Monday, April 30, 2018

BacterioFiles 337 - Gathering Gut Groupings Graphics

Bacteria labeled using FISH
By Velocity2222X
CC BY-SA 3.0
This episode: A simplified bacterial community in mouse guts doesn't have much community structure, relative to other body areas!

Download Episode (8.8 MB, 9.6 minutes)

Show notes:
Microbe of the episode: Rhodomicrobium vannielii

News item

Journal Paper:
Welch JLM, Hasegawa Y, McNulty NP, Gordon JI, Borisy GG. 2017. Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice. Proc Natl Acad Sci 114:E9105–E9114.

Other interesting stories:
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  • Sometimes bacteria modify their environment so hard, it kills them (paper)
  • Some ants' bacteria produce the pheromones they use for guidance
  • Modifying plants' microbiota might be difficult due to microbe diversity

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    Episode outline:
    • Background: Microbe communities, like in gut or elsewhere in body
      • Or soil, ocean, etc
      • Function and cooperation depends on structuring and layout of community in space
      • Changing structure can destabilize (or stabilize) community
    • In gut, microbes can stick to various things
      • Wall, mucus, food particles, each other
    • Understanding structure can give better awareness of how community works
    • What’s new: Now, scientists publishing in PNAS have looked at the structure that forms in gut communities of mice given a simplified human-like microbiota!
    • Methods: Used FISH, targeting different species with different colors of fluorescence
    • Community was artificial mix of 15 species taken from human gut, put in mice
      • Then gut removed and cut into sections and visualized
    • Found that bacteria weren't evenly distributed throughout gut
      • Many found right at wall of gut, and patches spread through inside of gut (lumen)
    • Then focused on individual species in 4 places
      • 2 dense: wall and patches
      • 2 sparse: rest of inside, and glands/crypts that secrete digestive enzymes
    • Found that communities in each place not identical, but major species found in all
      • Different but not super-different
    • But in microbe-world, these 4 places more like different countries
      • Each country different but has similar institutions
      • Real structure seen on smaller scale: some workers, academics, politicians, police, etc
    • Found that species called Ruminococcus torques was less present at border
      • And other species, Bacteroides cellulosilyticus, negatively correlated
      • But positively correlated with others
      • So possibly indicates interactions (competition, cooperation), or just different environments
      • Not much else stands out
    • Summary: Microbe community in gut, at least artificial mix of 15 human species in mice, is pretty diverse and well-mixed in each microenvironment
    • Applications and implications: Helpful for understanding gut community
      • Some details about specific types available
      • But don’t expect too much obvious structure
    • Only first step in understand though
      • Gotta find out more about interactions and functions
    • What do I think: So gut isn’t really much divided into microenvironments or compartments
      • More like incompletely mixed bioreactor
      • Makes sense, as contents constantly flowing
    • Possible that natural community might show different results
    • All pretty tricky to study though
      • Have to access specific area of gut with equipment like microscope
      • And unless in lab animals, can't be too invasive/destructive
    • Techniques and technology more advanced, better understanding awaits

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