more than a gut feeling: how the microbiota improves health · lactobacillus casei strain shirota...
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More than a gut feeling:
How the microbiota
improves health
Amanda Ramer-Tait, PhDHarold and Esther Edgerton Assistant Professor of
Immunology and Microbiology
Department of Food Science, University of Nebraska-Lincoln
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~200times as many
microbial genes in your body than human genes
100 trillionmicrobial cellsin your body
1,000species of gut
bacteria identified to date
Two-thirdsof the species of gut bacteria in your body
are unique to you
6 poundsis the combined weight of all the microbes in your body
(twice that of your brain)
You and your gut microbes
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+ =
Why are gut microbes important?
HolobiontYou Microbes
Gut Barrier Integrity
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What do we call our gut microbes?
What’s the difference between the microbiota,
the metagenome and the microbiome?
Total collection of genes,
genomes and products
of the microbiota
Microbiome
Genes and genomes
of the microbiota
(the genetic potential of
the population)
Metagenome
The community of
microbes in an
environment
Microbiota
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How do we know who’s there?
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How do we know who’s there?
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Can we culture them?
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ATGC…
So what do we do?
Metagenomics:
the study of the genes and genomes
present in the microbiota
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What do we do with the DNA data?
ATGGCACTTA… =
TCCGAAAGCC… =
GGGTCTAGCG… =
Microbiome A Microbiome B
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How do we visualize microbiome differences?
Microbiome A
Beta diversity
Microbiome B
Microbiome C
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Courtesy Rob Knight
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Courtesy Rob Knight
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Oral
Fecal
Vaginal
Skin
Courtesy Rob Knight
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Courtesy Rob Knight
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When does our gut microbiota
develop?
Illustration by Nishant Choksi,
The New Yorker
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When does our gut microbiota
develop?
Dominguez-Bello et. al.
2010. PNAS. 107:11971-5.
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Infant(Fecal)
Oral
Fecal
Vaginal
Skin
Courtesy Rob Knight
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Courtesy Rob Knight
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Courtesy Rob Knight
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Courtesy Rob Knight
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Courtesy Rob Knight
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Does our gut microbiota change
throughout our lives?
Ottman et. al. 2012. Front Cell Infect Microbiol. 2:104.
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Does our gut microbiota change
throughout our lives?
David et. al. 2014. Genome Biology. 15:R89.
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PathogenicMicrobes & Pathobionts
BeneficialMicrobes &Symbionts
Are changes in the gut microbiota
linked to disease?
A need exists to causally link the
identified differences in the
microbiota to a physiological
function or disease state
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Gnotobiotic: from Greek gnōtos “known” + biotē “life”
The status of the microbial community is known
How can we establish causation?
University of Nebraska
Gnotobiotic Mouse
Facility
Germ-free:
No microbes
Mono-associated:
Germ-free mouse colonized
with one bacterial species
Conventional:
Complex microbiota from
birth—NOT gnotobiotic
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Obesity: A connection to
the gut microbiota
20%–<25% 25%–<30% 30%–<35% ≥35%
Prevalence of Self-reported Obesity
in the United States (2016)
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Observations in people…
Ley et al. Nature. 2006.
Ley et al. PNAS. 2005.
observations in conventional mice…
Obesity: A connection to
the gut microbiota
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Backhed et al. PNAS. 2004 and 2007.
…and studies in germ-free mice.
Obesity: A connection to
the gut microbiota
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Gut microbes and obesity:
What else can we learn from germ-free mice?
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Ridaura et al. Science 2013;341:1241214
Gut microbes from twins discordant for
obesity modulate mouse metabolism
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How well do “lean” and “obese”
microbiomes compete with each other?
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How well do “lean” and “obese”
microbiomes compete with each other?
Ob
Ln
Ln
Ridaura et al. Science 2013;341:1241214
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“Lean” microbiomes outcompete
“obese” microbiomes
Ridaura et al. Science 2013;341:1241214
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How does
the
microbiota
contribute
to obesity
and
metabolic
disease?
Adapted from Gravitz, Nature 2012
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Immunity, inflammation and
the gut microbiota
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MacDonald and Monteleone, 2005. Science. 307:1920-25.
Gut microbes and the immune system:
a delicate balanceMicrobes
Single-cell
layer of
epithelial
cells
Immune
tissue
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Can individual microbiota members
modulate immunity?
Health
(probiotics)
Disease
(colitogenic)
Lactobacillus species
Bifidobacterium species
Faecalibacterium prauznitsii
Klebsiella pneumoniae
Proteus mirabilis
Adherent and invasive E. coli
Helicobacter spp.
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Some gut microbes promote the
development of Regulatory T Cells
Stops
immune
responses
and limits
inflammation
Helps initiate
immune
responses
and promotes
inflammation
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Clostridium species:
promoting protection
• Colonized germ-free mice with 46 Clostridium species
• Expanded the numbers of Foxp3+ Regulatory T Cells
• Induced TGF-b1 secretion from intestinal epithelial cells
Atarashi et. al. 2011. Science 331:337.
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Clostridium species:
promoting protection
• Subsets of Clostridium species thought to protect against
inflammation are reduced in patients with Inflammatory
Bowel Diseases
• Can providing a cocktail of Clostridium species to mice
provide protection against colitis?
Atarashi et. al. 2011. Science 331:337.
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By producing
metabolites and
by-products of
fermentation called
short-chain fatty acids
(butyrate)Baas, T. SciBX 6(46);
10.1038/scibx.2013.1310
How do gut
microbes
provide
protection
against
inflammation?
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Should we change the composition
of the gut microbiota? How?
Antibiotics
Bacteriophages (viruses)
Fecal transplantation
Diet
Probiotics
Prebiotics
Fiber and whole grains
Other food components
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dietary supplements containing potentially
beneficial bacteria or yeasts
According to the currently adopted definition by
FAO/WHO, probiotics are:
Report of a Joint FAO/WHO Expert Consultation on
Evaluation of Health and Nutritional Properties of Probiotics
in Food Including Powder Milk with Live Lactic Acid Bacteria
(October 2001)
“Live microorganisms
which when
administered in
adequate amounts
confer a health benefit
on the host.”
Probiotics
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Adapted from Crittenden, 2006.
Role of probiotics in gut health
2
1
4
3
5
6
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Challenges along the way
Kok and Hutkins, 2018
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Challenges: colonization resistance
Intestinal
epithelium
Mucus layer
Commensal
microbiota
Antimicrobial
peptides
pH changes
(SCFAs)
Nutrient
limitation
Attachment site
restriction
Food associated
microbes
Bacteriocins
Adapted from Sassone-Corsi and Raffatellu, 2015.
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Consume probiotics regularly at high doses
How do we overcome these challenges?
David et. al. 2014. Genome Biology. 15:R89.
Bifidobacterium
Regular yogurt consumption maintains
bifidobacteria in the gut
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Probiotic consumption does not routinely
alter microbiota composition…
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…but probiotic consumption does alter
microbiota function
McNulty et. al., Science Translational Medicine. 2011.
Urinary metabolites change in mice after
consuming a fermented milk product:
• Bifidobacterium animalis subsp. lactis
• Two strains of Lactobacillus delbrueckii
subsp. bulgaricus
• Lactococcus lactis subsp. cremoris
• Streptococcus thermophilus
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…or probiotic consumption may promote
gut microbiota homeostasis
(and maybe minimize the effects of
microbiota disturbances)
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Probiotics Everywhere!
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Dairy Foods as Sources of Probiotics
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Plant-based yogurt
products + probiotics
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Nutrition
Bars
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Beverages
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Fruit-and Veggie-based
Beverages
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Breakfast Cereals
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The Kambucha Kraze
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Gaga for Gummies
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Probiotics for Kids
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Babies and Infants
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Probiotics Are Just About Everywhere
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Probiotic Supplements Galore
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Up close and personal:
The science of naming microbes
and why it matters
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What’s in a name?
Why does it matter?
Bifidobacterium
lactis
genus
species
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Lactobacillus
acidophilus LA-5
strain
Different species and even strains
can deliver different benefits
genus
species
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Lactobacillus Probiotic strains that have been
evaluated in clinical trials
Lactobacillus johnsoni LA1 (Nestle)
Lactobacillus acidophilus NCFM (Danisco)
Lactobacillus acidophilus SBT (Snow Brand)
Lactobacillus acidophilus ADH (Dupont)
Lactobacillus rhamnosus GG (Valio)
Lactobacillus reuteri DS2112 (Biogaia)
Lactobacillus casei strain Shirota (Yakult)
Lactobacillus plantarum 299v (Probi Foods)
Lactobacillus crispatus CTV05 (Osel, Inc.)
Lactobacillus casei F19 (Alra Foods)
Lactobacillus casei DN-114001 (Dannon)
Lactobacillus rhamnosus Lcr35 (Lycocentre)
Lactobacillus fermentum RC-14 (Urex Biotech)
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Lactobacillus Probiotic strains that have been
evaluated in clinical trials
Lactobacillus johnsoni LA1 (Nestle)
Lactobacillus acidophilus NCFM (Danisco)
Lactobacillus acidophilus SBT (Snow Brand)
Lactobacillus acidophilus ADH (Dupont)
Lactobacillus rhamnosus GG (Valio)
Lactobacillus reuteri DS2112 (Biogaia)
Lactobacillus casei strain Shirota (Yakult)
Lactobacillus plantarum 299v (Probi Foods)
Lactobacillus crispatus CTV05 (Osel, Inc.)
Lactobacillus casei F19 (Alra Foods)
Lactobacillus casei DN-114001 (Dannon)
Lactobacillus rhamnosus Lcr35 (Lycocentre)
Lactobacillus fermentum RC-14 (Urex Biotech)
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Lactobacillus johnsoni LA1 (Nestle)
Lactobacillus acidophilus NCFM (Danisco)
Lactobacillus acidophilus SBT (Snow Brand)
Lactobacillus acidophilus ADH (Dupont)
Lactobacillus rhamnosus GG (Valio)
Lactobacillus reuteri DS2112 (Biogaia)
Lactobacillus casei strain Shirota (Yakult)
Lactobacillus plantarum 299v (Probi Foods)
Lactobacillus crispatus CTV05 (Osel, Inc.)
Lactobacillus casei F19 (Alra Foods)
Lactobacillus casei DN-114 001 (Dannon)
Lactobacillus rhamnosus Lcr35 (Lycocentre)
Lactobacillus fermentum RC-14 (Urex Biotech)
Lactobacillus Probiotic strains that have been
evaluated in clinical trials
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Lactobacillus johnsoni LA1 (Nestle)
Lactobacillus acidophilus NCFM (Danisco)
Lactobacillus acidophilus SBT (Snow Brand)
Lactobacillus acidophilus ADH (Dupont)
Lactobacillus rhamnosus GG (Valio)
Lactobacillus reuteri DS2112 (Biogaia)
Lactobacillus casei strain Shirota (Yakult)
Lactobacillus plantarum 299v (Probi Foods)
Lactobacillus crispatus CTV05 (Osel, Inc.)
Lactobacillus casei F19 (Alra Foods)
Lactobacillus casei DN-114 001 (Dannon)
Lactobacillus rhamnosus Lcr35 (Lycocentre)
Lactobacillus fermentum RC-14 (Urex Biotech)
Lactobacillus Probiotic strains that have been
evaluated in clinical trials
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Bifidobacterium
Bifidobacterium longum BB536 (Moringa)
Bifidobacterium bifidum (Yakult)
Bifidobacterium infantis (Shirota)
Bifidobacterium breve (Yakult)
Bifidobacterium lactis DS 920 (DSM Foods)
Bifidobacterium animalis DN 173010 (Dannon)
Bifidobacterium lactis Bb12 (Chr Hansen)
Bifidobacterium essensis (Danone)
Commercial strains that have been evaluated in clinical trials
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Bifidobacterium longum BB536 (Moringa)
Bifidobacterium bifidum (Yakult)
Bifidobacterium infantis (Shirota)
Bifidobacterium breve (Yakult)
Bifidobacterium lactis DS 920 (DSM Foods)
Bifidobacterium animalis DN 173 010 (Dannon)
Bifidobacterium lactis Bb12 (Chr Hansen)
Bifidobacterium essensis (Danone)
Bifidobacterium Commercial strains that have been evaluated in clinical trials
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Probiotics Q and A
Q. How to know what’s in the yogurt, kefir or capsule?
Q. What is an appropriate dose? And in what units?
Q. Food versus supplement?
A. Read the label and look for species and strains
A. Usually, 100 million cells per g is the minimum.
Many products will contain 1 - 5 billion cells per g
A. Foods components may protect cells from digestion butmost supplements are now well protected
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Which probiotic should I choose?Clinical guides summarize the
scientific literaturehttps://isappscience.org
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Which probiotic should I choose?Clinical guides summarize the
scientific literaturehttps://isappscience.org
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Manipulating the gut microbiota through better eating
The population of oligosaccharide-fermenting strains is
enriched, at the expense of OS non-fermenting organisms
In the colon, these oligosaccharides are fermented, but
only by select members of the GI tract
Prebiotics are usually non-digestible oligosaccharides that
survive gastric digestion and reach the colon intact
Among the bacteria capable of metabolizing prebiotics are
bifidobacteria and lactobacilli
The prebiotic concept
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microbiota enriched with
bifidobacteria and lactobacillidiverse microbiota
+ prebiotic
The prebiotic concept
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21
4
3
5
6
Adapted from Crittenden, 2006.
prebioticsfermentable fiber
oligosaccharides
selective
fermentation
Role of prebiotics in gut health
by natural
inhabitants
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Prebiotic oligosaccharides are normal dietary components
Naturally present in wide variety of fiber-rich foods
Inulin, fructooligosaccharides, galactooligosaccharides + others
Extracted or synthesized and added as ingredients
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Synbiotics
Probiotic Prebiotic Synbiotic
Bifidobacteria +
fructooligosaccharides
Lactobacillus rhamnosus GG +
inulins
How synbiotics are
formulated can have
considerable influence on
their potential
effectiveness!
• Complementary: components are
chosen independently of one another,
with each responsible for a particular
effect or health benefit
• Synergistic: combination is specifically
designed with a prebiotic substrate
synergistically supporting the
competitiveness, survival or metabolic
activity of a cognate probiotic strain
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We think diet is the best tool available for
manipulating the gut microbiome
AND influencing health!
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Mission: Identify food molecules with clinically proven effects
Audacious Goal:
Crops and Foods with Real Health Claims
https://foodforhealth.unl.edu
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Thank you!