5 - Microbiome in ID Flashcards
Define:
The combined genetic material of the microorganisms in a particular environment
MICROBIOME
Define:
A condition in which all the forms of life present within an organism can be accounted for.
Typically ________ organisms are GERM FREE
GNOTOBIOSIS
Define:
Living with, on, or in another
without injury to either
COMMENSAL
Define:
Specialized plant fiber that beneficially nourishes the GOOD bacteria
that is already in the Large bowel or Colon
PRE-BIOTIC
FOOD FOR BACTERIA
Define:
- *Introduction of a fecal suspension** derived from a
- *healthy doner –> GI tract of a DISEASED individual**
FMT
Fecal Microbiota Transplantation
List major components of the microbiome.
Include:
- Prokaryotes (Bacteria)**+**Viruses (Phage*)**
- *Eukaryotes** = Yeast / Protozoa / Helminth
Microbial DIversity
Diversity between BOTH Body Sites & Individuals
- *GUT MICROBIOTA_ = _NOT as Diverse**
- *ProteoBacteria** / ActinoBacteria / Firmicutes / Bacteriodetes
FUNCTIONAL REDUNDENCY
microbiota that yield SIMILAR proteins/metabolite profiles
Gene Diversity
- *Bacteria** = 8-Million genes
- *99% are beneficial** // 1% pathogenic
Fungi = 500k genes
Archaea = 80k genes
Human = 22k genes
List the major functions of the microbiome critical for human health.
HOST-MICROBIAL MUTUALISM
Production of Beneficial METABOLITES
Short Chain Fatty Acids = Acetate / Propionate / Butyrate
Secondary Bile Acids / Neurotransmitters
Choline-Derived metabolites
Vitamin Synthesis
RESISTANCE against invading pathogens
Maturation of MUCOSAL IMMUNE SYSTEM & Cells
Know the major factors that cause dysbiosis in humans.
MEDICATIONS
Prescription medication effects the microbiome diversity in large human cohorts
Even those that DONT directly effect the GUT
STATINS / ANTIDEPRESSANTS / METFORMIN
Antibiotics w/ MAJOR alterations in Microbiome Composition
B-Lactam / Fluoroquinolonges / Tigecycline / Clinda
Favorable perturbation = Rifaximin
Know the major factors that cause dysbiosis in humans.
Disease
↑Th1 ↑Th2 ↑Th17
Health
↑Treg cells
Host Genetics
mutations in NOD2 / IL23R / ATG16L / IGRM
LIFESTYLE
Diet / Stress
Early Colonization
Birth in hospitals –> exposure ot microbes
Medical Practices
VACCINATIONS / Antibiotics
Know the rational for fecal microbiota transplant (FMT).
C.DIFF & MICROBIOTA
↓Microbial Diversity (w/ AB use)
= Associated with Severe & recurrent C.DIFF INFECTION
Modifiable Risk Factors:
BROAD SPECTRUM AB’s & PPI’s
RECURRENT CDI
due to the regrowth of vegetative bacteria from SPORES that are resistant to antibiotics
Occurs within 1-2 weeks of completing treatment
Risk Factors for Recurrent CDI:
Age / AB’s / PPI / Renal insufficiency
Know the rational for fecal microbiota transplant (FMT).
C.DIFF
RE-INTRODUCE a complete & stable community
of GUT MICROBIAL COMMUNITIES
in order to
Repair or Replace
Disrupted Native Microbiota
Methods:
Nasoduodenal Tube / Colonoscopy / Rectal Enema
Know the rational for fecal microbiota transplant (FMT).
REDUCE ANTIMICROBIAL RESISTANCE GENES
AB’s in Agriculture & healthcare
has led to a dramatic INCREASE in
PREVALENCE & INCIDENCEof
ANTIBIOTIC RESISTANT BACTERIA = RESISTOME
List the major metabolites of probiotic species.
BIFIDOBACTERIUM
Found in Human & Animal Intestines & Vaginas
- *Strict Anaerobe**
- does NOT like OXYGEN*
ACETIC ACID** + **LACTIC ACID
lactic acids help control pH
+
SECONDARY BILE ACIDS
List the major metabolites of probiotic species.
LACTOBACILLUS
In nature, milk & dairy products, human & animal intestines & vaginas
Fermented foods
Facultative Anaerobe
LACTIC ACIDS
SECONDARY BILE ACIDS
Know the difference between
probiotics and prebiotics.
Probiotics:
Microorganisms that have HEALTH BENEFITS when consumed
THE SEEDS
PREbiotics
Non-Living / Non-digestable carbohydrates
that stimulate the healthy metabolism of gut microbiota
THE FOOD FOR THE PROBIOTICS / FETILIZER
FDA REGULATORY STATUS for
PROBIOTICS
LBP = Live BioTherapeutic Products
FDA’s Center for FOOD SAFETY & APPLIED NUTRITION
oversees the probiotic supplement industry:
•Dietary supplements may make structure/function, nutrient content or approved health claims on their labels or in marketing but not disease claims, i.e., that they can treat, mitigate, cure or prevent disease
FDA REGULATORY STATUS for FMT
Human Stool = Biological Agent
- *RCDI**
- *Recurrent C.Diff Infection**
- *does NOT require IND, but is strongly encouraged**
IND required for ANY OTHER INDICATION than RCDI
Discuss why there is so much conflicting evidence regarding the use of probiotics for antibiotic associated diarrhea.
Research shows that individuals respond very differently to the same probiotic depending on their diet, genetics, microbiome and other aspects of health
GONE BOTH WAYS
but GENERALLY SAFE
Types of Probiotics
Sources = Yogurt & Supplements
LACTIC ACID BACTERIA
LactoBacillus
BifidoBacterium
- *NON-LACTIC ACID BACTERIA**
- *Bacillus**
NON-PATHOGENIC YEAST
SaccharoMyces Boulardii
Types of PRE-BIOTICS
•Non-living, non-digestible carbohydrates that stimulate the healthy metabolism of gut microbiota
- Resists metabolism by mammalian enzymes and absorption in upper GI
- Is fermented by intestinal bacteria
- Selectively stimulates growth or activity of intestinal bacteria associated with health.
- *INULIN**
- *FructoOligoSaccharides**
Resistant Starch
Gums
Dosage & Use of
PROBIOTICS
Typical dose between 6-9 billion CFUs
Post antibiotic dose 10-15 billion CFUs
Moderately healthy GI tract 1 billion CFUs
Timing = WITH or Directly AFTER a Meal
ADR:
Gas / Bloating / Ab tenderness or Pain
