The Human Microbiome

Question 1

What is the human microbiome project?

Answer 1

The human microbiome is the most rapidly changing field in human biology
The aim of the HMP is to characterise the microbial communities found in human body sites and look at correlations between their micro biomes and healthy humans. Uses culture independent methods of microbial communities and characterisation as well as whole genome sequencing of individual bacterial species. Started in 2008, five year long project ($15 million). Emphasis of gut, vaginal, skin, oral and nasal/lung

Question 2

How are microbiomes different?

Answer 2

Strong niche specilisation both within and among individuals = different sites different microbes
Diversity and abundance of each habitats signature microbes vary widely
One individual’s gut bacteria have 50 times the genetic diversity of the human genome
Everyone has ~160 species. The community can change but the functions don’t as much.

Question 3

What does the microbiome do for us?

Answer 3

Prevent pathogens from being successful
Blocks colonisation niches
Competes for nutrients
Lowers pH
Cause host to thicken mucus layer
Cause host to upregualte anti microbial peptides
Primes host neutrophils and macrophages

Question 4

What four human microbial communities are dominant?

Answer 4

Firmicutes
Bacteroidetes
Actinobacteria
Proteobacteria
Few bacterial groups but many different species and strains

Question 5

What are functions of the gut microbiome?

Answer 5

The gut microbiota creates SCFAs that modulate our metabolisms and affects our defence against pathogens
Synthesises vitamins (vitamin B and K)
Modulates the immune response
Alters drug delivery

Question 6

What is a functional food?

Answer 6

Food claimed to have a health promoting or disease preventing property beyond the basic function of supplying nutrients

Question 7

What is a probiotic?

Answer 7

Live microorganisms found in fermented foods e.g. yoghurt
Survive transit through stomach and duodenum (first part of small intestine)

Question 8

What are some potential benefits of probiotics?

Answer 8

Prevent chronic intestinal inflammatory diseases
Prevention and treatment of pathogen-induced diarrhea
Prevent urogenital infections

Question 9

What are prebiotics?

Answer 9

An ingredient that beneficially nourishes the good bacteria already in the large bowel or colon
Prebiotics stimulate the growth of probiotics
Mostly obtained from oligosaccharides
Examples: whole grains, bananas, onions, garlic, honey and artichokes

Question 10

How does modifying our microbiome influence us?

Answer 10

We are a colonised ecosystem : colonising microbes can be good, bad or neutral
All are simply extracting carbon and energy

Question 11

What are C. difficle and Lactobacillus ?

Answer 11

Two gut species that both use sialic acids from mucin as carbon/energy source -> heterotrophs
Speed of growth and presence of accessory genes are the only factors making C. difficile a pathogen

Question 12

How are fecal matter transplant effective?

Answer 12

Fecal microbiota transplantation (FMT) is a highly successful treatment for multiple recurrences of Clostridium difficile infection (CDI)

Question 13

What are the five goals of the human microbiome project?

Answer 13

1. To develop a reference set of microbial genome sequences and to perform preliminary characterisation of the human microbiome.
2. To explore the relationship between existing disease and change in the human microbiome
3. To develop new technologies and tools for computer analysis
4. To establish a resource repository
5. To study the ethical, legal and social implications of human microbiome research