Outline

• Clinical impact gut microbes

• HIV dysbiosis

• Engraftment

Microbiome as space occupying communityC. difficile infection (CDI)

• Disease associated with exposure to antibiotics– Antibiotic is first-line tx

• Recurrence rate of 30% after first episode – 50% after 2nd episode

• Fecal transplant (FMT) is curative in 90+%

Van Nood et al., NEJM 2013; Seekatz AM Mbio, 2014

Microbes process diet to produce metabolites that affect CV disease

Koeth et al., Nat Med 2013; Tang et al., NEJM 2013

Inhibiting microbial TMA lyase to treat atherosclerosis

Wang Z et al. Cell, 2015

Foamy macrophage

Atherosclerotic lesions

Microbiome and nutrition/metabolism

Ridaura et al. Science, 2013

OFID, 2015

Microbiome as a pharmacoactive agent

• Digoxin (unsaturated lactone) levels vary by patients

– 20% of patients have excess dihydrolactone

– Antibiotics increase serum levels of active agent

• Eggerthella lenta + cardiac glycoside reductase (cgr) alters digoxin levels

» Haiser & Turnbaugh et al. Science 2013

Brief Summary

• Microbiota – as a community e.g., C diff.

– as a metabolic agent e.g., TMAO, insulin resistance

– as a pharmacoactive agent e.g., digoxin, lovastatin

– as an immunomodulatory e.g., CTLA4, PD-1

• Consider the microbiota in clinical conditions that vary by: – Antibiotics / diet

– Intravenous vs. oral formulation

– Altered pharmacokinetics

Microbiome

• Clinical impact

• HIV dysbiosis

• Engraftment

Morbidity

MortalityHIV Inflammation

Immune activation

(IL-6, sCD14, K/T, D-

dimer, CD38+ etc.)

Microbiome as a potential source of persistent immune activation

Gut CD4 cells are eliminated during HIV infection

Sanos Immunology, 2011

Sato et al. Nature, 2011

• CD4 (Th17/22) subsets preferentially eliminated

• CD4 provides immunity to bacteria & maintain the epithelial barrier– Stimulates epithelial cells to make

mucins & antimicrobial peptides

– Absence leads to mucocutaneouscandidiasis and S. aureus infection

Microbiota profile linked to HIV infection

Vujkovic & Somsouk. Current HIV AIDS Rpts, 2019

Dysbiosis during treated HIV associate with markers of inflammation

Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG,

Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M,

Deeks SG, Hunt PW, Lynch SV, McCune JM. Sci Trans Med, 2013

Enzymatic pathways for tryptophan catabolism (IDO) overrepresented in HIV microbiota

Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG,

Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M,

Deeks SG, Hunt PW, Lynch SV, McCune JM. Sci Trans Med, 2013

Microbes or their metabolites may affect host immune function

• Can a ‘healthy’ microbiome reduce systemic inflammation?

• How can a microbiome be altered and stably reconstituted?

– Rifaxamin had no significant effect on T cell activation / microbial translocation

» Tenorio et al. J Infect Disease, 2015

– Abtx + FMT in SIV macaques reduced immune activation» Hensley McBain et al. J Virol, 2016

– Vancomycin induced dysbiosis did not accelerate untreated SIV disease progression

» Ortiz AM et al. Nat Med, 2018

– Cotrimoxazole reduced systemic (CRP) and intestinal inflammation (myeloperoxidase)

» Bourke et al. Sci Trans Med, 2019

Questions

Fecal transplant study in patients with HIV

Inclusion criteria HIV-infected, ART for >= 1 year Favored CD4 T cell < 500 cells/mL, CD4:CD8 ratio < 1.0

Donors Selected for low Proteobacteria and low Prevotella abundance

ClinicalTrials.gov Identifier: NCT02256592

Vujkovic-Cvijin & Somsouk et al. Gut Microbes, 2017

Shift in microbiome towards donor communityoccurs post-FMT

-0.2

-0.1

0.0

0.1

0.2

0.3

-0.2 -0.1 0.0 0.1 0.2

PC1 (21.76%)

PC

2 (

19

.89

%)

Recipients

P1713 (donor: D01)

P2112 (donor: D37)

P2150 (donor: D01)

P2294 (donor: D01)

P2356 (donor: D37)

P3164 (donor: D37)

Donors

D01

D37

DONOR

RECIPIENTS

After FMT, recipient microbiome profiles remained distinctly separated from the donors

FMT for C. difficile infection results in large microbial shifts

Vujkovic-Cvijin & Somsouk et al. Gut Microbes, 2017

Why is engraftment limited?

C. difficile infection with drastically reduced alpha diversity

Infection /

Antibiotics?

Antibiotic conditioning pre-FMT

Cipro/Flagyl x 5d

-7

Pre-antibiotic treatment

After antibiotic treatment

22

After FMT

23

Engraftment remained variable & modest

Very low alpha diversity associated with greater degree of engraftment (n=1)

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30

40

50

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24

Microbiome

• Clinical impact

• HIV dysbiosis

• Engraftment (learn from other studies)

Lessons from other interventions

• Mucosal vs. stool microbes

• Anaerobic processing

• Pooled donors

• Antibiotic pre-tx

• Prebiotics, probiotics, and synbiotics

Stool

Mucus

Colon

Clostridia

Bacteroidiaα-proteobacteria

β-proteobacteria

γ-proteobacteria

δ-proteobacteria

Bacterial Taxonomic Class

Actinobacteria

Bacilli

Sphingobacteriia ErysipelotrichiaCoriobacteriia

Microbial profile varies across stool, mucus, and colonic lining

Keir & Somsouk, Courtesy of GenentechWilliams BB et al. Path & Immunity, 2019.

Abundance of live species altered during aerobic processing

Bacteroidaceae

O2 tolerant orgs enriched O2 sensitive orgs depleted

Veillonellaceae

Courtesy of OpenBiome

Anaerobically processed FMT for ulcerative colitis

• Early trials using FMT for UC– Generally negative but promising

– No antibiotics

– Superdonor with f. Lachnospiraceaeand g. Ruminococcus

Costello SP JAMA, 2019; Moayyedi Gastro, 2015; Rossen Gastro, 2015; Lloyd-Price Nature, 2019

• 2019, anaerobic processing from pooled donor vs. autologous FMT– 32% vs. 9% response, P=0.03

– Fecalibacterium prausnitzii and other obligate anaerobes preserved

Probiotics

• Intact microbial community resists probiotic colonization» Zmora N et al. Cell, 2018

» Kristensen NB et al. Genome Medicine, 2016

• May be effective in prevention of infant sepsis– L. plantarum + fructooligosaccharide effective

» Panigrahi P et al. Nature, 2017

– Strep thermophlus, B. infantis, B. lactis» Jacobs SE et al. Pediatrics 2013

– B. breve BBG001» Costeloe K et al. Lancet, 2016

– VSL#3» Sinha A et al. BMJ Open, 2015

What is the natural history of the microbiome after abtx?

• Microbiome spontaneously reconstitutes over time

• FMT accelerates microbial reconstitution

• Probiotics delay reconstitution

Suez J et al. Cell, 2018

Human

Summary

• Microbiome well described in specific health conditions

– Microbial community naturally resists infection and probiotic supplements

– Enzymatic pathways a target for drug development

– Metabolic and immune pathways continue to be advanced

• Fecal transplantation is an evidence based intervention (but inconsistent) for engraftment

– Lack of microbial diversity may predict engraftment

– Super donor, anaerobic preparation, repeat dosing can enhance engraftment