MICROBIOTA

Question 1

1. What is the difference between microbiota and microbiome?

Answer 1

• Microbiota: microbial community, including bacteria, archaea, viruses (phages), fungi, protozoa.
• Microbiome: microbial community and their “theatre of activity”. The latter involves the whole spectrum of molecules produced by the microorganisms, including their structural elements (nucleic acids, proteins, lipids, polysaccharides), metabolites (signaling molecules, toxins, organic and inorganic molecules), and molecules produced by the coexisting host and structures by the surrounding environmental conditions.

Question 2

Briefly explain the difference between ‘16S profiling’ and ‘Whole-genome sequencing’.

Answer 2

For the sequencing of the microbiota, you have to options, either perform a 16S rDNA profiling or perform a whole-genome (shotgun) sequencing.
To study the members of a microbial community, two sequencing strategies can be utilized. For amplicon sequencing (left), primers are utilized that amplify conserved regions within a kingdom. For bacteria, the 16S ribosomal RNA (rRNA) region of the ribosomal gene is amplified, whereas for fungi, the internal transcribed spacer 1 (ITS1) region is amplified. By contrast, whole genome sequencing (right) captures the entire complement of genetic material in a sample without a targeted amplification step. Analyses of sequenced amplicons can identify the genus-level and the species-level community composition, but only shotgun metagenomics can reveal kingdom relative abundances and resolution to the strain level. Colours not defined may be grouped as ‘Other’.
WGS: expensive longer turnaround high res. (species + genes)
16S rRNA: cheap, fast and has low resolution (OTU)

Question 3

Name the 2 dominant phyla of mammalian large intestinal bacteria.

Answer 3

Firmicutes and Bacteroidetes

Question 4

Roughly how many different bacterial species colonize an individual human’s intestinal tract?

Answer 4

About 300 species can colonize an individual human’s intestinal tract.

Question 5

Which of the following statements is/are correct?

Answer 5

a) Is a hypoxic environment.
b) Is covered by a compact inner and loose outer mucus layer.
c) Contains crypts and villi.
d) Is the densest microbial ecosystem of the human body.

Question 6

Which of the following statement(s) on human intestinal metatranscriptome signatures is/are correct?

Answer 6

a) Metatranscriptomic profiles are less individualized than metagenomic profiles.
b) A person’s metatranscriptome is more variable over time than that person’s metagenome.

Question 7

Explain the “Commensal Koch´s postulates”.

Answer 7

Koch’s postulates keep being very important today. They talk about the causality in infectious diseases. But we can apply these postulates to commensal causality in microbiome research. We mean, study that some bacteria can actually protect us from disease.
• The suspected commensal bacteria must be present in all healthy individuals and absent from sick ones.
• The suspected commensal bacteria should be grown in pure culture
• Microorganisms from the pure culture should cause protection in another animal
• The microorganism should be reisolated and shown to be the same as the original.

Question 8

What are gnotobiotic animals?

Answer 8

The term generally describes biological systems wherein all present organisms can be accounted for. In the present context, the term refers to ex-germ-free animals that were inoculated and colonized with a defined bacterial species or consortium.

Question 9

Name a mucus-degrading gut bacterial species.

Answer 9

Bacteroide sthetaiotaomicron

Question 10

10. Name a metabolite produced by Bacteroides thetaiotaomicron that can inhibit growth of Salmonella enterica.

Answer 10

Propionate