©FYNDLAY.
MCB4422 Exam 3 Study Guide.
Microbiome - Answers✔the full complement of microbes, their genes, and genomes in a
particular environment
microbiota - Answers✔the microorganisms that live in an established environment
commensalism - Answers✔one organism benefits and the other in unaffected (mycobacteria in
the ear)
mutualism - Answers✔both organisms benefit (e. Coli in colon synthesizes vitamin K)
parasitism - Answers✔one organism benefits at the expense of the other (disease-causing
bacteria)
define the constituents of the microbiota** - Answers✔Microorganisms begin colonization in
and on the surface of the body soon after birth
Normal microbiota: microorganisms that establish permanent colonies inside or on the body
without producing disease
Staphylococcus on epidermis and mucous membranes
Escherichia coli in colon
Transient microbiota: are microbes that are present for various periods and then disappear
16S rRNA sequencing - Answers✔16S rRNA gene present in all bacteria and archaea
Gene contains highly conserved and more viable regions
Amplify 16S rRNA genes using primers directed at conserved regions but flanking variable
regions
Align gene sequences, resolve phylogenetic relationships at different depths
Most 16S rRNA sequences come from previously undescribed microbes
Limitations of 16S rRNA - Answers✔Many genomes have multiple and nearly identical copies
of 16S rRNA operons
Not always possible to accurately normalize 16S data
1
, ©FYNDLAY.
Cannot always obtain accurate estimates of diversity and abundance
Strain-level resolution of the microbial community is not always possible
Strains of the same species can have different phenotypes and functional capabilities
Not possible to accurately infer or reconstruct functional and metabolic capabilities
Conservation of 16S gene sequence can mask sequence diversity in rest of the genome
shotgun metagenomic approach - Answers✔sequence community dna, compare sequences,
identify them
other methods for studying microbial communities - Answers✔metabolomics, imaging,
phylogenetic diversity and action, reference genomes, metatranscriptomics
Metagenomic sequencing - Answers✔functional predictions based on gene content
metatranscriptomic sequencing - Answers✔functional predictions based on gene expression
metagenomics - Answers✔taxonomic composition, accurate strain level resolution and
abundance, functional composition and metabolic potential
roles of microbiota in host - Answers✔Seal body spaces
Mitigate intestinal pathogens
Maintain tissue homeostasis
Facilitate fermentation of dietary fiber (inulin, pectin)
Critical energy yield
immune maturation/immune balance
Metabolic end products and therapeutic drug processing
Signaling among cells and organ systems
Butyrate: energy for gut epithelial cells
Acetate and propionate: lipogenesis and gluconeogenesis
factors that modify the microbiota - Answers✔Our microbiome changes:
As we mature and age
With puberty or pregnancy
As our diet changes
Medical conditions and treatments
Pets in the home
2
MCB4422 Exam 3 Study Guide.
Microbiome - Answers✔the full complement of microbes, their genes, and genomes in a
particular environment
microbiota - Answers✔the microorganisms that live in an established environment
commensalism - Answers✔one organism benefits and the other in unaffected (mycobacteria in
the ear)
mutualism - Answers✔both organisms benefit (e. Coli in colon synthesizes vitamin K)
parasitism - Answers✔one organism benefits at the expense of the other (disease-causing
bacteria)
define the constituents of the microbiota** - Answers✔Microorganisms begin colonization in
and on the surface of the body soon after birth
Normal microbiota: microorganisms that establish permanent colonies inside or on the body
without producing disease
Staphylococcus on epidermis and mucous membranes
Escherichia coli in colon
Transient microbiota: are microbes that are present for various periods and then disappear
16S rRNA sequencing - Answers✔16S rRNA gene present in all bacteria and archaea
Gene contains highly conserved and more viable regions
Amplify 16S rRNA genes using primers directed at conserved regions but flanking variable
regions
Align gene sequences, resolve phylogenetic relationships at different depths
Most 16S rRNA sequences come from previously undescribed microbes
Limitations of 16S rRNA - Answers✔Many genomes have multiple and nearly identical copies
of 16S rRNA operons
Not always possible to accurately normalize 16S data
1
, ©FYNDLAY.
Cannot always obtain accurate estimates of diversity and abundance
Strain-level resolution of the microbial community is not always possible
Strains of the same species can have different phenotypes and functional capabilities
Not possible to accurately infer or reconstruct functional and metabolic capabilities
Conservation of 16S gene sequence can mask sequence diversity in rest of the genome
shotgun metagenomic approach - Answers✔sequence community dna, compare sequences,
identify them
other methods for studying microbial communities - Answers✔metabolomics, imaging,
phylogenetic diversity and action, reference genomes, metatranscriptomics
Metagenomic sequencing - Answers✔functional predictions based on gene content
metatranscriptomic sequencing - Answers✔functional predictions based on gene expression
metagenomics - Answers✔taxonomic composition, accurate strain level resolution and
abundance, functional composition and metabolic potential
roles of microbiota in host - Answers✔Seal body spaces
Mitigate intestinal pathogens
Maintain tissue homeostasis
Facilitate fermentation of dietary fiber (inulin, pectin)
Critical energy yield
immune maturation/immune balance
Metabolic end products and therapeutic drug processing
Signaling among cells and organ systems
Butyrate: energy for gut epithelial cells
Acetate and propionate: lipogenesis and gluconeogenesis
factors that modify the microbiota - Answers✔Our microbiome changes:
As we mature and age
With puberty or pregnancy
As our diet changes
Medical conditions and treatments
Pets in the home
2
