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.

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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

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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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