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1. Héctor Maldonado-Pérez
Taylor Sehein
Katia Chadaideh

2. The ecosystem inside us
◦ The Microbiome = microbes, their
genomes, and the habitat they are
found
◦ The gut microbiome:
◦ The most diverse (over 100 trillion
bacteria)
◦ Implicated in a range of metabolic
processes

3. Influences on Gut Microbial Composition

4. Main Driver: Diet or Genetics?
Turnbaugh et al. (2009)

5. Main Driver: Diet or Genetics?
Goodrich et al. (2014)

6. Outline
• Part 1: Examining the effects of Diet vs Host Genotype
• Part 2: Evaluating Responsiveness to Diet
• Part 3: Assessing Memory associated with Past Diets
• Evaluation and Critiques
• Conclusions and Significance

7. Part 1: Diet vs Host Genotype

8. Part 1: Computational Methods
• Data generated by 16s rRNA Illumina
Sequencing
Analyses:
•Operational taxonomic unit (OTU)
relative abundance
•Bray-Curtis dissimilarity-based
principal coordinate analysis

9. Part 1: Diet drives gut microbial variance

10. Part 2: Responsiveness to Shifts in Diet

11. Part 2: Computational Methods
•Use of OTU relative abundance
Analysis:
•Microbial Counts Trajectories
Infinite Mixture Model Engine (MC-
TIMME) modeling

12. Part 2: Diet drives reproducible microbial shifts

13. Part 3: Memory Associated with Past Diets
• Oscillation of number
dependent or stable
abundances for OTUs
• Determination of “microbial
memory”

14. Part 3: Computational Methods
• Relative abundance of species-level
OTUs
Analysis:
• Normalization of specific OTU trends
per 10k reads in individual mice

15. Part 3: Memory trends in specific OTUs
Phylum Firmicutes:
Phylum Bacteroidetes:

16. Part 3: Memory trends in specific OTUs

17. Part 3: Memory trends in specific OTUs

18. A Critical Appraisal
• No reported conflicts of
interest
Sources of funding:
• the NIH
• Brigham and Women’s
• General Mills Bell Institute

19. Conclusions and Significance
• Dietary factors provide
greatest impact on gut
microbiome
• Reproducible
• Past-diet impacts
Future directions:
• Functional significance of
OTUs
• Public health implications
• Trends in obesity linked to
microbiome
• Cross-cultural variation
Yang, et al (2009)

20. References
Carmody, Rachel N., et al. "Diet dominates host genotype in shaping the murine gut microbiota." Cell
host & microbe 17.1 (2015): 72-84.
Turnbaugh, Peter J., et al. "The effect of diet on the human gut microbiome: a metagenomic analysis
in humanized gnotobiotic mice." Science translational medicine 1.6 (2009): 6ra14-6ra14.
Goodrich, Julia K., et al. "Human genetics shape the gut microbiome." Cell. 159.4 (2014): 789-799.
Yang, Xing, et al. "More than 9,000,000 unique genes in human gut bacterial community: estimating
gene numbers inside a human body." PLoS One 4.6 (2009): e6074.