1. Human microbiome

Microbiome

The combine genomes of the microbiota

Microbiota

The complete collection of organisms colonizing humans

Which types of relationships are more common in the human microbiome

Mutualistic and commensal relationships predominate over parasitic

Human microbiome project (HMP)

Started in 2008 to understand microbiome impacts to health and disease

Phase 1 focused on characterizing the microbiome of healthy individuals, why healthy?

To establish a baseline of a “normal” microbiome to reference and compare against in studies of disease and health.

Finding from HMP phase 1

Humans are home to 1000s of species, there is significant person-person variation as well as intra-person variation overtime

Role of microbiome in disease

They produce factors that both promote and decrease disease risk

Role of microbiome in nutrients

aids in the digestion and absorption of nutrients, synthesizes essential vitamins, and contributes to metabolic processes.

How does the microbiome contribute to obesity

obese microbiotas have a greater ability to recover energy from food

Mice study on contribution of microbiome to obesity

Microbiota transplant from both lean and obese humans was transplanted into mice, and even on the same diet, the mice took on the composition of the donor

What happens to the vaginal microbiome during pregnancy

Transforms into low diversity, lactobacillus dominated microbiota

What if vaginal microbiome diversity doesn’t decrease properly throughout pregnancy

High diversity is linked to preterm birth, which could be fatal

There are multiple different relationships that can be
had between a microbe and a human host (e.g.,
parasitic, mutualistic, commensal). What is the
definition of a commensal relationship?

relationship in which one organism benefits from the
interaction while the second organism is unaffected

Metagenomics from fecal samples: Sequences were aligned and contigs (≥500 bp) were generated (totaling 10.6 Gb in length).
What happened to the rest of the sequence data?

Likely was short read and poor quality or redundant data that did not meet quality standards for analysis.

How did they use NextGen sequencing data to assess
species abundance from the set of common genes in the fecal sample contigs

They used illumina sequencing to sequence everything and compare it to a reference to positively identify species abundance based on the presence of specific genes.

Prenatal factors that influence newborn microbiota

Maternal gut microbiota
Vaginal Infection
Periodontitis

Factors during birth that affect newborn microbiota

vaginal delivery or c-section

Post-natal factors that affect newborn microbiome

Antibiotics
Breastfeeding
Host genetics
Environment

When do babies acquire an adult like microbiota and why?

Around 1-3 years old once they have a full adult diet

Microbe exposure during vaginal delivery

Good lactobacillus (Bacteroides)

Microbe exposure during c-section

Pathogens from hospital environment (Enterococcus)

Primary epidemiological studies have shown that c-section babies have increased risk of

Asthma, IMB, obesity, allergies

How would newborn antibiotic exposure affect the development of microbiome

can disrupt the ecosystem of the microbiome and is
particularly a worry for the nascent infant microbiome

How does breastfeeding impact the newborn microbiota development

Breastmilk carbohydrates feed the developing microbiome and also contains bacteria as well

Burkina Faso toddlers early diet

Low in protein but higher in fiber, carbohydrates, and veggies leading to decreased obesity

European toddlers early diet

Higher in animal protein and fat, but lower in fiber leading to increased obesity

What is the hypothesis surrounding the BF toddlers and why they had more Bacteroidetes?

gut microbiota coevolved with the polysaccharide-rich diet in BF, maximizing energy intake from plant fibers

There is a correlation between factors that
disrupt the microbiota during childhood and
certain immune and metabolic conditions (e.g.,
asthma, allergies, obesity, etc.). Which answer
is NOT a factor that can lead to a suboptimal
infant microbiota?

having siblings