You Are What You Eat

by Karen Schwarzberg and Mike Gur­ney

De­spite the rise of a global cul­ture, de­li­ciously dis­tinct dif­fer­ences in diet still per­sist among var­i­ous na­tion­al­i­ties. Makes one won­der if, along with each cui­sine, comes a dis­tinc­tive mi­cro­biome. We now have the re­search tools needed to be­gin to ex­plore such pos­si­bil­i­ties. A pa­per re­cently pub­lished in Na­ture by Hehe­mann et al. re­ports that, in at least one par­tic­u­lar in­stance, we do har­bor bac­te­ria adapted to the tra­di­tional diet of our cul­ture.

B. ple­beius, the re­cip­i­ent of the β‑porphyranase genes. Source (link dead in 2026).

All of us hu­mans rely on our gut bac­te­ria to sup­ply en­zymes that we lack but that we need in or­der to di­gest the poly­sac­cha­rides found in ter­res­trial plants. But the en­zymes (gly­co­side hy­dro­lases) needed to break­down poly­sac­cha­rides unique to ma­rine al­gae, such as car­rageenan and agar, are an­other story. Such en­zymes had been iden­ti­fied only in some ma­rine bac­te­ria. Hehe­mann and col­leagues won­dered about the Japan­ese, who con­sume, on av­er­age, 14 grams of sea­weed per day (mostly the Por­phyra spp. of red al­gae known as nori).

Nori au na­turel. Source

Nori con­tains the sul­phated poly­sac­cha­ride por­phyran, so they be­gan their in­ves­ti­ga­tion by search­ing for por­phyranases within the genome se­quence of a ma­rine Bac­teroidetes that lives on an­other red alga, Zo­bel­lia galac­tanivo­rans. Sure enough, they found two such en­zymes (β‑porphyranases). Struc­ture analy­sis pro­vided knowl­edge of the ac­tive site, mak­ing it pos­si­ble to mine for more por­phyranases in the Gen­Bank non-re­dun­dant data­base. This net­ted them six more likely β‑porphyranases. All of these en­zymes were from ma­rine bac­te­ria with the ex­cep­tion of one found in Bac­teroides ple­beius, a hu­man gut bac­terium. No­tably, all 6 strains of B. ple­beius de­scribed so far have been iso­lated from the mi­cro­biota of Japan­ese in­di­vid­u­als. This in­cludes the type strain that was se­quenced as part of the Hu­man Mi­cro­biome Project.

Nori sheets in the mar­ket­place. Source

Next, in or­der to see if por­phyranases are com­mon in Japan­ese — and only Japan­ese — in­testi­nal mi­cro­biota, these re­searchers screened sam­ples from 13 Japan­ese and 18 North Amer­i­can vol­un­teers. Strik­ingly, these en­zymes were found in four of the 13 Japan­ese tested, but in none of the North Amer­i­cans. Thus the Japan­ese can di­gest their nori (Por­phyra) cour­tesy of the par­tic­u­lar strains of B. ple­beius that they carry, strains that are not found in North Amer­i­cans. Fur­ther­more, ge­nomic ev­i­dence sug­gests that the ini­tial ac­qui­si­tion of the β‑porphyranase genes by B. ple­beius was by hor­i­zon­tal trans­fer from a ma­rine Bac­teroidetes. The likely site for the trans­fer might well have been within the hu­man GI tract since such Bac­teroidetes are present on the un­cooked sea­weeds that have been avidly eaten by the Japan­ese since at least the eighth cen­tury. The trans­fer would have pro­vided the host with a se­lec­tive ad­van­tage: the abil­ity to me­tab­o­lize and de­rive en­ergy from a fre­quently-eaten car­bo­hy­drate source that oth­ers in the pop­u­la­tion could not di­gest. In­ter­est­ingly, the pa­per re­ports an in­ci­dent of trans­fer from mother to in­fant, im­ply­ing that we can pass those mod­i­fied bac­te­ria to close fam­ily mem­bers and per­haps oth­ers.

Nori on the plate. Source

Now, what are the im­pli­ca­tions of these find­ings? Could our mi­cro­biota in­flu­ence the in­ci­dence of obe­sity or even coro­nary heart dis­ease and stroke? Could the eti­ol­ogy be as sim­ple as hav­ing a few genes in a few bac­te­ria some­where in the small in­tes­tine? Clearly, the di­etary choices we make pro­vide on­go­ing se­lec­tion pres­sure, de­ter­min­ing which bac­te­r­ial strains — even which genes — are main­tained or lost. This pa­per strongly sug­gests that, at least in the case of the por­phyranases, rare oc­cur­rences of hor­i­zon­tal trans­fer can in­tro­duce "good" genes that can be­come es­tab­lished within the res­i­dent gut con­sor­tium of a pop­u­la­tion. But per­haps the genes that pro­vide a se­lec­tive meta­bolic ad­van­tage to mem­bers of our mi­cro­biome are, for us, "path­o­genic."

As hu­mans, we are born ster­ile and sub­se­quently ac­quire a mi­cro­biota from our food and/or our en­vi­ron­ment. Our race and na­tion­al­ity don't mat­ter, but what we eat does. Through­out our lives, there will al­ways be or­gan­isms com­ing in. How­ever, for an or­gan­ism to suc­cess­fully col­o­nize and be­come es­tab­lished in our gut flora, it has to com­pete ef­fec­tively with what is al­ready there. Var­i­ous bac­te­r­ial strains can come and go with shifts in our diet, an­tibi­otic ther­apy, and other fac­tors. Thus the grow­ing rev­enue stream for the pro­bi­otics in­dus­try that of­fers us "good" bac­te­ria in con­ve­nient, easy-to-in­gest forms. For these "good" bac­te­ria to per­sist, though, we must eat a diet rich in foods that gives them a se­lec­tive ad­van­tage; oth­er­wise, the mi­cro­bial com­mu­nity will even­tu­ally re­turn to its orig­i­nal con­fig­u­ra­tion. Con­se­quently, main­te­nance of the ben­e­fi­cial im­pact of pro­bi­otics would re­quire a change to a diet fa­vor­ing those or­gan­isms, pre­sum­ably a diet more healthy for us, too. How­ever, we would guess that the be­nign genes and good bac­te­ria are there al­ready, which would ren­der the need for pro­bi­otics moot.

Never has it been more true: You are what you eat.

Ref­er­ence

Hehe­mann, J., Cor­rec, G., Bar­bey­ron, T., Hel­bert, W., Czjzek, M, Michel, G. (2010). Trans­fer of car­bo­hy­drate-ac­tive en­zymes from ma­rine bac­te­ria to Japan­ese gut mi­cro­biota Na­ture, 464 (7290), 908−912. DOI 10.1038/nature08937

Mike Gur­ney and Karen Schwarzberg are stu­dents in the Spring 2010 grad­u­ate course in In­te­gra­tive Mi­cro­bi­ol­ogy at the Uni­ver­sity of Cal­i­for­nia at San Diego/San Diego State Uni­ver­sity Joint Doc­toral Pro­gram.

(we apol­o­gize for the poor qual­ity of Mike Gurney's pro­trait photo).