The Gut Microbiota:
The Intersection Between Diet and
Health
Sharon M. Donovan, PhD, RD
Department of Food Science & Human Nutrition
University of Illinois, Urbana, USA

Conflict of Interest Disclosure
Danone Institutes International paid for my travel
expenses to chair the session and present this talk,
but did not influence the content of the
presentation.

Presentation Outline
• What is the human microbiome?
• How do we study the microbiome?
– Techniques
– HMP and Metahit
– GF and Gnotobiotics
• What have we learned?
– What factors influence gut microbial communities?
– What diseases are linked to the microbiome?
• Conclusions and future directions

What is the Microbiome?
• The “microbiota” represents the
collection of microorganisms living on
and in the human body, the majority of
which inhabit the gastrointestinal tract
• Bacteria, fungi, yeasts, viruses, archaea,
and protozoa
• The majority live in our gut, particularly in
the large intestine
• The “microbiome” is the collective genomes of the microbiota
• The number of microbial genes is 100- times the number of genes
in the human genome.

We Are Mainly Microbes
Source: Gaby D’Allesandro (American Museum of Natural History)
Microbial Cells
(100 trillion)
Human Cells
(30 trillion)
Microbial
Genes(~2 million)
Human
Genes
(23,000)
70% 99%

Presentation Outline
• What is the human microbiome?
• How do we study the microbiome?
– Techniques
– HMP and Metahit
– GF and Gnotobiotics
• What have we learned?
– What factors influence gut microbial communities?
– What diseases are linked to the microbiome?
• Conclusions and future directions

How Do We Study the Microbiome?
• These techniques apply unbiased “omics” based approaches
• Variable regions of the 16S rRNA
• DNA
• In the past, microbial composition had been studied using
culture-based methods
• Underestimated diversity
• Only “grow what we know”
• Over the past decade, our
understanding of the composition
and diversity of the gut microbiota
has been advanced by next
generation sequencing approaches
Karlsson et al. Assessing the human gut microbiota in metabolic diseases. Diabetes 2013; 62:3341-3349.

Bacterial Identification using 16S rRNA
Tyler et al. Analyzing the human microbiome: a how to guide for physicians. Am J Gastroenterol 2014; 109: 983-993
• Unique to Bacteria & Archaea
• Present in all bacteria – allows use
of “Universal Primers”
• Design PCR primers that target
different “variable regions”
• Compare to database of available
16S rRNA sequences
Variable and Conserved regions
Most Commonly used

Zoetendal et al. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut
2008;57:1605-1615.
16S rRNA
approaches
O’mics Based Approaches to
Microbiome Analysis
Which microbes
are there?
What are the
microbes doing?
What is there
genetic potential?

Hierarchical Organization of Taxonomic
Levels (E. coli vs. Humans)
Tyler et al. Analyzing the human microbiome: a how to guide for physicians. Am J Gastroenterol 2014; 109: 983-993

Human Microbiome Sequencing Projects
NIH Human Microbiome Project
(FY 2007-2012)
Integrative Human
Microbiome Project
(FY 2013-2015)
MetaHit
(FY 2008-2012)
2007 2008 2009 2010 2011 2012 2013 2014 2015
Year

NIH-Funded Projects
Human Microbiome Project (HMP): FY 2007-2012
http://commonfund.nih.gov/hmp/index
• Funded by NIH
• Objective: to develop datasets and tools that the community can use to
evaluate which biological properties of the microbiome and host will yield
important new insights in understanding human health and disease.
• Five body sites (15-18 subsites) from 300 young, healthy adults (18-40 yrs)
• 6 initiatives for data sets and analytical tools
• Objective: to create integrated longitudinal datasets of biological properties from both the
microbiome and host from three different cohort studies of microbiome-associated conditions
using multiple "omics" technologies.
• Pregnancy and preterm birth – Virginia Commonwealth University
• IBD – Broad Institute and Harvard
• Prediabetes – Stanford and Jackson Laboratory
Integrative Human Microbiome Project (iHMP): FY 2013-2015
http://hmp2.org/

• Funded by European Commission – 13 partners from academia & industry
• 8 countries in Europe and China
• Its total cost has been evaluated at more than 21.2 million €
• European Commission set an upper limit of 11.4 million €
• Objective: to establish associations between the genes of the human intestinal
microbiota and our health and disease.
• Sequenced metagenomes (DNA)
• Focused on Inflammatory Bowel Disease (IBD) and Obesity
• Research is continuing to be published from the consortium
Metagenomics of the Human Intestinal Tract (MetaHit): 2008-2012
http://www.metahit.eu/index.php?id=410
European-Funded Projects

Mechanisms of Action Using of Germ-free
and Gnotobiotic Animal Models
• Germ-free animals have shown that the gut microbiota are
essential for normal gastrointestinal, immune, metabolic and
cognitive development and function
“Gnotobiotic”
Karlsson et al. Assessing the human gut microbiota in metabolic diseases. Diabetes 2013; 62:3341-3349.

Presentation Outline
• What is the human microbiome?
• How do we study the microbiome?
– Techniques
– HMP and Metahit
– GF and Gnotobiotics
• What have we learned?
– What factors influence gut microbial communities?
– What diseases are linked to the microbiome?
• Future directions of microbiome, nutrition and health
research

Functions of the Microbiome for
Health Maintenance

What Have We Learned?
– We have redefined what it means to be
human...
1. “We” are mainly microbes and the microbiome comprises 99% of our
“metagenome”
• Gut microbiome has 1014 resident microorganisms
2. The microbiome is diverse and representing all 3 domains of life
• Microbes, Fungi, Archea
3. The microbiota shows remarkable diversity at different anatomical sites
4. Microbiome function is more highly conserved between sites than
microbial composition
• Different bacteria can fill the same functional niche

Bacterial Phyla
by Anatomical
Site
Cho & Blaser. The human microbiome: at the interface of health and disease. Nature Rev. Gen. 2012; 13: 260
Firmicutes
Bacteroidetes
Proteobacteria
Actinobacteria

HMP Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486: 207
Microbial Ecosystems have Functional
Redundancy Across Body Sites and Individuals
Phyla – Who is there?
Metabolic Pathways – What are they doing?

Presentation Outline
• What is the human microbiome?
• How do we study the microbiome?
– Techniques
– HMP and Metahit
– GF and Gnotobiotics
• What have we learned?
– What factors influence gut microbial communities?
– What diseases are linked to the microbiome?
• Conclusions and future directions

Factors that Influence Microbiome
Composition
Cresci and Bawden. Gut microbiome: What we do and don’t know. Nutr Clin Prac 2015; 30: 734-746.

Microbiota Change Across the Lifespan
Ottman et al. The function of our microbiota: who is out there and what do they do? Front Cell Inf Micro 2012; 2: 104

Birth
day 1-
6 mos
6 mos –
3 yrs
3 years-
adult
Advanced
Age
Variability among
Individuals*
• After age 65, the number of microbial
species decreases, and populations are
more similar among individuals
* Gender, diet, age, hygiene, body
site, antibiotic use
Adapted from: http://learn.genetics.utah.edu/content/microbiome/intro/
Increaseddiversityinchildhood
Reduceddiversityinelderly
• Family members
and pets
• More complex diet
• By age 3, resembles adult
• More stable, but affected by
puberty, pregnancy,
menopause
• Early diet
• Weaning foods
• Route of delivery
Key Factors Across the Life Span

Dietary Factors Influencing
the Microbiome
Singh RK et al. Influence of diet on the gut microbiome and implications for human health. J Transl Med 2017; 15:73
• Dietary patterns, specific nutrients and dietary bioactive components all play
significant roles in shaping the gut microbiome
• Microbiome composition, metagenome and metabolome are associated with
long-term dietary patterns
• Macronutrients (Wu G et al. Science 2011; 334: 105-108)
• Vegetarian diets (Wu G et al. Gut 2016; 65: 63-72)
• Dietary alterations can induce large, temporary microbial shifts within 24 h
(David et al. Nature 2014; 505:559-563)
• Pre and probiotics are commonly used for microbiome modulation
• Yogurt has been relatively understudied in terms of its effects on the
microbiome

Impact of Dietary Protein on Intestinal
Microbiota & Health Outcomes
Singh RK et al. Influence of diet on the gut microbiome and implications for human health. J Transl Med 2017; 15:73
TMAO = trimethylamine N-oxide

Impact of Dietary Fat on Intestinal
Microbiota & Host Metabolism
Singh RK et al. Influence of diet on the gut microbiome and implications for human health. J Transl Med 2017; 15:73

Presentation Outline
• What is the human microbiome?
• How do we study the microbiome?
– Techniques
– HMP and Metahit
– GF and Gnotobiotics
• What have we learned?
– What factors influence gut microbial communities?
– What diseases are linked to the microbiome?
• Conclusions and future directions

Diet, Microbiome and Health
• Dysbiosis, or an abnormal
microbiota, has been associated
with diseases across organ systems
• Some cause-and effect
relationships have been
established with gnotobiotic
animals.
• Moderated by host genetics and
other environmental factors
• Nutrition, probiotics (and prebiotics)
modulate the gut microbiome
• Microbes interact with gut
epithelium and host immune system
• Microbial products also influence
host physiology (e.g. SCFA, LPS)

Potential Mechanisms – Leaky Gut
• Loss of intestinal
barrier function
• Bacterial translocation
and LPS in circulation
• Immune activation
• Local and systemic
inflammation
Sanz et al. Understanding the role of gut microbiome in metabolic disease risk. Pediatr Res 2015; 77: 236-

Potential Mechanisms – Microbial
Metabolites
Sanz et al. Understanding the role of gut microbiome in metabolic disease risk. Pediatr Res 2015; 77: 236-
Healthy Diet High Fat Diet

Potential Mechanisms
• Nutrition, probiotics (and
prebiotics) modulate the gut
microbiome
• Microbes interact with gut
epithelium and host immune
system
• Microbial products also
influence host physiology (e.g.
SCFA, LPS)

Presentation Outline
• What is the human microbiome?
• How do we study the microbiome?
– Techniques
– HMP and Metahit
– GF and Gnotobiotics
• What have we learned?
– What factors influence gut microbial communities?
– What diseases are linked to the microbiome?
• Conclusions and future directions

Future Directions
• Our knowledge of composition has
rapidly expanded, our understanding of
function remains limited
– Relatively small sample sizes – are they
representative?
• Longer-term observational studies with
detailed metadata and stool samples are
needed
• Prospective yogurt
intervention with to
establish dose and
mechanisms of
action

Microbiome in Health and Disease
Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. Host-gut microbiota metabolic interactions.
Science. 2012; 336 :1262-1267