Microbiome

NSCI 4143/5353
HUMAN NUTRITION AND METABOLISM II
 MICROBIOME-OBJECTIVES
Key concepts:
 Microstructure of the GI wall

 Definition of Microbiome

 Short chain fatty acids

 Fecal transplant

 Commensal microbiota vs opportunistic bacterial pathogen

 Prebiotics and probiotics and synbiotics

 Bifidobacterium

 Akkermansia muciniphila

 Gut dysbiosis and chronic inflammation

 Lipopolysaccharides (LPS)

 Tight junction and gut permeability

 Intestine alkaline phosphatase (IAP)

EXERCISE-GROUP DISCUSSION
 Illustrate (draw a picture) the GI wall with positioning of the
following key elements:
 Gut immune cells (marcrophages, dendritic cells, neutrophils, T cells,
NK cells, Treg cells, B cells, ...)
 Lamina propria
 Mucosal cells (brush boarder membranes vs apical membrane vs basal
lateral membrane)
 Mucus (inner layer vs outer layer)
 Commensal vs pathogenic microbes
 Lipopolysaccharides, tight junction, and leaky gut
 Short chain fatty acids
 Gut hormones (GLP1 &2, …)
 Anti-microbial peptides
 Goblet cells, L cells
 https://www.youtube.com/watch?v=5DTrENdWvvM

 Microbiome
 The ecological community of commensal, symbiotic and
pathogenic microorganisms that literally share our body space
 Gut microbiome
 Commensal microbiota (“good” microbiota): an ensemble of
microorganisms that reside in close proximity and in mutualistic relation
with a host organism
 Opportunistic bacterial pathogen (OBP, “bad”): Microbes cause diseases
 Microbiota dysbiosis: a microbial imbalance or maladaptation on or
inside the body
 Relative sizes of major host cells and their components versus those of bacteria and viruses.

Patrice D Cani Gut doi:10.1136/gutjnl-2018-316723

Copyright © BMJ Publishing Group Ltd & British Society of Gastroenterology. All rights reserved.
IAP: INTESTINAL ALKALINE PHOSPHATASE

LPS
Mucus layer
(mucins)

Mucosal
layer/epitheli
al cell
layer/enteroc
ytes

Lamina
propria
INTERACTIONS BETWEEN THE DIET AND THE GUT MICROBIOTA DICTATE THE
PRODUCTION OF SHORT-CHAIN FATTY ACIDS-BIFIDOBACTERIUM AND OTHERS

Dietary fibers and other prebiotics

Doi: 10.1038/nature18846
SIGNALING FROM THE GUT MICROBIOTA TO THE HOST

1. Enterocytes, also called mucosal

layer, epithelial
layer-barrier/absorption
2. L cells-produce GLP-1
3. Goblet cells-synthesis of mucin

Doi: 10.1038/nature18846
SIGNALING FROM THE GUT MICROBIOTA TO THE HOST (CONTINUED)

 The colonic lamina propria is a thin layer of loose

connective tissue. The cells of the lamina propria
are variable and can include small blood vessels,
fibroblasts, dendritic cells, plasma cells, B cells,
neutrophils, macrophages, etc. These immune cells
exert their roles in the host immune responses to
the homeostasis of the gut microbiome.
 Association between Akkermansia muciniphila and several diseases: what is known? What are
the major confounding factors. The picture illustrated different pathological situations where the
abundance of the bacteria A. muciniphila has been found to be increased or decreased.

Patrice D Cani Gut doi:10.1136/gutjnl-2018-316723

Copyright © BMJ Publishing Group Ltd & British Society of Gastroenterology. All rights reserved.
EXERCISE (YOU CAN WORK ON IT AT HOME)
 Illustrate (draw a picture) the GI wall with positioning of the
following key elements:
 Gut immune cells (marcrophages, dendritic cells, neutrophils, T cells,
NK cells, Treg cells, B cells, ...)
 Lamina propria
 Mucosal cells (brush boarder membranes vs apical membrane vs basal
lateral membrane)
 Mucus (inner layer vs outer layer)
 Commensal vs pathogenic microbes
 Lipopolysaccharides, tight junction, and leaky gut
 Short chain fatty acids
 Gut hormones (GLP1 &2, …)
 Anti-microbial peptides
 Goblet cells, L cells
GUT MICROBIOME DYSBIOSIS
 Microbial dysbiosis refers to a change in the structural and/or functional
configuration of gut microbiota, which causes disruption of gut homeostasis
and is associated with a variety of diseases, such as obesity, diabetes,
autoimmune diseases, neurological disorders, allergies, and inflammatory
and infectious diseases. An altered microbiome, directly reflecting changes
in microbiota, is not only a marker of disease but also actively contributes
to disease pathogenesis.
FACTORS IMPACT GUT MICROBIOME DYSBIOSIS
CONSEQUENCES OF GUT DYSBIOSIS
APPROACHES TO ASSESS MICROBIOME DYSBIOSIS

 Common assess approaches include 16S rRNA

sequencing (testing compositional changes of the
microbiome), metagenomics (deep microbiome
sequencing to evaluate the functional changes/genetic
variants of the microbiome), metatranscriptomics
(microbiota functional changes at the transcription
level), meta-proteomics (microbiota functional changes
at the translation/protein level), and metabolomics
(microbiome metabolism changes by testing the
metabolite profiling).
 APPROACHES EMPLOYED IN MICROBIOME STUDIES
 Group of 3-4
 Sequencing (16S rRNA vs metagenomics)
 16S rRNA: a gene encode the prokaryotic ribosome 30S
subunit. It is highly conserved in gut bacteria so useful in
classifying bacteria
 Metagenome: total genome of all microbes
 Fecal metabolomics-functional readout of gut
microbiome
 Fecal transplant into germ free mice
 Biomarkers: SCFA, LPS, other metabolites
WHY 16S RRNA SEQUENCING
 Characterize non-cultivable bacteria
 Profile hundreds of microorganisms from a single analysis
 Semi-quantify the relative abundance of microbiome
members
 Study complex microbiomes 
 Provide faster and more accurate classification than
traditional identification methods like cloning and culturing
 Identify low-abundance bacteria
 more cost-effective microbiome characterization
https://www.jennycraig.com/dna-innovation
FECAL METABOLOMICS
 Gut microbiota metabolism
 CHO-polysaccharides
 Lipids
 Proteins
 Metabolomics:
 profile the fecal metabolites through LC-MS,
NMR, GC-MS, etc.
HUMAN FECAL METABOLOME DATABASE
APPLICATIONS OF HUMAN FECAL METABOLOMICS

 The use of fecal metabolomics analysis to assess human

health and disease is particularly attractive due to its non-
invasive sampling nature
 Clinical applications:
 Microbiome and metabolome interaction (SCFA, …)
 Profiling metabolic changes in various GI conditions and diseases
 Liver disease
 Non-clinical studies:
 Diet-microbiome-metabolome interactions
FECAL TRANSPLANT
The approach of microbiota transplantation
has been conducted in studies of multiple
diseases, such as colitis, type 1 diabetes,
and metabolic diseases.
GUT MICROBIOME RESEARCH IN LIN LAB

Commensal OBP (opportunistic

microbiota bacterial pathogen) carotenoids
LPS

MIP-2
TNF-α
Myd88 IFN-γ

IgA
T reg
B cell
Plasma cell
PREBIOTICS AS NUTRACEUTICALS & FUNCTIONAL FOODS
 FUNCTIONAL FOODS

 Foods that provide health benefits beyond basic nutrition

 Sold as dietary supplements and nutraceuticals (isolated or purified
forms)
 (International Food Information Council)

 Foods in which concentrations of one or more ingredients have

been manipulated or modified to enhance their contribution to
a healthful diet
 (Institute of Medicine, National Academies Of Sciences)
 FUNCTIONAL FOODS IN MEDITERRANEAN DIET

 Olive oil- cold-pressed olive oil preserves the

natural antioxidants and flavor
 Oleuropein, hydroxytyrosol
 Carotenoids
 Phytosterols (squalene)
 Tocopherols
 Monounsaturated fatty acids
 Functions???
 (Stark et al. Nutr Rev. 2002)
 DIET AND GUT MICROBIOME

Burcelin et al. Gut microbiota and diabetes: from pathogenesis to therapeutic perspective
Acta Diabetol. 2011
 PREBIOTICS AND PROBIOTICS

Probiotics and prebiotics have a long history as

therapeutic tools in treating GI related
diseases, now known as approaches to
maintain gut microbiome homeostasis.
PREBIOTICS
 Non-absorbable food component that beneficially
stimulates one or more of the gut-beneficial microbe
groups and thus has a positive effect on human
health 
 Any food ingredient that enters the large intestine is
a candidate prebiotics
 Non-digestible oligosaccharides derived from
fructose, xylose, soy, galactose, glucose, and
mannose
SOURCES OF PREBIOTICS
 Oligosaccharides
 onion, asparagus, chicory, Jerusalem artichoke, garlic, wheat and oat 
 Inulin
 Storage carbohydrate in plants, commercially added as fillers to processed
foods
 Fructooligosaccharides (FOS)
 Obtained from inulin, shown to promote growth of beneficial
Bifidobacterium
 Isomalto-oligosaccharides
 Fermented soy products

Sarao & Arora, Probiotics, prebiotics, and microencapsulation: A review. Critical Rev Food Sci Nutr 2017
MECHANISM OF ACTION OF PREBIOTICS
  regulation of intestinal mucosal biology
 higher villi, deeper crypts, increased number of goblet
cells and a thicker mucus layer on the colonic
epithelium
 inhibition of intestinal permeability to agents such as
LPS (lipopolysaccharide, bacterial toxin)

Martinez et al. Scientific evidence for health effects attributed to the consumption
probiotics and prebiotics: an update for current perspectives and future of
challenges.Br J Nutr 2015
MECHANISM OF ACTION OF PREBIOTICS
 Intestinal enteroendocrine functions could also
be targeted by prebiotics
 Fructoligosaccharides (FOS) increase the production
of glucagon-like peptide 1 (GLP-1) by L cells that
could favor insulin secretion and activate the gut-
brain axis for the control of glucose metabolism

Martinez et al. Scientific evidence for health effects attributed to the consumption
probiotics and prebiotics: an update for current perspectives and future of
challenges.Br J Nutr 2015
PREBIOTICS & BIFIDOBACTERIAL (A PROBIOTIC)
 bifidobacteria may use a wide variety of oligosaccharides and
complex carbohydrates as C and energy sources

 in presence of several non-digestible oligosaccharides,

bifidobacteria have higher growth rates, when compared with
pathogenic bacteria in the intestine environment

Martinez et al. Scientific evidence for health effects attributed to the consumption
probiotics and prebiotics: an update for current perspectives and future of
challenges.Br J Nutr 2015
PROBIOTIC
 live microorganisms, which, when administered in
adequate amounts, confer a health benefit on the
host

Sarao & Arora, Probiotics, prebiotics, and microencapsulation: A review. Critical Rev Food Sci Nutr 2017
SYNERGY BETWEEN PREBIOTICS AND PROBIOTICS-’SYNBIOSIS’

 Synbiotics is the word coined for the combined

administration of specific probiotics with prebiotics
to provide definite health benefits by synergistic
action
 Examples:
 Bifidobacteria and Fructooligosaccharides (FOS)
 Lactobacillus rhamnosus GG and inulins
 Bifidobacteria or lactobacilli with FOS or inulins or 
galactooligosaccharides (GOS)
Druart et al. Modulation of the Gut Microbiota by Nutrients with Prebiotic and Probiotic Properties
Adv Nutr. 2014
FOOD GROUPS CONTAINING PREBIOTICS WHICH ARE WELL STUDIED

 Fruits and vegetables

 Cruciferous vegetables
 Legumes
 Nuts
 Whole grains
 Tea
 Coffee
 Thus, the health benefits of plant-based diets in
many chronic diseases…
QUESTIONS-
 What is a prebiotic? A food compound promote
the beneficial microbiota intensity/abundance
 What is a probiotic? A live microorganism with
health benefits
 What is a synbiotic? Combination of pre- and pro-
biotics
 MICROBIOME AND FUNCTIONAL FOODS:

OBJECTIVES
 Gut dysbiosis and chronic inflammation
 Lipopolysaccharides (LPS)
 Gut permeability and tight junction
 Intestine alkaline phosphatase (IAP)
CELL JUNCTIONS VS TIGHT JUNCTION
 occluding junctions or zonulae occludentes
(singular, zonula occludens), are the closely
associated areas of two cells whose membranes
join together forming a virtually impermeable
barrier to fluid.

https://www.youtube.com/watch?v=gJ9WTD0XEnc
Gut Permeability: the control of material passing from inside
the GI tract through the cells lining the gut wall, into the rest of the
body
IAP: INTESTINAL ALKALINE PHOSPHATASE

LPS
INTERACTIONS BETWEEN DIET, GUT MICROBIOTA, AND THE HOST
WITHIN THE INTESTINAL LUMEN
DISCUSSION
 From the gut microbiome perspective, specifically
discuss why the Mediterranean Diet is considered
as a healthier diet, compared to the Western Diet
(high sugar/high fat (including cholesterol)/low
fiber (and/or whole grains), in chronic
inflammation and obesity.
IN SUM

“bad”

Endotoxemia induced
inflammation
“good”
TAKE AWAY
 Gut microbiome homeostasis is critical in human health and
diseases
 Disruption of the homeostasis has been associated with a
number of diseases
 Changes in lifestyles may be beneficial to gut health through
rescuing and remodeling the gut microbiome homeostasis
 Increased intake of functional foods matters
 Be familiar with the key concepts listed in the section of
objectives