chapter 11, the human microbiome

microbiome

• community of microorganisms living in/on the human body, they colonize the human body. They play rules in health digestion, immunity

• The microbiome differs by microenvironment and body site.

• Pathogens that are in different environments only affect specific parts. (One bacteria can cause troubles in the stomach, but not in the intestine).

• Majority is in the gut (gastrointestinal tract) in order to digest food and produce vitamins. This helps support the immune system and its development.

  (Microenvironment: immediate, small-scale environment surrounding a particular entity (cell, tissue, organism) and it has distinct physical/ chemical/ biological conditions compared to its broader surroundings. The conditions can influence behavior, survival and function of the organism)

where do microbes come form?

• Passage through the birth canal. 

• Exposure to other humans (and animals)

• Ingestion of food and fluids

• Inhalation of air-borne microbes

• Mostly of early life. Exposing microbes in early life builds up a diverse microbiome (this is good!)

What changes our microbiota?

• Everything

• Microbiome is not static 

• ex// diet, lifestyle, settings/ env, change in microbes

• Weather: temperature and moisture (in different parts of the country)

• Age: children have more varied microbiota

• Diet: metabolites = nutrients

• Hygiene habits

• Health status (& antibiotics). Taking antibiotics frequently is NOT good. The immune system is not as developed

1. Microbiota: term that refers to the accrual community of microorganisms living in a specific environment (human skin, gut, soil) they are the same bacterial species that colonize the same anatomical sites in all people

2. Static: the composition and function of microbial communities are dynamic and constantly changing in response to various internal and external factors

host- microbe interactions: (5)

1. Benefits to the microbes

2. Benefits to the host

3. Adaptation (intermicrobe conditions). Competition between microbes

4. Harmful aspects. Competition between microbes

5. Other potential consequences. Abundance of microbes

(1) host- microbe interactions: benefits to microbes

• Nutrient availability: host provides continuous source of nutrients (depending where in the body)

• Environmental stability: host temperature, solutes, etc are tightly regulated (in human health)

• Transportation: host carries and spreads microbes

(2) host- microbe interactions: benefits to host (3)

(1) Microbial antagonism: ways microbes prevent pathogen infection (competition & niches). This minimizes the host susceptibility to pathogens

• C diff establishes infection when people are on antibiotics for long periods of time

• stool is harvested from a healthy donor and dried out

• stool is transplanted into the intestines of the patient with C. Difficile infection

• The organisms from the donor sample restores a healthy gut microbiome in the patient

• Not very effective

(2) Nutritional synergism: host provides habitat and food/ produce vitamins and nutrients, microbes metabolize things we can’t (indigestible fibres)

• mutually beneficial relationship between gut microbiota and the human body where microbes produce essential vitamins and nutrients we cannot make ourselves, break down indigestible fibers into beneficial compounds, enhance absorption of minerals and other nutrients

• vitamin K2 produced my e. coli

(3) Immune stimulation: regulate and stimulate immune system

• The gut microbe actively communicates with the host immune system playing a crucial role in training immune cells to distinguish friend from foe, preventing excessive inflammation, enhancing pathogen defense. The process is called immune stimulation. Immune modulation. 

• This allows them to react to pathogens or non- pathogens accordingly

• Epithelial cells with receptors:

  • They have pathogen recognition receptors PRRs that trigger immune response. They are surrounded by mucus

  • Microbes will produce antimicrobial substances (peptides)

  • Body will start producing IGA antibodies, they neutralize pathogens if they enter your body

(3) host- microbe interactions: adaptation (intermicrobe conditions, competition between microbes)

• microbes adapting to host niches: pH, O2 levels, nutrient availability

(4) host- microbe interactions: harmful aspects. (competition between microbes)

Certain resident microbes can become pathogenic if conditions change. One type of bacterium outgrows the others it establishes infection

• Grow to high density

• Move to another location in the body (e.g. E. coli in intestine OK... UTI)

• Host becomes unhealthy

Opportunistic pathogens

1. Pathogenic: to microorganisms that can cause disease in a host by invading tissues, producing toxins, triggering harmful immune responses

2. Opportunistic pathogens: harmless resident microbes that turn pathogenic under specific conditions. Normally would not cause infection, but overgrowth can cause infection

(5) host- microbe interactions: other potential consequences, abundance of microbes

Microbes produce compounds that have local or global effects

Gut-brain axis:

• The things produce by microbes can affects brain cell development

• Parkinson's, MS, Alzheimer’s, depression, PTSD, anxiety

Growth & Development:

• Immunity & allergic disease

The microbiome has massive impacts on our health. Understanding these processes is helpful to maintain health and prevent disease. Microbiome profiling is necessary to figure out which taxa are present

1. Microbiome profiling: process of identifying and analyzing the microbial communities in a specific environment, the human gut, skin, soil to understand the composition, diversity and function

Microbiome profiling

• necessary to figure out which taxa are present

• process of identifying and analyzing the microbial communities in a specific environment, the human gut, skin, soil to understand the composition, diversity and function

• sequence a part of the DNA from every microbe in the community

  • DNA sequences tell which species present (or taxonomic groups present)

  • Amount of DNA from each species tells you the species abundance of the species. See who and what is there

Which part of the DNA is sequenced in microbiome profiling?

• Ideal: 16S rRNA, found in all life forms, sequences change without losing function, changes accumulate very slowly

• Bacterial groups have unique 16S rRNA sequences. When you sequence rRNA, we can identify the bacteria present and their relative abundance

• 16S rRNA: what makes ribosomes

microbial diversities (3)

1. richness

2. abundance

3. phylogenetic distance

(1) microbial diversities: richness

• number of unique species

• More species, higher richness, higher diversity

(2) microbial diversities: abundance

• prevalence of unique species (inverse of evenness) 

• High % of one species, high abundance, low evenness, lower diversity

• Yellow is more abundant than green species

• Opposite: evenness: same repetitive proportion of diff species, even microbial community

(3) microbial diversities: phylogenetic distance

• relatedness of species/ distance of diff species on phylogenetic tree

• Higher phylogenetic distance, more diversity

Define human microbiome.. What is it and where do you find it?

What factors affect the composition/diversity of your microbiome?

What are some pros and cons of human-microbiome interactions?

What is 16S rRNA and why is it used to study microbiome diversity?

What are some common ways to measure diversity?