The Human Microbiome (Lec. 20)
Monday, November 23, 2020 9:19 PM
CONTAGION
• Postulates of microbial ecology: (1) microbes are found in every earth environment, and • Science advisor: Ian Lipkin
(2) every molecule can be used by a microbe. • Origin: Meat market in Asia(Hong Kong). Know it was spread thru livestock.
• Years of co-evolution has evolved bacteria and phage species. • Virus in movie is based off of MEV-1.
• Leeuwenhoek created the first microscope and observed microbes w/in his own dental • Quicker means "less chance to spread," as in it kills its victims before the virus can find another
plaque(1st uncultured view of the human microbiome was oral). host.
• Before, microbes were isolated and cultured in single strains of bacteria. Now, we know to • 103 cases in 5 days, mainly children. Mortality rate is most likely low 20s.
grow microbes together to see how communities interact and cycle nutrients. • Believe its respiratory illness, and fomite (surface) spread.
• In 1970s, restriction enzymes were used to characterize microbiomes; now we sequence • R0: R-naught. Reproductive rate of virus. Decides whether an illness is an epidemic. Ex. Polio
microbial genomes to characterize them. 4/6.
Mass spectrometry: used to detect small molecules metabolized (produced) by • Incubation period: <10days.
microbes. • Virus contains both bat and pig sequences. Viral receptors found in respiratory tract and NS.
• How-to analyze the human microbiome: • Do we need to grow the virus in order to vaccinate against it? Yes! Sequences are an
important start for an mRNA virus; you would need to pick an epitope that generates an
immune response though.
• Their thought-to-be vaccine: Forsythia. Real vaccine massed-produced and distributed: MEV-
1.
• Buying in bulk, ppl in Asia wearing masks to prevent spread, riots(but not from social
injustice).
• Tried dead viruses -> moved to live, attenuated viruses, being tested on monkeys.
• R0: 2 then <4. -> 1/4 people will contract the disease; 26mil have died worldwide.
• Very rare, but a live attenuated virus can revert to WT and re-infect the host, if taken as a
vaccine.
○ That’s why flu mist(live attenuated) is not recommended for elderly, pediatric, pregnant or
immunocompromised.
• Found out the bat feces was eaten by pig; pig prepared by Hong Kong chef. Chef interacted w/
• patient zero via hand shake.
ACTIVE LEARNING (11/30/20)
• Abundance: inside a sample, how much is a particular species is present.
• Richness: how many species are in one sample.
• Prevalence: if you look across one sample, how many of those species are their across
the pop.
○ Does NOT tell you about abundance.
• Based on daily fecal samples, the gut microbiome changes dramatically over short periods
of time for a given individual.
• Concept check 23.2: Microbes from obese individuals cause mice to gain weight.
• C. Difficile: flora microbes can become pathogenic if they overgrow or reach new sites fo
• SEQUENCING APPROACHES the body.
• 16S rRNA sequencing: 16S rRNA is a universal gene present across all organisms. (1) ○ May be caused by excessive antibiotic use: kills normal flora, C. difficile
Amplify that gene, then (2) sequence the amplicons to study them. overgrowth…
○ Approach can be used for bacteria, but amplicon sequencing cannot be used for C. Difficile diarrhea is an opportunistic infection-- arises when we take too many
viruses (have no ribosomes of their own). antibiotics.
○ Used to compare variable regions w/in the bacterial 16S rRNA gene. -> Can
determine different bacterial types in the sample.
• Whole-genome sequencing: (1) isolate the microbes, (2) grow them*, then (3) sequence
their whole genome.
• Metagenomic sequencing: (1) extract ALL DNA from the sample and (2) shotgun
sequence the whole microbe community. -> "Metagenome-Assembled Genome (MAG)"
• Multivariate analysis of community composition: amplicons undergo sequence homology
to cluster similar sequences w/ one another.
○ Can make an abundance table of different bacterial taxa.
○ Can study how clusters compare b/w treatments.
• Microbial composition is different based on anatomic site it is found in.
• Yatsunenko's scatter plot (slide 17):
○ Measuring the microbial diversity from people in 3 different geographic locations, w/
age.
Monday, November 23, 2020 9:19 PM
CONTAGION
• Postulates of microbial ecology: (1) microbes are found in every earth environment, and • Science advisor: Ian Lipkin
(2) every molecule can be used by a microbe. • Origin: Meat market in Asia(Hong Kong). Know it was spread thru livestock.
• Years of co-evolution has evolved bacteria and phage species. • Virus in movie is based off of MEV-1.
• Leeuwenhoek created the first microscope and observed microbes w/in his own dental • Quicker means "less chance to spread," as in it kills its victims before the virus can find another
plaque(1st uncultured view of the human microbiome was oral). host.
• Before, microbes were isolated and cultured in single strains of bacteria. Now, we know to • 103 cases in 5 days, mainly children. Mortality rate is most likely low 20s.
grow microbes together to see how communities interact and cycle nutrients. • Believe its respiratory illness, and fomite (surface) spread.
• In 1970s, restriction enzymes were used to characterize microbiomes; now we sequence • R0: R-naught. Reproductive rate of virus. Decides whether an illness is an epidemic. Ex. Polio
microbial genomes to characterize them. 4/6.
Mass spectrometry: used to detect small molecules metabolized (produced) by • Incubation period: <10days.
microbes. • Virus contains both bat and pig sequences. Viral receptors found in respiratory tract and NS.
• How-to analyze the human microbiome: • Do we need to grow the virus in order to vaccinate against it? Yes! Sequences are an
important start for an mRNA virus; you would need to pick an epitope that generates an
immune response though.
• Their thought-to-be vaccine: Forsythia. Real vaccine massed-produced and distributed: MEV-
1.
• Buying in bulk, ppl in Asia wearing masks to prevent spread, riots(but not from social
injustice).
• Tried dead viruses -> moved to live, attenuated viruses, being tested on monkeys.
• R0: 2 then <4. -> 1/4 people will contract the disease; 26mil have died worldwide.
• Very rare, but a live attenuated virus can revert to WT and re-infect the host, if taken as a
vaccine.
○ That’s why flu mist(live attenuated) is not recommended for elderly, pediatric, pregnant or
immunocompromised.
• Found out the bat feces was eaten by pig; pig prepared by Hong Kong chef. Chef interacted w/
• patient zero via hand shake.
ACTIVE LEARNING (11/30/20)
• Abundance: inside a sample, how much is a particular species is present.
• Richness: how many species are in one sample.
• Prevalence: if you look across one sample, how many of those species are their across
the pop.
○ Does NOT tell you about abundance.
• Based on daily fecal samples, the gut microbiome changes dramatically over short periods
of time for a given individual.
• Concept check 23.2: Microbes from obese individuals cause mice to gain weight.
• C. Difficile: flora microbes can become pathogenic if they overgrow or reach new sites fo
• SEQUENCING APPROACHES the body.
• 16S rRNA sequencing: 16S rRNA is a universal gene present across all organisms. (1) ○ May be caused by excessive antibiotic use: kills normal flora, C. difficile
Amplify that gene, then (2) sequence the amplicons to study them. overgrowth…
○ Approach can be used for bacteria, but amplicon sequencing cannot be used for C. Difficile diarrhea is an opportunistic infection-- arises when we take too many
viruses (have no ribosomes of their own). antibiotics.
○ Used to compare variable regions w/in the bacterial 16S rRNA gene. -> Can
determine different bacterial types in the sample.
• Whole-genome sequencing: (1) isolate the microbes, (2) grow them*, then (3) sequence
their whole genome.
• Metagenomic sequencing: (1) extract ALL DNA from the sample and (2) shotgun
sequence the whole microbe community. -> "Metagenome-Assembled Genome (MAG)"
• Multivariate analysis of community composition: amplicons undergo sequence homology
to cluster similar sequences w/ one another.
○ Can make an abundance table of different bacterial taxa.
○ Can study how clusters compare b/w treatments.
• Microbial composition is different based on anatomic site it is found in.
• Yatsunenko's scatter plot (slide 17):
○ Measuring the microbial diversity from people in 3 different geographic locations, w/
age.
