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I am not a microbiome expert but I have always wondered how dynamic is the gut microbiome? For example, maybe I travel for a week and consume a bunch of fast f

by gww 7y ago

I am not a microbiome expert but I have always wondered how dynamic is the gut microbiome? For example, maybe I travel for a week and consume a bunch of fast food and drink a bunch of alcohol or I contracted food poisoning. Would my gut microbiome be substantially different than if I followed my regular diet of relatively healthy home made foods? and how long would it take to go back to its default state before I travelled (if ever).

berdon 7y ago
I've been told (by someone who has had C. diff and dealt with a number of gastro issues) that it can take up to 7 years for your gut to stabilize after simply taking antibiotics. With that being said, some googling just now to make sure I'm not just spouting nonsense hasn't turned up a 7 year figure. But it has returned a bunch of articles pointing to studies that suggest it takes a long time. [1] says after 10 months there's still a disturbance. [1] https://health.howstuffworks.com/medicine/medication/long-does-it-take-gut-flora-to-recover-from-antibiotics.htm https://health.howstuffworks.com/medicine/medication/long-do...
- akozak 7y ago
  I recall reading some news recently about studies of the microbiome in immigrants that suggest it can be a relatively quick shift. e.g. see: https://www.theatlantic.com/health/archive/2018/11/how-immigration-affects-microbiome/574585/ https://www.theatlantic.com/health/archive/2018/11/how-immig...
- zmmmmm 7y ago
  I have seen fairly convincing evidence presented quite recently that for the vast majority of people it may take months but after that period the intestinal microbiome is nearly indistinguishable from how it was before administering antibiotics.
tsomctl 7y ago
Yes. There's a long list of different starches and other molecules (e.g. connective tissue in joints) that your gut bacteria feed off of, and different strains of bacteria prefer different types of food. In the FODMAP diet, you avoid certain starches in a deliberate attempt to shift your biome diversity.
gnode 7y ago
Different bacteria thrive on different nutrients, so changing your nutrient intake will affect their populations. I wouldn't expect a week of fast food to be significant compared to going on a ketogenic diet (starving all carbohydrate eating bacteria). Also, intake of new bacteria affects them, as it changes the competitive landscape. Taking antibiotics massively reduces the quantity of gut bacteria. It often radically changes the balance as their numbers recover, resulting in a proportional increase in resistant strains.
- pkaye 7y ago
  Wonder what is the impact for those who just take Soylent for their meals. Does the lack of variety of nutrients kill of some bacteria in the gut and are they worse off for it?
  - gnode 7y ago
    I'm not sure it's correct to say Soylent constitutes a lack of variety of nutrients. Soylent and similar products contain a balance of macronutrients (carbohydrate, lipids, amino acids), vitamins and minerals. Eating a ketogenic (almost no carbs) or fruitarian (almost entirely carbs) diet, is much more likely to create an imbalance in types of gut flora.
XzetaU8 7y ago
https://github.com/MaximilianKohler/HumanMicrobiome/wiki https://github.com/MaximilianKohler/HumanMicrobiome/wiki
jakear 7y ago
As you can see on charts like [1], it's really quite dynamic. You can tell when major life events occur from a plot of gut bacteria over time. [1]: https://www.sciencenews.org/sites/default/files/2016/09/100116_scivis_inline.png?mode=magazine&context=192334 https://www.sciencenews.org/sites/default/files/2016/09/1001...
atombender 7y ago
There was an interesting post on Reddit recently by someone who tracked their gut microbiome composition over a three-year period, with some nice graphs [1] and source code. The data were compiled with uBiome SmartGut and Explorer kits over a 3 year period. I directly parsed the .json files they provided. The plots were generated with matplotlib and the source code is available here: https://github.com/isaacgerg/ubiome_longitudinal_analysis Not sure how scientific this is, but it was interesting to me that someone would even do this. [1] https://www.reddit.com/r/dataisbeautiful/comments/bnrkqm/oc_my_gut_microbiome_over_a_3year_period/ https://www.reddit.com/r/dataisbeautiful/comments/bnrkqm/oc_...
- tomrod 7y ago
  It isn't scientific because there is no hypothesis, but it is certainly good quality data.

by gww 7y ago

berdon 7y ago

I've been told (by someone who has had C. diff and dealt with a number of gastro issues) that it can take up to 7 years for your gut to stabilize after simply taking antibiotics. With that being said, some googling just now to make sure I'm not just spouting nonsense hasn't turned up a 7 year figure. But it has returned a bunch of articles pointing to studies that suggest it takes a long time. [1] says after 10 months there's still a disturbance. [1] https://health.howstuffworks.com/medicine/medication/long-does-it-take-gut-flora-to-recover-from-antibiotics.htm https://health.howstuffworks.com/medicine/medication/long-do...

akozak 7y ago
I recall reading some news recently about studies of the microbiome in immigrants that suggest it can be a relatively quick shift. e.g. see: https://www.theatlantic.com/health/archive/2018/11/how-immigration-affects-microbiome/574585/ https://www.theatlantic.com/health/archive/2018/11/how-immig...
zmmmmm 7y ago
I have seen fairly convincing evidence presented quite recently that for the vast majority of people it may take months but after that period the intestinal microbiome is nearly indistinguishable from how it was before administering antibiotics.

tsomctl 7y ago

Yes. There's a long list of different starches and other molecules (e.g. connective tissue in joints) that your gut bacteria feed off of, and different strains of bacteria prefer different types of food. In the FODMAP diet, you avoid certain starches in a deliberate attempt to shift your biome diversity.

gnode 7y ago

Different bacteria thrive on different nutrients, so changing your nutrient intake will affect their populations. I wouldn't expect a week of fast food to be significant compared to going on a ketogenic diet (starving all carbohydrate eating bacteria). Also, intake of new bacteria affects them, as it changes the competitive landscape. Taking antibiotics massively reduces the quantity of gut bacteria. It often radically changes the balance as their numbers recover, resulting in a proportional increase in resistant strains.

pkaye 7y ago
Wonder what is the impact for those who just take Soylent for their meals. Does the lack of variety of nutrients kill of some bacteria in the gut and are they worse off for it?
- gnode 7y ago
  I'm not sure it's correct to say Soylent constitutes a lack of variety of nutrients. Soylent and similar products contain a balance of macronutrients (carbohydrate, lipids, amino acids), vitamins and minerals. Eating a ketogenic (almost no carbs) or fruitarian (almost entirely carbs) diet, is much more likely to create an imbalance in types of gut flora.

XzetaU8 7y ago

https://github.com/MaximilianKohler/HumanMicrobiome/wiki https://github.com/MaximilianKohler/HumanMicrobiome/wiki

jakear 7y ago

As you can see on charts like [1], it's really quite dynamic. You can tell when major life events occur from a plot of gut bacteria over time. [1]: https://www.sciencenews.org/sites/default/files/2016/09/100116_scivis_inline.png?mode=magazine&context=192334 https://www.sciencenews.org/sites/default/files/2016/09/1001...

atombender 7y ago

There was an interesting post on Reddit recently by someone who tracked their gut microbiome composition over a three-year period, with some nice graphs [1] and source code. The data were compiled with uBiome SmartGut and Explorer kits over a 3 year period. I directly parsed the .json files they provided. The plots were generated with matplotlib and the source code is available here: https://github.com/isaacgerg/ubiome_longitudinal_analysis Not sure how scientific this is, but it was interesting to me that someone would even do this. [1] https://www.reddit.com/r/dataisbeautiful/comments/bnrkqm/oc_my_gut_microbiome_over_a_3year_period/ https://www.reddit.com/r/dataisbeautiful/comments/bnrkqm/oc_...

tomrod 7y ago
It isn't scientific because there is no hypothesis, but it is certainly good quality data.