Fine Read­ing: Mi­cro­bial Ge­nomics and In­fec­tious Dis­eases

by Elio

Would you like to read a con­cise and well-writ­ten re­view about how ge­nomics has in­flu­enced our un­der­stand­ing of in­fec­tious dis­eases? Click here for a sat­is­fy­ing ac­count by David Rel­man, one of the lead­ing con­trib­u­tors to this field.

Af­ter sum­ma­riz­ing the dizzy­ing ac­cel­er­at­ing pace at which com­plete genome se­quences are be­ing ac­quiredeukary­otic, vi­ral, bac­te­r­ial, archaeal—Relman dis­cusses how mi­cro­bial ge­nomic di­ver­sity im­pacts on health and dis­ease, as il­lus­trated by con­cepts such as the pangenome, genome re­duc­tion, ge­nomic is­lands, CRISPR loci, and oth­ers. We read about the evo­lu­tion of pathogens such as the plague bacil­lus, in­clud­ing its ori­gin be­tween 2600 and 28,000 years ago in China, and that the com­mon an­ces­tor of all the strains in the USA to­day prob­a­bly ar­rived in San Fran­cisco in 1899. We learn that com­par­ing ge­nomic se­quences of He­li­cobac­ter py­lori strains has been used to de­ter­mine the tim­ing and di­rec­tion of hu­man mi­gra­tions, and that Vib­rio cholerae trav­eled, with hu­man help, from South Asia to Haiti.

Mi­cro­bial Ge­nomics and Tool De­vel­op­ment. A genome se­quence fa­cil­i­tates the de­velopment of a va­ri­ety of tools and ap­proaches for un­der­stand­ing, ma­ni­pulating, and mit­i­gat­ing the over­all ef­fect of a mi­crobe. The se­quence pro­vides in­sight into the pop­u­la­tion struc­ture and evo­lu­tion­ary his­tory of a mi­crobe for epi­demi­o­logic in­ves­ti­ga­tion, in­for­ma­tion with which to de­velop new di­ag­nos­tic tests and cul­ti­va­tion meth­ods, new tar­gets of drug de­vel­op­ment, and anti­gens for vac­cine develop­ment. Source

Sym­bio­sis and patho­gen­e­sis are smartly in­ter­wo­ven here. Rel­man high­lights the im­por­tance of hor­i­zon­tal gene trans­fer and ge­nomic is­lands. He points out that in­nocu­ous mi­crobes of­ten carry vir­u­lence fac­tors, which sug­gests that these fac­tors have other uses, such as aid­ing col­o­niza­tion or re­sis­tance to phago­cytes. Some of them likely orig­i­nated as pro­tec­tion against pre­da­tion by pro­tists and worms. As ex­pected for a pa­per from a lead­ing hu­man mi­cro­bio­mi­cist, the mi­cro­biome re­ceives am­ple cov­er­age. Lastly, he dis­cusses the pro­duc­tive use of ge­nomic con­cepts and tools in the dis­cov­ery of pathogens and in the de­vel­op­ment of di­ag­nos­tic and ther­a­peu­tic tools. Al­though this piece is in­tended pri­mar­ily for physi­cians, I be­lieve that Relman's lu­cid overview will ben­e­fit many oth­ers as well.