The document discusses the significance of the gut microbiome and potential roles of probiotics. It notes that the gut microbiome contains trillions of microbes and plays an important role in health, immunity, and metabolism. Factors like diet, lifestyle, antibiotics, and other medications can disrupt the normal gut microbiome and lead to dysbiosis, which has been linked to various conditions. Probiotics may help maintain a balanced gut microbiome and mitigate disruption through interactions with the immune system and production of metabolites. Future research could further explore probiotics and manipulation of gut flora to treat certain diseases.

1. The Significance of Our Gut
Microbiome and Potential Roles
of Probiotics
Lincoln Westfall, DO
Family Physician in Sunnyside, WA (soon in Chelan, WA)
AAPCE San Diego 11/1/2019

2. Objectives
• Recognize the significance of a balanced gut microbiome
• Identify factors that can disrupt healthy gut flora
• Identify conditions affected by disruption of healthy gut flora
• Offer ways to mitigate disruption of a healthy microbiome
• Explore possible future studies to pursue further application of
probiotics and other manipulation of bowel flora

3. Microbiome / Microbiota
• “Ecological community of commensal, symbiotic And pathogenic
microorganisms within a body Space or other environment.”
Lederberg & McCray 2001
• "All animals and plants establish symbiotic relationships with
microorganisms.“
Rosenberg & Rosenberg Microbiol Rev 2008 32(5):723-35

4. The intestinal microbiome
• Composed of microbes that reside in the gut and may be altered by
diet, lifestyle, exposure to toxins, and antibiotic use.
• There is a relationship between disease, health, the immune system,
and changes in the microbiota.
• Probiotics have an important role in the maintenance of immunologic
equilibrium in the GI tract through direct interaction with immune
cells.
• The microbiome diversity is likely important in health maintenance,
and it is likely that broad-spectrum probiotics may increase the
effectiveness of treatment.

5. In the human body
• 1013 human cells
• 1014 microbial cells
• 1012 bacteriophages/g of feces
• 1011 bacteria/g of feces
• Gut microbes add an average of 600,000 genes to each human

6. Gut microbiota
• >3 million microbial genes in our gut microbiota – 150 times more
genes than in the human genome.
• Microbiota, in total, can weigh up to 2 kg.
• More than 1,000 different known bacterial species can be found in
human gut microbiota, but only 150 to 170 predominate in any given
subject.
• One third of our gut microbiota is common to most people, while two
thirds are specific to each one of us.
gutmicrobiotaforhealth.com

7. Ghoshal UC, Ghoshal U. Small Intestinal
Bacterial Overgrowth and Other Intestinal
Disorders. Gastroenterol Clin North Am.
2017 Mar;46(1):103-120. doi:
10.1016/j.gtc.2016.09.008.

10. Boer, C.G., Radjabzadeh, D., Medina-Gomez, C. et al. Intestinal microbiome composition and its relation to joint
pain and inflammation.Nat Commun 10, 4881 (2019) doi:10.1038/s41467-019-12873-4

12. Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial Ecology along the Gastrointestinal Tract. Microbes Environ. 2017;32(4):300–313.
doi:10.1264/jsme2.ME17017

13. Function of Gut Microbiota
• Metabolism of nondigestible carbohydrates, which include large polysaccharides,
such as resistant starches, cellulose, hemicellulose, pectins, and gums; some
oligosaccharides that escape digestion; unabsorbed sugars and alcohols from the
diet; and host-derived mucins.
• Produce antimicrobial compounds and compete for nutrients and sites of
attachment in the gut lining, thereby preventing colonization by pathogens.
• Prevention of allergy (ie, a disproportionate reaction of the immune system to
nonharmful antigens). Allergic infants and young children have been found to
have a different composition of intestinal bacteria than those who do not develop
allergies.
• The gut–brain axis is a communication system that integrates neural, hormonal,
and immunological signaling between the gut and the brain, offering the
intestinal microbiota and its metabolites a potential route through which to
access the brain.

14. Important metabolites produced by the
microbiota
• Folate
• Indoles
• Secondary bile acids
• Trimethylamine-N-oxide (TMAO)
• Short-chain fatty acids (SCFAs) (i.e. butyrate, propionate and acetate).
• Neurotransmitters like serotonin and gamma amino butyric acid
• 90% of the body's serotonin is made in the digestive tract!

15. Proposed Mechanisms of Probiotics
• Block the adhesion of pathogenic bacteria to the intestinal epithelium; produce
inhibitory agents
• Enhance the intestinal immune response
• Maintain normal levels of short-chain fatty acids
• Modulate immune system function, such as suppression of intestinal
proinflammatory cytokines
• Repair intestinal permeability
• Suppress the growth of pathogenic bacteria by directly binding to gram-negative
bacteria
• Upregulate intestinal electrolyte absorption
Probiotics for Gastrointestinal Conditions: A Summary of the Evidence. Thad
Wilkins, Jacqueline Sequoia. Am Fam Physician. 2017 Aug 1; 96(3): 170–178.

16. Cani PD. Human gut microbiome: hopes, threats and promises Gut 2018;67:1716-1725.

17. • Saltzman, E. T. et
all. Intestinal
Microbiome
Shifts, Dysbiosis,
Inflammation, and
Non-alcoholic
Fatty Liver
Disease. Frontiers
in Microbiology.
30 January 2018.

18. Dysbiosis
• Stress has been shown to influence the integrity of the gut epithelium and
to alter peristalsis, secretions, and mucin production
• IBS patients have shown a 2-fold increase in the ratio of Firmicutes to
Bacteroidetes
• IBD patients have shown greatly reduced diversity of Firmicutes (producers
of anti-inflammatory SCFA)
• Diverting ileostomy resolves IBD.
• Differences in microbiota between obese and lean people.
• Decreased diversity of Bacteroidetes at 12 months of age in atopic-eczema
patients.
Bull MJ, Plummer NT. Part 1: The Human Gut Microbiome in Health and
Disease. Integr Med (Encinitas). 2014;13(6):17–22.

19. The Human Microbiome and Its
Potential Importance to Pediatrics.
Coreen L. Johnson, James Versalovic
Pediatrics May 2012, 129 (5) 950-
960; DOI: 10.1542/peds. 2011-2736

20. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova et al. Science 29 April 2016 Vol 352.

21. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova et al. Science 29 April 2016 Vol 352.

22. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova et al. Science 29 April 2016 Vol 352.

23. Dietary markers for gut microbiome diversity
• Drinking buttermilk (sour milk with a low fat content) was associated with high diversity, while drinking high-
fat (whole) milk (3.5% fat content) was associated with lower diversity (table S6). Two of the species most
strongly associated with drinking buttermilk are Leuconostoc mesenteroides (q=9.1×10−46) and Lactococcus
lactis (q=2.5×10−8), both used as a starter culture for industrial fermentation (table S11). The abundance of
dairy-fermentation-related bacteria increased with increasing dairy consumption, indicating potential for the
use of probiotic drinks to augment and alter the gut microbiome composition.
• Consumption of alcohol-containing products, coffee, tea, and sugar-sweetened drinks were also correlated
with microbial composition. Consumption of sugar-sweetened soda had a negative effect on microbial
diversity (adjusted P=5×10−4), whereas consumption of coffee, tea and red wine, which all have a high
polyphenol content, was associated with increased diversity (19–21). Red wine consumption correlated
with F. prausnitzii abundance, which has anti-inflammatory properties, correlates negatively with
inflammatory bowel disease (22), and shows higher abundance in high-richness microbiota (23).
• Apart from the negative associations between sugar-sweetened soda and bacterial diversity, other features
of a Western-style diet, such as higher intake of total energy, snacking, and high-fat (whole) milk, were also
associated with lower microbiota diversity (Fig. 3). A higher amount of carbohydrates in the diet was
associated with lower microbiome diversity. Total carbohydrate intake was positively associated
with Bifidobacteria, but negatively with Lactobacillus, Streptococcus, and Roseburiaspecies. A low
carbohydrate diet consistently showed opposite directions for these species.
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova et al. Science 29 April 2016 Vol 352.

24. Medication effects on gut microbiome
• As expected, the use of antibiotics was significantly associated with microbiome
composition, in particular with strong and significant decreases in two species from the
genus Bifidobacterium (Actinobacteriaphylum).
• PPI users were found to have profound changes in 33 bacterial pathways. The most
significant positive correlation of PPIs was observed with the pathway of 2,3-butanediol
biosynthesis, and PPI use was correlated with calprotectin levels, particularly for bacteria
typical of the oral microbiome. Levels of calprotectin were positively correlated with age
and metabolic phenotypes (body mass index (BMI), diabetes, use of statins and
metformin, HBAc1, and systolic blood pressure), but negatively correlated with the
consumption of vegetables, plant proteins, chocolate, and breads.
• Multivariate analysis correcting for all factors revealed 14 species (table S13) and 114
bacterial metabolic pathways (table S14) exclusively associated with calprotectin,
suggesting calprotectin is robustly associated with gut microbiome.
• In 15 metformin users, we observed an increased abundance of Escherichia coli (E. coli)
and a positive correlation with specific pathways, including the degradation and
utilization of D-glucarate and D-galactarate and pyruvate fermentation pathways. SCFA
levels were consistently higher in metformin-users, especially for propionate.
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova et al. Science 29 April 2016 Vol 352.

25. Correlation between disease and dysbiosis
• IBS was reported by 9.9% of participants (n=112, table S1) and was associated with changes in the
gut microbiome and a lower microbial diversity (adjusted P=0.05).
• Species from the Eggerthella and Coprobacillus genera were positively associated with medication
and food allergies, respectively.
• Individuals who had suffered a heart attack (n=10) in the past had a significantly lower abundance
of Eubacterium eligens bacterium.
• Higher BMI was associated with lower level of two species from the family Rikenellaceae, Alistipes
finegoldii, and Alistipes senegalensis, while blood lipids were associated with other two
species, Alistipes shahii and Alistipes putredinis.
• Correlations with the number of different species were also found for other bacteria
including Roseburia hominis, Coprococcus catus, and Barnesiella intestinihominis and unclassified
species from genus Anaerotruncus that also showed correlation both with fruit, vegetable, and
nut consumption and with intrinsic phenotypes like HDL, triglycerides and quality of life. Based on
this data, it would be interesting to explore the potential to modulate disease-associated species
through medication or diet, although we still need to address the causality and underlying
mechanism.
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova et al. Science 29 April 2016 Vol 352.

28. Prebiotics - You are what your microbiome eats!
• non-digestible by host enzymes
• fermented in the GI tract by anaerobic endogenous
colon bacteria
• Selective in stimulation of intestinal flora
Patrick Hanaway, Treating Dysbiosis: Weed, Seed, and Feed, IFM GI AFP, Oct 2018.

29. Antibiotics affect colon flora
Jernberg C, Löfmark S, Edlund C, Jansson J. Long-term impacts of antibiotic exposure on the human intestinal
microbiota. Microbiology (Reading, England). 2010;156:3216–23.

30. Post-treatment with Clindamycin
Jernberg C, Löfmark S, Edlund C, Jansson J. Long-term impacts of antibiotic exposure on the human intestinal
microbiota. Microbiology (Reading, England). 2010;156:3216–23.

31. Association of Antibiotics in Infancy With
Early Childhood Obesity
• CONCLUSIONS AND RELEVANCE
Repeated exposure to broad-spectrum antibiotics at ages 0 to 23
months is associated with early childhood obesity. Because common
childhood infections were the most frequent diagnoses co-occurring
with broad-spectrum antibiotic prescription, narrowing antibiotic
selection is potentially a modifiable risk factor for childhood obesity
Bailey LC et al. Association of antibiotics in infancy with early childhood obesity. JAMA Pediatr. 2014 Nov;168(11):1063-
9. doi: 10.1001/jamapediatrics.2014.1539.

32. Yeast colonization
• Candida colonization of GI tract is associated with GI illnesses and
perpetual inflammation.
• Pro-inflammatory cytokine IL-17 elevated in IBD and in Candida
colonization.
Kumamoto, C. A. (2011). Inflammation and gastrointestinal Candida colonization. Current Opinion in Microbiology,
14(4), 386–391. http://doi.org/10.1016/j.mib.2011.07.015

33. Yeast eradication
• Yeast thrives on sugar. Just stop feeding it!
• Probiotics: Saccharomyces boulardii, Lactobacilli, Bifidobacter
• Enzymes: amylase, peptidase, lipase.
• Oregano, thyme, garlic, goldenseal
• Nystatin, fluconazole, amphotericin B, ketoconazole, terbinafine,
itraconazole.
Consider parasite testing and eradication.
Patrick Hanaway, Treating Dysbiosis: Weed, Seed, and Feed, IFM GI AFP, Oct 2018.

34. SushrMJ, Hallen-Adams HE. The human gut mycobiome: pitfalls and potentials —a mycologist' s perspective Mycologia, 107(6), 2015,
pp. 1057–1073. DOI: 10.3852/15-147.

35. Prebiotics = Food for healthy gut microbiota
• Bran, psyllium, resistant starch (high amylose), breast milk,
oligofructose, inulin, germinated barley foodstuff (GBF), synthetic
oligosaccharides, guar, & lactulose.
• FOS (fructooligosaccharides) 4g+/day - found in onions, garlic, rye,
chicory, blueberries, and bananas.
• promote growth of bifidobacteria
• Lower colon pH
• Discourage growth of clostridia
• Inulins 1-10g/day - derived from chicory and artichoke.
• reduce biomarkers of metabolic syndrome.
• Modified citrus pectin 3-5g BID.
• Larch (arabinogalactans) 500-5000mg BID
Langen L, Dieleman L. Prebiotics in chronic intestinal inflammation. Inflammatory bowel diseases. 2008;15(3):454–62.

36. Prebiotic Rich Foods
• Jerusalem artichokes
• Onions
• Chicory root
• Garlic
• Leeks
• Bananas
• Fruit
• Soybeans
• Burdock root
• Asparagus
• Agave
• Sugar maple
• Chinese chives
• Peas
• Legumes
• Eggplant
• Honey
• Green Tea
• Agave
• Pine nut
• Fava bean
• Yacon root

37. Dietary Fiber
• Soluble fiber is completely fermented by the bacterial: pectins, gums,
inulin type fructans, and mucilages.
• Insoluble fiber is only slightly fermented: cellulose, waxes, beta
glucan, and lignins (mainly in plant cell walls).
• Wheat is 90% insoluble and 10% soluble
• Oats are 50% insoluble and 50% soluble
• Psyllium is 10% insoluble and 90% soluble
J.M. Lattimer & M.D. Haub. Nutrients 2010, 2, 1266-1289

38. Dietary Fiber
• Recommended intake for adult is 30-40 g/day (for child is age + 5).
• Forms gel, increases stool bulk, holds water, binds minerals.
• Inverse correlation to obesity, DM2, CVD, cancer.
• > SCFA, > gut hormones, < transit time, change in intestinal viscosity
(less contact with mucosal cells)
• > estrogen excretion, > antioxidant nutrients, < inflammation

39. Probiotic Rich Foods
• Mushrooms
• Yeast
• Olives
• Fermented cabbage (sauerkraut, kimchi)
• Vinegars, wines
• Fermented dairy (cheeses, kefir, buttermilk, sour cream, yogurt)
• Cucumber pickles

40. Probiotics
• Probiotics are only recoverable in stool samples for one to two weeks.
• Use the specific probiotic species and strains that have been studied.
• Make sure that the product states that the dosage recommended is
viable at the expiration date, and that the expiration date is printed
on the bottle. Good Manufacturing Practice!
• Their viability is temperature-dependent. Keep in fridge. Give in cool
food/drink.
• They are not well regulated in general.

41. Risks of Probiotics
• Bacteremia (rare)
• Endocarditis: 16 reported cases (1992 2001)
5 cases with yogurt or probiotic
Only 1 confirmed to be identical to probiotic
• Liver abscess (74 year old woman)
Daily consumption of probiotic drink
Indistinguishable from probiotic strain
• Several reports of fungemia associated with use of yeast-based
probiotics (S. boulardii) – usually critically ill host and polymicrobial

42. • “Only three out of the seven products (43%) contained the claimed
culture concentration or more.”
• None of the multispecies products contained all the labeled probiotic
bacteria.
• Misidentification of some species occurred.
Fredua-Agyeman M. , Parab S. & Gaisford S. (2016) “Evaluation of Commercial Probiotic
Products”, British Journal of Pharmacy. 1(1). doi: https://doi.org/10.5920/bjpharm.2016.11

43. • Only 4 of 13 products (31%) were in accordance with label claims.
• Our results suggest the need for adequate control of probiotic
production as well as periodical screenings by competent
organizations to monitor the effect of storage on product quality.
Drago L, Rodighiero V, Celeste T, Rovetto L, De Vecchi E. Microbiological evaluation of commercial
probiotic products available in the USA in 2009. J Chemother. 2010 Dec;22(6):373-7.

44. Fredua-Agyeman M. , Parab S. & Gaisford S. (2016) “Evaluation of Commercial Probiotic
Products”, British Journal of Pharmacy. 1(1). doi: https://doi.org/10.5920/bjpharm.2016.11

46. Łukaszewicz M. Saccharomyces cerevisiae var. boulardii Probiotic Yeast. In: Rigobelo EC, ed., Probiotics. InTech; 2012. https://www.intechopen.com/books/probiotics

47. Ritchie ML, Romanuk TN. A Meta-
Analysis of Probiotic Efficacy for
Gastrointestinal Diseases. Heimesaat
MM, ed. PLoS ONE. 2012;7(4):e34938.
doi:10.1371/journal.pone.0034938.

48. Am J Gastroenterol. 2006 Apr;101(4):812-22.
Meta-analysis of probiotics for the prevention of antibiotic associated diarrhea and the treatment of Clostridium difficile disease.
McFarland LV1. Department of Health Services Research and Development, Veterans Administration Puget Sound Health Care System, Seattle, Washington
98101, USA.
CONTEXT:
Antibiotic-associated diarrhea (AAD) is a common complication of most antibiotics and Clostridium difficile disease (CDD), which also is incited by
antibiotics, is a leading cause of nosocomial outbreaks of diarrhea and colitis. The use of probiotics for these two related diseases remains controversial.
OBJECTIVE:
To compare the efficacy of probiotics for the prevention of AAD and the treatment of CDD based on the published randomized, controlled clinical trials.
DATA SOURCES:
PubMed, Medline, Google Scholar, NIH registry of clinical trials, metaRegister, and Cochrane Central Register of Controlled Trials were searched from 1977 to
2005, unrestricted by language. Secondary searches of reference lists, authors, reviews, commentaries, associated diseases, books, and meeting abstracts.
STUDY SELECTION:
Trials were included in which specific probiotics given to either prevent or treat the diseases of interest. Trials were required to be randomized, controlled,
blinded efficacy trials in humans published in peer-reviewed journals. Trials that were excluded were pre-clinical, safety, Phase 1 studies in volunteers,
reviews, duplicate reports, trials of unspecified probiotics, trials of prebiotics, not the disease being studied, or inconsistent outcome measures. Thirty-one
of 180 screened studies (totally 3,164 subjects) met the inclusion and exclusion criteria.
DATA EXTRACTION:
One reviewer identified studies and abstracted data on sample size, population characteristics, treatments, and outcomes.
DATA SYNTHESIS:
From 25 randomized controlled trials (RCTs), probiotics significantly reduced the relative risk of AAD (RR = 0.43, 95% CI 0.31, 0.58, p < 0.001). From six
randomized trials, probiotics had significant efficacy for CDD (RR = 0.59, 95% CI 0.41, 0.85, p = 0.005).
CONCLUSION:
A variety of different types of probiotics show promise as effective therapies for these two diseases. Using meta-analyses, three types of probiotics
(Saccharomyces boulardii, Lactobacillus rhamnosus GG, and probiotic mixtures) significantly reduced the development of antibiotic-associated diarrhea.
Only S. boulardii was effective for CDD.

49. Ritchie ML, Romanuk TN. A Meta-
Analysis of Probiotic Efficacy for
Gastrointestinal Diseases. Heimesaat
MM, ed. PLoS ONE. 2012;7(4):e34938.
doi:10.1371/journal.pone.0034938.

50. Ritchie ML, Romanuk TN. A Meta-
Analysis of Probiotic Efficacy for
Gastrointestinal Diseases. Heimesaat
MM, ed. PLoS ONE. 2012;7(4):e34938.
doi:10.1371/journal.pone.0034938.

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86. FMT for C. diff infection
• Fecal microbiota transplantation (FMT) involves administration of the whole microbial
community from healthy donor stool into the recipient's intestinal tract to normalize or
modify intestinal microbiota composition and function
• Overall suppression of microbiota and disruption of its community structure in the colon,
most commonly resulting from antibiotic therapies, is the fundamental problem
underlying the pathogenesis of Clostridium difficile infection (CDI)
• FMT results in normalization of microbial diversity and community structure in patients
being treated for CDI, with high rates of clinical cure
• The restored colon microbial community could inhibit C. difficile by multiple
mechanisms: competition for nutrients; direct suppression by antimicrobial peptides;
bile-acid-mediated inhibition of spore germination and vegetative growth; and activation
of immune-mediated colonization resistance
Understanding the mechanisms of faecal microbiota transplantation. Khoruts A. &
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90. SushrMJ, Hallen-Adams HE. The human gut mycobiome: pitfalls and potentials —a mycologist' s perspective.
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