20161020 general meeting 1 - mycrobes.berkeley.edu · • winter 2016 - assembled team, established...

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 axisBull and Plummer, Part 1: The Human Gut Microbiome in Health and Disease, IMCJ, 2014.

• mainly two bacterial phyla: Bacteriodetes Firmicutes

• influenced by many factors, including host age, genetics and diet

gut microbiome diversity

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 logevery night, submit an electronic form:

• diet

• sampling information

• bristol stool rating

• health notes

next weekstudy 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?