Microbiome Overview Part 2 Flashcards by Tansy Stewart

Traditional View of Microbiome (4)

(1) Unavoidable expansion of microbial ecosystems in exposed body spaces
(2) Symbiotic host-microbe relationship
(3) Interface for immune recognition of microbial antigens
(4) Microbes confined by surfaces of host compartments

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Symbiotic relationship based on

Accessing and processing nutrients

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Confinement to host compartments

Can be disrupted and cause disease

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Evolving view of microbiome

There is highly regulated microbial/host interactions and different faucets

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Continuous and interchanging interactions between host and microbes and differences in…

Immunology, metabolism, neurology (behavior), co-evolution

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Number of species in GI microbiota per individual

> 160 (124 studies)

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Predominant Genera in GI microbiota

Firmicutes –> Bacteriodetes –> Actinobacteria –> Verrucomicrobiota

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Types of Firmicutes

Lactobacillus, mycoplasma, bacillus, clostridium…

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General of Firmicutes

> 250

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Genera of Bacteroidetes

~20

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Core mircobibiome

18 species shared in all participants in GI microbiome (huge variability)

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Normal bacterial colonisation populated through

Maternal vaginal/fecal flora and oral feeding (breast vs formumla)

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Age of complete adult colonization of gut microbiota

3 years

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Factors affecting gut microbiome (7)

Genetics + Birth Route + Geography + Hygiene + Diet/nutrition + Stress + Drugs

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Microbiome complexity and stability

Increase to adult and then decrease in elderly

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Microbiome complexity and diversity over time in healthy (3)

Protects against pathogens + Train and stimulate the IS + Supply nutrients, energy, vitamins, SCFAs

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Microbiome complexity and diversity over time due to perturbation (4)

Local and systemic inflammation + Oxidative stress + Increase in GNB and infection with opportunistic bacteria + altered metabolite production

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Perturbations led to

Infectious disease + metabolic disease + Inflammatory disorders

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Perturbations and IBD

Contributes to different stages of disease (maybe)

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Perturbations rapidly decrease

Microbiome complexity and stability

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Microbiome acquired from

Immediate environment after birth

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Steps to obtaining microbiome in infant

1) Obtain microbes from mother and environment with mode of delivery having impact
2) Microbial succession for 1-2 years
3) Microbiome becomes adult like in 1-2 years

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Caesarean section has microbes similar to

Mom’s skin

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Mom’s body habitats

Very different from each other

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Species of bacteria in baby over 1-2 years

Firmicutes mostly --> Actinobacteria --> Firmi and bacteriodetes but really all kinds

Microbiome changes with (6)

Age, puberty, pregnancy, diet, medical conditions and treatment, pets...

How the microbiome changes (4)

Kinds of microbes present, number of each type, relative amount of each microbe, active genes even if kind and number of microbe do not change

Active microbial genes usually change due to

Diet

Treatment that changes microbiome

Antibiotics

Human microbiome project goals

1) Reference set of sequences 2) Disease and microbiome changes 3) Develop technology for computational analysis 4) Establish a data analysis and coordinating center 5) Establish research repositories 6) Examine ethicals, legal, and social implications 7) Evaluate multiomic data

Develop reference set of sequences -->

Preliminary characterisation of human microbiome

Develop new technologies and tools for computational analysis

Need to analyze

Establish a data analysis and coordinating center

Analyze in similar way so you can compare

Establish research repository

Data available to different groups

Each body part has

Distinct microbial community

PCA plot

Shows how microbes are distinct in different body parts

Similar microbes are in the ...

Skin and Nasal

Comparison of microbiome in different parts of body

Very different microbiomes but similar metabolic pathways so different microbes rely on same metabolic capabilities

5 most abundant microbes in 16s RNA and metagenomic sequencing

Firumicutes, Bacteroidetes, Actinobacteria, protobacteria, Fusobacteria

Number of bacteria for each cm2 of skin

1 million

Number of species on skin or in deep layers

100-200

Non-infectious skin pathology due to

imbalances in normal ecosystem

Skin Pathology

Atopic dermatitis Psoriasis Rosacea Acne

P. acnes

Population structure different between healthy and acne cohorts

Acne prevalence

85% teens

Rosacea affects

3% worldwide

Immunocompromised and skin microbiomes

Altered with increased colonization of pathogenic bacteria and fungi

Novel approaches for skin

Therapies that restore microbiota instead of antibiotics

Animal models to study microbiomes association with disease

Mouse: Liver Cirrhosis, obesity, autism, stress, non-alcholic fatty liver disease, diabetes...

Mechanistic correlations of microbiome as whole with disease

Most at single species level and cannot yet tell what microbiome is causing what disease but can use info as biomarkers to detect disease

Gastric cancer microbiome

Toxin-producing strains pertubation of colonic epithelium --> risk of developing malignancies but could not find what caused disease just correlation studies

Gastric cancer microbiome value

Monitor microbiota, circulating metabolites, host biomarkers in healthy and diseased

In gastric cancer, microbe populations can be

Disease progression indicators based on 16s rRNA analysis

3 components that must interact for IBD

Environment, microbiota, genes

IBD pathogenesis

Inappropriate activation of GI immune system toward a gut microbiota in susceptible host under the influence of environmental factors

What moves the balance of pro vs anti-inflammatory bacteria in IBD?

Environment and genetics

Health vs IBD

Balanced vs imbalanced anti vs pro inflammatory bacteria

Noninvasive microbial ecology diagnostics

Looks at which phylum are more abundant per what disease

UC toward

Proteobacteria

CD toward

Actinobacteria

Healthy toward

Bacteriodetes or Firmicutes depending on person

Functional Bowel Disorder (FBD)

IBS, functional bloating, constipation, diarrhoea

FBD changes in microbiota

Abnormal fermentation of dietary substances --> excess stimulation of mucosal immune system through leaky gut --> low grade inflammation, visceral hypersensitivity, and effects gut motor responses

Immune stimulation through leaky gut...

Low grade inflammation, gut motor response changes, and visceral hypersensitivity

Decreased in IBS

Lactobacillus and Bifidobacterium

Compromised permeability causes

Antigen introduction

Microbiome plays role in

Immune development (HMP)

Factors that shift microbiota found through HMP

Sanitisation, antibiotics, immunisations

Microbiome Overview Part 2 Flashcards

(68 cards)