American gut microbiome-2

1. Microbiome Biomarkers from the
Human Gut Microbiome
Based on samples from the American Gut Project (http://americangut.org)

2. Biological Background
The human body is home to a diverse ecosystem of trillions of
bacteria. In fact, your digestive tract alone — including your small
and large intestine — houses about 99% of your entire
microbiome. In fact, the human body has more microbes than
human cells. Some of these bacteria can make you sick, but the
overwhelming majority are important for keeping you healthy and
fending off infections. Sometimes, the same bacteria can do both.
Recently, scientists began studying the correlation between the
health of the gut microecosystem, and other health issues, and
found that gut bacteria are closely tied to other aspects of health.
The american gut microbiome project used over 11,000 16s rRNA
samples from people across the United States in their analyses.
Phenotypic attributes and geolocation allowed for examination of
the association between the human microbiome and external
environmental factors like age, race, diet, and place of residence.
The American gut microbiome project has fecal, oral, skin, and
other body site samples collected from thousands of participants.

3. American Gut Project Background and Summary
Human microbiome reference datasets provide epidemiological context for researchers. This enables them to
uncover new insights into their own data through meta-analyses. In addition, large and comprehensive
reference sets offer a means to develop or test hypotheses and can pave the way for addressing practical
study design considerations such as sample size decisions. Through engaging the general public, the
American Gut Project aims to address many of the issues present in existing reference resources,
characterizing health and disease, lifestyle, and dietary choices of the participants while extending its efforts
globally through international collaborations.
American Gut Project has completed sequencing and analysis of gut, skin, and oral bacteria from the first
4,658 samples of 3,624 participants in the American Gut study.
Pine Biotech selected all microbiome samples from patients that gave more than one type of sample: Mouth &
Skin, Mouth & Stool for further analysis.
16S gene (leading to two distinct datasets—V1-3 and V3-5)
• http://www.ebi.ac.uk/ena/data/view/ERP012803&display=html

4. Data Information
Laboratory: Knight Labs
Extracted Molecule: 16 s rRNA /rDNA
Extraction Protocol: PowerMag Soil DNA Isolation Kit
Extraction Link: https://microbio.me/AmericanGut/faq/#faq25
Protocol Link: http://www.earthmicrobiome.org/emp-
standard-protocols/dna-extraction-protocol/
Instrument Model: Illumina MiSeq
16S software package: QIIME using raw sequence data
http://qiime.org
Sample #: 651
Sample Type: Mouthl, Skin, Stool
Study:http://www.ebi.ac.uk/ena/data/view/PRJEB11419

5. T-Bioinfo Analysis Steps
1) mapping on a database of known 16S rRNA databases
2) generating Abundance tables for samples with both skin and stool
samples; samples with both stool and mouth.
3) Using the BiAssociation /P-clustering method to find pairs of associated
bacteria and detect clusters between bacterial species from two separate
body sites such as stool and skin.
Microbiome Data Analysis Machine Learning

6. Preliminary Conclusions
Unsupervised detection of many-to-
many associations by BiAssociation
procedure allowed for new insights
into the data.
Unsupervised analysis has identified
“outstanding” samples
More Updates soon!
An ASD teenager was found in a group of senior patients
as having the same specificity in abundances of linked set
of bacteria from mouth and gut