izzy's concept map by Izzy Chiang

start your journey here! the microbiome

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the microorganisms inside us

the self or the host

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brain

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immune system

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gut brain axis

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network of connections through multiple biological systems allowing for bidirectional communication between gut microbiome and brain

chemical signalling

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such as neurotransmitters in the blood

neuronal pathways

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such as through the vagus nerve which is part of the enteric nervous system. afferent fibres carry signals from gut to brain, and efferent fibres carry signals from gut to brain

metabolism

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alpha diversity

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the number or relative abundance of taxa within a sample.

beta diversity

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differences in the number or abundance and phylogenetic relationships of taxa between samples

human development

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in utero colonisation hypothesis

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suggests that the womb is not sterile, and microbial colonisation begins before birth

sterile womb hypothesis

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suggests that the womb is sterile, and babies are born without any microbiome

"window of oppourtunity"

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the time between late fetal period to early infancy, which greatly shapes the baby's immune system through sufficient and proper environmental exposure for microbial colonisaiton

short chain fatty acids (SCFAs for short)

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metabolite produced by gut microbiome

butyrate

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a SCFA that regulates glucose metabolism, and prevents against inflammation, obesity, diabetes, cancer

16s rRNA sequencing

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a sequencing method used to identify and compare bacteria present within a given sample. this works because the 16S rRNA gene found in the prokaryotic ribosome can serve as a molecular marker for bacterial identification. the gene exhibits both conserved regions that are essential for ribosomal function and variable regions that are unique to different bacterial taxa.

differential abundance testing

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identifies the specific taxa that are different between the groups of interest to develop hypotheses about up-regulated and down-regulated taxa

metabolomics

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a comprehensive measurement of all metabolites and proteins produced within a sample, done through mass spectrometry

shotgun or metagenomic sequencing

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sequences short fragments from all types of DNA which allows this method to provide data about not just bacteria, but also the archaea, protozoa, fungi, and viruses present in the sample

autism spectrum disorder

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group of different neurodevelopmental disorders also linked to gastrointestinal dysfunction, including increased susceptibility to intestinal inflammation and altered gut permeability

fecal bacteria transplant

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antibiotics course to remove of existing gut bacteria, followed by transplant to create new gut microbiome

blood brain barrier (BBB for short)

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selective semi-permeable membrane between the blood and the interstitium of the brain, allows for regulation of molecule and ion movement between brain and the circulatory system.

tight junctions protiens

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creates a tight and selective barrier, ensuring limited and selective permeability

alzheimer's disease

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a progressive neurological disease, causes loss of memory

primary cancerous tumor

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uncontrollable and abnormal growth of cells that invades and destroys ordinary cell tissues

clonal selection

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continuous selection for advantageous mutations that contribute to rapid cancerous growth

oncomicrobe

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microorganism with cancer causing effects such as dna damage, altered Wnt/B-catenin signalling, pro-inflammatory programs

tumor microenvironment (TME for short)

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includes cancer cells, stromal tissue, and extracellular matrix

intratumoral microbe (ITM for short)

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present inside tumor, causing actin cytoskeleton reorganization which allows cancer cells to be more pliable and therefore more resistant to mechanical stresses

tumor resident microbe (TMR for short)

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stabilises the tumor

butyrate paradox

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has opposing affects on normal and cancerous colon cells: causes proliferation and growth for normal cells and apoptosis for cancerous cells

ischemic stroke

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can have drastically different outcomes based on alpha and beta diversity metrics for stroke patient

gut composition

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signficantly different for good and bad stroke outcomes, including microbiome composition, reduced motility, bacterial translocation

top-down pathways

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HPA axis, vagus nerve which directly innervates the intestinal tract, damage associated molecular patterns

bottom up pathways

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through gut-derived immune cells and microbial metabolites like SCFAs or Trp

probiotic therapy

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foods or supplements that contain live microorganisms to increase numbers of benefical bacteria in body

metastastis cancerous tumor

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secondary tumor far away from the original primary tumor

circulating cancer cells

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can be found in blood stream

intestinal gluconeogenesis

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production of glucose from non-carbohydrate compounds, this helps to regulate blood sugar and promote satiety

gut hormones

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such as GLP-1 and PYY, promoting insulin secretion, reducing digestion to increase feeling of satiety

obesity and type II diabetes

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methylamines

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atherosclerosis

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buildup of cholesterol and plaques in arteries

thrombosis

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excessive clot formation which can lead to heart disease or strokes

skin barrier

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is maintained by microbes which produce metabolites that maintain barrier function, protect against pathogens, and regulate the immune system

stapholococcus aureus

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invades broken skin and triggers virulence factors that cause inflammation and skin damage

atopic dermatitis

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drug biotransformation

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microbial enzymes

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can convert prodrugs to active drugs, or active drugs to inactive drugs

proton pump inhibitors

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can cause gut dysbiosis due to changes in stomach pH

metformin

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reduces bile salt formation

levodopa

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can be metabolised to dopamine by gut microbiome