Microbiome Overview Part 2 Flashcards
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
Symbiotic relationship based on
Accessing and processing nutrients
Confinement to host compartments
Can be disrupted and cause disease
Evolving view of microbiome
There is highly regulated microbial/host interactions and different faucets
Continuous and interchanging interactions between host and microbes and differences in…
Immunology, metabolism, neurology (behavior), co-evolution
Number of species in GI microbiota per individual
> 160 (124 studies)
Predominant Genera in GI microbiota
Firmicutes –> Bacteriodetes –> Actinobacteria –> Verrucomicrobiota
Types of Firmicutes
Lactobacillus, mycoplasma, bacillus, clostridium…
General of Firmicutes
> 250
Genera of Bacteroidetes
~20
Core mircobibiome
18 species shared in all participants in GI microbiome (huge variability)
Normal bacterial colonisation populated through
Maternal vaginal/fecal flora and oral feeding (breast vs formumla)
Age of complete adult colonization of gut microbiota
3 years
Factors affecting gut microbiome (7)
Genetics + Birth Route + Geography + Hygiene + Diet/nutrition + Stress + Drugs
Microbiome complexity and stability
Increase to adult and then decrease in elderly
Microbiome complexity and diversity over time in healthy (3)
Protects against pathogens + Train and stimulate the IS + Supply nutrients, energy, vitamins, SCFAs
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
Perturbations led to
Infectious disease + metabolic disease + Inflammatory disorders
Perturbations and IBD
Contributes to different stages of disease (maybe)
Perturbations rapidly decrease
Microbiome complexity and stability
Microbiome acquired from
Immediate environment after birth
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
Caesarean section has microbes similar to
Mom’s skin
Mom’s body habitats
Very different from each other
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
