microbio lecture 24 (microbiomes)

microbiota

the microorganisms inhabiting a specific environment/habitat

microbiome

the collective gene pool of the microbiota (are microbial ecosystems)

carl woese

discovered 16S used to build a molecular clock AND identify unculturable microbes (how we study microbiomes)

study microbiome methods

• 16S rRNA amplicon sequencing

• metagenomic sequencing

• transcriptomics/RNAseq, metabolomics and proteomics

16S rRNA amplicon sequencing

way we study microbiomes:

• identifies which microbes are there

metagenomic sequencing

way we study microbiomes:

• identifies which microbes are there and what functions they have

transcriptomics/RNAseq, metabolomics and proteomics

way we study microbiomes:

• identify what functions microbes are actively doing

alpha diversity, beta diversity, taxonomic abundance

We examine differences in microbial communities using three common metrics:

alpha diversity

• Within-sample diversity

• How diverse are the microbial taxa the microbial taxa in a single sample?

• Species richness – the number of microbial taxa

• Species diversity – the evenness of microbial taxa

beta diversity

• Between-sample diversity

• How do microbial communities differ between samples?

• Community level similarity or dissimilarity

• How much overlap in species composition is there between two samples?

relative abundance

what proportion of our sequences are assigned to a taxa

where do we study microbiomes

Virtually every habitat on earth:

• Water (marine and freshwater)

• Air

• Soil

• Plant surfaces

• Animals

• Thermal vents

• Buildings

human microbiome project goals

• Determine whether individuals share a core human microbiome

• Understand whether changes in the human microbiome are correlated with changes in human health

• Develop the new technological and bioinformatic tools needed to support these goals

• Address the ethical, legal and social implications raised by human microbiome research

human microbiome project sample collection

• Microbiome samples collected from 300 healthy individuals

• Initially, to characterize the complexity of the microbial communities, samples were subjected to 16S RNA sequencing

• Metagenomic sequencing was used to provide insights into functions performed by the human microbiome

human microbiome

• Humans have more microbial cells than human cells (~1.3:1 ratio)

• Extensive variation within and between people

• Alterations in the microbiome are associated with health and phenotype

• Microbiome-based therapies are being developed

phenotype

our microbiome influences our ______:

• fecal transplant from lean twin conferred a lean ______

• fecal transplant from obese twin conferred an obese _____

short chain fatty acids (SCFA)

Our microbiome influences our phenotype – How?

• through ________: by-products of microbial fermentation

• Some trigger anti-inflammatory immune pathways (butyrate and sometimes propionate)

gut microbiome

this develops rapidly during first 3 years of life

• geography, lifestyle and parasite infection status ALL were associated with ___ _____ composition

we have evolved with our microbes

diet, environment and disease exposure all shape both our genome and our microbiome

• ex: low lactase (low expression of LCT gene) = higher bifobacterium in intestines

• high lactase (low expression of LCT gene) = lower bifobacterium in intestines

gut microbiome and hypertension

• There is solid evidence that the gut microbiome plays a direct role in modulating blood pressure

• association has roots in infancy

probiotic

foods and supplements containing live microorganisms

prebiotics

food containing substrates for beneficial microbes (usually fiber)

fecal microbiota transplant

• transferring the microbiota from a health individual to a diseased individual

• Highly effective for C. difficile infections

• Not reliably effective for other diseases (and can be harmful)

toxins

Just as we use microbes to bioremediate toxic waste, many species rely on their gut microbiome to neutralize ___ in their diet

• Giant pandas have gut microbes that degrade cyanide, a toxin found in bamboo

• Pack rats (Neotoma spp.) have gut microbes that degrade creosote toxins

neotoma

Two different species of pack rat consume creosote bushes (Neotoma bryanti and N. lepida) in a portion of their range

rhizobium

is only one bacteria with a key role in plant-microbe interactions – there is an entire ecosystem of soil microbes

• A robust soil microbiome:

  • Provisions plants with nutrients

  • Helps exclude pathogens

• Soil microbiomes are affected by farming practices

built environment

microbiome of ____ ____:
Our human propensity to alter our environment has changed our interactions with microbes

• This changes which microbes we acquire from the environment

• May contribute to the decreased diversity of human-associated microbiomes in North America and Europe

→ The chemicals we use in building materials and in our daily lives affect the microorganisms around us

stress

Microbes in built environments experience more ___

• UV light exposure

• Low humidity

• Temperature variation

• Chemical exposure

Increased stress may induce the transfer of mobile genetic elements, facilitating the spread of antibiotic resistance

Additionally, increased stress selects for bacteria with resistance to stress (including resistance to antibiotics)

antibiotic resistance

• Increased stress may induce the transfer of mobile genetic elements, facilitating the spread of _____ _____

• Additionally, increased stress selects for bacteria with resistance to stress (including resistance to antibiotics)