Microbiota

What is the microbiota?

Community of microorganism that live in a specific environment

What is a microbiome?

Collective genomes of the microbiota/organisms in a particular environment

What does the Microbiome influence?

• Brain and mental health

• Immune system regulation

• Metabolism

• Protection against pathogens

• Development

• Nutrient synthesis

How do infants acquire the microbiota?

• Vaginal birth - colonised by bacteria in vaginal and gut - e.g. Lactobacillus and bifidobacterium

• C-section - skin associated as well as hospital microbes - e.g. Pseudomonas, Klebsiella, Staphylooccus

What does the microbiota of children and adults look like?

Stable and diverse, determined by diet

• Firmicutes

• Bacteroidetes

How is the microbiota studied

• 16s rRNA gene sequencing

• Shotgun metagenomics

• Metatranscriptomics

• Metabolomics

• Whole genome sequencing of isolated strains

• Culture-based methods

• GF animal models

What is the downside of Culture-based methods?

• Most gut-microbes are difficult to culture ~70-80%

When would you use shotgun metagenomics?

• To analyse/sequence DNA within a sample telling you about species within a community

• Detects viruses and fungi as well as bacteria

When would you do whole shotgun sequencing?

To study the whole genome of a single isolate that has been successfully cultured

• Useful on finding accurate strain resolution

• Study complete genomes

• Study functional genes

How does the microbiota influence BBB development?

SCFA travel to the brain and regulate expression of tight junction proteins like Claudin-5

What do GF mice show in their BBB and upon SCFA supplementation?

• Increased BBB permeability

• Restored BBB similar to SPF mice

How does the gut microbiota influence neurogenesis/ formation of new neurones and regeneration with age?

• Modulate neurotrophic factors and neurotransmitter levels

What neurotrophic factor does the gut microbiota modulate and how?

SCFAs can modulate brain-derived neurotrophic factor (BDNF)

What is the role of Brain derived neurotrophic factor?

• Neuronal survival

• Neuronal differentiation

• Neuronal circuits

What neurotransmitter biosynthesis is regulated by the gut microbiota?

Serotonin

What is the role of serotonin?

• Mood regulation

• Memory

• Sleep

• Digestion

How does the gut microbiota modulate serotonin biosynthesis?

• SCFA modulate the expression of Tryptophan 5-hydroxlase

How can the maternal microbiota influence foetal neurodevelopment?

1. PG can reach the foetal brain and stimulate TLR2 in microglia

2. This leads to expression of FOXG1 inducing neural proliferation

What disorders do individuals with Neurodevelopmental disorders show in their microbiota?

Less diverse microflora

• Missing or lower abundance of key: Bifidobacteria, Enterococcus and Lactobacillus

How can Bifidobacteria reduce stress and anxiety?

Enhance levels of serotonin precursor Tryptophan

• Acts of Hypothalamus-pituatry axis stress response

What probiotic supplementation saw improvement of what neurodevelopmental disorder?

• Saw higher Lactobacilli and Bifidiobacteria CFU and alleviated severity in autism syndrome

How does the gut microbiota influence immune development?

• Induction of Th17 cells

• Treg development

• Development of peyers patches, MLN, GALT

How does the microbiota influence the development of Th17 cells ?

Segmented filamentous bacteria

• Trigger epithelial cells to generate Serum amyloid A and IL-6

• This activates DCs to produce IL-6, IL-23 and TGF-beta

• This drives Th17 cell production

Importance of Th17 cells?

• Act against extracellular bacteria and fungi

What is the role of the microbiota in immunity

• Promotes IgA class switching

• Treg induction

• Antimicrobial peptides

• Viral pathogen clearance

What is the role of IgA

First line in mucosal defense within mucus layer

• Neutralises toxins and viruses

How does the Microbiota promote IgA production

• SCFAs bind to DC GPR43, promoting Retenoic Acid production

• RA promotes IgA class switching in B cells

How can the Microbiota promote viral clerance?

• Prime anti-viral/IFN responses ready for future infection

How does the microbiota prime antiviral responses and what viral infection was it useful against?

Single Clostridium bile acid-transforming bacteria

• Produce secondary bile acids

• sBAs act on TLR-7/MyD88, producing Type I IFN responses, inducing anti-viral state in DCs

• Led to reduced CHIKV permissibility in monocytes

How does the microbiota induce Tregs?

• SCFAs can cause epigenetic changes and enhance FoxP3 expression

• SCFAs can activate GPR43 which promotes e.g. Retenoic Acid production

• Bacteroides fragilis produces Polysaccharide A (PSA), which interacts with TLRs and induce cytokine environments promoting Treg development - e.g. IL-10 and TGF-beta

What key nutrients does the Microbiota produce?

• SCFAs

• Vitamin K

• Contribute to the availability of essential amino acids

• Neurotransmitter precursors

• Polyamines - e.g. Spermidine

Role of polyamines and examples?

e.g. Spermine, Spermidine

• Scavenge ROS

• Epithelial cell renewal

What is the importance of Vitamin K

• Bone health

• Blood clotting

What essential amino acids does the microbiota produce?

• Tryptophan

• Lysine

• Valine

What neurotransmitters does the gut microbiota produce?

GABA - Lactobacillus and Bifidobacterium

• Dopamine - Some Bacillus spp

• Norepinepherine - E. coli, Bacillus and Lactobacillus