Microbiology Publications in 2010s


Lozano, G. L., J. I. Bravo, M. F. Garavito Diago, H. B. Park, A. Hurley, S. B. Peterson, E. V. Stabb, J. M. Crawford, N. A. Broderick, J. Handelsman. 2019. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio. 10 (2) e02846-18 [pubmed: https://www.ncbi.nlm.nih.gov/pubmed/30837345]

Lozano, G. L., H. B. Park, J. I. Bravo, E. A. Armstrong, J. M. Denu, E. V. Stabb, N. A. Broderick, J. M. Crawford, J. Handelsman. 2019. Bacterial analogs of plant tetrahydropyridine alkaloids mediate microbial interactions in a rhizosphere model system. Appl. Environ. Microbiol.. AEM.03058-18 [pubmed: https://www.ncbi.nlm.nih.gov/pubmed/30877115]

Sivakumar, R., J. Ranjani, U. S. Vishnu, S. Jayashree, G. L. Lozano, J. Miles, N. A. Broderick, C. Guan, P. Gunasekaran, J. Handelsman, J. Rajendhran. 2019. Evaluation of INSeq To Identify Genes Essential for Pseudomonas aeruginosa PGPR2 Corn Root Colonization. G3: Genes, Genomes, Genetics. 9(3):651-661 [pubmed: https://www.ncbi.nlm.nih.gov/pubmed/30705119


Handelsman, J., Hernandez, S., Tsang, T., Bascom-Slack, C., and Broderick, N. 2018. Tiny Earth – A Research Guide to Studentsourcing Antibiotic Discovery, XanEdu Publishing Inc., Ann Arbor, MI. 203 pp.


Lozano G.L.,Bravo J.I., Handelsman J., Draft genome sequence of Pseudomonas koreensis CI12, a Bacillus cereus “hitchhiker” from the soybean rhizosphere. Genome Announcements  5:e00570-1.

Rodríguez MM, Herman R, Ghiglione B, Kerff F, D’Amico González G, 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-β-lactamase LRA-12 from an Alaskan soil metagenome. PLoS ONE 12(7):e0182043.

Bravo J.I., Lozano G.L., Handelsman J. 2017. Draft genome gequence of Flavobacterium johnsoniae CI04, an isolate from the soybean rhizosphere. Genome Announcements. 5:e01535-16.

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. 2 9;6.


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 Announcements. 4: e00910-16.

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


Allen H.K., An R., Handelsman J., Moe L.A. 2015. A response regulator from a soil metagenome enhances resistance to the β-lactam antibiotic carbenicillin in Escherichia coli. PLoS One. 10(3):e0120094.

Miles J., J.F. Holt, and J. Handelsman. 2015. Allies and adversaries: roles of the microbiome in infectious disease. Microbe Magazine. 10: 370-374.

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


Udikovic-Kolic, N., F. Wichmann, N.A. Broderick, and J. Handelsman. 2014. Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1409836111.

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

Wichmann, F., N. Udikovic-Kolic, S. Andrew, and J. Handelsman. 2014. Diverse antibiotic resistance genes in dairy cow manure. mBio. 5(2): e01017-13.


Blum, J.E., C.N. Fischer, J. Miles, and J. Handelsman. 2013. Frequent replenishment sustains the beneficial microbiome of Drosophila melanogaster. mBio. 4(6): e00860-13. doi:10.1128/mBio.00860-13.

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

Baraban, E.G., J.B. Morin, G.M. Phillips, A.J. Phillips, S.A. Strobel, and J. Handelsman. 2013. Xyolide, a bioactive nonenolide from an Amazonian endophytic fungus, Xylaria feejeensis. Tetrahedron Letters. doi: 10.1016/j.tetlet.2013.05.093.

Shade, A., J.G. Caporaso, J. Handelsman, R. Knight, and N. Fierer. 2013. A meta-analysis of changes in bacterial and archaeal communities with time. ISME Journal. doi: 10.1038/ismej.2013.54.

Shade, A., P.S. McManus, and J. Handelsman. 2013. Unexpected diversity during community succession in the apple flower microbiome. mBio. 4(2): e00602-12. doi:10.1128/mBio.00602-12.


Shade, A., H. Peter, S.D. Allison, D. Baho, M. Berga, H. Buergmann, D.H. Huber, S. Langenheder, J.T. Lennon, J.B. Martiny, K. Matulich, T.M. Schmidt, and J. Handelsman. 2012. Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology. 3: 417. doi: 10.3389/fmicb.2012.00417.

Araujo J.F., A.P. de Castro, M.M. Costa, R.C. Togawa, G.J. Júnior, B.F. Quirino, M.M. Bustamante, L. Williamson, J. Handelsman, and R.H. Krüger. 2012. Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance. Microb Ecol. 64(3): 760-770.

Shade, A., C.S. Hogan, A.K. Klimowicz, M. Linske, P.S. McManus, and J. Handelsman. 2012. Culturing captures members of the soil rare biosphere. Environmental Microbiology. 14(9): 2247-2252.

McMahon, M.D., C. Guan, J. Handelsman, and M.G. Thomas. 2012. Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression. Applied and Environmental Microbiology. 78:3622-3629.

Shade, A. and J. Handelsman. 2012. Beyond the Venn diagram: the hunt for a core microbiome. Environmental Microbiology. 14(1): 4-12.


de Castro, A.P., B.F. Quirino, H. Allen, L.L. Williamson, J. Handelsman, and R.H. Kruger. 2011. Construction and validation of two metagenomic DNA libraries from Cerrado soil with high clay content. Biotechnology Letters. 33: 2169-2175.

Mason, K.L., T.A. Stepien, J.E. Blum, J.F. Holt, N.H. Labbe, J.S. Rush, K.F. Raffa, and J. Handelsman. 2011. From commensal to pathogen: translocation of Enterococcus faecalis from the midgut to the hemocoel of Manduca sexta. mBio. 2(3): e00065-11.


Schloss, P.D., H.K. Allen, A.K. Klimowicz, C. Mlot, J.A. Gross, S. Savengsuksa, J. McEllin, J. Clardy, R.W. Ruess, and J. Handelsman. 2010. Psychotrophic strain of Janthinobacterium lividium from a cold Alaskan soil produces prodigiosin. DNA and Cell Biology. 29(9): 533-41. [PubMed]

Borlee, B.R., G.D. Geske, H.E. Blackwell, and J. Handelsman. 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. [PubMed]

Klimowicz, A.K., T.A. Benson, and J. Handelsman. 2010. A quadruple-enterotoxin-deficient mutant of Bacillus thuringiensis remains insecticidal. Microbiology. 156: 3575-3583. [PubMed]

Lang, K.S., J.M. Anderson, S. Schwarz, L. Williamson, J. Handelsman and R.S. Singer. 2010. Novel florfenicol and chloramphenicol resistance gene discovered in Alaskan soil by using functional metagenomics. Applied and Environmental Microbiology. 76(15): 5321-5326. [PubMed]

Donato, J., L.A. Moe, B.J. Converse, K.D. Smart, F.C. Berklein, P.S. McManus and J. Handelsman. 2010. Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Applied and Environmental Microbiology. 76(13): 4396-4401. [PubMed]

Broderick, N.A., E. Vasquez, J. Handelsman and K. F. Raffa. 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. [PubMed]

Broderick, N.A., K.F. Raffa and J. Handelsman. 2010. Chemical modulators of the innate immune response alter gypsy moth larval susceptibility to Bacillus thuringiensis. BMC Microbiology. 10(1):129. [PubMed]

Allen, H.K., J. Donato, H.H. Wang, K.A. Cloud-Hansen, J. Davies and J. Handelsman. 2010. Call of the wild: antibiotic resistance genes in natural environments. Nature Reviews Microbiology. 8(4): 251-259. [PubMed]

Robinson, C.J., P.D. Schloss, Y. Ramos, K.F. Raffa and J. Handelsman. 2010. Robustness of the bacterial community in the cabbage white butterfly larval midgut. Microbial Ecology 59(2): 199-211. [PubMed]