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TheScoop!
ThankyouforbeingamemberofTheBioCollectiveandhelpingusmakeconnectionstothemicrobiomeandhealth.

Youmightbewonderinghowmicrobescanbesoimportanttoyourhealth.Believeitornotthereare10timesas
manymicrobialcellsthanhumancellsinyourbody.Thesemicrobestinyorganismsincludingbacteriaareessential
for digestion, making vitamins and metabolites, brain and immune system health, and fighting bad pathogens. You
andyoursampleareapartofthetinyrevolutionthatismicrobiomescience!Everyonespoopismadeupofmicrobes.
Thelatestestimateapproximatesthatthereare100trillionbacterialivinginyourlargeintestine(abitoftrivia100
trillion bacteria weigh 3 pounds!). We used a DNA sequencing technique that detects the groups of bacteria that
makeupthemajorityofyourgutmicrobiome.(Sobacterialgroupswithlowabundancewontbeseeninyourreport).
WethencomparedthetypesandamountofbacteriainyoursampletoabunchofotherpoopersfromtheAmerican
GutprojectsothatyouhaveasenseofhowyoucomparetootherpeopleintheUS.


Yourgutmicrobiomeislikeafingerprintveryspecificanduniquetoyou.Whatsimportantisthatyouhaveavariety
ofbacteriainyourgutthatarehelpingtokeepyouhealthy.Asupereasywaytokeeptrackofyourbowelhealthisto
pay attention to the number and consistency your bowel movements. Poop that is too dry or too watery for long
periodsoftimetogetherwithlowenergy,feelingbadand/ornauseamightsignalthatitstimetocheckinwithyour
healthcareprovider.


Learnmoreaboutthemicrobiomebyclickinghere:http://www.thebiocollective.com/microbiome101

Disclaimer:Resultsarenotintendedfordiagnosticpurposes.Ifyouhavequestionsorconcernsaboutyourhealth,talk
toyourhealthcareprovider.
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Wedividedyourresultsintocategoriesthatareimportantforhealth.Bluebarsshowyourresultsandtheorangebars
representtheAmericanGut.Thebiggerthebarthemorebacteriainthatcategory.Onlythemostabundantbacterial
groups(>1%relativeabundance)arelistedandonlyshowtherelativeabundancenottheabsoluteamountofeach
bacterialgroupisshown.

Keep in mind that these sequencing results identify bacteria to genus level only and do not distinguish between
speciesand/orstrains,whichmaybehavequitedifferently.GermanShepherdsandChihuahuasbelongtothesame
species,butareclearlydifferentanimals!

Western/NonVegetariandiet

RuminococcusandBacteroides

Thetypicalwesterndietiscomposedofabout50%carbohydrates,15%protein,and35%fat.Itisrichinred
meat and dairy while being low in fruits and vegetables. This dietary composition favors bacterial groups such as
RuminococcusandBacteriodes,astheyhelpdigestcomplexcarbohydratesandanimalfats.
The group Ruminococcus is important for the digestion of resistant starches. Some foods that are high in
resistant starches include whole grains, beans, fruits, and vegetables. Resistant starches are a kind of carbohydrate
thatisnotdigestedintosmallsugarmoleculesinthesmallintestine,butratherarefermentedinthelargeintestine.
Thismeansthattheyaredigestedmoreslowlythancarbohydratesthatcanbequicklyandeasilybrokendown.The
slowerdigestionmakesresistantstarcheslesslikelytocauseabloodsugarspike,whichcanlaterleadtoasugarcrash,
leavingyoufeelinglethargicandfatigued.Ruminococcusisoneoftheprimaryfermentersofresistantstarchesinthe
largeintestine.TheproductsreleasedbythedegradationofresistantstarchbyRuminococcusareimportantforboth
thehealthofothergutmicrobiotaandyourintestines!(SeeSCFAformore).
Bacteroidesareanothergroupofbacteriathatareinvolvedincomplexsugarandproteinfermentationinthe
large intestine. They are part of an infants very first colonization of microflora. Not only are they a part of the
placentalmicrobiome,buttheyarealsothenpassedfrommothertochildasthechildtravelsthroughthebirthcanal.
Laterinlife,havingagutmicrobiomehighinBacteroidesisthoughttobeindicativeofalongtermdiethighinprotein
andanimalfats.Commonsourcesofproteinandanimalfatinthewesterndietareeggs,dairy,andbeef.

Plantbased/VegetarianDiet

Prevotella,Paraprevotella

Sinceavegetariandietremovesallmeat,individualswhoeatthiswayconsumelessproteinandanimalfats
than nonvegetarians do. Additionally, because meat in the diet is often times replaced with increased amounts of
fruits,vegetablesandbeanstheamountoffibertheindividualiseatingincreasesalso.Increasedconsumptionoffiber
and complex carbohydrates, such as those found in fruits and vegetables, are associated with higher levels of the
groupPrevotellainthegut.Prevotellamayalsoplayaroleinimprovedglucosemetabolismfollowingconsumptionof
barleykernel based bread, primarily through promoting increased glycogen storage. Glucose metabolism is a
mechanismbywhichcellsgetenergyfromthefoodyoueat.Disordersofglucosemetabolismcanresultindiseases
suchasdiabetes.Improvedglucosemetabolismincreasestheamountofenergyyourcellsgetfromyourdiet.
Prevotellaisfoundnotonlyinthegut,butinthemouthandvaginaaswell.Thoughtherelationshipbetween
Prevotallaandthehumanhostisoftencommensal,thisbacterialgroupalsocontainssomeopportunisticpathogens.
Some species have been associated with chronic inflammatory conditions such as arthritis, and oral disease such as
gingivitis.Generally,though,Prevotellaandthehumanhostcoexistharmlessly.

ComplexcarbohydratereducingandSCFAproducing

Clostridium,Blautia,Faecalibacterium,Rosebuira,Lachnospira,Coprococcus,Dialster,Parabacteroides,Eubacterium

Whenweingestfoodsthatarehighincomplexcarbohydratesandfiberourbodiescannotfullydigestthemin
our stomach and small intestine as it can with most other foods. Instead, we rely upon the bacterial groups listed
abovetohelpusgetnutritionfromcomplexcarbohydrates.Carbohydratesthatcanbeeasilybrokendownintosmall
sugarmoleculesarepassedthroughtheintestinalwallandabsorbedintoourbloodstream,providingourbodywith
energyandnutrition.However,ifconsumedingreatquantitiesthiscouldcauseaspikeinbloodglucoselevels.This
doesnothappenaftereatingcomplexcarbohydrates.
Complexcarbohydratesaremadeupofresistantstarches,namedfortheirabilitytoresistquickdigestionin
the small intestine. These foods make their way into the large intestine, or bowel, where many different bacterial
groups ferment them. Although your body alone cannot digest resistant starches, they become food that nourishes
your microbiome. The fermentation products of the initial bacterial fermenter become food for the next fermenter
andsoonasthestarchisbrokendownintosmallerandsmallerpieces.Thefinalfermentationproductiswhatscalled
shortchainfattyacids,orSCFA.
SCFAareimportantforkeepingtheguthealthybecausetheyaretheprimaryenergysourceforintestinalcells.
OnesuchSCFAisamoleculecalledbutyrate(commonproductofRoseburiagroup),whichisanimportantmolecule
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formaintainingintestinalhealth.Butyratehasseveralimportantfunctionsinthegut,andhasantiinflammatoryand
anticancerous properties. It increases blood flow to the lining of the intestine, keeping those cells healthy. It also
marks DNA damage in a cell, which can induce apoptosis, or programmed cell death, to prevent the buildup of
harmfulmutationsthatcouldeventuallyleadtoacancer.
Having increased or decreased levels of some of these bacterial groups is also associated with different diseases.
Clostridium is part of a healthy gut microbiome, but children with autism have been found to have higher levels of
somespecies.Conversely,Eubacteriumstrainshavebeenfoundtobelowerinchildrenwithautism.Eubacteriumare
allpartofourinitialmicroflorafollowingbirth,andareatparticularlyhighlevelsduringawomansfirsttrimesterof
pregnancy.Groupsassociatedwithantiinflammatoryproperties,suchasRoseburiaandParabacteroides,havebeen
foundtobelowerinthosewithirritableboweldisease(IBD),ulcerativecolitis,andliverdisease.

Probiotics

Bifidobacterium, Lactobacillus, Escherichia coli (E. coli), Streptococcus, and Lactococcus lactis, Enterococcus,
Pediococcus,

If you think about the microbiome as an ecosystem similar to the Earths ecosystem, you can begin to
comprehend the complexity that is the gut microbiota. Like any other ecosystem, the health and diversity of our
microbiome is governed by the availability of resources and competition for those resources. With the myriad of
antibacterial soaps, highly processed foods, and heavy antibiotic use, our industrialized, modern culture isnt very
conduciveformaintainingahealthy,diversemicrobiome.Andresearchersbelievethatthislackofdiversityinourgut
isabigclueintowhysomanyofusareafflictedbychronicdisease.
Probioticsarefoundinmanynaturalandfermentedfoodssuchasyogurt.Probioticsupplementshavebeen
successfullyusedtohelprecolonizeandbalancethegut,andtheycanevenhelpyoufightoffaninfection!Recently,
some exciting evidence has shown that probiotics may be an effective treatment for people with irritable bowel
syndrome/disease,obesity,andneurologicalandpsychologicaldisorderssuchasParkinsonsanddepression.
Yourmicrobiotaistrulyuniquetoyou,sothetrickypartisfindingaformulathatwillworkformorethanjust
one person! To make things even more complicated, different species have different mechanisms by which they
influence you and your gut ecosystem. Some species can actually colonize your gut, while others have a temporary
effectastheypassthrough.
Probiotics are capable of influencing the intestinal epithelial barrier, producing antimicrobial substances
(bacteriocins), immune modulation, influencing bacterial interspecies communication, and acting as placeholders to
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prevent colonization by bad bacteria. For example, some Bifidobacterium species produce a molecule called
autoinducer2,whichpromotesdiversecolonizationofthegutbyhelpingdifferentbacterialspeciescommunicate.

PotentialPathogens

Salmonella,E.coli,Campylobacter,Staphylococcus,Streptococcus,Enterococcus

Dysbiosisoccurswhenthegutmicrobiotabalanceisdisrupted.Whenthishappens,itleavesyourgutweakto
attackfrompotentialpathogens.E.coli,Campylobacter,Staphylococcus,Streptococcus, andEnterococcuscaneither
be part of your normal flora, or they can be pathogenic. Where in the body these organisms make contact, the
number of organisms present, as well as the specific species and/or strains present determines whether or not the
relationshipismutualistic.Salmonellaspeciesareopportunisticpathogens,whichmeanstheymaybepresentinyour
body without causing a disease state, however they are not considered normal flora. Streptococcus causes Strep
throatandE.coli,Campylobacter,StaphylococcusandSalmonellausuallycausefoodpoisoning.AndEnterococcuscan
causeurinarytractinfectionsorbacteremia.Again,keepinmindthatthesequencingresultsyouhavereceivedareto
thegenuslevelonlyanddonotdistinguishbetweencommensalandpathogenicspeciesand/orstrainswithinagiven
genus.
Since many of these species are also commensal, you may be wondering how the pathogenic ones get
introduced.Thiscouldoccurthroughtransferofgeneticmaterialorbecausethegutispoorlycolonized(forexample,
afteralongroundofantibiotics)allowingthepathogenicbacteriatooutcompetethenormalflora.Researchershave
shown that nonpathogenic E. coli in your normal flora may acquire genetic material from pathogenic E. coli and
become pathogenic. Advanced bioinformatics analysis has shown that both individuals with colorectal cancer and
irritable bowel syndrome/disease have a higher abundance of E. coli, relative to healthy controls. Currently, we are
interestedinwhetherornotspecificpathogenicitygenesorahighrelativeabundanceofthispotentiallypathogenic
groupcanbeusedasamarkerfordiseaserisk.

LacticAcidBacteria

Lactobacillus,Bifidobacterium

Lactic acid bacteria (LAB), particularly the lactobacilli and Bifidobacteria, have in common the ability to
producelacticacidastheendproductofcarbohydratefermentation.Theyarecommonlyfoundinfermentedfoods
(yogurt,cheese,pickles,sourdoughbread,curedmeatsetc.),silage,andtheoralcavities,gastrointestinaltractsand
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vaginas of humans and animals. LAB has a reputation as being prominent and stable members of a healthy gut
ecosystem.Intruth,adifferentpictureseemstobeemerginginwhichLABareforthemostparttransientresidentsof
thegutthatoriginatefromfoodortheoralcavity.Nevertheless,LABprovidesavarietyofbenefitstoourhealth.(See
Probiotics)
Like most other bacteria, lactic acid bacteria produce bacteriocins, small protein peptides that inhibit the
growthofcloselyrelatedspecies.Bacteriocinshaveantimicrobialproperties,butaredistinguishedfromtherapeutic
antibiotics in that they dont have the same issues with potentially eliciting an allergic response or other medical
complicationsandareeasilydigestedbyproteasesinthehumangutsotheydonotpersistintheenvironment.Some
LAB are able to produce bacteriocins with a broader range of target species, and so are being implemented as
biopreservativestoinhibitpathogensinfoodproducts.
Were not the only ones to find benefit from lactic acid bacteria. Honeybees carry a diverse population of
lacticacidbacteriaintheirhoneycrop(organusedforcollectionandtransportofnectar),whichhelpsprotecttheir
honey and beebread (long term food stores for adults and larvae) from bacteria, yeast and molds they might
encounterduringforaging.Theseharmfulmicrobescouldquicklydestroythebeeshardworkthroughfermentation
ofthehoney,ormoldgrowth,butinsteadarekilledinthebeesgutbeforetheyreachthehive.Scientiststhinkthis
symbiosismayhavebeengoingonfor80millionyears!Humanshavelongusedhoneytotreatwoundsandillness,
andnowweknowthereisgoodreasonotherthanthefactthatittastesyummy!

Xenobiotics

Eggerthella,Enterococcus

Xenobiotics are chemicals that are foreign to the body and may include things like drugs, pesticides and
industrialpollutants.Ourgutmicrobiotacantransformsuchchemicalsinwaysthatmaybebeneficialorharmfultous.
Mostofthesetransformationsareattributedtobroadgroupsofbacteriaandarenotuniquetoasinglespecies.One
interestingexamplewhereaxenobiotictransformationisattributedtotheactivityofasinglemicrobeisinthecaseof
digoxin,adrugusedtotreatatrialfibrillationandcongestiveheartfailure.ItwasdiscoveredthatEggerthellalentais
able to chemically reduce a lactone ring of digoxin, rendering it inactive. The importance of this transformation is
underscored by the fact that digoxin has a very narrow therapeutic range. The degree of inactivation is highly
individualized (likely dependent on the presence and activity of a specific strain of Eggerthella lenta), but in some
casesmorethan50%ofthedrugmaybeinactivated.
Onepositivebiotransformationcarriedoutbybacteriainourgutisthatinvolvingtwoclassesofplantderived
phytoestrogens,ligninsandisoflavones.Severalspeciesofbacteria(Enterococcusfaecium,Lactobacillusmucosae,
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Bifidobacterium sp., Coriobacteriaceae sp., Eggerthella sp.) are able to convert the isoflavones diadzin and diadzein,
foundprimarilyinsoyproducts,intoacompoundcalledequol,whichisapowerfulantioxidanthavingapotentialrole
in reducing both breast and prostate cancer. Similarly, certain plant lignins can be transformed by bacteria into
bioactivemoleculesthathavebeenlinkedtoabreastcancerprotectiveeffect.

AntiObese

Akkermansia

Akkermansiaarefoundthroughouttheanimalkingdomandinhumansmaycomprise14%ofthemicrobiome.
TheremaybeatleasteightspeciesoftheAkkermansiagenusthatarefoundinthegut,butonlyone,Akkermansia
muciniphila, has been cultured in the lab. It was isolated relatively recently (2004) and named for a Dutch
microbiologist,Dr.AntoonAkkermans.
The genus Akkermansia is illustrative of an essential mutualism between bacteria and their hosts. These
bacteriaarefedbyintestinalmucusfromthehost(you)andinreturncontributetothehealthoftheirhumanhostin
severalways.Thecolonhastwomucuslayers,aninnerattachedlayerthatprovidesabarriertotheintestinalwall
andanouterlooselayerinhabitedbycommensalbacteriaincludingAkkermansia.Inthishabitat,Akkermansiaare
uniqueintheirabilitytobreakdownthemucin(aglycoprotein)thatcomprisesthemucusanduseitasafoodsource.
Intheprocessofbreakingdownthemucin,smallersugarsandshortchainfattyacidsareproducedthatfeedother
commensal bacteria. In doing so, Akkermansia facilitate a kind of colonization resistance that helps outcompete
potentialpathogens.
SCFAs (specifically acetate and propionate) produced by Akkermansia also act as signaling molecules to
stimulate the host immune response and as metabolic signals to produce more mucus. A low population of
Akkermansia could be an indicator of a thin mucus layer and a weakened gut barrier. There have been numerous
studies in which in the population of Akkermansia was inversely correlated with inflammatory bowel diseases and
metabolicdisorderssuchasobesityandtype2diabetes.Researchwithanimalmodelshavemadeitincreasinglyclear
thatAkkermansiaplaysanimportantroleinregulatingenergymetabolismandimmuneresponsepathways.
All of this suggests that Akkermansia could be a potent probiotic someday soon. Very recently a group of
researchers demonstrated that pasteurized Akkermansia muciniphila was able to reduce fat mass development,
insulin resistance and excess blood lipids in mice. Furthermore, they were able to isolate and link this activity to a
specific protein, Amuc_1100. Some prebiotic substrates that are thought to promote Akkermansia colonization
include arabinoxylan, inulin and fructooligosachharides (FOS). If thats too much of a mouthful, try consuming
polyphenolrichfoodssuchaspomegranateandcranberries,andfishoil.
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FurtherReading

1.Themicrobiomeandinflammatoryboweldisease:isthereatherapeuticroleforfecalmicrobiotatransplantation?
Damman CJ, Miller SI, Surawicz CM, Zisman TL. Am J Gastroenterol. 2012 Oct;107(10):14529. doi:
10.1038/ajg.2012.93.

2.Thehealthadvantageofavegandiet:exploringthegutmicrobiotaconnection.GlickBauerM,YehMC.Nutrients.
2014Oct31;6(11):482238.doi:10.3390/nu6114822.

3. Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health. RosCovin D, RuasMadiedo P,
Margolles A, Gueimonde M, de Los ReyesGaviln CG, Salazar N. Front Microbiol. 2016 Feb 17;7:185. doi:
10.3389/fmicb.2016.00185.eCollection2016.

4. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Morrison DJ,
PrestonT.GutMicrobes.2016May3;7(3):189200.doi:10.1080/19490976.2015.1134082.Epub2016Mar10.

5.Probioticlacticacidbacteriathefledglingcuckoosofthegut?BerstadA,RaaJ,MidtvedtT,ValeurJ.MicrobEcol
HealthDis.2016May26;27:31557.doi:10.3402/mehd.v27.31557.eCollection2016.

6. Lactic Acid Bacteria as Cell Factories for the Generation of Bioactive Peptides. Brown L, Pingitore EV, Mozzi F,
Saavedra L, Villegas JM, Hebert EM. Protein Pept Lett. 2017;24(2):146155. doi:
10.2174/0929866524666161123111333.

7. Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism
and metabolic disorders during obesity in mice. Schneeberger M, Everard A, GmezValads AG, Matamoros S,
RamrezS,DelzenneNM,GomisR,ClaretM,CaniPD.SciRep.2015Nov13;5:16643.doi:10.1038/srep16643.

8. Developing a metagenomic view of xenobiotic metabolism. Haiser HJ, Turnbaugh PJ. Pharmacol Res. 2013
Mar;69(1):2131.doi:10.1016/j.phrs.2012.07.009.Epub2012Aug9.

9.Xenobioticsshapethephysiologyandgeneexpressionoftheactivehumangutmicrobiome.MauriceCF,HaiserHJ,
TurnbaughPJ.Cell.2013Jan17;152(12):3950.doi:10.1016/j.cell.2012.10.052.
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10. Role of commensal and probiotic bacteria in human health: a focus on inflammatory bowel disease. Martn R,
Miquel S, Ulmer J, Kechaou N, Langella P, BermdezHumarn LG. Microb Cell Fact. 2013 Jul 23;12:71. doi:
10.1186/147528591271.

11.RoleofProbioticsinhealthimprovement,infectioncontrolanddiseasetreatmentandmanagement.AmaraAA,
ShiblA.SaudiPharmJ.2015Apr;23(2):10714.doi:10.1016/j.jsps.2013.07.001.Epub2013Jul18.

12.Microbiomewideassociationstudieslinkdynamicmicrobialconsortiatodisease.GilbertJA,QuinnRA,DebeliusJ,
Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. Nature. 2016 Jul 7;535(7610):94103. doi:
10.1038/nature18850.

13. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. Ze, X.,
Duncan,S.H.,Louis,P.,&Flint,H.J.TheISMEJournal.20126(8),15351543.http://doi.org/10.1038/ismej.2012.4

14. Dietary fiberinduced improvement in glucose metabolism is associated with increased abundance of
Prevotella.KovatchevaDatchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., ... & Bckhed, F. Cell
metabolism.201522(6),971982.

15.LinkingLongTermDietaryPatternswithGutMicrobialEnterotypes.Wu,G.D.,Chen,J.,Hoffmann,C.,Bittinger,K.,
Chen,Y.Y.,Keilbaugh,S.A.,Lewis,J.D.Science2011334(6052),105108.http://doi.org/10.1126/science.1208344

Abundance

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Bacteroides

Bifidobacterium

Blautia

Probiotic
Bulleidia

Collinsella

Sulfur reducing
Plant based diet

Coprococcus

Potential pathogen

Western diet
Desulfovibrio

Dialister
Carbohydrate degrading

Dorea

Faecalibacterium

Short chain fatty acid producing


Fusobacterium

Oscillospira

Parabacteroides

Paraprevotella

Parvimonas

Phascolarctobacterium

Prevotella

Roseburia

Rubrivivax

Ruminococcus
Your Sample
American Gut

Sutterella