Influences of Probiotics and
Prebiotics on the Microbiome:
A Case for Lactose Intolerance
M. Andrea Azcarate-Peril, Ph. D. University of North Carolina at Chapel Hill
Disclosures
M. Andrea Azcarate-Peril, PhD, has disclosed that she has
served as a consultant for Ritter Pharmaceuticals.
Contact:
https://www.med.unc.edu/microbiome/
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facilities and expertise to characterize complex microbial
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Vitamins and
supplements Age Diet
Host genetic
background Surgical
interventions
Antibiotics
Pathogens
Probiotics
Fecal
microbiota
transplantation
Breast milk
Bacteriophages
Fiber
Nutraceuticals Meet Precision Medicine: Microbiome Modulators
Prebiotics
Any compound, microorganism, or
environmental factor that generates a compositional or functional modification
of the microbiome
Vitamins and
supplements
Age Diet
Host genetic background
Surgical
interventions
Antibiotics
Pathogens
Probiotics
Fecal microbiota
transplantation
Breast milk
Bacteriophages
Fiber
Nutraceuticals Meet Precision Medicine: Microbiome Modulators
Prebiotics
ISAPP definition 2017
ISAPP definition 2017
SCFAs
HDAC inhibition
Energy
GPR signaling
Liver
Prebiotics: A selectively fermented ingredient that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health (ISAPP, 2017)
β (1-4) Galacto-oligosaccharides (GOS)
Added to infant formulas to mimic
the beneficial effects of human
breast milk oligosaccharides
Generic formula is β (1-4)
[DGalactose]n-D-Glucose where
n ranges between 3 and 10 sugar molecules
Products of metabolism include SCFAs, lactate, and gases
Mean proportions of the three
individual samples taken
during the treatment periods
for each subject
Representative sequences of all OTUs
detected that were significantly affected by
GOS in individual subjects
Consumption of GOS Results in a Highly Specific Bifidogenic Response in Humans
Davis et al. 2011.
β (1-4) Galacto-oligosaccharides (GOS)
Modified from Misson et al., 2016
+
H20
-galactosyl
Acceptor Transgalactosylation
Hydrolysis 𝛃-galactosidase
𝛃-galactosidase
𝛃-galactosidase
Sporobolomyces singularis
Bruno-Barcena and Azcarate-Peril. J Funct Foods. 2015; Dagher et al. AEM. 2013.
Heterologous Expression of a Bioactive β-Hexosyl-Transferase, an
Enzyme Producer of Prebiotics, from Sporobolomyces singularis
1E-3
0.01
0.1
1
Rela
tive a
bundance (
%)
Control GOS90
Day 7
GOS90
Day 14
R NR.
GOS90 Day 14
Bifidobacterium
*
Pure GOS Enhance Bifidobacterium and Its Metabolic
Activity in the Mouse Gut Microbiome
Monteagudo-Mera et al. 2016.
Common symptoms of lactose intolerance include:
• Bloating, a feeling of fullness or swelling
• Pain
• Diarrhea
• Gas
• Nausea
What is lactose intolerance?
• Lactose in dairy products is usually digested in the
small intestine by the enzyme lactase.
• If small intestine does not produce enough lactase,
lactose cannot be broken down and goes to the colon
where bacteria will break down the lactose generating
fluid and gas, and causing symptoms
Source: NIH NIDDK
Glucose
Galactose Lactose
Lactase-phlorizin hydrolase
(LPH)
Lacta
se e
xpre
ssio
n
Time
Lactase persistence (LP)
Lactase deficience –
Lactose intolerance
birth weaning
Intestinal Lactase and Lactose Intolerance
Distribution of LP and the −13910*T Allele in the “Old World”
Ingram et al. 2008; Gerbault et al. 2011
Baseline
Lactose Challenge
Post-
Treatment
Lactose
Challenge
Follow-up
Lactose
Challenge
35-Days GOS
GOS
Placebo
(Sweetose)
Lactose/Dairy
consumption
Encouraged
Lactose
Avoidance Diet
Screening
Day 0 Day 36 Day 66 30 Days
(Stop Treatment)
Can Pure GOS Increase the Numbers of Lactose-Metabolizing Bacteria?
Savaiano et al. 2013.
Dairy Consumption Impacted the Overall Composition and Diversity of
the Gut Microbiome of Lactose Intolerant Individuals
Azcarate-Peril et al. 2017.
Taxa Significantly Associated with Specific Symptoms
M. Andrea Azcarate-Peril et al. PNAS. 2017;114:E367-E375.
Interindividual
variation
Intra-species
genomic and phenotypic variability
What Factors Impact GOS Response?
RE
SP
ON
DER
S N
ON
RESP
ON
DER
Host Genetic Variation Correlated with Bacterial Taxa
• By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, gathered
information on host genetic variation for 93 individuals for whom bacterial abundance data were also available.
• Found 83 associations between genetic variation in host coding sequence and abundance of specific microbial
taxa (genome-wide false discovery rate Q-value <0.1).
Relative abundances of the heritable genus Bifidobacterium are associated with genetic variants in the genomic locus containing
the gene LCT
Blekhman et al. 2015; Goodrich et al. 2016.
Interindividual
variation
Intra-species
genomic and phenotypic variability
What Factors Impact GOS Response?
RE
SP
ON
DER
S N
ON
RESP
ON
DER
Arnold et al. 2018a
Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus
A
A
A
A
B B
C B B
C
B B
C C C C
Arnold et al. 2018b
Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus
bgl PTS IIB p-βgal PTS IIA
⍺-gal
bgl PTS IIB p-βgal PTS IIA
PTS IIB bgl PTS IIA p-βgal
βgal-3 PTS IIB PTS IIC PTS IID PTS IIA
βgal-Large Subunit βgal-Small
Subunit
βgal AMC143_βgal: BT102_02540
AMC143: NA LGG: NA Lc705: NA
AMC143: BT102_00105 LGG: LGG_RS03055-03070 Lc705: Lc705_RS02930-02945
AMC143: BT102_01370-01385 LGG: NA Lc705: Lc705_RS01460-01475
AMC143: BT102_01435-01460 LGG: LGG_RS01605-01625 Lc705: Lc705_RS01540-01560
AMC143: NA LGG: NA Lc705: NA Lc705 Plasmid: Lc705_p00050
AMC010: NA LGG: LGG_RS02250 Lc705: NA
Absent 98.2% Absent
Absent Absent Absent 99.6%
Absent Absent Absent 99.6%
99% 98.8% 100%
Absent* Absent* Absent
99.2% 99% 100%
99.3% 99% 99.9%
97.7% 98.7% 100%
96.4% 97.5% 99.7%
97.4% Absent 100%
98.9% Absent 99.9%
98.1% Absent 100%
97.5% Absent 100%
99.8% 98.7% 100%
98.4% 98.6% 99.9%
98.1% 98.2% 100%
99.7% 98.8% 100%
Absent* Absent* Absent*
Absent* Absent* Absent*
Absent* Absent* Absent*
Absent Absent Absent
AMC010 – lac1: BVG98_13950-13965
AMC010 – lac2: BVG98_15885-15910
AMC010 – lac3: BVG98_10115-10130
AMC010 – lac4: BVG98_10195-10220
AMC010 – lac5: BVG98_07735-07750
Arnold et al. 2018b
A
A
A
A
B B
C B B
C
B B
C C C C
Arnold et al. 2018b
Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus
bgl PTS IIB p-βgal PTS IIA
⍺-gal
bgl PTS IIB p-βgal PTS IIA
PTS IIB bgl PTS IIA p-βgal
βgal-3 PTS IIB PTS IIC PTS IID PTS IIA
βgal-Large Subunit βgal-Small
Subunit
βgal AMC143_βgal: BT102_02540
AMC143: NA LGG: NA Lc705: NA
AMC143: BT102_00105 LGG: LGG_RS03055-03070 Lc705: Lc705_RS02930-02945
AMC143: BT102_01370-01385 LGG: NA Lc705: Lc705_RS01460-01475
AMC143: BT102_01435-01460 LGG: LGG_RS01605-01625 Lc705: Lc705_RS01540-01560
AMC143: NA LGG: NA Lc705: NA Lc705 Plasmid: Lc705_p00050
AMC010: NA LGG: LGG_RS02250 Lc705: NA
Absent 98.2% Absent
Absent Absent Absent 99.6%
Absent Absent Absent 99.6%
99% 98.8% 100%
Absent* Absent* Absent
99.2% 99% 100%
99.3% 99% 99.9%
97.7% 98.7% 100%
96.4% 97.5% 99.7%
97.4% Absent 100%
98.9% Absent 99.9%
98.1% Absent 100%
97.5% Absent 100%
99.8% 98.7% 100%
98.4% 98.6% 99.9%
98.1% 98.2% 100%
99.7% 98.8% 100%
Absent* Absent* Absent*
Absent* Absent* Absent*
Absent* Absent* Absent*
Absent Absent Absent
AMC010 – lac1: BVG98_13950-13965
AMC010 – lac2: BVG98_15885-15910
AMC010 – lac3: BVG98_10115-10130
AMC010 – lac4: BVG98_10195-10220
AMC010 – lac5: BVG98_07735-07750
Arnold et al. 2018b
Genomic and physiological characteristics of strains impact GOS utilization
Inactivation of p-𝛃gal_3 Abolished Growth and Utilization of
GOS and Lactose by AMC143 at 24 Hours
Arnold et al. 2018b
Conclusions
• The nature and purity of the prebiotic matters.
• Pure GOS has a marginal effect on overall gut microbiome composition and diversity
• They increase the abundance of intestinal lactose-metabolizing, beneficial bacteria.
• Lactose-metabolizing bacteria remove undigested lactose from the gut, thus reducing
the gas production and water secretion that produce symptoms.
• Increased bifidobacteria is inversely correlated with pain and cramps associated with
lactose intolerance.
• Host genotype impacts abundance of gut bifidobacteria potentially modulating
prebiotic response.
• Response to GOS can vary due to intra-species genetic and phenotypic differences
of intestinal bacteria.
Todd Klaenhammer
NC State University
Andrew Ritter
Ritter Pharmaceuticals
Dennis Savaiano
Purdue University
Scott Magness
UNC Chapel Hill
“The dependence of the intestinal microbes on the food
makes it possible to adopt
measures to modify the flora in
our bodies and to replace the harmful microbes by useful
microbes”
E. Metchnikoff, Optimistic studies
New York: Putman’s Sons, 1908, 161-183
Jose Bruno Barcena
NC State University
Acknowledgements