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| Everybody Poops! |
Quick plug for QIIME2. I am a bioinformatician...which means I am routinely breaking software in the name of biology! I am also a self-taught programmer (yes, my software engineer husband gasped at that too), which means, I can read code but I'm still a novice at writing it. SO, I know just enough to be truly annoying to these bioinformatics software developers. The QIIME crew are really fantastic and you don't have to fear about posting questions on their forum, unlike Stack Overflow which few novices would ever dare post on. They are supportive and really want you to use their tools and make them better, shout outs to Thermokarst and Nicholas_Bokulich who have dealt with me. Two more of the biggest metagenomics analysis packages that I have used are:
- MOTHUR v1.4 (Pat just recently overhauled the package, I have yet to dive in. He offers a ton of workshops on Mothur and R by the way)
- MGRAST - Completely online, nice crew of developers routinely overwhelmed which is good and bad right? You have tool that is so streamlined it's becoming super popular and everyone wants to use it, but that means finding the funding and manpower to keep it going. It's a very slick interface. They are very responsive to helpdesk emails. There are limitations and make sure you know what you are doing with your data when you set up the analysis. The metadata input is very specific in it's requirements so don't be shy about asking questions if you get errors in uploading. Sometimes using their API is a lot faster than the GUI interface on the webpage. At least that's been my experience.
I digress - back to the American Gut Project!
So Daniel presented a quick download on the American Gut project and what they are moving toward for the future - these poster talks are fast and meant to pique your interest such that you will check out their posters later!
The American Gut was launched in 2012 focusing on 16S rRNA microbial diversity analysis of fecal samples from anyone and everyone who desired to know more about their gut microbiome. They've collected fecal samples from over 10,000 individuals discovering how associations between lifestyle and health impact human microbiomes but also noting that there is still much more we don't know about our "microbial inhabitants." They have uncovered (i) "a wealth of small molecule diversity mediated by lifestyle choices" and (ii) discovered bacterial derived molecules that mimic host signaling molecules which were only 'theorized' to exist in the human gut!
This project is huge on the power of 'citizen science' and now, not just characterization of American guts but guts around the world (there is now a British Gut Project). The Human Food Project has a nice download of American and British Gut as well. As you can see we have tons of representation from the US, UK and Australia but efforts are underway to expand sampling to other parts of the globe and underrepresented populations. This will allow for some really cool questions to be asked about how culture and the environment impact microbiome development and maintenance within the human body.
Just read this excerpt from their abstract:
Science Daily also did a very nice download of their paper and the American Gut Project in their May 2018 posting...have a look. They also posted a really nice InfoGraphic on the project - courtesy of UC San Diego.
So Daniel presented a quick download on the American Gut project and what they are moving toward for the future - these poster talks are fast and meant to pique your interest such that you will check out their posters later!
The American Gut was launched in 2012 focusing on 16S rRNA microbial diversity analysis of fecal samples from anyone and everyone who desired to know more about their gut microbiome. They've collected fecal samples from over 10,000 individuals discovering how associations between lifestyle and health impact human microbiomes but also noting that there is still much more we don't know about our "microbial inhabitants." They have uncovered (i) "a wealth of small molecule diversity mediated by lifestyle choices" and (ii) discovered bacterial derived molecules that mimic host signaling molecules which were only 'theorized' to exist in the human gut!
This project is huge on the power of 'citizen science' and now, not just characterization of American guts but guts around the world (there is now a British Gut Project). The Human Food Project has a nice download of American and British Gut as well. As you can see we have tons of representation from the US, UK and Australia but efforts are underway to expand sampling to other parts of the globe and underrepresented populations. This will allow for some really cool questions to be asked about how culture and the environment impact microbiome development and maintenance within the human body.
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| McDonald et al., 2018. mSystems http://msystems.asm.org/content/3/3/e00031-18 |
"Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education."If that doesn't get you excited about your gut-possibilities, I don't know what will - give their paper a read!
Science Daily also did a very nice download of their paper and the American Gut Project in their May 2018 posting...have a look. They also posted a really nice InfoGraphic on the project - courtesy of UC San Diego.
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| American Gut Project, UC San Diego Health (credit) |
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