713 Lecture 15

Host metagenomics

Progression of techniques• Culture based

– Use phenotypes and genotypes to ID

• Non-culture based, focused on 16S rDNA– Clone 16S PCR products into vector and

sequence

• Non-culture based, no cloning, sequence 16s

• Future: non-culture based, no cloning, sequence all genes being used (RT-PCR of RNA into cDNA, sequence)

Some wild bugs detected in plaque

Metagenomics• Metagenome – Analysis of the genetic material

within a community of organisms

Extract DNA

Sequence DNA

Analyze the types found

More on the mammalian gut microbiome

• Adult monozygotic twins (and, to a lesser extent, dizygotic twins and siblings) have more similar gut microbes than to their marital partners

• Animals inherit their gut flora from their mothers

• Host genotype appears to affect relative abundance of community members, not composition

Mouse vs Fish

• 99% of mouse gut bacteria belong to Bacteroides and Firmicutes

• Mostly Proteobacteria in Fish

• Do gut bacteria differ because the residents of their typical environment differ?

• Or does the host animal select the resident bacteria?

Responses ofzebrafish to colonization with individual cultured gut microbes

The bacteria must be fed to be helpful

The Intestinal Microbiome

• The gut microbiome is largely shared among family members– Your intestinal flora is closer to your mom and dad’s than your

friend’s

• In a study of 154 individuals, there was no common shared species between all individuals

• There are 150 times more genes in the intestinal microbiome than in the human genome

• Many of these bacteria perform metabolic functions necessary for digestion

Co-Metabolism• The intestinal flora provide us with enzymes that can break

down foods that the human genome does not encode – Glycoside hydrolase breaks down polysaccharides (such as

pectin)

• Our intestinal flora co-metabolizes our food and provides us with nutrients– Vitamin K, short chain fatty acids, biotin, Tryptophan, other

amino acids, lipids, and indole-melanin

• In a study involving rats, antibiotic intervention drastically altered the intermediate metabolites for many nutrients– After antibiotic treatment the rats were observed every day for

the restoration of the metabolites to levels before antibiotic treatment

Co-Metabolism

• Antibiotics don’t just alter the microbial community

• Provides proof in mammals that antibiotic treatment has effects on digestion

• Reduced microbial flora changes metabolism

Intestinal Flora and Obesity

• Obese individuals have reduced microbial diversity

• The amount of bacteroidetes decreases and firmicutes increase (associated with high fat diets)– Although bacteroidetes decrease, a subgroup of this phyla,

Prevotellaceae, increases (No dietary restrictions)

• The energy that microbes harvest from foods is increased in obese individuals compared to lean individuals– They release more calories, which in turn are taken up by

the body

Diet Changes the Intestinal Flora

• A study using humanized mice with transplanted microbial communities from healthy individuals found that diet alters the intestinal community– The original community was heritable from generation to

generation– When switched to a high fat diet, bacteroidetes decreased,

firmicutes increased, and the mice started to gain weight– This new, alter community became transmissible from mother to

offspring

• This finding indicates that an unhealthy community can set up offspring for a less efficient microbial community

• A human study found that restricting calories and fat can change the microbial flora

• Obese subjects were monitored for one year and were found to have Firmicutes and Bacteroidetes compose 92% of the intestinal flora

• This trend was stable for all subjects for one year

Diet Changes the Intestinal Flora

• The subjects were then randomly assigned to fat restricted or carbohydrate restricted diets and monitored for another year

Diet Changes the Intestinal Flora

The Intestinal Flora and Autoimmune Diseases

• Not many direct links or causes have been made yet

• It is hypothesized that properly regulated microbes send metabolic signals to the innate immune system

• These signals can either suppress or stimulate the innate immune response

• More studies are being conducted to elucidate the possible mechanistic causes of this microbe-immune system interaction

• A trial treatment for Crohn’s disease and ulcerative colitis is fecal bacteriotherapy– Fecal transplant from healthy individuals into affected

individuals– Shows promising results so far but needs clinical trials– Many people are “grossed out” by the treatment

The Intestinal Flora and Autoimmune Diseases