general meeting 1 20 October 2016
introductions
today s topics the human microbiome about the study
the human microbiome
the human microbiome human microbiota: the microorganisms that live within and on humans human microbiome: the genomes of these microorganisms HMP: Human Microbiome Project Turnbaugh et al., The Human Microbiome Project, Nature, 2007.
the gut microbiome most symbiotic microbes located in the gut functions: - metabolism - host protection and immune-system development - gut-brain axis Bull and Plummer, Part 1: The Human Gut Microbiome in Health and Disease, IMCJ, 2014.
gut microbiome diversity mainly two bacterial phyla: Bacteriodetes Firmicutes influenced by many factors, including host age, genetics and diet De Filippo et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, PNAS, 2010.
microbiome and health obesity: - associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes - obese microbiome has increased capacity to harvest energy from the diet - colonization of germ-free mice with an 'obese microbiota' results in a significantly greater increase in total body fat than colonization with a 'lean microbiota Turnbaugh et al., An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 2006.
C. difficile infection (CDI) Clostridium difficile: anaerobic, antibiotic resistant, Gram-positive bacteria - commonly found in the human gut but outcompeted by other bacteria - after antibiotic treatment, C. difficile may take over - produces various toxins, including cytotoxin an enterotoxin symptoms include diarrhea, fever, and potentially deadly inflammation of the colon if antibiotic treatment fails, stool transplants are fairly effective in treating CDI https://en.wikipedia.org/wiki/clostridium_difficile_infection
impact of soylent consumption on human microbiome composition
history of the study fall 2015 - conception and ideas winter 2016 - assembled team, established RSO february 2016 - crowdfunding campaign
experiment.com /soylentmicrobiome crowdfunding, for science! funding sources: - friends and family - reddit.com/r/soylent - experiment.com community
history of the study fall 2016 - conception winter 2016 - assembled team, established RSO february 2016 - crowdfunding campaign january to october 2016 - IRB review
IRB review federally required documentation and paperwork for ethical biomedical human research 10 months 1 bajillion revisions 82 page document it means our study is approved and safe
history of the study fall 2015 - conception winter 2016 - assembled team, established RSO february 2016 - crowdfunding campaign january to october 2016 - IRB review october 2016 - first meeting! november 2016 - main study begins
why soylent? students are busy students want to be healthy more and more people are drinking soylent
participation in the study every participant receives 8 ubiome gut DNA kits if you are in the soylent group, 20 bottles of soylent full access to your personal sequencing data $700+ value!
revised study design 9 participants in soylent group 5 participants in control group soylent is consumed for 4 days
daily procedures diet microbiome sampling electronic log
diet regular diet - stick to your regular diet as described in screening protocol soylent diet - 1 bottle for breakfast - 2 bottles for lunch - 2 bottles for dinner
microbiome sampling keep a kit with you at all times 1. swab off used toilet paper 2. re-suspend in lysis buffer 3. seal kit in envelope
daily electronic log every night, submit an electronic form: diet sampling information bristol stool rating health notes
next week study logistics: 1. sign informed consent document 2. receive Participant ID 3. fill out health screening form topics: 1. next-generation dna sequencing 2. bioinformatics
questions?