7A The Human Microbiome

Define microbiome, microbiota, metagenome, and holobiont

microbiome - the entire habitat of microbes, their genome, and their surrounding environment

microbiota - microogranism that inhabit a particular environment

metagenome - The combined genetic material (DNA) of all microorganisms in a community.

holobiont - host and all of its mircroganisms

Classify the interactions of symbionts: mutualist, commensal, parasites, pathogens

mutualist +/+

commensal +/neutral or neutral/+

parasites -/+

pathogens- disease causing organism

Describe the common tools for studying the microbiome.

16S rDNA sequencing: measures species identity and abundance

Metogenomics (sequencing): survey of DNA in a sample; measures functional potential of the community (who is there and what they do)

Metatranscriptornics (sequencing): survey of mRNA in a sample; measures activity of the community (What genes are they using right now)

Metabolonics (liquid/gas chromatography + mass spectrometry or NMR): survey small molecules in a sample; Measures functional output and small molecules (What molecules are they producing)

Gnotobic animals: model organisms that can be reared germ-free (axenic) and colonized w/ defined microbes to see effects do these microbes have on the host

Define the terms “stability” and “resilience” as they relate to the human microbiome.

Stability - Refers to how well the human microbiome maintains certain levels without disturbance

Resilience - Describes the ability of the microbiome to recover to normal levels after being disturbed

Factors Influencing Human Microbiome Development (Birthing Process, breastfeeding, High-Fiber Foods)

Birthing Process

• The birthing process significantly impacts the baby's future microbiome

• Babies delivered vaginally and via C-section are expected to have different microbiomes due to varying exposure to maternal microbiota

• Evidence from 'The Human Microbiome Part 1' video suggests diversity of human microbiota is influenced by body habitat

Breastfeeding

• Breast milk contains human milk oligosaccharides (HMOs), which are complex sugars that infants cannot digest.

• HMOs serve as a food source for beneficial bacteria, especially Bifidobacteria.

• This promotes the growth of Bifidobacteria in the infant gut, helping establish a healthy microbiome and supporting immune system development.

High-Fiber Foods

• High-fiber foods produce beneficial molecules like short-chain fatty acids and alter the microbiome

• Key bacteria for digesting high-fiber foods is Bacteroidetes

Colonization Resistance in Adult Microbiota

Adult microbiota exhibit colonization resistance by overpowering and out-competing harmful bacteria for resources (indirect mechanism)

They produce factors that directly kill harmful bacteria (direct mechanism)

These mechanisms maintain stability by eliminating potential disturbances

Effects of Antibiotic Treatment

Antibiotic treatment can alter the adult microbiome by not discriminating effectively between good and bad microorganisms

Some taxa may not return even months after treatment, leading to a more permanent alteration of the microbiome

16S rRNA

bacterial fingerprints

ultilized the gene (DNA) that encode small ribosomal subunits (RNA

Alpha diversity

a quantitative measure of different microbes present in a sample

OTU (Operational Taxonomic Units)

Microbe ID

Beta diversity

a qualitative analysis; measures how similar/different microbiome communities are across different samples

Interpret 16S rRNA gene sequencing data

Use 16S rRNA sequencing data to find:
1. Genetic relatedness, sequence similarity, measure variation between samples. Compare the sequences to a database of known bacterial sequences (beta) => or can use it to take data from different parts of the body and look at phyla, abundance of particular phyla of microbes in certain body habitats
2. Find microbe's ID, OTU, Determine bacterial species and quantity of each species (Alpha)

- can use 16S rRNA to find specific taxa of microbes
- Abundance of microbial genes (shows metabolic pathways) does not use 16S rRNA sequencing, because need to use the whole genome to find all microbial pathway, all of these enzymes not coded for in 16S rRNA, but in the rest of the genome

Interpret data relating to microbe-microbe and microbiota-host interactions

Microbe-microbe: they can coexist or can take over causing the other microbe to no longer survive (i.e vibrio takes over and does not allow Aer to survive in gut)

Micro-Host: microbes allow host to digest food that host cannot, or can take over host actions
(i.e. vibrio causes smooth muscle to contract, which makes host cause Aer to be excluded it through intestinal interactions)

Describe ways in which the host can alter the microbiota and vice versa

Host: If host take antibiotics, develops new diet, the microbiota in the gut could be altered, or can come in contact, ingest, microbes

Microbiota: Allows host to digest food it host cannot or microbiota can take over host systems (i.e vibrio makes smooth muscle contract)

Discuss what constitutes a "healthy" microbiome

One that has high resilient microbiomes (fast to recover and withstand change) and has high biodiversity (many functions, able to extract more nutrients with more microbes)

Healthy: high diversity => higher resilience, more function (more microbes a lot more energy utilization, because more genes for organism to utilize), high stability

Not healthy: lower diversity => lower resilience, function, and stability