Mi­cro­bial Read­ing Roundup

by Daniel P. Haeusser

Fig­ure 1. A nat­ural com­mu­nity of bac­te­ria grow­ing on a sin­gle grain of sand. The sand was col­lec­ted from inter­tidal sed­i­ment on a beach near Boston, MA in Sep­tem­ber 2008 and im­aged us­ing a Scan­ning Elec­tron Mi­croscope (SEM). Ima­ge cour­tesy of the Lewis Lab at North­east­ern Uni­ver­sity. CC BY 2.0 im­age cre­ated by A. D'Ono­frio, WH. Fowle, EJ. Stew­art and K. Lewis. Source

To­day I wanted to catch up with some re­cent books that vis­i­tors to this blog may have in­ter­est in adding to their mi­cro­bi­o­log­i­cal li­brary. So here is a roundup of six aca­d­e­mic mi­cro­bial ti­tles of note that make up a trio of re­lated pairs.

An­tibi­otics & Al­lelopa­thy

An­tibi­otics: Chal­lenges, Mech­a­nisms, Op­por­tu­ni­ties by Christo­pher Walsh and Tim­o­thy Wencewicz. (2016) ASM Press. ISBN: 978–1‑555819–30‑9 (Hard­cover, 477 pages), 978–1‑555819–31‑6 (eBook).

The Bac­te­ri­ocins: Cur­rent Knowl­edge and Fu­ture Prospects by Robert Dorit, San­dra M. Roy, and Mar­garet A. Ri­ley (Ed­i­tors). (2016) Cais­ter Aca­d­e­mic Press. ISBN: 978–1‑910190–37‑1 (Pa­per­back, 158 pages), 978–1‑910190–38‑8 (eBook).

A sig­nif­i­cant up­date from its 2003 pre­cur­sor, An­tibi­otics: Ac­tions, Ori­gins, Re­sis­tance, this new an­tibi­otics text­book brings the con­cept of 'chal­lenges' to the fore, namely, the so­ci­etal need to de­velop next-gen­er­a­tion an­tibi­otics. The two open­ing chap­ters re­view the ma­jor classes and mech­a­nisms of cur­rent an­tibi­otics and also dis­cuss the process of an­tibi­otic de­vel­op­ment and the his­tory of re­sis­tance. The next sec­tions go into the mech­a­nisms of an­tibi­otic ac­tion and re­sis­tance de­vel­op­ment in greater de­tail, clos­ing the sec­tion with a case study on tu­ber­cu­lo­sis.

The au­thors then fo­cus on biosyn­the­sis of dif­fer­ent an­tibi­otic classes and close with two chap­ters on 'op­por­tu­ni­ties': un­der­ex­ploited pathways/targets and prospects for new an­tibi­otics. I be­lieve that these chap­ters are the most in­ter­est­ing be­cause they col­lect re­cent in­for­ma­tion on re­search and prospects that are sure to be in­spir­ing to re­searchers in the field and stu­dents alike. As some­one whose re­search in­ter­ests are in cell di­vi­sion, I watch­fully read sec­tions in the fi­nal chap­ters on bac­te­r­ial cell di­vi­sion and FtsZ as po­ten­tial pathways/targets for novel an­tibi­otics. The au­thors did a re­mark­able job of sum­ma­riz­ing the back­ground and pre­lim­i­nary find­ings in this field. They even pointed out the po­ten­tial harm that could come from caus­ing bac­te­ria to fil­a­ment with­out be­ing killed.

One el­e­ment miss­ing from this text is the im­por­tance of an­tibi­otics in mi­cro­bial com­pe­ti­tion, i.e. the eco­log­i­cal role and evo­lu­tion­ary ori­gin of an­tibi­otics. The text is fo­cused on an­tibi­otics as a tool for hu­man med­i­cine. Not a bad thing – every­thing needs fo­cus – but, in con­trast, the other book on an­tibi­otic com­pounds fea­tured here, The Bac­te­ri­ocins, cov­ers both en­vi­ron­men­tal and med­ical as­pects.

Bac­te­ri­ocins are an­timi­cro­bial pep­tides made by bac­te­ria through non-kin ex­clu­sion as tox­ins di­rected against com­peti­tors. First dis­cov­ered by An­dre Gra­tia close to a cen­tury ago in E. coli, sci­en­tists es­ti­mate that most bac­te­ria en­code at least one bac­te­ri­ocin. Sim­i­lar mol­e­cules, ar­chaeocins, are also made by the Ar­chaea. With a fam­ily so broadly dis­trib­uted, there is un­sur­pris­ingly a lot of di­ver­sity within it (Merry once wrote on them here, specif­i­cally on their re­la­tion to phages). The bac­te­ri­ocins range from small pep­tides to large pro­teins that tar­get a range of cel­lu­lar processes. Re­gard­less of their mol­e­c­u­lar tar­get, some bac­te­ri­ocins have broad ac­tiv­ity against large groups of bac­te­ria, while oth­ers are only po­tent against a nar­row range of bac­te­r­ial species. Their eco­log­i­cal role as weapons of de­fense (al­lelopa­thy) makes the bac­te­ri­ocins at­trac­tive can­di­dates for novel an­tibi­otics, and some have al­ready been used in­dus­tri­ally, e. g., in food preser­va­tion.

Ed­i­tors Dorit, Roy, and Ri­ley pack their rel­a­tively slim com­pi­la­tion with a com­pre­hen­sive sur­vey across the cur­rent knowl­edge on these an­timi­cro­bial com­pounds. Af­ter a fore­word by Richard James that gives the topic his­tor­i­cal and per­sonal per­spec­tive, two chap­ters re­view the ba­sic bi­ol­ogy of bac­te­ri­ocin di­ver­sity. In gen­eral, while sci­en­tists know a fair amount about the tar­gets and mech­a­nisms of some bac­te­ri­ocins, they know rel­a­tively lit­tle about ones out­side com­mon Gram-neg­a­tive or Gram-pos­i­tive model or­gan­isms, or about how their ac­tiv­ity is reg­u­lated in na­tive eco­log­i­cal set­tings of in­ter­spe­cific com­pe­ti­tion. More­over, the con­se­quences of their po­ten­tial use as an­tibi­otics, and the ease at which tar­gets may de­velop re­sis­tance are largely un­ex­plored.

The re­main­ing chap­ters em­pha­size some of the well-known sys­tems, from E. coli and Pseudomonas to Gram-pos­i­tive species, or re­search into the po­ten­tial use of bac­te­ri­ocins as oral mi­cro­biome pro­bi­otics and as an­tibi­otics in vet­eri­nary med­i­cine. Rather than end­ing with a re­view of fu­ture prospects, a group that in­cludes two of the ed­i­tors presents a short pa­per of data on 'The Phe­no­typic and Geno­typic Land­scape of Col­icin Re­sis­tance'. Though pre­lim­i­nary, the data sug­gest that re­sis­tance to E. coli bac­te­ri­ocins arises through a rel­a­tively small win­dow around toxin re­cep­tor bind­ing and up­take, and comes with se­vere costs to the re­sis­tant tar­get strain.

Any­one in­ter­ested in the top­ics of an­tibi­otics, ei­ther in their prac­ti­cal use or their nat­ural use as part of mi­cro­bial evo­lu­tion, will ap­pre­ci­ate both of these books. The an­tibi­otics text is use­ful for up­per level courses or ref­er­ence ma­te­r­ial, while that on the bac­te­ri­ocins is a use­ful ad­di­tion to mi­cro­bi­ol­ogy, med­ical, or eco­log­i­cal ref­er­ence li­braries.

Biofilms

Mi­cro­bial Biofilms, Sec­ond Edi­tion by Mah­moud Ghan­noum, Matthew Parsek, Mar­vin Whitely, and Pranab K. Mukher­jee (Ed­i­tors). (2015) ASM Press. ISBN: 978–1‑555817–45‑9 (Hard­cover, 404 pages), 978–1‑555817–46‑6 (eBook).

Aquatic Biofilms: Ecol­ogy, Wa­ter Qual­ity, and Waste­water Treat­ment by Anna M. Ro­maní, He­lena Guasch, and M. Do­lors Bal­a­guer (Ed­i­tors). (2016) Cais­ter Aca­d­e­mic Press. ISBN: 978–1‑910190–17‑3 (Hard­cover, 229 pages), 978–1‑910190–18‑0 (eBook).

A decade fol­low­ing its first edi­tion, Mi­cro­bial Biofilms ex­pands re­views of biofilm re­search be­yond its early foun­da­tional years of 'dis­cov­ery sci­ence'. Full of col­ored, high-qual­ity fig­ures to ac­com­pany the text, this vol­ume gives roughly equal at­ten­tion to both bac­te­r­ial and fun­gal biofilms. The con­tri­bu­tions fo­cus on de­vel­op­men­tal mech­a­nisms of biofilms, mol­e­c­u­lar prop­er­ties of their com­po­nents, and their med­ical consequences/applications. The first chap­ter, "New Tech­nolo­gies for Study­ing Biofilms" is a par­tic­u­larly use­ful ref­er­ence for the unini­ti­ated as it dis­cusses how mi­cro­bi­ol­o­gists are able to study biofilms in con­di­tions de­signed to mimic nat­ural states.

Some of the med­ically re­lated se­lec­tions are model-or­gan­ism spe­cific, such as re­views of fun­gal pathogens like Can­dida al­bi­cans and Cryp­to­coc­cus neo­for­mans, or of bac­te­r­ial pathogens like Es­cherichia coli and Pseudomonas aerug­i­nosa. Other con­tent fo­cuses on gen­eral path­o­genic roles of biofilms (e.g. an­timi­cro­bial tol­er­ance and host de­fense eva­sion), and on biofilm con­trol and com­bat.

For all its med­ical fo­cus, sev­eral sec­tions of Mi­cro­bial Biofilms cover top­ics of gen­eral rel­e­vance re­gard­less of en­vi­ron­men­tal con­text. This in­cludes the open­ing chap­ter and ba­sic re­views on biofilm for­ma­tion, de­vel­op­ment, and dis­per­sal. One chap­ter dis­cusses the ecological/evolutionary con­se­quences of in­ter­spe­cific com­pe­ti­tion in biofilms, while an­other, from the lab of our own Roberto Kolter, de­tails the mir­ror im­age of such in­ter­ac­tions: co­op­er­a­tion that per­mits biofilms a mul­ti­cel­lu­lar-es­que di­vi­sion of la­bor.

While the ASM Press vol­ume fo­cuses on the med­ical side of re­search, an­other re­cent col­lec­tion from Cais­ter Aca­d­e­mic Press fo­cuses on biofilms in aquatic set­tings. The open­ing ar­ti­cle nicely in­tro­duces the topic through his­tor­i­cal and prac­ti­cal con­sid­er­a­tions of what de­fines biofilms. No­tably, the au­thors dis­cuss the clas­si­fi­ca­tion of biofilms not just in con­sid­er­a­tion of the or­gan­ism in­volved, but also in re­la­tion to the abi­otic fac­tors of sub­strate and en­vi­ron­men­tal con­di­tions. This pro­vides an ecosys­tem per­spec­tive to a topic that is com­monly only con­sid­ered at the pop­u­la­tion or com­mu­nity ecol­ogy level. For all its strengths from the holis­tic-eco­log­i­cal view, Aquatic Biofilms does no­tably lack a broad overview on the tech­niques of biofilm study; it in­cludes only a sin­gle re­view, in this case on laser mi­croscopy imag­ing.

Yet, this omis­sion is more than bal­anced by the unique en­vi­ron­men­tal fo­cus of the rest of the vol­ume. The first of three parts in Aquatic Biofilms con­cludes by sum­ma­riz­ing mi­cro­bial di­ver­sity in biofilms and their role in bio­geo­chem­i­cal processes. This in­for­ma­tion sets up the sec­ond part on the role of biofilms in aquatic pol­lu­tion and their use for mon­i­tor­ing fresh­wa­ter com­mu­nity health. The fi­nal part con­sists of three re­views de­tail­ing new en­vi­ron­men­tal sci­ence tech­nolo­gies in­volv­ing biofilms, such as in the biodegra­da­tion of per­sis­tent or­ganic pol­lu­tants or bio­elec­tro­chem­i­cal sys­tem tech­nol­ogy for pol­lu­tant re­moval from con­t­a­m­i­nated wa­ter and air. These lat­ter fas­ci­nat­ing chap­ters may in­spire an up­com­ing piece for Small Things Con­sid­ered on a topic that our read­ers may be less fa­mil­iar with.

Even Mis­an­thropes Catch Dis­ease

In­fec­tions of Leisure, 5^th Edi­tion by David Schloss­berg (Ed­i­tor). (2016) ASM Press. ISBN: 978–1‑555819–22‑4 (Pa­per­back, 411 pages), 978–1‑555819–23‑1 (eBook).

Zoonoses: In­fec­tious Dis­eases Trans­mis­si­ble from An­i­mals to Hu­mans, Fourth Edi­tion by Rolf Bauer­feind, Alexan­der von Graevenitz, Pe­ter Kim­mig, Hans Gerd Schiefer, Tino Schwarz, Werner Slenczka, and Horst Zah­ner. (2016) ASM Press. ISBN: 978–1‑555819–25‑5 (Pa­per­back, 532 pages), 978–1‑555819–26‑2 (eBook).

If any ger­mo­phobes out there need some fresh night­mare fuel, this pair of up­dated vol­umes from ASM Press should be just the thing. Reg­u­lar read­ers of this blog prob­a­bly re­al­ize that the ma­jor­ity of mi­crobes are not 'germs' at all. How­ever, these texts re­mind us that many in­fec­tious agents are out there, in per­haps sur­pris­ing places, and that they of­ten aren't trans­mis­si­ble just through con­tact with other peo­ple.

Of the two books, In­fec­tions of Leisure will in­ter­est the broader au­di­ence sim­ply due to the read­abil­ity of the text in a new edi­tion that in­cludes color fig­ures. Some of the dis­eases in this vol­ume are ex­otic, and rel­a­tively rarely seen in oth­er­wise healthy in­di­vid­u­als. But the trans­mis­sion of these dis­eases oc­curs through mun­dane ac­tiv­i­ties of every­day hu­man life. Writ­ten by in­fec­tious dis­ease ex­perts, the con­tents are or­ga­nized by dis­ease source, from "In­fec­tions Ac­quired in the Gar­den" to "In­fec­tious Risks of Air Travel" and "In­fec­tions from Body Pierc­ing and Tat­toos".

This book has been an in­valu­able ref­er­ence for me while co-teach­ing for the first time a col­lege mi­cro­bi­ol­ogy course that in­te­grates ma­te­r­ial from path­o­genic mi­cro­bi­ol­ogy with an en­vi­ron­men­tal mi­cro­bi­ol­ogy per­spec­tive. For in­stance, the chap­ter "In­fec­tions Ac­quired via Fresh Wa­ter: from Lakes to Hot Tubs" pro­vided a foun­da­tion to ad­dress the mi­cro­bial ecol­ogy of fresh­wa­ter en­vi­ron­ments in re­la­tion to vi­ral, bac­te­r­ial, and eu­kary­otic pathogens of hu­mans, such as Norovirus, Le­gionella, and Acan­thamoeba.

Fol­low­ing the re­view of in­fec­tious agents found in the given en­vi­ron­ment, and their ef­fects, each chap­ter con­cludes with a bul­leted list of "prac­ti­cal tips" for avoid­ing dis­ease trans­mis­sion and ci­ta­tions of rec­om­mended pri­mary lit­er­a­ture read­ings, the lat­ter pro­vided ex­cel­lent ma­te­r­ial for as­sign­ing to stu­dents for read­ing and class dis­cus­sion.

The re­vised and up­dated Zoonoses is an ex­haus­tive cat­a­log of in­fec­tious agents that are trans­mit­ted to hu­mans from other an­i­mals. While it will be use­ful for clin­i­cal mi­cro­bi­ol­o­gists and ref­er­ence li­braries, it is not the type of book for a broad au­di­ence to pick up and read. En­cy­clo­pe­dic in na­ture, its or­ga­ni­za­tion sep­a­rates vi­ral, bac­te­r­ial, fun­gal, and par­a­sitic zoonoses each ac­cord­ing to dis­ease agent fam­i­lies. A typ­i­cal chap­ter in­cludes a broad in­tro­duc­tion fol­lowed by short sec­tions on oc­cur­rence, eti­ol­ogy, trans­mis­sion, di­ag­no­sis, and treat­ment. The ap­pen­dices high­light in­fec­tions by kind of an­i­mal bite, con­sump­tion of in­fected an­i­mal tis­sue, and in­clude other quickly ac­ces­si­ble prac­ti­cal in­for­ma­tion for clin­i­cians. For ed­u­ca­tors, a list of ref­er­ences at the end of each sec­tion could be use­ful for find­ing pri­mary lit­er­a­ture re­lated to a topic of fo­cus in class.

I hope these re­views are of some use to read­ers and fol­low­ers of Small Things Con­sid­ered. I have many more re­cent books on the shelf, so look for an­other roundup soon!