gut microbiome dysbiosis in the presenter has … ance/preidis_gut microbiome.pdf · 02.03.2018 ·...

Texas Children’s HospitalTCH128 PowerPoint System ProcessRound 6 Template Review

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DEPARTMENT NAME

Geoff Preidis, MD PhD

Section of Gastroenterology, Hepatology, and Nutrition

Department of Pediatrics

Baylor College of Medicine

Texas Children’s Hospital

GUT MICROBIOME DYSBIOSIS IN UNDERNUTRITION:Cause, Effect, or Both?

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• The presenter has received research support from:

• Young Investigator Grant for Probiotics Research – Global Probiotics Council (Danone, Yakult)

• Early Career Award – Thrasher Research Fund

• NASPGHAN Foundation Young Investigator Development Award/ Nestlé Nutrition Research Award

• The Texas Medical Center Digestive Disease Center (DDC) Pilot/Feasibility Award

• The Alkek Center for Metagenomics and Microbiome Research

• American Neurogastroenterology and Motility Society Research Grant

• AGA‐Rome Foundation Functional GI & Motility Disorders Pilot Award

• Chao Physician‐Scientist Award, Ting Tsung and Wei Fong Chao Foundation

• NIH/NIDDK (K08DK113113)

DISCLOSURES / FUNDING

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LEARNING OBJECTIVES

1. Identify the distinct patterns of gut bacterial community configurations in undernourished children

2. List dietary, environmental, and host factors that shape the gut microbiome of undernutrition, and understand how this “dysbiosis” can impair weight gain

3. Evaluate the clinical and preclinical evidence supporting the use of microbiome‐targeting therapies for undernutrition

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• Definitions

• Historical perspective

• How we assess the microbiome today

• Microbial diversity – what does it mean?

“MICROBIOME 101”

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THE HUMAN MICROBIOME (MICROBIOTA?)• Microbiota = an ecological

community of commensal, symbiotic and pathogenic microorganisms, which includes bacteria, archaea, protists, fungi and viruses

• Microbiome = the genomes contained within these organisms

• Many microbes are abundant in some individuals, and many microbes are prevalent among most individuals, but none are universal

• Although they can vary over time and share some similarity with some individuals, our intestinal contents appear to be highly personalized in terms of microbial presence, absence, and abundance

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THE “BAD OLD DAYS”: IF IT CAN’T BE GROWN, IT CAN’T BE STUDIED!

• Plating samples on specialized media selective for the growth of that organism

• Identification by colony morphology, growth on different media, metabolic production or consumption

• This approach limited the range of organisms that could be detected to those that would actively grow in laboratory culture

• The vast majority of microbial species have never been grown in the laboratory


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HOW DO WE STUDY BACTERIA IF WE CAN’T GROW THEM IN THE LABORATORY?

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Intestinal epithelial cells

Mucus layer

Lactobacillus

It doesn’t have to be grown to be studied!

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• Like a human, a bacterial community consists of a collection of individual cells, each carrying its own genomic DNA

• Unlike a human, a bacterial community’s individual cells may or may not carry identical genomes (they usually don’t!)

CHARACTERIZING AN ENTIRE MICROBIAL COMMUNITY (A MICROBIOTA) BY ITS DNA

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HOW TO DETERMINE “WHO’S THERE”

Sequence DNA

• Mapping = matching your sample’s As, Ts, Cs, and Gs to a bacterial DNA library

• Some sequences can be identified as coming from specific bacterial species, others will be “unclassified”

• New species that are not yet cataloged, sequencing errors, etc.

Extract DNA

“Map” DNA

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• Microbiota = the bacteria, archaea, protists, fungi and viruses that are present within a microbial community

• Microbiome = these organisms’ collective genetic material

• Standard sequencing workflow:

• Isolatingmicrobial DNA from a biological sample

• High‐throughput sequencing (typically on an Illumina platform)

• Mapping the As, Ts, Cs, and Gs to publicly available microbial DNA libraries

“MICROBIOME 101” SUMMARY (PART 1)

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WHY MEASURE MICROBIOTA DIVERSITY?

• No known bacterial groups are widely and consistently shared among the human microbiome

• Decreased microbial diversity is associated with multiple human diseases


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ALPHA VS BETA DIVERSITY

• Alpha diversity: the number of unique microbes (richness) and their relative distribution (evenness) within a sample

• Summary statistics within an individual sample

• Examples: Simpson, Shannon, Chao diversity indices

• Beta diversity: a similarity score between samples

• Allows analysis by sample clustering or by dimensionality reductions such as Principal Component Analysis (PCA).

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ALPHA DIVERSITY ‐ EXAMPLES

E. coli

Bifidobacterium

Clostridium

Lactobacillus

Streptococcus

Vibrio

TOTAL

Quiz: what is the richness of Sample 1?

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ALPHA DIVERSITY ‐ EXAMPLES

# of members

100

50

0

E. coli

Bifidobacterium

Clostridium

Lactobacillus

Streptococcus

Vibrio

TOTAL

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ALPHA DIVERSITY

Relative abundan

ce (%)

100

50

0

Relative abundance (%)

E. coli

Bifidobacterium

Clostridium

Lactobacillus

Streptococcus

Vibrio

TOTAL

E. coli

Bifidobacterium

Clostridium

Lactobacillus

Streptococcus

Vibrio

TOTAL

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ALPHA DIVERSITY: REAL‐LIFE EXAMPLES

Preidis et al. Therap Adv Gastroenterol 2016.Preidis et al. J Nutr Biochem 2015.

*

*

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• Richness = 6

• Evenness = High

• Diversity = High

ALPHA DIVERSITY QUIZ

• Richness = 2

• Evenness = Low

• Diversity = Low

• Richness = 1

• Evenness = N/A

• Diversity = Low

#

?

?

#

?

?

#

?

?


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STABILITY = RESILIENCE + RESISTANCE

Perturbation

PerturbationDEPARTMENT NAME

BETA DIVERSITY: A SIMILARITY SCORE BETWEEN INDIVIDUAL SAMPLES

Preidis..Petrosino. J Nutr Biochem 2015;26:1050‐7.

Samples 1‐14 Samples 15‐30 Samples 31‐45

• Principal Components Analysis (PCA)

• Each point is a mathematical description of an entire microbial community from an individual sample

• Samples that are closer to one another on the PCA plot are more “similar” than samples that are far away

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• Alpha diversity = descriptions within a single community

• Richness = total number of unique bacteria present

• Evenness = how community population is divided among bacteria

• Beta diversity = relative similarity between communities, often visualized using a Principal Component Analysis (PCA) plot

“MICROBIOME 101” SUMMARY (PART 2)

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LEARNING OBJECTIVES




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• Globally, undernutrition contributes to 3.1 million child deaths per year.

• 96 million children (14%) are underweight and 159 million (24%) are stunted.

THE #1 HEALTH PROBLEM PLAGUING CHILDREN TODAY

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• Gut microbes help regulate growth and body weight

• Most undernourished children in our care are very sick – medical illnesses (and medical treatments such as antibiotics) dramatically alter the microbiome

• Most studies of protein‐energy undernutrition enroll underweight but otherwise healthy children –they may offer the best insights into microbiome‐nutrition interactions

IS THE GUT MICROBIOME OF CHILDREN WITH PROTEIN‐ENERGY UNDERNUTRITION RELEVANT TO OUR PRACTICE?


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DEPARTMENT NAME

STOOL FROM UNDERNOURISHED VS HEALTHY CHILDREN CONTAINS DECREASED MICROBIAL ALPHA‐DIVERSITY

Adapted from: Monira.. Alam. Front Microbiol 2011;2:228.

Healthy Undernourished

#Unique Bacteria 546

310

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UNDERNOURISHED VS HEALTHY CHILDREN HAVE…

Ghosh.. Nair. PLoS One 2014;9:1‐13.Gupta.. Mande. Gut Pathog 2011;3:1‐7.

Monira.. Alam. Front Microbiol 2011;2:228.Dinh.. Ward. PLoS One 2016;11:e0155405.

• Increasedabundance of pathogenic genera within the phylum Proteobacteria, including Enterobacter, Escherichia, Klebsiella, and Shigella, even in the absence of diarrhea.

• Decreasedabundance of genera with potentially beneficial microbes, including

Roseburia, Faecalibacterium,

Butyrivibrio, Lactobacillus, and Bifidobacterium.

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ANOREXIA NERVOSA PATIENTS ALSO HAVE DYSBIOSIS WITH DECREASED DIVERSITY

Healthy controls

Anorexia nervosa

Borgo..Borghi. PLoS One 2017; 12:e0179739.Kleiman..Carroll. PsychosomMed 2015;77:969‐81.

Healthy controls

Anorexia nervosa

Proteobacteria, including Enterobacteriaceae, are overrepresented vs healthy controls

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ALPHA DIVERSITY IS DECREASED IN UNDERNOURISHED (LOW BIRTHWEIGHT – LBW) VS NORMAL BIRTHWEIGHT (NBW) NEONATES

Zheng..Xu. Nutrients. 2015;7:6924‐37.

Proteobacteria are overrepresented compared to normal birthweight neonates

RichnessChao Diversity

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DECREASED ALPHA DIVERSITY IN LBW NEONATES MIGHT PREDICT POOR OUTCOMES

Madan..Hibberd. Arch Dis Child Fetal Neonatal Ed. 2012;97:F456‐62.

Shan

non Diversity In

dex

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• Gut microbiota diversity increases over time during childhood

• As richness and diversity increase, the functional potential of the microbiota increases as well

• Hypothesis: might the decreased microbial community richness of undernutrition = delayed acquisition of important microbial functions?

HUMAN GUT MICROBIOTA DEVELOP & MATURE


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A GUT MICROBIOTA “GROWTH CURVE”

Smith..Gordon. Science 2013;339:548‐54.

317 Malawian twin pairs studied during their first 3 years of life – half remained well‐nourished.

Their fecal microbial DNA revealed a distinct pattern of maturation with increasing age.

One can predict a healthy child’s age based on his/her fecal microbial DNA!

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GUT MICROBIOTA MATURITY IS IMPAIRED IN UNDERNUTRITION


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• Children who are undernourished from a variety of causes have gut microbial community alterations (dysbiosis), characterized by:

• Decreased alpha‐diversity, including decreased richness (fewer unique bacteria) and decreased evenness

• Increased abundance of potentially pathogenic bacteria

• Decreased abundance of potentially beneficial bacteria

• Delayed microbiota maturation

KEY POINT 1

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LEARNING OBJECTIVES




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EXPLORING

Velly..Preidis. Gut Microbes 2017;8:98‐112.

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Compared to healthy Italian children, stool from healthy children in Burkina Faso was enriched with microbes (e.g., Prevotella, Xylanibacter) that carry enzymes for metabolizing non‐digestible dietary cellulose and xylans, key components of the Burkina Faso diet.

DIET (CARBOHYDRATE CONTENT) INFLUENCES A CHILD’S MICROBIOME

De Filippo..Lionetti. Proc Natl Acad Sci USA 2010;107:14691‐6.


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DEPARTMENT NAME

Compared to formula‐fed infants, the gut microbiota of breastfed infants is less diverse, consistent with enrichment of genes required for the degradation of human milk oligosaccharides (HMOs) from breast milk.

DIET (BREAST MILK VS FORMULA) INFLUENCES AN INFANT’S MICROBIOME

Backhed..Wang. Cell Host Microbe 2015;17:690‐703.

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• Not all breastmilk is equal!

• Breast milk analysis (mass spectrometry) from Malawian mothers with severely stunted vs healthy infants revealed decreased human milk oligosaccharides (HMOs)

• How do HMOs affect growth?

DIET INFLUENCES THE INFANT MICROBIOME

Charbonneau..Gordon. Cell 2016;164:859‐71.

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DIET‐INDUCED GUT MICROBIAL DYSBIOSIS CAN CONFER SUSCEPTIBILITY TO INFECTION

Desai..Martens. Cell 2016;167:1339‐53.

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EXPLORING



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DEPARTMENT NAME DEPARTMENT NAME

FECAL MICROBES FROM UNDERNOURISHEDCHILDREN CAN CAUSE UNDERNUTRITION IN GERM‐FREE MICE!


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EXPLORING


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• Dysbiosis of undernutrition can be shaped by many factors, including:

• Prenatal/perinatal factors, carbohydrate composition of breast milk or the post‐wean diet, inflammation, presence of pathogens…

• Mechanisms by which dysbiosis can impair weight gain are less clear, but might include:

• Bacterial toxins, subclinical inflammation, decreased efficiency of energy harvest from diet, impaired micronutrient biosynthesis…

KEY POINT 2

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LEARNING OBJECTIVES




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HOW CAN WE MODIFY THE MICROBIOME?


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DEPARTMENT NAME

• Randomized, placebo controlled trial enrolled 795 Malawian children hospitalized for nutritional rehabilitation

• Children randomized to RUTF + placebo vs RUTF + Synbiotic 2000 Forte

• 4 probiotics: Pediococcus pentosaceus, Leuconostocmesenteroides, Lactobacillus paracasei, Lactobacillus plantarum

• 4 prebiotics: oat bran, inulin, pectin, resistant starch

• Median 33 days of treatment

THE PRONUT STUDY: TESTING A PREBIOTIC + PROBIOTIC IN CHILD UNDERNUTRITION

Kerac..Collins. Lancet 2009;374:136‐44.

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• Result: No significant effect on nutritional cure or on any other nutritional outcome

• Reasons for this negative result?

THE PRONUT STUDY: TESTING A PREBIOTIC + PROBIOTIC IN CHILD UNDERNUTRITION

Kerac..Collins. Lancet 2009;374:136‐44.

DEPARTMENT NAME

• 2,767 Malawian children prescribed RUTF as outpatient treatment for severe acute undernutrition

• Children randomly assigned to twice‐daily placebo vs amoxicillin (80‐90 mg/kg/day) or cefdinir (14 mg/kg/day) for 7 days

• Placebo increased the relative risk of treatment failure:

• RR 1.32 [1.04 – 1.68] vs amoxicillin

• RR 1.64 [1.27 – 2.11] vs cefdinir

• Placebo increased the relative risk of mortality:

• RR 1.55 [1.07 – 2.24] vs amoxicillin

• RR 1.80 [1.22 – 2.64] vs cefdinir

A PROMISING TRIAL OF ANTIBIOTICS FOR CHILDREN WITH SEVERE ACUTE UNDERNUTRITION

Trehan..Manary. N Engl J Med 2013;368:425‐35.

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• 2,412 children in Niger with severe acute undernutrition randomized to twice‐daily placebo vs amoxicillin (80 mg/kg/day) x7 days

• No effect on nutritional recovery over 8 week follow‐up

• 1,778 children in Kenya who had recovered from severe acute undernutrition randomized to daily placebo vs co‐trimoxazole (120 or 240 mg/day) x6 months

• No effect on mortality over 12 month follow‐up

TWO OTHER LARGE TRIALS FAILED TO SHOW BENEFIT OF ANTIBIOTICS FOR UNDERNOURISHED CHILDREN

Isanaka..Grais. N Engl J Med 2016;374:444‐53.Berkley..Fegan. Lancet Global Health 2016;4:e464‐73.

DEPARTMENT NAME

• None of these landmark studies assessed how placebo vs treatment affected the gut microbiome!

• Would a beneficial effect of a broad‐spectrum antibiotic be worth the risks?

SUMMARY OF LARGE RANDOMIZED, PLACEBO‐CONTROLLED CLINICAL TRIALS TO DATE


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• 199 preterm infants (mean gestational age 29 weeks) randomized to receive placebo vs Bifidobacterium lactisvs Bifidobacterium longum vs both probiotics

• No difference in weight, length, or head circumference

IN THE NICU, OBSERVATIONAL STUDIES SHOW MODEST BENEFITS OF PROBIOTIC THERAPY, BUT WELL‐DESIGNED RANDOMIZED CONTROLLED TRIALS HAVE NOT YET CONFIRMED THE EFFECT

Hays..Picaud. Clin Nutr 2016;35:802‐11.


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DEPARTMENT NAME

Antibiotic

Probiotic

Prebiotic

Restoration of a healthy microbiome

Sustained healthy growth

+ Elimination of pathogenic bacteria,

functions, andmaturation trajectories

- Multiple adverse effects

+ Enhancement of beneficial bacteria

and functions- Commensal

targets may be missing in the

undernourished gut

Development of low-cost biomarkers to: A) Identify children who would benefit

from microbiome-targeting therapies B) Select the specific agents needed to

address an individual’s functional imbalances

Undernourished child with gut

microbial “dysbiosis"

+ Restoration of a healthy microbiota

- Species/strain selection currently not based on

mechanistic data

Diagnostics

SUMMARY/WHAT LIES AHEAD?


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LEARNING OBJECTIVES




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CLOSING THOUGHTS• We must more accurately detect all gut microorganisms (including

viruses and fungi) and understand their biological functions

• Microbes detected in stool are often not the same microbes that colonize the large/small bowel including the GI mucus layer – which might have a greater influence on health

• Microbial communities in early life are unstable – at no other stage in a healthy person’s life are microbiota in such a state of flux, making it difficult to determine which microbes associate with health vs disease

• It is even more difficult to determine whether specific microbes actually promote health, or whether they simply thrive in a healthy gut environment

• One day we might be able to modify a child’s growth trajectory, vitamin stores, and other developmental parameters by manipulating the gut microbiota – but a great deal of research is still needed before these intriguing possibilities are ready for clinical practice

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ACKNOWLEDGEMENTS

Funding Young Investigator Grant for Probiotics

Research, Global Probiotics Council

Early Career Award, Thrasher Research

Fund

Pediatric GI Training Grant, NIH/NIDDK

T32DK007664 (PI: Shulman)

NASPGHAN Foundation / Nestlé Nutrition

Research Young Investigator Development

Award

Pilot/Feasibility Award, Texas Medical

Center Digestive Disease Center (PHS grant

P30DK56338)

Functional and Mechanistic Award, Alkek

Center for Metagenomics and Microbiome

Research

Research Grant, American

Neurogastroenterology and Motility

Society

AGA‐Rome Foundation Functional GI &

Motility Disorders Pilot Research Award

Chao Physician‐Scientist Award

NIH/NIDDK K08DK113114

•Pediatric GI, Hepatology &

Nutrition Research Laboratories

•Tripti Halder

•Sanjiv Harpavat

•Swapna Krishnamoorthy

•Subapradha Narayanan

•Benjamin Shneider

•Krishnakant Soni

•Sundararajah Thevananther

•Elizabeth Tessier

•Jennifer Yeh

•Moore Laboratory

•Sungwoo Choi

•Kangho Kim

•David Moore

•Robert Britton

•Rui Chen

•Cristian Coarfa

•Margaret Conner

•Sridevi Devaraj

•Milton Finegold

•Robert Shulman

•Jennifer Spinler

•Lanlan Shen

•Arun Sreekumar

•James Versalovic

•Lisa White

gut microbiome dysbiosis in the presenter has … ance/preidis_gut microbiome.pdf · 02.03.2018 ·...

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