Lecture 16: Microbiota Guest Lecture

Microbiota

Community of microorganisms (includes bacteria, viruses, fungi)

• Varies between body sites

• Today we are focusing on the gut (colon) microbiota

Microbiota development

Exposed to microbes from birth

• Vaginal microbes / skin microbes (C-section) →

• Rapid increases in complexity

• Community develops with facultative microbes

• Transitions to anaerobes → after they use up the oxygen

The Microbiota in the Adult colon

• Dense colonization

• Varies from person to person

  • More in composition than function

• Anaerobic (during healthy state)

• Dominated by Firmicutes (Bacillota) and Bacteroidetes (Bacteroidota) phyla;

• small numbers of Proteobacteria (Pseudomonadota), Actinobacteria (Actinomycetota) and others

Beneficial functions

• Digestion of complex carbohydrates in anaerobic fermentation à short-chain fatty acids (SCFA)

• Produce diverse metabolites that influence host locally (gut) and systemically

  • Great Chemists/Biochemists!

    • Biosynthetic gene clusters

    • Host compounds; mucus, bile acids

    • Xenobiotics

    • Microbial products

• Provide colonization resistance

An Ancient Connection between microbes and the immune system

• immune system evolved in presence of microbes

• used to think the microbiota was largely ignored – the immune system was only on lookout for pathogens

• Now: recognize that the microbiota trigger a response

• The catch → response occurs without inducing overt inflammation → homeostatic immunity

• Relationship stressed by rapid changes (on an evolutionary scale) in microbiota

  • Increased autoimmune, inflammatory disorders

When you are born, is the immune system fully developed?

no

• proteobacteria → use oxygen

Window of Opportunity

• Adult like stability in gut microbiota and immune system occurs by 2-3 years

• window of opportunity refers to privileged period of development where influences of the microbiota on the immune system are durable

• After birth; immune system goes through a developmental trajectory that balances tolerance of new antigens and ability to respond to infections

Key factors affecting this dynamic system

• Route of delivery → helps determine the starting point for microbiota

• Antibiotics

• Environmental exposure to different microbes & antigens

• Feeding: Breastmilk or formula

Development Crosstalk Example 1: An Early Start

• A mother’s microbiota influences their offspring's immune system before birth

• Small metabolites (SCFA) reach the fetus

• Experiments using transient colonization of germfree mice show alterations of innate lymphoid cell populations in pups

  • immune cells of the developing fetus is affected by the mothers microbes

Development Crosstalk Example 2: LPS & Type 1 Diabetes

• finland has more type 1 diabetes than Russia (5-6x more)

• theres is a difference in HMO utilizing bacteria between the populations 

• Finland → higher bacteroides while other have e coli 

• bacteroids and e coli are both gram negative → have LPS which causes differential activation of ———- by the macrobiotic

  

Example 2: The Microbiota and T Cells

• The microbiota controls the differentiation of T cells

  • Specific microbes: SFB Segmented filamentous bacteria

  • Microbial Metabolites:

    • Butyrate, or secondary bile acids

study with the microbiota and T cells?

• Germfree mice have low numbers of TH17 cells

• Mice from different vendors had different numbers of TH17 cells

• Compare microbiota between vendors:

  • Jackson mice lack SFB!

• Mono-colonizing mice rescues TH17

• Induces a major shift in immune system

Bile acids: The Microbiota and T Cells

We secrete primary bile acids (CA, CDCA)

• Helps with digestion

• The microbiota converts these into secondary bile acids

• DCA, LCA

• That used to be the end… but now we are realizing there are many more modifications!

New modifications are being discovered

• Modified bile acids alter T cell differentiation

• Bile acid metabolism is another axis of cross talk between immune system and microbiota

Bile acids and aging: The Microbiota and T Cells

Some secondary bile acids are further

modified

• These modified bile acids alter T cell

differentiation

• Bile acid metabolism is another axis of

cross talk between immune system and

microbiota

The Microbiota and Innate Immunity

• NOD1 and NOD2 detect peptidoglycan

• Activate NF-kB

• Respond to peptidoglycan released microbiota

• Is this important?

• Mutations of NOD2 à strongest risk factor for Crohn’s disease

• Overall model: microbiota releases PG; immunomodulatory function

• Who? →

  

Dysbiosis

Disrupted communities have altered interactions with the immune system.

Changes in microbiota:immune interactions have been associated with many diseases:

Crohn’s and Ulcerative Colitis

Colorectal Cancer

many extra-intestinal conditions.

Chemotherapy/radiation

Trying to treat cancer by

targeting the tumor

Cancer immunotherapy

Broad range of approaches to

manipulate the immune

system to treat cancer

A war on cancer

Paul Ehrlich 1900s: We are constantl generating cancerous cells

• They are being eliminated by our immune system

• Recognition of cancer neo-antigens by T cells

• Altered expression of cell surface markers à killing by NK cells

• Our immune system effectively wages a constant war on cancer!

• In cancer immunotherapy, we try to harness and accelerate this function

• Much focus devoted to T cells

T cell basics

TCR recognizes antigen in the context of MHC

Class II (CD4) MHC Class I (CD8)

• But need co-stimulation

• CD28 and related receptors

• Potent co stimulatory molecules

• Recognize CD80/86 (B7-1/-2) Provided by APC

• After T cell activation: Inhibitory receptors are

also induced

Checkpoint

molecules

CTLA4: T. lymphocyte assoc.

protein 4

• PD1: programmed death 1

• CTLA4/PD1: Most potent T cell

immune checkpoints

• Prevent hyperactivation

What if you cut the T Cell’s brake lines?

1996 Allison lab

Inject mice with colon carcinoma cells. Inject Anti-CD28, Anti-CTLA-4 or control Antibodies

Combination immunotherapy

Previously, about 10% survival at 24 months

But not everybody responds to the checkpoint blockade. How can you ID responders and Non-responders?

Is dysbiosis during disease or antibiotic

use associated with lack of PD-1 blockade

response?

The microbiota has been implicated in response to chemotherapies

1. Disruption with antibiotics à less

response

2. Survival and response to cancer

immunotherapy is associated with

differences in the microbiome

Are these microbes causative?

Fecal microbiota transplantation (FMT)

Transfer of complex, incompletely defined community of microorganisms

• Transfer from a healthy donor

• Screening for pathogens is critical

• Goal is the rapid re-establishment of community

• Actively investigated for a range of conditions;

• C. difficile

• Multidrug resistant infection Enterobacteriaceae

• Can be as high as 90% effective for treating recurrent C. difficile infections

Concerns with FMT

Classes of Microbiome-directed therapeutics

Supplementation of microbiota-target substrates

such as specific dietary fibers to promote a desired

compositional change in the microbiota, or

production of a desired metabolite

• Transfer of a group of isolates, selected or designed

to promote specific microbiota functions

• Transfer of bacteria that colonize the targeted site

and are engineered to have a desired function or

deliver a desired product/metabolite

• Direct supplementation with beneficial proteins or

metabolites (i.e SCFA)

Microbiome-targeted therapeutics

There is lots of excitement in developing microbiome-targeted therapeutics

• Two new first in class live biotherapeutics were FDA approved in 2023

• There is lots of work yet to do in developing microbiome-based therapeutics

• As we learn more about the interaction with the immune system, new opportunities