Module 4: Gut Bacteria Flashcards
3 core function of a healthy microbiome
- breakdown of dietary fiberes
- production of short chain fatty acids (propionate, acetate, butyrate)
- production of vitamins and other co-factors
2 ways to study the gut microbiome
- Traditional culturing
- bacteria grown in petri dish
-away from communities - Classification using SSU rRNA
-SSU rRNA reads mRNA, determines evolutionary relationdship s
Traditional culturing limitations/challenges
-O2 rich environments
-growing individual bacteria apart from their communities
SSU rRNA approach limitations/challenges
- Analysis done w fecal famples-microbes that reside in other regions of gut can be missed (eg. small intestine)
2.Comparisons made w “healthy” gut
3.Identification vs function
-can tell what microbes are present, no info on what they do
2 ways to define healthy gut
1.stability
- resist change in face of stress
- return to equilibrium following stress-induced perturbation
2. Diversity
-range of species with a range of functions
Metagenomics
Application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environment
-bypasses need for isolation and lab cultivation
2 branches of metagenomics
- Sequence-based
- Determine what genes are
2.Function-based
- Determine what genes do
Sequence-based metagenomics
-sequence DNA to create a “catalogue of genes” present
-investigate genetic potential to predict functions
Function based metagenomics
-discoever new functions
-work backwards to figure out genes underlying functions
Upside & downside of function-based metagenomis
Upside: discover new biological advances
Downside: laborious and time consuming
Establishing the gut microbiome –> birth - first few years) aerobic/anaerobic
-Fetile intesine is sterile
-initial O2 abundance in newborn gut influences first colonizers
(gut environ favours aerobic bacteria)
-As they grow/expand O2 consumed
(gut environ now favours anaerobic)
-In a few years: anaerobic >aerobic
3 factors that have a significant impact on infant gut bacteria development
- Mode of delivery
- Antibiodics
- Diet
Mode of delivery affect on infant gut bacteria
Vaginal: colonized with vaginal and distal gut bacteria of mom
C-section: colonized by skin bacteria of the mom
Antibiotics affect on infant gut bacteria
Alters microbial diversity and number
Newborn diet affect on infant gut bacteria (breast fed vs formula)
Breast milk: bacteria and HMO - promote growth of specific microbial communities
Formula feeding + probiotic use can show similar microbial community to breast fed
Example of HMO on microbial community
encourage growth of Bifidobacterium
-inhibit growth of pathogenic organisms, maintain mucosal barrier function, regulate inflammatory respoonses
Core gut microbiome
Basic functions shared by bacteria from all people
-basic cell functions
-energy harvesting (sugars to SCFA)
-degrades xenobiotics (foreign substancess)
-vitamin production
Short-chain fatty acids and what they do
Acetate C2:0 - influence cholesterol and fatty acid production
Propionate C3:0 - used by liver for gluconeogenesis
Butyrate C4:0 - used for energy for intestinal enterocytes
Gut bacteria and obesity relation
Obesity = less diversity in gut bacteria
When in life is gut bacteria more stable?
Adulthood
-decrease in infancy and old age
When is gut bacteria the most diverse
childhood - late senior
Probiotic
Live microorganisms that when administered in adequate amounts confer a health benefit on the host
Prebiotic
A substrate that is selectively utilized by host microorganisms conferring a health benefit
Synbiotic
A mixture, comprimising live microorganisms and substrate(s) selectively utilized by host microorganisms, that confers a health benefit on the host
Does the presence of gut bacteria influence mouse body weight?
Gut bacteria presence associated with higher body fat and larger fat pads
Gut bacteria and plasma markers of metabolism
Gut bacteria associated w higher fasting leptin, insulin and glucose levels in blood
Gut bacteria and hepatic production of TAGs
Gut bacteria associated w more liver triglycerides and greater expression of hepatic genes (involved in de novo lipogensis)
Gut bacteria and adipocyte lipid storage
-LPL hydrolyzes blood TAG -allows for fatty acid takeup into adipocyte
-LPL inhibited by FIAF
-Gut bacteria suppress FIAF production
-Higher LPL = higher body weight (increased fat storage)
Is obesity associated w changes in the gut microbiota in mice?
Obese mice showed:
-reduction in bacteriodetes
-increase in fermicutes
How do firmicutes efficiently extract energy from food
-rich in glycoside hydrolases (digest dietary starch)
-enriched with proteins that impoart glycoside hydrolases, metabolize them and generate SCFA
Are obese or lean mice more efficient at extracting energy from food?
Obsese mice
-less energy remaining in feces relative to lean mice
Can gut microbiota be remodelled by fecal transplants?
-obese patients received transplant from lean healthy donor, microbiome shifted to that of lean donor
-increased microbial diversity
-bile acids reduced
Do gut microbiota influence diet-induced obesity
-Germ free mice resistant to diet-induced obesity
Germ free vs conventional mice TAG
Germ free mice have higher levels of blood TAG
Relationship between gut bacteria and fat oxidation in liver and muscle
Fat oxidation reduced in animals w gut bacteria by reducing AMPK signalling
AMPK activation promotes (1)
Fat oxidation
FIAF
LPL inhibitor
LPL
encourage TAG uptake into adipose tissue
Glycoside hydrolases
Enzymes needed for digestion of complex plant polysaccharides
-human genome poor
-microbial genome rich(bacteria efficient at breaking down to produce SCFA)
SCFA - what pathway do they activate
-signalling molecules
-activate GPR41 pathwas
GPR41-/- mice
-energy content in feces higher
-more SCFA in cecum and feces
-weakens energy absorption
GPR41 and body weight relationship
GPR41-/- -colonized with gut bacteria weight less
GPR41 +/+ - weigh more
Can dietary habits (animal vs. plant based) shape human gut bacteria?
Animal: rapidly changed bacterial community
Plant: did not
Mango study 280g/day on plasma metabolic markers and gut microbiome
-3.5% reduction in SBP, 10.5% reduction in 2hr pl glucose
-Increased abundance of specific species, enhanced gut microbial diversity
Diet-induced or genetic obesity is characterized by(3)
-low-level chronic inflammation
-increased expression/secretion of cytokines ans chemokines (TNF-a, IL-6, etc)
*cytokines promote crosstalk between tissues = insulin resistance
What does LPS impact
Gut permeability
(High LPS = high gut perm)
LPS production/transportation
-Produced by death of gram-negative bacteria (bacteroidetes)
-Transported out of intestine and through body bound to LPS-binding proteins
What does LPS interact with/what does it do
Interacts with receptor CD14 on immune cells, increases production of pro-inflammatory cytokines
HFD and LPS
HFD increases blood LPS levels
–> higher body weight & fat pads, higher bl glucose and insulin, whole body insulin resistance
–> increased inflammatory markers
CD14-/-
No change in inflammatory markers, no change in body weight, no change in blood glucose or liver fat
