Microbiology Publications in the 2010s


Lozano, G. L., Bravo, J. I., Diago, M. F. G., Park, H. B., Hurley, A., Peterson, S. B., Stabb, E. V., Crawford, J. M., Broderick, N. A., Handelsman, J. (2019). Introducing THOR, a model microbiome for genetic dissection of community behavior. mBio, 10(2).

Lozano, G. L., Park, H. B., Bravo, J. I., Armstrong, E. A., Denu, J. M., Stabb, E. V., Broderick, N. A., Crawford, J. M., Handelsman, J. (2019). Bacterial analogs of plant tetrahydropyridine alkaloids mediate microbial interactions in a rhizosphere model system. Applied and Environmental Microbiology, 85(10).

Sivakumar, R., Ranjani, J., Vishnu, U. S., Jayashree, S., Lozano, G. L., Miles, J., Broderick, N. A., Guan, C., Gunasekaran, P., Handelsman, J., Rajendhran, J. (2019). Evaluation of INSeq To identify genes essential for Pseudomonas aeruginosa PGPR2 corn root colonization. G3-Genes Genomes Genetics, 9(3), 651-661. doi.org/10.1534/g3.118.200928


Handelsman, J., Hernandez, S., Tsang, T., Bascom-Slack, C., & Broderick, N. (2018). Tiny Earth: A Research Guide to Studentsourcing Antibiotic Discovery, XanEdu Publishing Inc.


Bravo, J. I., Lozano, G. L., & Handelsman, J. (2017). Draft genome sequence of Flavobacterium johnsoniae CI04, an isolate from the soybean rhizosphere. Genome Announcement, 5(4). doi.org/10.1128/genomeA.01535-16

Fischer, C. N., Trautman, E. P., Crawford, J. M., Stabb, E. V., Handelsman, J., & Broderick, N. A. (2017). Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior. Elife, 6, e18855. doi.org/10.7554/eLife.18855

Lozano, G. L., Bravo, J. I., & Handelsman, J. (2017). Draft genome sequence of Pseudomonas koreensis CI12, a Bacillus cereus “hitchhiker” from the soybean rhizosphere. Microbiology Resource Announcements, 5(26). doi.org/ARTN e00570-1710.1128/genomeA.00570-17

Rodriguez, M. M., Herman, R., Ghiglione, B., Kerff, F., González, G. D., Bouillenne, F., Galleni, M., Handelsman, J., Charlier, P., Gutkind, G., Sauvage, E., Power, P. (2017). Crystal structure and kinetic analysis of the class B3 di-zinc metallo-beta-lactamase LRA-12 from an Alaskan soil metagenome. PLoS One, 12(7). doi.org/ARTN 018204310.1371/journal.pone.0182043


Lozano, G. L., Holt, J., Ravel, J., Rasko, D. A., Thomas, M. G., & Handelsman, J. (2016). Draft genome sequence of biocontrol agent Bacillus cereus UW85. Genome Announcement, 4(5). doi.org/10.1128/genomeA.00910-16

Stulberg, E. R., Lozano, G. L., Morin, J. B., Park, H., Baraban, E. G., Mlot, C., Heffelfinger, C., Phillips, G. M., Rush, J. S., Phillips, A. J., Broderick, N. A., Thomas, M. G., Stabb, E. V., Handelsman, J. (2016). Genomic and secondary metabolite analyses of Streptomyces sp. 2AW provide insight into the evolution of the cycloheximide pathway. Frontiers in Microbiology, 7, 573. doi.org/10.3389/fmicb.2016.00573


Allen, H. K., An, R., Handelsman, J., & Moe, L. A. (2015). A response regulator from a soil metagenome enhances resistance to the beta-lactam antibiotic carbenicillin in Escherichia coli. PLoS One, 10(3), e0120094. doi.org/10.1371/journal.pone.0120094

Holt, J. F., Kiedrowski, M. R., Frank, K. L., Du, J., Guan, C. H., Broderick, N. A., Dunny, G. M., Handelsman, J. (2015). Enterococcus faecalis 6-phosphogluconolactonase is required for both commensal and pathogenic interactions with Manduca sexta. Infection and Immunity, 83(1), 396-404. doi.org/10.1128/Iai.02442-14

Miles, J., Holt, J., & Handelsman, J. (2015). Allies and adversaries: Roles of the microbiome in infectious disease. Microbe Magazine. doi.org/10.1128/microbe.10.370.1


Shade, A., Jones, S. E., Caporaso, J. G., Handelsman, J., Knight, R., Fierer, N., & Gilbert, J. A. (2014). Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio, 5(4). doi.org/ARTN e01371-1410.1128/mBio.01371-14

Udikovic-Kolic, N., Wichmann, F., Broderick, N. A., & Handelsman, J. (2014). Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proceedings of the National Academy of Sciences of the United States of America, 111(42), 15202-15207. doi.org/10.1073/pnas.1409836111

Wichmann, F., Udikovic-Kolic, N., Andrew, S., & Handelsman, J. (2014). Diverse antibiotic resistance genes in dairy cow manure. mBio, 5(2). doi.org/ARTN e01017-1310.1128/mBio.01017-13


Baraban, E. G., Morin, J. B., Phillips, G. M., Phillips, A. J., Strobel, S. A., & Handelsman, J. (2013). Xyolide, a bioactive nonenolide from an Amazonian endophytic fungus, Xylaria feejeensis. Tetrahedron Letters, 54(31), 4058-4060. doi.org/10.1016/j.tetlet.2013.05.093

Blum, J. E., Fischer, C. N., Miles, J., & Handelsman, J. (2013). Frequent replenishment sustains the beneficial microbiome of Drosophila melanogaster. mBio, 4(6). doi.org/ARTN e00860-1310.1128/mBio.00860-13

Shade, A., Caporaso, J. G., Handelsman, J., Knight, R., & Fierer, N. (2013). A meta-analysis of changes in bacterial and archaeal communities with time. ISME Journal, 7(8), 1493-1506. doi.org/10.1038/ismej.2013.54

Shade, A., Klimowicz, A. K., Spear, R. N., Linske, M., Donato, J. J., Hogan, C. S., McManus, P., Handelsman, J. (2013). Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil. Applied and Environmental Microbiology, 79(21), 6617-6625. doi.org/10.1128/Aem.02017-13

Shade, A., McManus, P. S., & Handelsman, J. (2013). Unexpected diversity during community succession in the apple flower microbiome. mBio, 4(2). doi.org/ARTN e00602-1210.1128/mBio.00602-12


Araujo, J. F., de Castro, A. P., Costa, M. M. C., Togawa, R. C., Pappas, G. J., Quirino, B. F., Bustamante M. M. C., Williamson, L., Handelsman, J., Kruger, R. H. (2012). Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals Acidobacteria dominance. Microbial ecology, 64(3), 760-770. doi.org/10.1007/s00248-012-0057-3

McMahon, M. D., Guan, C., Handelsman, J., & Thomas, M. G. (2012). Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression. Applied and Environmental Microbiology, 78(10), 3622-3629. doi.org/10.1128/AEM.00044-12

Shade, A., & Handelsman, J. (2012). Beyond the Venn diagram: the hunt for a core microbiome. Environmental Microbiology, 14(1), 4-12. doi.org/10.1111/j.1462-2920.2011.02585.x

Shade, A., Hogan, C. S., Klimowicz, A. K., Linske, M., McManus, P. S., & Handelsman, J. (2012). Culturing captures members of the soil rare biosphere. Environmental Microbiology. 14(9): 2247-2252. doi.org/10.1111/j.1462-2920.2012.02817.x

Shade, A., Peter, H., Allison, S. D., Baho, D. L., Berga, M., Bürgmann, H., Huber, D. H., Langenheder, S., Lennon, J. T., Martiny, J. B. H., Matulich, K. L., Schmidt, T. M., Handelsman, J. (2012). Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology, 3. doi.org/ARTN 41710.3389/fmicb.2012.00417


de Castro, A. P., Quirino, B. F., Allen, H., Williamson, L. L., Handelsman, J., & Kruger, R. H. (2011). Construction and validation of two metagenomic DNA libraries from Cerrado soil with high clay content. Biotechnology Letters, 33(11), 2169-2175. doi.org/10.1007/s10529-011-0693-6

Handelsman, J. (2011). Metamicrobiology: Analyzing microbial behavior at the community level. In G. Storz & R. Hengge (Eds.), Bacterial Stress Responses (2nd ed., pp. 419-424). ASM Press. doi.org/10.1128/9781555816841.ch25

Mason, K. L., Stepien, T. A., Blum, J. E., Holt, J. F., Labbe, N. H., Rush, J. S., Raffa, K. F., Handelsman, J. (2011). From Commensal to Pathogen: Translocation of Enterococcus faecalis from the Midgut to the Hemocoel of Manduca sexta. mBio, 2(3). doi.org/ARTN e00065-1110.1128/mBio.00065-11


Allen, H. K., Donato, J., Wang, H. H., Cloud-Hansen, K. A., Davies, J., & Handelsman, J. (2010). Call of the wild: Antibiotic resistance genes in natural environments. Nature Reviews Microbiology, 8(4), 251-259. doi.org/10.1038/nrmicro2312

Borlee, B. R., Geske, G. D., Blackwell, H. E., & Handelsman, J. (2010). Identification of synthetic inducers and inhibitors of the quorum-sensing regulator LasR in Pseudomonas aeruginosa by high-throughput screening. Applied and Environmental Microbiology, 76(24), 8255-8258. doi.org/10.1128/Aem.00499-10

Broderick, N. A., Raffa, K. F., & Handelsman, J. (2010). Chemical modulators of the innate immune response alter gypsy moth larval susceptibility to Bacillus thuringiensis. BMC Microbiology, 10. doi.org/Artn12910.1186/1471-2180-10-129

Broderick, N. A., Vasquez, E., Handelsman, J., & Raffa, K. F. (2010). Effect of clonal variation among hybrid poplars on susceptibility of gypsy moth (Lepidoptera: Lymantriidae) to Bacillus thuringiensis subsp. kurstaki. Journal of Economic Entomology, 103(3), 718-725. doi.org/10.1603/Ec09377

Donato, J. J., Moe, L. A., Converse, B. J., Smart, K. D., Berklein, F. C., McManus, P. S., & Handelsman, J. (2010). Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Applied and Environmental Microbiology, 76(13), 4396-4401. doi.org/10.1128/Aem.01763-09

Klimowicz, A. K., Benson, T. A., & Handelsman, J. (2010). A quadruple-enterotoxin-deficient mutant of Bacillus thuringiensis remains insecticidal. Microbiology-Sgm, 156, 3575-3583. doi.org/10.1099/mic.0.039925-0

Lang, K. S., Anderson, J. M., Schwarz, S., Williamson, L., Handelsman, J., & Singer, R. S. (2010). Novel florfenicol and chloramphenicol resistance gene discovered in Alaskan soil by using functional metagenomics. Applied and Environmental Microbiology, 76(15), 5321-5326. doi.org/10.1128/Aem.00323-10

Robinson, C. J., Schloss, P., Ramos, Y., Raffa, K., & Handelsman, J. (2010). Robustness of the bacterial community in the cabbage white butterfly larval midgut. Microbial ecology, 59(2), 199-211. doi.org/10.1007/s00248-009-9595-8

Schloss, P. D., Allen, H. K., Klimowicz, A. K., Mlot, C., Gross, J. A., Savengsuksa, S., McEllin, J., Clardy, J., Reuss, R. W., Handelsman, J. (2010). Psychrotrophic strain of Janthinobacterium lividum from a cold Alaskan soil produces prodigiosin. DNA Cell Biology, 29(9), 533-541. doi.org/10.1089/dna.2010.1020