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
