Commensal Bacteria

The most current, literature-based information on human studies related to increased * Under certain conditions, environmental factors may influence specific commensals or decreased levels of the commensal bacteria is summarized in the following chart. to become pathobionts. Pathobionts are distinguished from true infectious agents; Note that the findings in the literature may not be consistent with Genova’s findings they are potential pathogens under certain conditions. It is unknown whether due to different methodologies, thus treatment efficacy may vary. Most therapeutic these organisms play a causative role in disease or are a consequence of a disease interventions do not work in isolation, meaning they do not exclusively only target state. Literature is evolving regarding the definition of a pathobiont and the role of 1-3 that one organism. Genova has not conducted outcome studies on the impact of commensal bacteria. certain therapeutics on the microbiome markers. Clinician discretion is advised for appropriateness of therapeutics.

Organism Description Increased Levels Decreased Levels Bacteroides-Prevotella group Bacteroides historically included multiple taxonomic groups including A Bacteroides-dominated microbiome is positively correlated with long-term diets Tart cherry juice may normalize high or low levels.19 Prevotella and others. New classification has separated them into rich in animal protein and saturated fat.9,18 A small study on 11 healthy volunteers Bacteroides, Prevotella, and other groups, however it is challenging to showed that an animal-based diet increased the abundance of bile-tolerant Reduced with inulin from Jerusalem artichoke or chicory.29 separate many of the species. For this reason, the Bacteroides- microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of A systematic review of inulin supplementation in humans Prevotella group includes mainly Bacteroides and some Prevotella.4-6 Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium showed an increase in Bifidobacterium, and a relative rectale and Ruminococcus bromii).9 increase in Faecalibacterium and Lactobacillus, and decrease Displays flexibility to adapt to many environmental in relative abundance of Bacteroides.30 conditions/diets Tart cherry juice may normalize high or low levels.19 Lactobacillus kefiri was given to 20 healthy volunteers for Bacteroides consist of bile-tolerant organisms and has the capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet20 one month and after the probiotic was discontinued for a utilizing polysaccharides and mucins.7-9 month, Bacteroides, Barnesiella, Clostridium, Veillonella and Increased in overweight men drinking low glycinin soymilk compared to regular other species were significantly reduced compared to Produces beta glucuronidase,10 secondary bile acids,11 acetate, soymilk or bovine milk21 baseline samples.31 propionate,12,13 products of protein breakdown,9 and is involved in vitamin metabolism7 Levels of Bacteroides, Faecalibacterium, Odoribacter, and others enriched after A study on 250 vegetarian and vegan individuals showed pomegranate extract consumption in overweight-obese subjects. Serum lower counts of Bifidobacterium spp. (vegan), Bacteroides Associated with reduced bacterial gene richness14 endotoxemia marker LBP was reduced.22 spp. (vegan) and E. coli (vegan and vegetarian).32

Along with Methanobrevibacter smithii, certain Clostridium and Four bacteria are enriched with aspirin use versus no medication and includes Bacteroides spp. can produce methane gas.15 Bacteroides spp., Prevotella spp., Barnesiella spp. and the family Ruminococaceae. Furthermore, Bacteroides spp. was seen with other medications including NSAIDs with Generally associated with industrialized populations consuming a PPIs, and NSAIDs with antidepressants and laxatives.23 Western diet16 Cigarette smoking is associated with increased levels.24 Bacteroides growth in culture and propionate formation is favored at a close-to-neutral pH of 6.5, in contrast to butyrate-producing Red wine was positively associated with the relative abundance of Bacteroides in 23 Faecalibacterium prausnitzii and Roseburia spp., which are favored at a allergic patients,25 and in 10 healthy males.26 lower pH of 5.5.17 A high beef diet was associated with increases in Bacteroides fragilis, B. vulgatus and Pathobiont* some species Clostridium spp. in 10 volunteers.27

A ketogenic low-carbohydrate high-fat diet was associated with a reduction of Faecalibacterium and abundance of Bacteroides and Dorea spp. in race walkers.28

1

Commensal Bacteria

Organism Description Increased Levels Decreased Levels Bacteroides- vulgatusPrevotella group BacteroidesGenerally considered historically a beneficialincluded multiple gut commensal, taxonomic although groups isincluding capable A Bacteroideshigh beef diet-dominated was associated microbiome with increases is positively in Bacteroides correlated fragilis,with long B. -vulgatusterm diets and TartDecreased cherry levelsjuice maywere normalize found in 7high-12- oryear low olds levels who.19 ofPrevotella attaching and to others. and invading New classification colonic epithelial has separated cells and them inducing into pro- richClostridium in animal spp. protein in 10 volunteers.and saturated27 fat.9,18 A small study on 11 healthy volunteers consumed oligofructose-enriched inulin (BENEO's prebiotic inflammatoryBacteroides, Prevotella, cytokines and33 other groups, however it is challenging to showed that an animal-based diet increased the abundance of bile-tolerant Reducedfiber Synergy1 with) ifornulin 16 fromweeks Jerusalem in a double artichoke-blind-controlled or chicory .29 separate many of the species. For this reason, the Bacteroides- microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of trialA systematic.36 review of inulin supplementation in humans PrevotellaProduces beta group-glucuronidase includes mainly10 Bacteroides and some Prevotella.4-6 Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium showed an increase in Bifidobacterium, and a relative rectale and Ruminococcus bromii).9 increaseDietary inulin in Faecalibacterium-type fructan prebiotics and Lactobacillus, decreased and Bacteroides decrease 34 AssociatedDisplays flexibility with insulin to adapt resistance to many environmental vulgatusin relative in abundance obese women of Bacteroides. which positively30 correlated with 37 conditions/diets Tart cherry juice may normalize high or low levels.19 changes in body composition and glucose homeostasis. 35 Contains bile salt hydrolases to metabolize bile Lactobacillus kefiri was given to 20 healthy volunteers for Barnesiella spp. Barnesiella spp. is a small group made up of two species with B. Four bacteria are enriched with aspirin use versus no medication and includes 20 Lactobacillus kefiri was given to 20 healthy volunteers for Bacteroides consist of bile-tolerant organisms38,39 and has the capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted die23t one month and after the probiotic was discontinued for a utilizingintestinihominis polysaccharides isolated inand humans mucins. .7-9 Bacteroides spp., Prevotella spp., Barnesiella spp. and the family Ruminococaceae. month,one month Bacteroides and after, Barnesiella, the probiotic Clostridium was discontinued, Veillonella for and a month, Bacteroides, Barnesiella, Clostridium, Veillonella and Increased in overweight men drinking low glycinin soymilk compared to regular other species were significantly reduced compared to B. intestinihominis is found in individuals10 in industrialized11 populations 21 other species were31 significantly reduced compared to Produces beta glucuronidase, secondary bile acids, acetate, soymilk or bovine milk baseline samples.31 versus hunter12,13-gatherer societies and generally correlat9 es with baseline samples. propionate, products of protein40,41 breakdown, and is involved in beneficial effects on the7 human gut. vitamin metabolism Levels of Bacteroides, Faecalibacterium, Odoribacter, and others enriched after A study on 250 vegetarian and vegan individuals showed Barnesiella colonization correlates with reduced antibiotic-resistant pomegranate extract consumption in overweight-obese subjects. Serum lower counts of Bifidobacterium spp. (vegan), Bacteroides 14 22 32 EnterococcusAssociated with species reduced,42 eradication bacterial of gene Klebsiella richness pneumoniae ,43 and has endotoxemia marker LBP was reduced. spp. (vegan) and E. coli (vegan and vegetarian). other beneficial immunoregulatory effects including potential applicationsAlong with Methanobrevibacter in cancer treatment smithii,.44,45 certain Clostridium and Four bacteria are enriched with aspirin use versus no medication and includes 15 Bacteroides spp. can produce methane gas. Bacteroides spp., Prevotella spp., Barnesiella spp. and the family Ruminococaceae. Positively correlates with plasma cholesterol in mice46 Furthermore, Bacteroides spp. was seen with other medications including NSAIDs with Odoribacter spp. GenerallyThis genus associatedincludes three with species industrialized: O. denticanis populations, O. laneus consuming, O. a PPIs,Animal and based NSAIDs diet withs have antidepressants been found to andincrease laxatives. Odoribacter23 spp.48 Higher fiber intake is associated with lower abundance of Westernsplanchnicus diet.4716 Odoribacter.49 LevelsCigarette of Bacteroides,smoking is associated Faecalibacterium, with increased Odoribacter, levels. and24 others enriched after BacteroidesProduces butyrate, growth aincetate culture, propionate and propionate, indole formation from tryptophan, is favored at a pomegranate extract consumption in overweight-obese subjects. Serum closeproducts-to- neutralof protein pH breakdownof 6.5, in contrast, hydrogen to butyrate and H2S-producing47 Redendotoxemia wine was marker positively LBP associated was reduced. with22 the relative abundance of Bacteroides in 23 Prevotella spp. FaecalibacteriumThe Prevotella genus prausnitzii is comprised and Roseburia of more thanspp., 4which0 species, are favored and three at a allergicA Prevotella patients-dominated,25 and in microbiome 10 healthy malesis richer.26 in response to plant-based, complex Lactobacillus kefiri was given to 20 healthy volunteers and predominatelower pH of 5.5. in 17the gut with P. copri being most abundant. The carb, high-fiber diet.18 at the end of one month, Prevotella and other species were majority of Prevotella spp. are found in the oral cavity.51 A high beef diet was associated with increases in Bacteroides fragilis, B. vulgatus and reduced compared to baseline samples.31 Pathobiont* some species IClostridiumndividuals withspp. ina high10 volunteers. Prevotella27-to -Bacteroides ratio lost more body weight and Prevotella has been linked with chronic inflammatory conditions and body fat compared to individuals with low P/B, confirming that individuals with a A Standard American Diet (low-fiber/high-animal based) insulin resistance,51 however others have linked P. copri with improved highA ketogenic P/B are low more-carbohydrate susceptible tohigh weight-fat diet loss was on aassociated diet rich in with dietary a reduction fiber of has been associated with reduced levels and less diversity glucose tolerance in diets rich in fiber. Prevotella effects may be diet- (30+grams)Faecalibacterium.16 and abundance of Bacteroides and Dorea spp. in race walkers.28 of Prevotella.56 dependent. For example, P. copri strains associated with an omnivorous diet may result in higher BCAA synthesis, a risk factor for Four bacteria are enriched with aspirin use versus no medication and includes 23 glucose intolerance and DM2, whereas fiber-rich diets were linked to P. Bacteroides spp., Prevotella spp., Barnesiella spp. and the family Ruminococaceae. copri types with enhanced potential for carbohydrate metabolism.52,53 Cigarette smoking is associated with increased levels.24 Acetate, propionate, and succinate producer;13,54 mucin degrader55 Red wine polyphenol intake for 4 weeks in 10 healthy males was associated with Generally associated with traditional, agrarian diets across Africa, Asia, increased Prevotella.26 and South America16

Pathobiont50* some species

2

Commensal Bacteria

Organism Description Increased Levels Decreased Levels BacteroidesAnaerotruncus-Prevotella colihominis group BacteroidesButyrate and historically acetate producer included57 multiple taxonomic groups including A Bacteroides-dominated microbiome is positively correlated with long-term diets Tart cherry juice may normalize high or low levels.19 Prevotella and others. New classification has separated them into rich in animal protein and saturated fat.9,18 A small study on 11 healthy volunteers AbundanceBacteroides, a Prevotella,ssociated with and otherhigher groups, bacterial however gene richness it is challenging in the gu tto14 showed that an animal-based diet increased the abundance of bile-tolerant Reduced with inulin from Jerusalem artichoke or chicory.29 separate many of the species. For this reason, the Bacteroides- microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of A systematic review of inulin supplementation in humans IncreasedPrevotella ingroup healthy includes individuals mainly and Bacteroides presumed and to some be anti Prevotella.- 4-6 Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium showed an increase in Bifidobacterium, and a relative inflammatory 58 rectale and Ruminococcus bromii).9 increase in Faecalibacterium and Lactobacillus, and decrease Displays flexibility to adapt to many environmental in relative abundance of Bacteroides.30 Inverseconditions/diets correlation with high BMI and elevated serum triglycerides in Tart cherry juice may normalize high or low levels.19 older Amish adults59 Lactobacillus kefiri was given to 20 healthy volunteers for Butyrivibrio crossotus BacteroidesButyrate producer consist14 of bile-tolerant organisms and has the capability of IncreasedB. crossotus in correlated obese adolescents with xylanase/xylosida who lost morese than enzymes 4 kg on that a calorie break- downrestricted complex diet20 one month and after the probiotic was discontinued for a utilizing polysaccharides and mucins.7-9 carbohydrates, mainly from grains.60 month, Bacteroides, Barnesiella, Clostridium, Veillonella and Abundance may help protect against weight gain14 Increased in overweight men drinking low glycinin soymilk compared to regular other species were significantly reduced compared to Produces beta glucuronidase,10 secondary bile acids,11 acetate, Highersoymilk counts or bovine of Butyrivibrio milk21 spp. appear to be associated with a diet richer in baseline samples.31 propionate,Abundance associated12,13 products with of higher protein bacterial breakdown gene richness,9 and is in involved the gut14 in complex carbohydrates than animal protein.61 Clostridium spp. vitaminClostridium metabolism spp. is a genus7 belonging to the phylum Firmicutes. While LevelsCigarette of Bacteroides,smoking is associated Faecalibacterium, with increased Odoribacter, levels. and24 others enriched after ALactobacillus study on 250 kefiri vegetarian was given and to vegan 20 healthy individuals volunteers showed for interpreting the literature, careful attention should be paid to the pomegranate extract consumption in overweight-obese subjects. Serum lowerone month counts and of afterBifidobacterium the probiotic spp. was (vegan) discontinued, Bacteroides for a phylogeneticAssociated with classification reduced bacterialof this group gene due ri chnessto minor14 spelling Coffeeendotoxemia was positively marker LBPassociated was reduced. with the22 relative abundance of Clostridium, monthspp. (vegan), Bacteroides, and E. coli Barnesiella, (vegan and Clostridium, vegetarian) Veillonella.32 and differences between the taxonomic levels. Beyond the phylum level, it Lactobacillus, and Lactococcus in 23 allergic patients.25 other species were significantly reduced compared to isAlong broken with down Methanobrevibacter as follows: Class: smithii, Clostridia, certain Order: Clostridium Clostridiales and, Family: Four bacteria are enriched with aspirin use versus no medication and includes baseline samples.31 Clostridiaceae,Bacteroides spp. and can finally, produce Genus: methane Clostridium. gas.15 The Clostridium genus BacteroidesA high beef spp.,diet was Prevotella associated spp., with Barnesiella increases spp. in andBacteroides the family and Ruminococaceae. Clostridium spp. in contains more than 100 species, most of which are commensal, Furthermore,10 volunteers. Bacteroides27 spp. was seen with other medications including NSAIDs with After 12 weeks, a significant increase in Bifidobacteria, and howeverGenerally it associateddoes include with pathogens industrialized. The literature populations discusses consuming Clostridial a PPIs, and NSAIDs with antidepressants and laxatives.23 decrease in pathogenic Clostridium spp. (C. histolyticum and clustersWestern, which diet16 may include other species belonging to Eubacterium, C. coccoides clusters) were observed in 57 HIV positive Ruminococcus, Roseburia, Butyrivibrio, Faecalibacterium and other Cigarette smoking is associated with increased levels.24 adults supplemented with a prebiotic oligosaccharide genera.Bacteroides These growth clusters in cultureexist due and to propionate historic issues formation with classification, is favored at a powder (15 or 30 g short chain whereclose-to unclassified-neutral pH species of 6.5, wouldin contrast be moved to butyrate into the-producing Clostridium Red wine was positively associated with the relative abundance of Bacteroides in 23 galactooligosaccharides/long chain category.Faecalibacterium62,63 prausnitzii and Roseburia spp., which are favored at a allergic patients,25 and in 10 healthy males.26 fructooligosaccharides/pectin hydrolysate-derived acidic lower pH of 5.5.17 oligosaccharides (scGOS/lcFOS/pAOS).66 The Clostridium spp. probe is not meant to diagnose pathogenic A high beef diet was associated with increases in Bacteroides fragilis, B. vulgatus and ClostridiumPathobiont* infections. some species An add -on Clostridium difficile EIA stool test is Clostridium spp. in 10 volunteers.27 available if patient symptoms warrant testing. A ketogenic low-carbohydrate high-fat diet was associated with a reduction of Produces butyrate, acetate, hydrogen, secondary bile acids, beta- Faecalibacterium and abundance of Bacteroides and Dorea spp. in race walkers.28 glucuronidase10,64,65

Along with Methanobrevibacter smithii, certain Clostridium and Bacteroides spp. can produce methane gas.15

Necessary for immune homeostasis62

Many of its species are associated with lower bacterial gene richness.34 Coprococcus eutactus Butyrate producer13,67 Higher abundance was seen on a very low protein diet supplemented with select amino acids in patients with chronic kidney disease. C. eutactus correlated with fiber, Abundance associated with greater bacterial gene richness in the gut14 vegetable proteins, potassium, and ketoanalogs.68

3

Commensal Bacteria

Organism Description Increased Levels Decreased Levels BacteroidesFaecalibacterium-Prevotella prausnitzii group BacteroidesFaecalibacterium historically prausnitzii included belongs multiple to the taxonomic Clostridium groups cluster including IV, also AThere Bacteroides are many-dominated studies on microbiome the beneficial is positively effects of correlatedfiber and prebiotics with long on-term increasing diets TartA small cherry study juice of 10may healthy normalize subjects high showed or low levels reduced.19 F. knownPrevotella as theand Clostridium others. New leptum classification group.63,69 has separated them into F.rich prausnitzii in animal levels, protein however and saturated some studies fat.9,18 showA small mixed study results on 11 in healthy various volunteers populations. prausnitzii after 1 month on a gluten-free diet (GFD).80 Bacteroides, Prevotella, and other groups, however it is challenging to Thisshowed may that be due an animal to the -manybased strains diet increased of F. prausnitzii the abundance responding of bile to different-tolerant AnotherReduced study with didinulin not from find aJerusalem change in artichoke F. prausnitzii or chicory levels. 29 Predominantseparate many butyrate of the species-producer. For contributing this reason, tothe a Bacteroideshealthy mucosa- and substrates.microorganisms69,70 (Alistipes, Bilophila and Bacteroides) and decreased the levels of onA systematic a GFD in healthy review individuals, of inulin supplementation but did observe in a humansdecrease barrierPrevotella function group. Controlsincludes inflammationmainly Bacteroides through and inflammatory some Prevotella. 4-6 Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium inshowed abundance an increase of other in butyrateBifidobacterium,-producing and bacteria a relative in the cytokine inhibition. F. prausnitzii produces an anti-inflammatory Higherrectale andfiber Ruminococcus intake is associated bromii ).with9 higher abundance of Faecalibacterium.49,71 Fincreaseirmicutes in phylum.Faecalibacterium81 and Lactobacillus, and decrease proteinDisplays called flexibility Microbial to adapt Anti- inflammatoryto many environmental Molecule (MAM) which in relative abundance of Bacteroides.30 inhibitsconditions/diets the activation of NF-κB.70,71 LongTart cherry-term juiceconsumption may normalize of a low high-fat, or high low complex levels.19 carbohydrate diet was associated A low FODMAP diet in 52 IBD patients resulted in lower with increased abundance of F. prausnitzii, in an obese population.72 LactobacillusBifidobacterium kefiri adolescentis, was given toBifidobacterium 20 healthy volunteers longum, andfor ThereBacteroides are many consist strains of bile of -F.tolerant prausnitzii organisms that respond and has to the different capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet20 oneFaecalibacterium month and after prausnitzii the probiotic than patients was disconti on a controlnued for diet. a utilizingsubstrates polysaccharides including simple and carbohydrates, mucins.7-9 amino acids, pectin, non- Levels of Bacteroides, Faecalibacterium, Odoribacter, and others enriched after month,However, Bacteroides microbiome, Barnesiella, diversity andClostridium markers, Veillonellaof and digestive polysaccharides, and host-derived mucosal substrates.70 It Increasedpomegranate in overweight extract consumption men drinking in overweight low glycinin-obese soymilk subjects. compared Serum to regular otherinflammation species were did not significantly differ between reduced the compared IBD and control to fermentsProduces glucose beta glucuronidase, and acetate to10 produce secondary formate, bile acids, D-lactate11 acetate,, and soymilkendotoxemia or bovine marker milk LBP21 was reduced.22 baselinegroups.82 samples. Lower F.31 prausnitzii and Bifidobacterium was butyrate.propionate,71 12,13 products of protein breakdown,9 and is involved in observed in 20 patients with IBS-D or IBS-M on a low vitamin metabolism7 Levels increasedof Bacteroides, after Faecalibacterium,polydextrose and Odoribacter,soluble corn andfiber others intake enriched.73 after AFODMAP study on diet. 250 Additionally, vegetarian and total vegan SCFAs individuals and n-butyrate showed F. prausnitzii is an extremely oxygen-sensitive anaerobe. Therefore, the pomegranate extract consumption in overweight-obese subjects. Serum lowerwere lower. counts77 of Bifidobacterium spp. (vegan), Bacteroides Associateddevelopment with of a reduced therapeutic bacterial supplement gene riproveschness challenging.14 71 endotoxemiaF. prausnitzii was marker more LBP abundant was reduced. in a raffinose22 and chick pea diet compared to spp. (vegan) and E. coli (vegan and vegetarian).32 controls .69 Excess bile salt70 F.Along prausnitzii with Methanobrevibacter growth and butyrate smithii, production certain is Clostridium favored at aand lower pH Four bacteria are enriched with aspirin use versus no medication and includes inBacteroides culture, around spp. can 5. 7produce to 6.7.17,70 methane gas.15 BacteroidesInulin and inulin spp.,- Prevotellatype fructans spp., increased Barnesiella Bifidobacterium spp. and the familyand F. prausnitziiRuminococaceae..37,71,74 A A ketogenic, low-carbohydrate, high-fat diet was Furthermore,systematic review Bacteroides of inulin spp. supplementation was seen with inother humans medications showed including an increase NSAIDs in with associated with a reduction of Faecalibacterium and BeneficialGenerally bacteriaassociated with industrialized populations consuming a PPIs,Bifidobacterium, and NSAIDs and with a antidepressantsrelative increase and in Faecalibacterium laxatives.23 and Lactobacillus, and abundance of Bacteroides and Dorea spp. in competitive Western diet16 decrease in relative abundance of Bacteroides.30 race walkers.28 However another study on a ketogenic diet Cigarette smoking is associated with increased levels.24 in 6 patients with GLUT1 Deficiency Syndrome did not have 83 Bacteroides growth in culture and propionate formation is favored at a Red wine consumption was associated with an increased abundance of F. an effect on F. prausnitzii. 75 close-to-neutral pH of 6.5, in contrast to butyrate-producing Redprauznitzii wine was. In positively ten metabolic associated syndrome with patients,the relative red abundance wine polyphenols of Bacteroides significantly in 23 Faecalibacterium prausnitzii and Roseburia spp., which are favored at a allergicincreased patients the number,25 and of in fecal 10 healthy Bifidobacteria males.26 and Lactobacillus (intestinal barrier Oral versus IV iron supplementation in iron-deficient IBD lower pH of 5.5.17 protectors) and butyrate-producing bacteria (Faecalibacterium prausnitzii and patients resulted in decreased abundances of RoseburiaA high beef) at diet the was expense associated of less with desirable increases groups in Bacteroides of bacteria fragilis,such as B.LPS vulgatus producers and Faecalibacterium prausnitzii, Ruminococcus bromii, Dorea 76 84 Pathobiont* some species (ClostridiumEscherichia spp. coli andin 10 Enterobacter volunteers. 27cloacae ). spp., and Collinsella aerofaciens.

70 MostA ketogenic strains lowcan- growcarbohydrate on apple high pectin.-fat diet was associated with a reduction of Faecalibacterium and abundance of Bacteroides and Dorea spp. in race walkers.28 A decline in F. prausnitzii in 20 patients with IBS on a low FODMAP diet can be 77 recovered with supplementation of prebiotic fructo-oligosaccharides (FOS).

Physical activity at doses as low as the minimum recommended by the WHO may increase health-promoting species including Bifidobacterium spp., Roseburia hominis, Akkermansia muciniphila and Faecalibacterium prausnitzii. However, in a study comparing sedentary to active women, dietary differences were noted, which may account for the bacterial differences. The active group consumed more fiber, fruits and vegetables, and the sedentary group consumed more processed meats.78

The poorly absorbed antibiotic rifaximin was associated with increases in beneficial bacteria F. prausnitzii, Bifidobacterium, and Lactobacillus in human studies.79

4

Commensal Bacteria

Organism Description Increased Levels Decreased Levels BacteroidesLactobacillus-Prevotella spp. group BacteroidesThere are over historically 170 species included of Lactobacillus. multiple taxonomic85 Many species groups and including strains AWhey Bacteroides and pea-dominated protein, a Mediterranean microbiome is positivelydiet, polyphenols correlated (catechins, with long flavonols,-term diets ATart small cherry study juice of 10may healthy normalize subjects high showed or low levels reduced.19 arePrevotella found iandn probiotic others. supplementsNew classification and fermented has separated foods them. There into are flavones,rich in animal anthocyanins, protein and proanthocyanidins, saturated fat.9,18 A phenolic small study acids on found 11 healthy in fruits, volunteers seeds, Lactobacillus, Bifidobacterium and Bifidobacterium longum numerousBacteroides studies, Prevotella, on the and therapeutic other groups, benefit howevers of probiotics. it is challenging86 to vegetables,showed that tea, an animalcocoa, -winebased) increase diet increased beneficial the bacteriaabundance Lactobacillus of bile-tolerant and afterReduced 1 month with on inulin a gluten from- freeJerusalem diet (GFD). artichoke80 or chicory.29 separate many of the species. For this reason, the Bacteroides- microorganismsBifidobacterium. 89(Alistipes, Bilophila and Bacteroides) and decreased the levels of A systematic review of inulin supplementation in humans FermentsPrevotella carbohydratesgroup includes to mainly produce Bacteroides lactic acid and, inhibits some Prevotella.the 4-6 Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium showedHigh saturated an increase and transin Bifidobacterium,-fat, found in a and Western a relative diet , colon ization of pathogens, enhances barrier integrity, and beneficially Arectale study and using Ruminococcus a partially hydrolyzed bromii).9 guar gum preparation was administered to 15 increaseincreases in the Faecalibacterium risk of cardiovascular and Lactobacillus, disease and and reduces decrease 86 87 modulates the immune system constipated women for 3 weeks. Lactobacillus spp. increased and constipation Lactobacillus. 30 Displays flexibility to adapt to many environmental 90 in relative abundance of Bacteroides. conditions/diets improved.Tart cherry juice may normalize high or low levels.19 Both Lactobacillus and Bifidobacterium (probiotic bacteria) are involved A Western diet is associated with decreased Lactobacilli and Lactobacillus kefiri was given to 20 healthy volunteers for in the process of converting polyphenols to phytoestrogens, converting In ten metabolic syndrome patients, red wine polyphenols significantly increased the Bifidobacteria.89 Bacteroides consist of bile-tolerant organisms and has the capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet20 one month and after the probiotic was discontinued for a glucosinolates from cruciferous vegetables7-9 to isothiocyanates which number of fecal Bifidobacteria and Lactobacillus (intestinal barrier protectors) and areutilizing cytoprotective polysaccharides and antioxidative and mucins,. B vitamin production, and SCFA butyrate-producing bacteria (Faecalibacterium prausnitzii and Roseburia) at the month, Bacteroides, Barnesiella, Clostridium, Veillonella and production. 87 Along with Oxalobacter formigenes, Lactobacillus and expenseIncreased of in less overweight desirable men groups drinking of bacteria low glycinin such as soymilkLPS producers compared (Escherichia to regular coli and other species were significantly reduced compared to 10 11 21 31 BifidobacteriumProduces beta glucuronidase,are also capable o secondaryf consuming bile oxalate. acids,88 acetate, Enterobactersoymilk or bovine cloacae milk).76 baseline samples. 12,13 9 propionate, products of protein breakdown, and is involved in 7 Beneficvitaminial metabolism bacteria, probiotic ALevels systematic of Bacteroides, review of Faecalibacterium, inulin supplementation Odoribacter, in humans and others showed enriched an increase after in A study on 250 vegetarian and vegan individuals showed Bifidobacterium,pomegranate extract and a consumption relative increase in overweight in Faecalibacterium-obese subjects. and Lactobacillus, Serum and lower counts of Bifidobacterium spp. (vegan), Bacteroides Associated with reduced bacterial gene richness14 decreaseendotoxemia in relative marker abundance LBP was reduced. of Bacteroides.22 30 spp. (vegan) and E. coli (vegan and vegetarian).32

Along with Methanobrevibacter smithii, certain Clostridium and FourCoffee bacteria was positively are enriched associated with aspirin with the use relative versus abundanceno medication of Clostridium, and includes Bacteroides spp. can produce methane gas.15 BacteroidesLactobacillus, spp., and Prevotella Lactococcus spp., in 23Barnesiella allergic patients. spp. and25 the family Ruminococaceae. Furthermore, Bacteroides spp. was seen with other medications including NSAIDs with Generally associated with industrialized populations consuming a PPIs,The poorly and NSAIDs absorbed with antibiotic antidepressants rifaximin and was laxatives. associated23 with increases in beneficial Western diet16 bacteria F. prausnitzii, Bifidobacterium, and Lactobacillus in human studies.79 Pseudoflavonifractor spp. Small group made up of two species: Pseudoflavonifractor capillosus Cigarette smoking is associated with increased levels.24 Decreased in long-term users of proton pump inhibitors93 91 Bacteroidesand Pseudoflavonifractor growth in culture phocaeensis and propionate formation is favored at a close -to-neutral pH of 6.5, in contrast to butyrate-producing Red wine was positively associated with the relative abundance of Bacteroides in 23 Study participants who succeeded in losing weight consistently had a 25 26 Faecalibacterium prausnitzii and Roseburia spp., which are92 favored at a allergic patients, and in 10 healthy males. lowermicrobiota pH of enriched 5.5.17 in Pseudoflavonifractor at baseline. Roseburia spp. The genus Roseburia includes 5 species: R. intestinalis, R. hominis, R. HigherA high beefRoseburia diet was is associated associated with with consuming increases in a plantBacteroides-based fragilis, diet, Mediterranean B. vulgatus and diet R. faecis decreased on a gluten-free diet in 21 healthy inulinivorans, R. faecis and R. cecicola.71,94 and fiber-rich foods.72,96,97 volunteers.81 Pathobiont* some species Clostridium spp. in 10 volunteers.27

The Roseburia genus, along with Faecalibacterium are the predominant Roseburia increased on a resistant starch diet.98 A small study on 11 healthy volunteers showed that an 95 A ketogenic low-carbohydrate high-fat diet was associated with a reduction of butyrate producers in the human GI tract. 28 animal-based diet increased the abundance of bile-tolerant FaecalibacteriumIn ten metabolic syandndrome abundance patients, of Bacteroides red wine polyphenols and Dorea spp. significantly in race walkers. increased the microorganisms (Alistipes, Bilophila and Bacteroides) and Roseburia is involved in immune maintenance and is anti- number of fecal Bifidobacteria and Lactobacillus (intestinal barrier protectors) and decreased the levels of Firmicutes that metabolize dietary inflammatory.94 butyrate -producing bacteria (Faecalibacterium prausnitzii and Roseburia) at the plant polysaccharides (Roseburia, Eubacterium rectale and expense of less desirable groups of bacteria such as LPS producers (Escherichia coli and Ruminococcus bromii).9 Enterobacter cloacae).76 Roseburia decreased on a high-protein, low-carbohydrate Physical activity at doses as low as the minimum recommended by the WHO may weight loss diet in 14 overweight men.98 increase health-promoting species including Bifidobacterium spp., Roseburia hominis, Akkermansia muciniphila and Faecalibacterium prausnitzii. However, in a study comparing sedentary to active women, dietary differences were noted, which may account for the bacterial differences. The active group consumed more fiber, fruits and vegetables, and the sedentary group consumed more processed meats.78

5

Commensal Bacteria

Organism Description Increased Levels Decreased Levels BacteroidesRuminococcus-Prevotella spp. group BacteroidesThere are 11 historically species of Ruminococcusincluded multiple, many taxonomic in need ofgroups including AR. Bacteroidesbromii increased-dominated on a resistant microbiome starch is diet.positively81,98 correlated with long-term diets TartR. bromii cherry decreased juice may o nnormalize a gluten- highfree dietor low in 21levels healthy.19 Prevotellareclassification and others..99 New classification has separated them into rich in animal protein and saturated fat.9,18 A small study on 11 healthy volunteers volunteers.81 Bacteroides, Prevotella, and other groups, however it is challenging to showedDaily walnut that anconsumption animal-based (43 dietg) in increased 194 healthy the individuals abundance was of bile associated-tolerant with Reduced with inulin from Jerusalem artichoke or chicory.29 105 Variousseparate species many ofproduce the species short. chainFor this fatty reason, acids the butyrate Bacteroides, acetate- and microorganismsincreased abundance (Alistipes, of Ruminococcus Bilophila and and Bacteroides Bifidobacterium) and decreased. the levels of A systematicsmall study review on 11 healthyof inulin volunteers supplementation showed in that humans an 100-102 propionatePrevotella group. includes mainly Bacteroides and some Prevotella.4-6 Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium animalshowed- basedan increase diet increased in Bifidobacterium, the abundance and a of relative bile-tolerant Ruminococcus is associated with long-term fruit and vegetable consumption. Species microorganisms (Alistipes, Bilophila and Bacteroides) and rectale and Ruminococcus bromii).9 increase in Faecalibacterium and Lactobacillus, and decrease Ruminococcus has been implicated in negative health outcomes, are specialized in degrading complex carbohydrates, such as cellulose and resistant decreased the levels of Firmicutes that metabolize dietary Displays flexibility to adapt to many environmental in relative abundance of Bacteroides.30 however studies are mixed likely due to different species or strains starch, found in plant-based foods. However, it has19 also been linked to low dietary plant polysaccharides (Roseburia, Eubacterium rectale and conditions/dietshaving diverse metabolic capabilities. R. gnavus is mucolytic and fiberTart cherry consumption juice may due normalize to its ability high to or break low levelsdown. the resistant starches found in Ruminococcus bromii).9 produces an inflammatory polysaccharide.103,104 However, R. bromii refined grain products.87,106 Lactobacillus kefiri was given to 20 healthy volunteers for 20 fermentsBacteroides re sistantconsist starchof bile which-tolerant produces organisms beneficial and has butyrate. the capability101 R. of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet oneOral monthversus IVand iron after supplementation the probiotic was in irondisconti-deficientnued forIBD a champanellensisutilizing polysaccharides is known and to fermentmucins. 7cellulose,-9 cellobiose and xylan month,patients B resultedacteroides in, decreasedBarnesiella, abundances Clostridium of, Veillonella and from plants and produces acetate and succinate.100 Increased in overweight men drinking low glycinin soymilk compared to regular otherFaecalibacterium species were prausnitzii, significantly Ruminococcus reduced compared bromii, Dorea to Produces beta glucuronidase,10 secondary bile acids,11 acetate, soymilk or bovine milk21 baselinespp., and samples. Collinsella31 aerofaciens.84 propionate,Studies are mixed12,13 products as to whether of protein Ruminococcus breakdown is influenced,9 and is involved by both in vitaminanimal and metabolism plant-based7 diets. Differences in study outcomes may be Levels of Bacteroides, Faecalibacterium, Odoribacter, and others enriched after A study on 250 vegetarian and vegan individuals showed due to the presence of different Ruminococcus species. One mouse and pomegranate extract consumption in overweight-obese subjects. Serum lower counts of Bifidobacterium spp. (vegan), Bacteroides Associatedone human studywith reduced showed possiblebacterial correlation gene richness with 14Ruminococcus and endotoxemia marker LBP was reduced.22 spp. (vegan) and E. coli (vegan and vegetarian).32 TMAO levels, which is derived from animal-based dietary carnitine and 87 Alongcholine with. Methanobrevibacter smithii, certain Clostridium and Four bacteria are enriched with aspirin use versus no medication and includes Veillonella spp. TheBacteroides genera Veilspp.lonella can produce contains methane 12 Gram gas.-negative15 species. This BacteroidesPostprandial spp., levels Prevotella of lactose spp., after Barnesiella milk intake spp. in and14 healthy the family men Ruminococaceae. were positively Lactobacillus kefiri was given to 20 healthy volunteers for phylogenetic grouping is unusual as the larger Firmicutes phylum is correlated with the abundance of Veillonella.112 one month and after the probiotic was discontinued for a Furthermore, Bacteroides spp. was seen with other medications including NSAIDs with comprised of Gram-positive bacteria.107 V. parvula is often isolated month, Bacteroides, Barnesiella, Clostridium, Veillonella and Generally associated with industrialized populations consuming a PPIs, and NSAIDs with antidepressants and laxatives.23 from the human16 oral cavity and has also been found in the intestinal The family Veillonellaceae increased with supplemental polydextrose and soluble corn other species were significantly reduced compared to Westerntract. Like diet other gram-negative bacteria, it produces LPS and in the fiber in 20 healthy adult males.113 This family includes genera other than Veillonella, baseline samples.31 24 oral cavity it is known to produce biofilm.108,109 althoughCigarette Veillonellasmoking is representsassociated thewith majority increased of thislevels. family .107 Bacteroides growth in culture and propionate formation is favored at a The family Veillonellaceae was decreased on a gluten-free closeUtilizes-to lactate-neutral to pH produce of 6.5, SCFAsin contrast acetate to butyrateand propionate-producing;64,110 H2 RedVeillonella wine was spp. positively increased associated following withRoux the-en -relativeY gastric abundance bypass RYGB of Bacteroides within the firstin 23 diet in 21 healthy volunteers.81 This family includes genera Faecalibacteriumproducer111 prausnitzii and Roseburia spp., which are favored at a 3allergic months patients and remained,25 and in elevated 10 healthy for malesthe first.26 year.114 other than Veillonella, although Veillonella represents the lower pH of 5.5.17 majority of this family.107 Bifidobacterium spp. Many species and strains are found in probiotic supplements and there WheyA high and beef pea diet protein was associated increase beneficial with increases bacteria in Bacteroides Lactobacillus fragilis, and Bifidobacterium. B. vulgatus and89 Cigarette smoking is associated with decreased levels.24 Pathobiont*are extensive some studies species on the therapeutic benefits of probiotics. Clostridium spp. in 10 volunteers.27 Probiotics can beneficially modulate the microbiome and immune Human studies on individuals consuming partially hydrolyzed guar gum show an A high beef diet was associated with a decrease in B. system.115 increaseA ketogenic in Bifidobacterium low-carbohydrate and high butyrate-fat diet-producing was associated bacteria. with118-120 a reduction of adolescentis in 10 volunteers.27 Faecalibacterium and abundance of Bacteroides and Dorea spp. in race walkers.28 Both Lactobacillus and Bifidobacterium (probiotic bacteria) are involved Da ily walnut consumption (43 g) in 194 healthy individuals was associated with A low FODMAP diet in 52 IBD patients resulted in lower 105 in the process of converting polyphenols to phytoestrogens, converting increased abundance of Ruminococcus and Bifidobacterium. Bifidobacterium adolescentis, Bifidobacterium longum, and glucosinolates from cruciferous vegetables to isothiocyanates which Faecalibacterium prausnitzii than in patients on a control

are cytoprotective and antioxidative, B vitamin production, and SCFA Red wine polyphenol intake for 4 weeks in 10 healthy males was associated with diet. However, microbiome diversity and markers of production.87 Along with Oxalobacter formigenes, Lactobacillus and increased Bifidobacterium.26 In ten metabolic syndrome patients, red wine inflammation did not differ between the IBD and control Bifidobacterium are also capable of consuming oxalate.88 polyphenols significantly increased the number of fecal Bifidobacteria and groups.82 Lower F. prausnitzii and Bifidobacterium was Lactobacillus (intestinal barrier protectors) and butyrate-producing bacteria observed in 20 patients with IBS-D or IBS-M on a low Bifidobacteria can prevent GI infections by competitive exclusion of (Faecalibacterium prausnitzii and Roseburia) at the expense of less desirable groups of FODMAP diet. Additionally, total SCFAs and n-butyrate pathogens.115 They are equipped with genes related to carbohydrate bacteria such as LPS producers (Escherichia coli and Enterobacter cloacae).76 were lower.77 Another study in patients with functional GI metabolism from plants in the diet, milk oligosaccharides, and host- disorders with flatulence compared a low FODMAP diet derived glycans. They produce acetate that facilitates the cross-feeding The prebiotic effects of FOS, GOS, inulin, and lactulose have been thoroughly assessed with the effects of a prebiotic supplement. Bifidobacterium of other bacteria, including butyrate-producers.71 They also produce in human trials and suggest a beneficial impact on the microbiome by increasing was reduced in the low FODMAP group and increased in the lactic acid.116 Bifidobacterial levels and decreasing E. coli and enterococci.115 A systematic review of prebiotic group.121 inulin supplementation in humans showed an increase in Bifidobacterium, and a

6

Commensal Bacteria

Organism Description Increased Levels Decreased Levels Bacteroides-Prevotella group BacteroidesAlong with Collinsellahistorically, can included modify multiple bile acids taxonomic to modulate groups the including virulence Arelative Bacteroides increase-dominated in Faecalibacterium microbiome and is positivelyLactobacillus, correlated and decrease with long in relative-term diets TartA small cherry study juice of 10may healthy normalize subjects high showed or low levels reduced.19 andPrevotella pathogenicity and others. of enteric New classification pathogens117 has separated them into richabundance in animal of Bacteroides.protein and 30saturated fat.9,18 A small study on 11 healthy volunteers Lactobacillus, Bifidobacterium and Bifidobacterium longum Bacteroides , Prevotella, and other groups, however it is challenging to showed that an animal-based diet increased the abundance of bile-tolerant afterReduced 1 month with on inulin a gluten from- freeJerusalem diet (GFD). artichoke80 or chicory.29 separateBeneficial many bacteria, of the probiotic species . For this reason, the Bacteroides- Physicalmicroorganisms activity at(Alistipes, doses as Bilophila low as the and minimum Bacteroides recommended) and decreased by the the WHO levels may of A systematic review of inulin supplementation in humans Prevotella group includes mainly Bacteroides and some Prevotella.4-6 increaseFirmicutes health that -metabolizepromoting speciesdietary plantincluding polysaccharides Bifidobacterium (Roseburia, spp., Roseburia Eubacterium hominis, showedA study onan 2increase50 vegetarian in Bifidobacterium, and vegan individuals and a relative showed Akkermansiarectale and Ruminococcus muciniphila and bromii Faecalibacterium).9 prausnitzii. However, in a study increaselower counts in Faecalibacterium of Bifidobacterium and spp. Lactobacillus, (vegan), Bacteroides and decrease 32 Displays flexibility to adapt to many environmental comparing sedentary to active women, dietary differences were noted, which may inspp. relative (vegan) abundance and E. coli of (vegan Bacteroides. and vegetarian)30 . conditions/diets Tartaccount cherry for juicethe bacterial may normalize differences. high Theor low active levels group.19 consumed more fiber, fruits and 78 vegetables, and the sedentary group consumed more processed meats. Lactobacillus kefiri was given to 20 healthy volunteers for Bacteroides consist of bile-tolerant organisms and has the capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet20 one month and after the probiotic was discontinued for a 7-9 The poorly absorbed antibiotic rifaximin was associated with increases in beneficial utilizing polysaccharides and mucins. 79 month, Bacteroides, Barnesiella, Clostridium, Veillonella and Increasedbacteria F. inprausnitzii, overweight Bifidobacterium, men drinking lowand glycininLactobacillus soymilk in human compared studies. to regular other species were significantly reduced compared to Bifidobacterium longum Bifidobacterium longum is comprised10 of multiple subspecies11 the Long-term consumption21 of Mediterranean diet partially restored B. longum in B. longum and B. adolescentis31 suppressed by rice in 26 Produces beta glucuronidase, secondary115,122 bile acids, acetate, soymilk or bovine milk 123 baseline samples. beneficiallypropionate, modulate12,13 products the immune of protein system breakdown. It ,is9 andfound is ininvolved probiotic in m etabolic syndrome patients. Mongolian individuals who consumed wheat, rice, and oat supplements and fermented foods. as the sole carbohydrate staple food for a week each.60 vitamin metabolism7 Levels of Bacteroides, Faecalibacterium, Odoribacter, and others enriched after A study on 250 vegetarian and vegan individuals showed

pomegranate extract consumption in overweight-obese subjects. Serum lower counts of Bifidobacterium spp. (vegan), Bacteroides Lactate producer; acetate producer A low FODMAP diet in 52 IBD patients resulted in lower Associated with reduced bacterial gene richness14 endotoxemia marker LBP was reduced.22 spp. (vegan) and E. coli (vegan and vegetarian).32 Bifidobacterium adolescentis, Bifidobacterium longum, and

Utilizes diet-derived carbohydrates115 Faecalibacterium prausnitzii than patients on a control diet. Along with Methanobrevibacter smithii, certain Clostridium and Four bacteria are enriched with aspirin use versus no medication and includes 15 However, microbiome diversity and markers of BacteroidesBeneficial bacteria, spp. can probiotic produce methane gas. Bacteroides spp., Prevotella spp., Barnesiella spp. and the family Ruminococaceae. inflammation did not differ between the IBD and control Furthermore, Bacteroides spp. was seen with other medications including NSAIDs with groups.82 23 Generally associated with industrialized populations consuming a PPIs, and NSAIDs with antidepressants and laxatives. 16 Western diet A small study of 10 healthy subjects showed reduced 24 Cigarette smoking is associated with increased levels. Lactobacillus, Bifidobacterium and Bifidobacterium longum Bacteroides growth in culture and propionate formation is favored at a after 1 month on a gluten-free diet (GFD).80 Collinsella aerofaciens Possiblyclose-to- proinflammatoryneutral pH of 6.5,, inm aycontrast play a torole butyrate in altering-producing intestinal barrier RedHigher wine C. aerofacienswas positively levels associated in healthy with adults the relativeconsuming abundance a whole of grain Bacteroides diet (40 ing 23 Decreased on a high-protein, low-carb weight loss diet in a integrityFaecalibacterium124,125 prausnitzii and Roseburia spp., which are favored at a allergicfiber) compared patients ,to25 anda red in meat 10 healthy diet.128 males Studies.26 are mixed on the association with fiber study in 14 overweight men.98 lower pH of 5.5.17 and the Collinsella genus,129 which contains at least 6 species.130 Produces H2, ethanol, short-chain fatty acids including butyrate, and A high beef diet was associated with increases in Bacteroides fragilis, B. vulgatus and C. aerofaciens reduced in elderly subjects taking NSAIDs lactatePathobiont* and is some a major species utilizer of lactose.117,126 HigherClostridium levels spp. were in 10found volunteers. in non-vegetarian27 versus vegetarian Thai adults that were compared to elderly subjects not taking NSAIDs, or in young healthy .131 adults.132 Contains bile salt hydrolases to metabolize bile,35 and along with A ketogenic low-carbohydrate high-fat diet was associated with a reduction of Bifidobacterium, can modify bile acids to modulate the virulence and Faecalibacterium and abundance of Bacteroides and Dorea spp. in race walkers.28 Oral versus IV iron supplementation in iron-deficient IBD pathogenicity of enteric pathogens.117 patients resulted in decreased abundances of Faecalibacterium prausnitzii, Ruminococcus bromii, Dorea Consumes oligosaccharides and simple sugars127 spp., and Collinsella aerofaciens.84 Desulfovibrio piger Desulfovibrio piger is Gram-negative and the most common sulfate- A study on sigmoid biopsies from 9 healthy subjects over 9 months showed D. piger was reduced with supplemental Lactobacillus reducing bacteria (SRB) in healthy adults. Although SRB are positively correlation with Desulfovibrio spp. and red meat and cholesterol intake.136 The plantarum.137 associated with inflammation, both pro- and anti-inflammatory Desulfovibrio genus contains several species, so it is not clear whether this correlation signaling have been attributed to H2S.127 pertains to D. piger, specifically. A study on 10 healthy individuals showed reduction of H2S with bismuth subsalicylate. The study only looked at H2S Utilizes H2 and lactate and releases acetate and hydrogen sulfide levels, not bacterial composition.138 (H2S). H2S is highly toxic to colonic mucosa. H2S may create colonic cellular energy deficiency by inhibiting the beta-oxidation of A diet containing whole grains, traditional Chinese butyrate.133,134 May work together with Collinsella aerofaciens, a medicinal foods and prebiotics was given to 93 overweight hydrogen producer.127 individuals and resulted in a decrease in the family Desulfovibrionaceae.139 The Desulfovibrionaceae family

7

Commensal Bacteria Organism Description Increased Levels Decreased Levels Bacteroides-Prevotella group BacteroidesH2S can be derivedhistorically from included sulfur compounds multiple taxonomic in the diet groups including including sulfur - A Bacteroides-dominated microbiome is positively correlated with long-term diets Tartcontains cherry several juice mayspecies, normalize so it is nothigh clear or low whether levels .this19 containingPrevotella and amino others. acids New or endogenous classification mucin. has separated133 Sulfate them and sulfiteinto are rich in animal protein and saturated fat.9,18 A small study on 11 healthy volunteers correlation pertains to D. piger, specifically. Bacteroidesused as preservatives,, Prevotella, additives and other and groups, antioxidants however in it foods is challenging such as to showed that an animal-based diet increased the abundance of bile-tolerant Reduced with inulin from Jerusalem artichoke or chicory.29 separatebread, preserved many of meat,the species dried. fruit, For this carrageenan, reason, the and Bacteroides wine, and- is also microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of A systematic review of inulin supplementation in humans 127 Prevotellapresent in groupthe supplement includes mainly chondroitin Bacteroides sulfate. and some Prevotella.4-6 Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium showed an increase in Bifidobacterium, and a relative rectale and Ruminococcus bromii).9 increase in Faecalibacterium and Lactobacillus, and decrease Displays resistance to most broad-spectrum antibiotics, as H2S is a 30 Displays flexibility to adapt to many environmental135 in relative abundance of Bacteroides. conditions/dietsdefense mechanism against antimicrobials Tart cherry juice may normalize high or low levels.19

Lactobacillus kefiri was given to 20 healthy volunteers for Pathobiont* Bacteroides consist of bile-tolerant organisms and has the capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet20 one month and after the probiotic was discontinued for a Escherichia coli Escherichia coli is a Gram-negative facultative anaerobe.140 Many strains A small study of 10 healthy subjects showed increased E. coli and reduced In ten metabolic syndrome patients, red wine polyphenols utilizing polysaccharides and mucins.7-9 month, Bacteroides, Barnesiella, Clostridium, Veillonella and belong to the species Escherichia coli, and most strains are harmless, Lactobacillus, Bifidobacterium and Bifidobacterium longum after 1 month on a gluten- significantly increased the number of fecal Bifidobacteria Increased in overweight80 men drinking low glycinin soymilk compared to regular other species were significantly reduced compared to normal GI inhabitants. The Escherichia10 coli probe is not meant11 to free diet (GFD). 21 and Lactobacillus (intestinal31 barrier protectors) and Producesdiagnose pathogenic beta glucuronidase, E. coli infections. secondary An add bile-on shigaacids,-toxin acetate, soymilk or bovine milk baselinebutyrate -samples.producing bacteria (Faecalibacterium prausnitzii 12,13 9 propionate,producing E. coli EIAproducts stool test of proteinis available breakdown if patient, symptoms and is involved warrant in and Roseburia) at the expense of less desirable groups of 7 vitamintesting. metabolism Levels of Bacteroides, Faecalibacterium, Odoribacter, and others enriched after Abacteria study on such 250 as vegetarian LPS producers and (veganEscherichia individuals coli and showed pomegranate extract consumption in overweight-obese subjects. Serum lowerEnterobacter counts cloacaeof Bifidobacterium).76 spp. (vegan), Bacteroides AssociatedH2S producer with,135 E reducedthanol producer bacterial which gene may richness promote14 gut endotoxemia marker LBP was reduced.22 spp. (vegan) and E. coli (vegan and vegetarian).32 permeability ,141 Produces vitamin K and vitamin B12.140 A study on 250 vegetarian and vegan individuals showed Along with Methanobrevibacter smithii, certain Clostridium and Four bacteria are enriched with aspirin use versus no medication and includes lower counts of Bifidobacterium spp. (vegan), Bacteroides BacteroidesBoth commensal spp. can and produce pathogenic methane strains gas. capable15 of biofilm production. Bacteroides spp., Prevotella spp., Barnesiella spp. and the family Ruminococaceae. spp. (vegan) and E. coli (vegan and vegetarian). E. coli was The presence of mucin stimulates biofilm formation and E. coli utilizes Furthermore, Bacteroides spp. was seen with other medications including NSAIDs with lower in groups with lower stool pH, as seen in higher Generallymono-, disaccharides associated and with other industrialized simple glycoprotein populations degradation consuming a PPIs, and NSAIDs with antidepressants and laxatives.23 carbohydrate and fiber diets.32 moleculesWestern diet to form16 the biofilm.142 Cigarette smoking is associated with increased levels.24 The prebiotic effects of FOS, GOS, inulin, and lactulose have BacteroidesE. coli has been growth associated in culture with and intestinal propionate inflammatory formation disordersis favored in at a been thoroughly assessed in human trials and suggest a 142 closeanimal-to and-neutral human pH studies. of 6.5, in contrast to butyrate-producing Red wine was positively associated with the relative abundance of Bacteroides in 23 beneficial impact on the microbiome by increasing Faecalibacterium prausnitzii and Roseburia spp., which are favored at a allergic patients,25 and in 10 healthy males.26 Bifidobacterial levels and decreasing E. coli and 115 Consumes oligosaccharides17 and simple sugars and ferments amino enterococci. lower127 pH of 5.5. acids . Consumes oxygen, thus maintaining an environment for A high beef diet was associated with increases in Bacteroides fragilis, B. vulgatus and strictly anaerobic bacteria. Competitively excludes pathogens.140 Pathobiont* some species Clostridium spp. in 10 volunteers.27

E. coli Nissle is a probiotic that has a protective effect on the intestinal 143,144 A ketogenic low-carbohydrate high-fat diet was associated with a reduction of barrier and can ameliorate certain GI disorders. 28 Faecalibacterium and abundance of Bacteroides and Dorea spp. in race walkers. E. coli thrives in higher stool pH environments, as seen in omnivorous diets higher in animal protein.32

Pathobiont* some species Oxalobacter formigenes Gram negative anaerobic bacteria that depends on oxalate metabolism Sensitive to and reduced with commonly used antibiotics.88 for energy. Key bacterium responsible for the degradation of oxalate, therefore reducing oxalate absorption, oxalate excretion in urine, and the risk of calcium oxalate kidney stones developing.88,145

Lactobacillus and Bifidobacterium are also capable of consuming oxalate.88

8

Commensal Bacteria

Organism Description Increased Levels Decreased Levels BacteroidesMethanobrevibacter-Prevotella smithii group BacteroidesMethanobrevibacter historically smithii included is not multiple a bacteria, taxonomic but rather groups an archaea, including and AM. Bacteroides smithii is present-dominated in milk microbiome products and is positively their consumption correlated maywith determine long-term archael diets TartA smaller cherry study juice on may 11 normalize prediabetic, high obese or low patients levels .who19 were Prevotellais the most and common others. methanogen New classification in humans. has separated146 It uses themCO2 and into H2 to richgut colonizationin animal protein in children. and saturated150 fat.9,18 A small study on 11 healthy volunteers treated with Rifaximin and Neomycin eradicated M. smithii Bacteroidesproduce methane, Prevotella, gas.147 and M. other smithii groups, levels correlatehowever itwith is challenging breath to showed that an animal-based diet increased the abundance of bile-tolerant andReduced lower withed breath inulin methane from Jerusalem levels. Additionally, artichoke or chicoryLDL, total.29 146 152 separatemethane manylevels. of the (This species correlation. For this was reason, also observed the Bacteroides in an internal- microorganismsMethanobrevibacter (Alistipes, levels Bilophilawere positively and Bacteroides associated) and with decreased diets high the in levels of cholesterolA systematic, and review insulin of inulin levels supplementation improved. in humans 151 PrevotellaGenova data group analysis.) includes mainly Bacteroides and some Prevotella.4-6 Firmicutescarbohydrates. that metabolize dietary plant polysaccharides (Roseburia, Eubacterium showed an increase in Bifidobacterium, and a relative rectale and Ruminococcus bromii).9 Statinsincrease are in beingFaecalibacterium studied for andtheir Lactobacillus, ability to lower and decrease Certain Clostridium and Bacteroides spp. can produce methane gas.15 methanogen and thus, methane levels.147 Displays flexibility to adapt to many environmental in relative abundance of Bacteroides.30

conditions/diets Tart cherry juice may normalize high or low levels.19 Methane has been associated with constipation, possibly due to the Twenty-one healthy adults received a probiotic containing gasotransmitter effect on intestinal transit.15 Lactobacillus andkefiri Bifidobacterium was given to 20 strains healthy for volunteers 60 days and for 20 Bacteroides consist of bile-tolerant organisms and has the capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet oneabundance month andof Methanobrevibacter after the probiotic was reduced.discontinued153 for a 7-9 utilizingIt is suggested polysaccharides that since andmethanogens mucins. consume hydrogen, flatulence month, Bacteroides, Barnesiella, Clostridium, Veillonella and is reduced through a 4:1 conversion of hydrogen gas to methane gas.148 Increased in overweight men drinking low glycinin soymilk compared to regular other species were significantly reduced compared to Produces beta glucuronidase,10 secondary bile acids,11 acetate, soymilk or bovine milk21 baseline samples.31 Mpropionate,. smithii is strongly12,13 products associated of protein with the breakdown presence ,of9 and the isparasite involved in Blastocystis.vitamin metabolism149 (This correlation7 was also observed in an internal Levels of Bacteroides, Faecalibacterium, Odoribacter, and others enriched after A study on 250 vegetarian and vegan individuals showed Genova data analysis.) pomegranate extract consumption in overweight-obese subjects. Serum lower counts of Bifidobacterium spp. (vegan), Bacteroides Associated with reduced bacterial gene richness14 endotoxemia marker LBP was reduced.22 spp. (vegan) and E. coli (vegan and vegetarian).32 Pathobiont* Fusobacterium spp. AlongThe genus with Fusobacterium Methanobrevibacter has approximately smithii, certain 20 Clostridiumspecies.154 Though and FourLow fiber,bacteria high are fat enriched diet in Africans with aspirin was associateduse versus withno medication an increase and of includesF. nucleatum .157 The green and black tea extracts (EGCG) and theaflavins mostBacteroides of the spp.members can produce of the F methaneusobacterium gas. 15genus are normal Bacteroides spp., Prevotella spp., Barnesiella spp. and the family Ruminococaceae. decreased the adherence of F. nucleatum to oral epithelial commensals, the genus also comprises some questionably pathogenic Furthermore, Bacteroides spp. was seen with other medications including NSAIDs with cells and attenuated F. nucleatum-mediated hemolysis and 158 speciesGenerally – ( F.associated nucleatum with has someindustrialized association populations with colorectal consuming cancer). a PPIs, and NSAIDs with antidepressants and laxatives.23 H2S production. Although the prevalence of Fusobacterium is higher in fecal samples in Western diet16 patients with CRC, Fusobacterium is a passenger that multiplies in the Levels of Fusobacteria decreased after ingestion of barley Cigarette smoking is associated with increased levels.24 more favorable conditions caused by malignancy rather than a causal β-glucans (whole grain barley pasta and durum wheat factorBacteroides in cancer growth development in culture. and Commensal propionate Fusobacterium formation is are favored also at a flour).159 foundclose-to in- theneutral oral pHcavity of 6.5, and in have contrast been to implicated butyrate- inproducing periodontal Red wine was positively associated with the relative abundance of Bacteroides in 23 25 26 diseaseFaecalibacterium.155 prausnitzii and Roseburia spp., which are favored at a allergic patients, and in 10 healthy males. No statistically significant associations were found between 17 lower pH of 5.5. dietary and lifestyle exposures except for a positive May be proinflammatory; some species produce butyrate and H2S135,156 A high beef diet was associated with increases in Bacteroides fragilis, B. vulgatus and association between higher BMI and inverse association Pathobiont* some species Clostridium spp. in 10 volunteers.27 between vegetable consumption and Fusobacterium in Pathobiont* some species advanced adenoma patients.155 Akkermansia muciniphila Mucin degrading bacteria.160 Low levels associated with obesity, ResveratrolA ketogenic supplementation low-carbohydrate led high to -increasefat diet wasA. muciniphila associated in with obese, a reduction insulin- resistantof Lower abundance on low FODMAP diet63,168 diabetes, inflammation, and gut permeability.71 FaecalibacteriumUSA Caucasians, but and not abundance other ethnic of Bacteroides groups.163 and Dorea spp. in race walkers.28

Produces acetate and propionate – supports the growth of butyrate Pomegranate (1000 mg of pomegranate extract daily) increased levels of Akkermansia 164 producers by degrading mucin and providing acetate. Can use in 20 healthy participants. pseudovitamin B12 produced by other bacteria for its propionate production.160 Significant increase in A. muciniphila after inulin and butyrate supplementation in 60 overweight and obese diabetic patients.165 May limit toxicity of sulfate-reducing bacteria – there is a release of sulfate during mucin degradation. This sulfate might be used by Akkermansia increased with polydextrose – but lowered Ruminococcus and sulfate-reducing bacteria, producing hydrogen sulfide. In turn, A. Coprococcus.73 muciniphila predictively harbors genes in L-cysteine biosynthesis using hydrogen sulfide, suggesting that it has a role in the detoxification of In a study on 28 patients with diabetes, those taking metformin had higher hydrogen sulfide in the intestines.161 Akkermansia compared to those not taking metformin.166

In development as a probiotic supplement for metabolic conditions162

9

Commensal Bacteria

Organism Description Increased Levels Decreased Levels Bacteroides-Prevotella group BacteroidesBeneficial bacteria historically included multiple taxonomic groups including APhysical Bacteroides activity-dominated at doses asmicrobiome low as the isminimum positively recommended correlated with by long the WHO-term may diets Tart cherry juice may normalize high or low levels.19 Prevotella and others. New classification has separated them into richincrease in animal health protein-promoting and saturated species including fat.9,18 A Bifidobacteriumsmall study on 11 spp., healthy Roseburia volunteers hominis, Bacteroides, Prevotella, and other groups, however it is challenging to showedAkkermansia that anmuciniphila animal-based and Faecalibacterium diet increased the prausnitzii. abundance However, of bile- tolerantin a study Reduced with inulin from Jerusalem artichoke or chicory.29 separate many of the species. For this reason, the Bacteroides- microorganismscomparing sedentary (Alistipes, to active Bilophila women, and dietary Bacteroides differences) and decreased were noted, the whichlevels mayof A systematic review of inulin supplementation in humans 4-6 account for the bacterial differences. The active group consumed more fiber, fruits and Prevotella group includes mainly Bacteroides and some Prevotella. Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium78 showed an increase in Bifidobacterium, and a relative rectalevegetables, and Ruminococcus and the sedentary bromii group).9 consumed more processed meats. A study on a increase in Faecalibacterium and Lactobacillus, and decrease group of 40 rugby players showed higher proportions of Akkermansia compared with Displays flexibility to adapt to many environmental in relative abundance of Bacteroides.30 higher BMI controls. Athletes consumed more protein in the form of meat and protein conditions/diets Tart cherry juice may normalize high or low levels.19 supplements, as well as more vegetables, fiber, and mono/polyunsaturated fats.167 Lactobacillus kefiri was given to 20 healthy volunteers for Bacteroides consist of bile-tolerant organisms and has the capability of Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet20 one month and after the probiotic was discontinued for a REFERENCES 7-9 utilizing polysaccharides and mucins. month, Bacteroides, Barnesiella, Clostridium, Veillonella and 1. Hornef M. Pathogens, commensal symbionts, and pathobionts: discovery and functional effects on the host. ILAR journal. Increased in overweight men drinking low glycinin soymilk compared to33. regular Cuiv PO, Klaassens ES, Durkinother AS, specieset al. 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