The human microbiome Flashcards
What is the content of the microbial ecosystem?
Humans = eukaryotes + bacteria + archaeabacteria + viruses + parasites
What type of interactions occur between microorganisms and humans?
Anything on the symbiosis spectrum
Relevance of the microbiome?
-Metabolism of xenobiotic
-Synthesis of essential vitamins and nutrients, metabolism of polysaccharides and modulate the immune system
-Change animal behaviour and mating preferences
-Makes you unique - 2 humans will have highly similar genomes, but tremedously varying microbiomes
What method, generally used, is unusable for the study of the microbiome?
Traditionally - culture-based methods but most bacterial cell are unculturable (appropriate nutrients, growth requirements, microbial interactions - need bacterial consortium)
What methods has replaced culture based methods for the microbiome?
16S rDNA-based sequencing methods (who is there)
depp genomic sequencing studies (metogenomics) (what do they do)
mRNA sequencing (metatranscriptomics) (what are they doing)
metabolomics (what are they doing
How do 16S rDNA gene analyses work?
Its a phylogenetic marker found in all species, that has both slow evolving and fast evolving regions
After PCR amplification, sequencing allows for the comparison with other members of the microbial communities
What is metagenomics? What’s it use?
Sequences all genomic DNA present in a sample
Human sequences can be removed with bioinformatic tools
Tells us what genes are present, and allows for inference of metabolic activity
(can also inform about community composition - same result as 16S rDNA sequencing, but with different intermediate info)
How do microbial communities differ in/on the body?
Overall diversity of bacteria + within the human microbiome?
They are site-specific due to their exposure to very different conditions
**clustered by site
>50 phyla, with human microbiome containing mostly 3-5 phyla
**microbial diversity explodes at a species/strain level
What causes body odor?
Metabolic by products of the skin bacteria - volatile fatty acids
How does the microbiome vary within the mouth?
Not a homogeneous system - diff parts hav diff conditions and thus different microbial communities
Teeth: predominant anaerobes
Non teeth: aerobes
*involved in tooth decay + linked to GI microbiota
Role of the microbiome within the urogenital tract?
-Production of lactic acid to maintain low pH (inhibition of other microorganism growth)
-Variance between individuals and with menstrual cycle
Properties of the penis microbiome?
-Penis and urethra have diff microbiomes
-Circumsion reduces anaerobic bacteria
-Sexual activity alters microbial diversity
Where is most of the human microbiome located?
70% is in the colon
Describe the composition of the gut microbiome?
-Mostly anaerobe, some facultative
-Mostly Bacteroides and firmicutes
-Many different species (~1000)
What can be used as a proxy for gut microbiome analysis?
Fecal samples
*note: not a perfect match
Describe the foetus microbiome?
Foetus are considered sterile - a study came out indicating the placenta has a unique microbiome: mostly disproven, there is a tiny microbiome, but if its detectable the pregnancy is generally unhealthy (at risk)
When do we aquire the microbiome?
Large amounts of microbes are aquired at birth (colonization varies with delivery mode)
How does the microbiome change with early human development? (timeline)
-Starts with facultative anaerobes and bifidobacteria
-After 6 months, obligate anaerobes predominate
-At 3 years you have your adult microbiota
How does the microbiome change with human development? (properties)
-high variance in first 3 years
-altered by type of milk environments exposure, pertubations (pets, antibiotics..)
-follows major life changes (pregnancy, illness, travel…)
How does the bacterial composition of the microbiome change with time?
Phyla will remain generally stable
species and strain are much more variable
What three major studies are used to get past correlation and actually establish causation in microbiome studies?
In vitro
Animal
Human
Advantages of mouse models?
Mammalian models with controlled conditions and interventions
Mice can be made to be sterile (no microbiota) - axenic
Mice are coprophagic - eat each others fecal mass - so populations will have a high level of shared bacterial species
What are gnotobiotic mice?
Mice where all microbes are known
Individual microbes or population can be reintroduced into germ free or antibiotic treated mice.
What is a holobiont?
A unit of biological organization composed of a host and its microbiota
Define the human microbiome
Collection of genes from microbes present on and within our body
Define the human microbiota
Collection of microbial cells present on and within our body
Effect of diet on gut microbiota?
Major driver of diversity
What does obesity put you at risk for?
Type 2 diabetes, cardiovascular disease, musculoskeletal disorder, inflammation, cancer
Economic effect of diabetes?
Huge economic burder (4.6 billion direct , 7.1 bill indirect in 2008)
Link between obesity and the gut microbiome?
Gut microbiome of obese individuals is distinct from that of lean individuals (however there are some confounding variables making it difficult to establish a clear correlation - diet, genetics…)
What is leptin?
hormone made by fat cells that regulate the amount of fat stored in the body (satiety hormone)
How were mouse models used in the study of obese microbiomes?
Comparison of leptin mutant mice (ob/ob) with WT lean mince - same diet
amplicon sequencing (16S rDNA)
-ob/ob: Higher firmicutes, lower bacteroids
(obisety didn’t always present with this gut microbiome, but a transferred microbiome with this composition always caused obesity)
Why does obesity occur? How was this determined in the mice experiment?
Shotgun sequencing of the gut microbiomes, with subsequent bioinformatic analysis of pathways demonstrated:
Genes harvesting energy from carbs higher in obese mice
Fecal matter calorimetry: less energy left in fecal matter in lean mice
How does the mice obesity experiment translate to humans? How was this determined
Microbiome colonization into mice from discordant twins (one obese one lean) caused one mouse to be lean, and the other obese (with same diet)
Relationship of diet to obesity?
Diet remains key: A lean microbiota cannot colonize well when mices are fed high fat, low fiber diets
What is the effect of antibiotics on the microbiota?
+specific results of performed experiment
Drastic reduction of gut microbiota diversity
Disruption of gut bacterial diversity (especially in early childhood)
Can promote weight gain
(7 day antibiotics, 24 month observation)
for 9 months: only one clindamycin strain detectable
After 24 months, gut microbiota diversity super low
What is C. difficile? Properties
Infection: antibiotic associated diarrhea
-2% of population are healthy carriers (infection found in low quantities in the microbiome)
-Naturally present in environment
-A healthy microbiota prevents colonization (and infection)
-Broad spectrum antibiotics are high risk factors
How do you treat C. difficile? How effective is it? Mortality?
1st line of treatment: discontinue antibiotic usage
metronidazole or vancomycin course (best if with probiotics)
25% of people are treatment resistant or have recurrent C. difficile
relapse is common (up to 10 times has been seen)
14,000 deaths in the US yearly
Last resort is FMT (fecal matter transfer)
What is FMT?
Result of study?
Infusion of feces from healthy donor - demonstrated in a randomized clinical trial to be highly effective
15/16 as opposed to 3-4/16
Study was stopped prematurely due to unethicality of only giving it to some people in the study given how good the results were
Cons in the use of FMT for the treatment of C. difficile?
-Total community transplant : how do you choose the right healthy host, what other pathogens or pathobionts might be transferred, would the microbiome then be transferred to the child, could it cause disease…
-Societal taboo
-Defined bacterial mixtures would be easier to regulate
What other disease are considered for use of FMT?
inflammatory bowel disease, autoimmune, metabolic syndrome, obesity, diabetes…
How do microorganisms in the gut affect the brain?
The production of short chain fatty acids (acetate, propionate, butyrate) occurs at the end of fermentation of dietary carbohydrates. Along with some neurotransmitters, they are considered to be bacterial metabolites and cross the BBB
What is the gut brain axis?
Bi-directional communication between the gut and the brain (bacterial metabolites, immune cells, cytokines)
What is an example of body wide microbial interactions?
Diseases having co-occuring pathologies
-IBD/IBS : lung function
-asthma : function gut microbiome changes
-oral microbiome changes : preterm birth and abortions
-rheumatoid arthritis : periodontal disease
-IBD : psoriasis
What are the 4 subsections of the microbiome?
Bacteriobiome
Mycobiome
Macrobiota
Virome
(all in the 10 to the power of 13-15 range, apart from macrobiota which is 0-10^4)
What is a probiotic?
Live microorganism which, when administered in adequate amounts confer a health benefit to the host
What is the issue with the use of probiotics in the manipulation of the microbiome?
-Inadeqaure studies
-Limited mechanistic understanding of effects
-Largely unregulated industry
-Publication of negative studies (not just positive studies)
-Need for standardization of the idea of “health benefit to the host”
-No adequate test to predict functionality of probiotics in the human body
-Lack of information (strain, dosage, duration…)
-Rare cases, but infection
-Transferably microbioal properties to other microorganisms within the microbiota
Interaction of probiotics with antibiotics? (mice and humans)
Comparison of probiotic usage with FMT usage
Mice with native gut microbiotas do not allow for probiotic colonization: probiotic colonization mildly enhance by antibiotics
In humans: site and person specific
Post antibiotics, probiotics delay microbiota reconstitution
FMT from the same person restores mucosal microbial diversity
Can the gut microbiome be manipulated by helminths?
Intestinal helminths possess immunomodulatory capacities and can alleviate bleeding in IBD (inflammatory bowel disease), and decreases the number of bacteroide species involved in intestinal inflammation
-can alleviate asthma symptoms
Three major assemblages of parasitic helminths?
Nematodes, cestodes and trematodes
Bacteriophage : bacteria
Typical and in humans
10 : 1 (typical)
Between 0.1 and 3 (much lower)
Phage community?
Effect of phages in the body?
immune response?
Form ‘phageome’ : unique, temporally stable communities (similar within households) - dynamic based on bacteria - viral interactions
**phages are viruses
Can cause stunting (globally, 22% of <5 year olds) - irreversible after the first 2-3 years
Can directly or indirectly modulate immune response
How do phages cause child stunting?
Healhty and stunted phages cange gut bacterial communities in an age specific manner
Stunted phages allow for proteobacteria to develop
Can be fixed (within 23 months) by microbiome manipulation
Phage population dynamics:
kid - adult
healthy - inflammed (gut)
More phages in kid
More bacteria in adult
More bacteria in healhty gut
More phages in inflammed gut
What do phages regulate?
Bacterial abundance, diversity, phenotype
