rRNA gene for studying the microbiota
Advantages (compared to whole genome sequencing)
- cost per sample (is cheaper)
- amplicon length (improves accuracy for detecting species)
- good for well characterised ecosystems
Disadvantages
- limited to one region of the 16S
- amplicon bias (PCR step)
Why is it so hard to define what is a ‘normal/healthy microbiota’
Individuals have specific gut microbiota and different does not necessarily mean better
What is meant by the term ‘core microbiome’
Set of genes (functional capabilities) present in a determined habitat in all or the vast majority of humans
What is the difference between alpha and beta diversity?
Alpha: alpha diversity indexes reflect the species diversity and or evenness at a local scale (skin). Diversity within the site.
Beta: reflects the differences in compositions between two sites (hands/arms). Compared between sites
