BIOL 2960 Lecture 40: Microbiome

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Washington University in St. Louis
Biology And Biomedical Sciences
Biology And Biomedical Sciences BIOL 2960
Kunkel Barbara

Lecture 40 & 41 Wednesday, April 26, 2017 10:17 AM MICROBIAL ECOLOGY & THE HUMAN MICROBE • Introduction to Microbial Ecology ○ Microbial communities ▪ Microbial ecology: the study of interactions among microorganisms, with each other and with their environment (human host, soil, etc.) ▪ Community: an assemblage or association of populations of two or more different species occupying the same area at a particular time □ Competition: competing for resources □ Predation: one species is trying to eat the other □ Mutualism: both species cooperate and benefit ▪ Microbial organisms are able to grow essentially anywhere, obtain nutrients, produce biomass, cycle nutrients ▪ Diverse groups of microbes determine the quality of the soil, air water -- essential for animal and plant life ▪ Examples of key activities of microbial communities: □ Soil: nitrogen cycle -- fixing N2 into biologically useful forms, oxidation of NH4, denitrification □ Termite guts: degradation of wood (complex carbohydrates) into digestible sugars  Termite guts host a complex microbial community, consisting of diverse microorganisms from all 3 domains of life (bacteria, archaea, eukarya (protists))  Extract DNA from the gut and compare sequences of 16S rRNA genes with databases of rRNA sequences, predominant microorganisms in the gut community have been identified as well as their functions in the termite gut  Enzymes that break down wood into sugars ◊ Cell wall components (e.g. cellulose) are broken down into oligomers & monomers ◊ These are further broken down into sugars, organic acids, etc. □ Human gut: nutrient flow, regulation of metabolism, immune response, mood, etc. ○ Key questions ▪ Where do we find microbial communities? Microbial organisms have evolved to colonize every habitat our biosphere ▪ Which microbes are present in a given ecosystem? □ Identification of different species or taxonomic groups □ Quantifying diversity and relative abundance □ Compare differences between communities -- healthy and compromised systems ▪ What functions do microbes perform? ▪ How do individual microbes impact and respond to their environment? ▪ How do modern life styles impact human-associated microbial communities? • Identification of microbes present in a community ○ How do we classify organisms? ▪ Domain: bacteria, archaea, eukaryotes ▪ Kingdom, phylum, class, order, family, genus, species □ Human classification, domain: eukarya □ Kingdom: animalia □ Phylum: chordata □ Phylum: chordata □ Class: mammalia □ Order: primates □ Family: hominidae □ Genus: homo (human, from "hominis" □ Species: sapien ("wise") ▪ In microbiome studies, often don't provide enough information to distinguish genus or species ▪ OUT = operational taxonomic unit ○ Phylogenetic tree showing diversity of bacteria compared to other organisms: ○ How to figure out who is there: ▪ Examine samples under microscope ▪ Culture -- a large number of microbes seen under a microscope cannot currently be grown under laboratory conditions □ May have as-yet-unidentified nutritional requirements □ In their native environments, microbes live in communities and may rely on the metabolic outputs of other organisms (food webs) □ May exist in non-cultivatable "resting states" in their environment □ May need to receive signals from other microbes to grow □ New culture-independent methods have allowed major advances in characterizing microbiomes!  Rely on sequencing the DNA of the organisms within a community  Metagenomics: the study of genetic material recovered directly from environmental samples  Two approaches: ◊ Targeted metagenomics: sequence single genetic locus (e.g., 16S rRNA gene) within community DNA ◊ Shotgun metagenomics: sequence community DNA in unbiased manner (i.e. whole genomes) -- allows analysis of various functions in community  Steps: 1. Sample from habitat 2. Filter particles 3. Lysis and DNA extraction 4. PCR amplify gene of interest or library construction 5. Sequence DNA 6. Analysis of sequence 7. Identification of operational taxonomic units -- sequencing RNA can provide more information about activity provide more information about activity ▪ Culture-independent techniques -- isolate total DNA from environmental sample & sequence ▪ Why use 16S rRNA gene? Acts are a "molecular fingerprint" that can be used to identify different bacteria □ Every bacterial genome has at least one copy of the 16S rRNA gene □ Presence of conserved and variable regions makes it a good diagnostic □ Conserved, slow-evolving regions can be targeted with "universal" primers □ Faster evolving, "hyper-variable" regions (V1-V9) allow distinction of different taxonomic groups -- the red arrows serve as primer sequences that facilitate PCR amplification to identify organisms because they are conserved sequences, anneal to every microbial sequence available and then the hyper-variable regions all for the identification of that microbe □ 16S sequences for many reference organisms available; comparing new sequences to known references tells us about the taxonomy of an organism □ 16S sequences useful for comparing both individual organisms and communities • The human microbiome ○ As soon as a baby is born, they are populated by microbes -- in utero, no microbes ○ Colonization occurs where the body meets the external environment: ▪ Skin ▪ Mouth, nose ▪ Gastrointestinal (GI) tract ○ Most internal tissues are sterile (unless there is an infection) ○ Eventually there will be 10x as many microbial cells (mostly bacterial) than human cells in the body ○ "Microbiota" often referr
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