How We Tell The Good Bac­te­ria From The Bad

by Micah Ma­n­ary

Re­cently, Yale's Richard Flavell led a team of re­searchers into the most talked about and yet one of the least un­der­stood of mi­cro­bial en­vi­ron­ments — the hu­man gut. Rather than present the usual metage­nomic char­ac­ter­i­za­tion of the mi­cro­bial pop­u­la­tion, he teamed up with Jeff Gor­don at Wash­ing­ton Uni­ver­sity in Saint Louis and oth­ers to in­ves­ti­gate one of the most im­por­tant ques­tions in the field: how does the host or­gan­ism de­tect and re­spond to the re­place­ment of its 'nor­mal' gut bac­te­ria with 'ab­nor­mal?'

To get into this topic we need to spend a minute on the in­nate im­mune re­sponse and, specif­i­cally, the in­flam­ma­somes. These com­po­nents of the in­nate im­mune sys­tem are mul­ti­pro­tein com­plexes that sense dam­age to the host. As the name sug­gests, they fos­ter in­flam­ma­tion by pro­mot­ing the mat­u­ra­tion of pre­cur­sors of cy­tokines in­volved in in­flam­ma­tion, such as in­ter­leukin 1‑β and in­ter­leukin 18. When in­flam­ma­somes rec­og­nize one of many rel­e­vant sig­nals, they as­sem­ble into a mul­ti­pro­tein com­plex, usu­ally to­gether with an adap­tor pro­tein called ASC (for apop­to­sis-as­so­ci­ated speck-like pro­tein con­tain­ing a CARD). This com­plex gov­erns ac­ti­va­tion of the pro­tease caspase‑1 with sub­se­quent cleav­age of the proin­flam­ma­tory cy­tokines (in­clud­ing pro-IL-1β and pro-IL-18) into their ac­tive forms.

Schematic di­a­gram of the mouse col­i­tis show­ing the ef­fect of the NLRP6 dele­tion and co­hab­i­ta­tion of var­i­ous mouse strains. Bac­te­ria in the lu­men rep­re­sent the nor­mal mi­cro­biome (light col­ored) or the col­i­tis-as­so­ci­ated Pre­votella (dark col­ored). Source

Flavell and col­le­gaues found that a dele­tion mu­ta­tion in the in­flam­ma­some NLRP6 (NLR stands for Nod-Like Re­cep­tor) led to col­i­tis in a mouse model. In­ter­est­ingly, this led to dra­matic changes in the com­po­si­tion of the gut mi­cro­biota. Specif­i­cally, the num­ber of nor­mal bac­te­r­ial species de­creased, with an in­crease in Pre­votel­laceae, mem­bers of the phy­lum Bac­teroidetes. When germ-free wild-type mice were co­housed with con­ven­tional, non-germ free NLRP6 knock­out mice, they de­vel­oped the same gut mi­cro­biota com­po­si­tion as the mu­tants. Wild-type mice with nor­mal gut mi­cro­biota co­housed with the mu­tants also showed an in­crease in Bac­teroidetes, though to a lesser ex­tent. The in­flam­ma­some re­sponse in the wild-type mice with the changed gut mi­cro­biota was sim­i­lar to that in the NLRP6 knock­outs. This sug­gests that the NRLP6-de­pen­dent sig­nal­ing path­way is nec­es­sary for the de­vel­op­ment of col­i­tis. Serum lev­els of IL-18 were in­creased in all of these mice. The au­thors also noted an in­crease in the CCL5 cy­tokine sig­nal­ing path­way, which is known to drive the cleav­age of pro-IL-18 to IL-18. The con­clu­sion here is that the col­i­tis-caus­ing ac­tiv­ity of the gut mi­cro­biota can be trans­ferred to mice housed in the same en­vi­ron­ment.

Next, wild-type mice that had been in­fected with the Bac­teroidetes-en­riched mi­cro­biota from the knock­out mice were co­housed with un­af­fected wild-type mice. The mi­cro­biota com­po­si­tion of these mice re­turned to nor­mal, but only af­ter sev­eral gen­er­a­tions. The ver­ti­cal trans­fer of the high-Bac­teroidetes mi­cro­biota com­po­si­tion con­tin­ued for sev­eral gen­er­a­tions and re­mained in­def­i­nitely as long as there was no ex­po­sure to the wild-type gut mi­cro­biota. In ad­di­tion, these later gen­er­a­tions also de­velop col­i­tis-like symp­toms sim­i­lar to the orig­i­nal knock­outs. There­fore, the col­i­tis-caus­ing ac­tiv­ity of the gut mi­cro­biota can be trans­ferred to prog­eny as well as to mice housed in the same en­vi­ron­ment. The sever­ity of the col­i­tis was re­duced when the mice were treated with an­tibi­otics, fur­ther sug­gest­ing that the Provatel­laceae played an im­por­tant role in this dis­ease.

This pa­per has im­pli­ca­tions for re­search in in­flam­ma­tory bowel dis­ease. First, the au­thors have un­cov­ered a pos­si­ble mech­a­nism that gen­er­ates an in­flam­ma­some re­sponse when the gut mi­cro­biota is al­tered. Fur­ther, the mech­a­nism of this re­sponse is be­com­ing un­der­stood: it uti­lizes a known cy­tokine path­way. The trans­fer­able prop­erty of these in­flam­ma­tory symp­toms, through the trans­ferred gut bac­te­ria, is cer­tainly sur­pris­ing. The in­duc­tion by these Bac­teroidetes of the in­flam­ma­tory re­sponse in mice with­out any ge­netic ab­nor­mal­ity gives us a pow­er­ful in­sight into the eti­ol­ogy of in­flam­ma­tory bowel dis­eases. It is per­haps sur­pris­ing that the loss of NLRP6 re­sults in the ac­ti­va­tion of an in­flam­ma­tory cas­cade. The gut epithelium's reg­u­la­tion of in­flam­ma­tory re­sponses is thus shown to be a bal­ance be­tween dri­ving and in­hibitory fac­tors.

While clin­i­cal im­pli­ca­tions seem to lie on the hori­zon, us­ing per­haps a me­di­a­tion of in­flam­ma­tory ef­fects through down­reg­u­la­tion of its cas­cade, per­haps the most in­ter­est­ing part of this pa­per is the mi­cro­bi­ol­ogy. Through NLRP6 and other in­flam­ma­somes, the body is able to gen­er­ate an in­flam­ma­tory re­sponse to bac­te­ria that it rec­og­nizes as "for­eign." This re­sponse is ab­sent where the mi­cro­biota is nor­mal in com­po­si­tion. The species in the al­tered mi­cro­biome are not pathogens in the clas­si­cal sense, yet these re­sults give us valu­able in­sight into the reg­u­la­tion of "good" ver­sus "bad" bac­te­ria. This in­sight has fur­ther im­pli­ca­tions for the co­evo­lu­tion of ver­te­brates and their gut mi­cro­biota. Bac­te­ria in the in­testines are not merely par­a­sites or even com­men­sals; they are an in­te­gral part of our gas­troin­testi­nal tract and a dis­rup­tion in their com­po­si­tion leads to dra­matic changes in the body, in an ef­fort to re­store the "nor­mal" state.

Ref­er­ence

Eli­nav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J, Eisen­barth SC, Gor­don JI, Flavell RA (2011). NLRP6 In­flam­ma­some Reg­u­lates Colonic Mi­cro­bial Ecol­ogy and Risk for Col­i­tis. Cell, 145 (5), 745−757. PMID 21565393

Micah is in the MD/PhD pro­gram at the Uni­ver­sity of Cal­i­for­nia, San Diego and a stu­dent in the In­te­gra­tive Mi­cro­bi­ol­ogy grad­u­ate course.