Microbes, our other genome Flashcards
(37 cards)
Learning objectives
- Define the terms microbiome, microbiota, dysbiosis
- Describe the determinants of microbiome composition
- Understand the methods for measuring microbiome composition
- Describe different measures for microbiome diversity
- Describe the role of the gut microbiota in human health and
disease - Understand the hygiene hypothesis in relation to the microbiome
- Describe the role of the microbiome in metabolizing xenobiotics
- Describe the role of the microbiome as a source of antimicrobial
compounds - Describe the non-bacterial components of the microbiome, and
how we measure them - Describe interventions to manipulate the microbiota
Bacteria are the predominant life form on earth
- Stars in the universe vs. bacteria on earth?
– 5x1030 bacteria vs. 1x1024 stars - Bacteria or human cells in the human body?
– 3.8x1013 bacteria vs 3.0x1013 human cells - Total weight of all humans vs. all bacteria on earth?
– Bacterial mass 100 million-fold greater than human mass - Bacteria have an evolutionary history of 4 billion years
– Modern humans < 100,000 years
– Bacteria changed the earth’s atmosphere (cyanobacteria
created the Great Oxygenation Event)
– Marine microbial communities are responsible for half of
the oxygen produced on earth
- Competition and collaboration between microbes
– positive: cross-feeding
– negative: bacteria produce antibiotics (bacteriocins) that inhibit the
growth of competing bacteria
– Stochastic (unpredictable) forces - e.g., dispersal, dormancy
– Rapid evolution
Definitions
- Microbiota
– The micro-organisms present in a specific site - Bacteria
- Viruses
- Fungi
- Parasites
What influences the composition of microbial
communities?
Interactions between biological / physical / chemical
environment
– Environmental parameters
* e.g., oxygen tension, pH, temperature, energy sources
– Interactions between microbes
Interactions between biological / physical / chemical
environment
Definitions
- Microbiome:
– Microbial community that occupies a well-defined habitat; or
– Collective genome of a microbial community
Determinants: intestinal microbiota and food intake
People of Japanese origin can harvest energy from seaweed, whereas most other
people cannot.
* Japanese people have Bacteroidetes bacteria in their gut microbiota which
contain porphyranase enzymes which degrade sulfated polysaccharides found
in edible seaweed (such as nori).
* Marine Bacteroidetes bacteria which grow on seaweed possess similar
porphyranase enzymes.
* Transfer of genes from marine Bacteroidetes bacteria on nori was the likely
origin of enzymes to the Japanese human gut microbiota.
Determinants: intestinal microbiota and food intake
- Most complex plant polysaccharides are not
digested by humans and enter the colon as a
potential food source for the microbiota. - Bacteria have a diverse ability to break down
different substrates. - Change in diet can alter the degradative activity
of the colonic microbiota.
– Environmental parameters
* e.g., oxygen tension, pH, temperature, energy sources
– Interactions between microbes
* Microbial communities typically comprise complex, interacting
mixtures of bacteria, viruses, archaea and micro-eukaryotes (parasites,
fungi)
Dynamics of the microbiome
- Loss of commensals (e.g., antibiotic therapy)
– Often accompanied by pathogen/pathobiont overgrowth,
e.g., Clostridiodes difficile associated colitis - Loss of diversity
– Low bacterial diversity has been documented in association
with inflammatory bowel disease, HIV and type 1 diabetes
mellitus
*pathobiont=a potentially pathogenic organism which under normal circumstances lives as a symbiont
Dysbiosis
An imbalance in the microbial community associated with disease
- Bloom of pathobionts*
– Overgrowth of members of the commensal microbiota, e.g.,
Enterobacteriaceae, in inflammatory bowel disease
16S rRNA gene sequencing
How do we measure the microbiota and its function?
The two key sequence-based methods for measuring the microbiota
Measures of diversity
- Diversity estimates incorporate information regarding
species richness and evenness
– Alpha diversity is a measure of the mean diversity within a
sample
– Beta diversity is a measure of diversity between samples
The gut microbiome: determinants and metabolic niches
Alpha Diversity = richness and evenness of individuals within a site/sample. For example
in the figure below, Alpha Diversity of Site A = 7 species, Site B = 5 species, Site C = 7
species.
Beta Diversity = diversity between sites/samples. In the example below, the
greatest Beta Diversity is observed between Site A and C with 10 species that differ
between them and only 2 species in common.
Obesity and the gut microbiota
Microbiota, immune education and the hygiene hypothesis
- Microbiota shape immune homeostasis:
– Germ-free animals show deficiency in lymphoid organ development and
immune cell activity
