Aktukmak, M., Zhu, H., Chevrette, M. G., Nepper, J., Magesh, S., Handelsman, J., Hero, A. (2023). A Graphical Model for Fusing Diverse Microbiome Data. IEEE Transactions on Signal Processing, 71, 3399-3412. https://doi.org/10.1109/TSP.2023.3309464

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

Allen, H. K., Cloud-Hansen, K. A., Wolinski, J. M., Guan, C. H., Greene, S., Lu, S., Boeyink, M., Broderick, N. A., Raffa, K. F., Handelsman, J. (2009). Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants. DNA and Cell Biology, 28(3), 109-117. https://doi.org/10.1089/dna.2008.0812

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. https://doi.org/10.1038/nrmicro2312

Allen, H. K., Moe, L. A., Rodbumrer, J., Gaarder, A., & Handelsman, J. (2009). Functional metagenomics reveals diverse ?-lactamases in a remote Alaskan soil. ISME Journal, 3(2), 243-251. https://doi.org/10.1038/ismej.2008.86

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. https://doi.org/10.1007/s00248-012-0057-3

Araujo, R. S., Robleto, E. A., & Handelsman, J. (1994). A hydrophobic mutant of Rhizobium etli altered in nodulation competitiveness and growth in the rhizosphere. Applied and Environmental Microbiology, 60(5), 1430-1436. https://doi.org/10.1128/Aem.60.5.1430-1436.1994

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. https://doi.org/10.1016/j.tetlet.2013.05.093

Beattie, G. A., & Handelsman, J. (1989). A rapid method for the isolation and identification of Rhizobium from root nodules. Journal of Microbiological Methods, 9(1), 29-33. https://doi.org/10.1016/0167-7012(89)90027-4

Beattie, G. A., & Handelsman, J. (1993). Evaluation of a strategy for identifying nodulation competitiveness genes in Rhizobium leguminosarum biovar phaseoli. Journal of General Microbiology, 139(3), 529-538. https://doi.org/10.1099/00221287-139-3-529

Beattie, G. A., Clayton, M. K., & Handelsman, J. (1989). Quantitative comparison of the laboratory and field competitiveness of Rhizobium leguminosarum biovar phaseoli. Applied and Environmental Microbiology, 55(11), 2755-2761.

Biermann, B. J., de Banzie, J. S., Handelsman, J., Thompson, J. F., & Madison, J. T. (1998). Methionine and sulfate increase a Bowman-Birk-type protease inhibitor and its messenger RNA in soybeans. Journal of Agricultural and Food Chemistry, 46(7), 2858-2862. https://doi.org/10.1021/jf971086r

Bintrim, S. B., Donohue, T. J., Handelsman, J., Roberts, G. P., & Goodman, R. M. (1997). Molecular phylogeny of archaea from soil. Proceedings of the National Academy of Sciences of the United States of America, 94(1), 277-282. https://doi.org/10.1073/pnas.94.1.277

Bittinger, M. A., & Handelsman, J. (2000). Identification of genes in the RosR regulon of Rhizobium etli. Journal of Bacteriology, 182(6), 1706-1713. https://doi.org/10.1128/Jb.182.6.1706-1713.2000

Bittinger, M. A., Gross, J. A., Widom, J., Clardy, J., & Handelsman, J. (2000). Rhizobium etli CE3 carries vir gene homologs on a self-transmissible plasmid. Molecular Plant-Microbe Interactions, 13(9), 1019-1021. https://doi.org/10.1094/Mpmi.2000.13.9.1019

Bittinger, M. A., Milner, J. L., Saville, B. J., & Handelsman, J. (1997). rosR, a determinant of nodulation competitiveness in Rhizobium etli. Molecular Plant-Microbe Interactions, 10(2), 180-186. https://doi.org/10.1094/Mpmi.1997.10.2.180

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

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. https://doi.org/10.1128/Aem.00499-10

Borlee, B. R., Geske, G. D., Robinson, C. J., Blackwell, H. E., & Handelsman, J. (2008). Quorum-sensing signals in the microbial community of the cabbage white butterfly larval midgut. ISME Journal, 2(11), 1101-1111. https://doi.org/10.1038/ismej.2008.70

Brady, S. F., Chao, C. J., Handelsman, J., & Clardy, J. (2001). Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Organic Letters, 3(13), 1981-1984. https://doi.org/10.1021/ol015949k

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). https://doi.org/10.1128/genomeA.01535-16

Broderick, N. A., Goodman, R. M., Handelsman, J., & Raffa, K. F. (2003). Effect of host diet and insect source on synergy of gypsy moth (Lepidoptera: Lymantriidae) mortality to Bacillus thuringiensis subsp. kurstaki by zwittermicin A. Environmental Entomology, 32(2), 387-391. https://doi.org/10.1603/0046-225x-32.2.387

Broderick, N. A., Goodman, R. M., Raffa, K. F., & Handelsman, J. (2000). Synergy between zwittermicin A and Bacillus thuringiensis subsp. kurstaki against gypsy moth (Lepidoptera: Lymantriidae). Environmental Entomology, 29(1), 101-107. https://doi.org/10.1603/0046-225x-29.1.101

Broderick, N. A., Raffa, K. F., & Handelsman, J. (2006). Midgut bacteria required for Bacillus thuringiensis insecticidal activity. Proceedings of the National Academy of Sciences of the United States of America, 103(41), 15196-15199. https://doi.org/10.1073/pnas.0604865103

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. https://doi.org/Artn12910.1186/1471-2180-10-129

Broderick, N. A., Raffa, K. F., Goodman, R. M., & Handelsman, J. (2004). Census of the bacterial community of the gypsy moth larval midgut by using culturing and culture-independent methods. Applied and Environmental Microbiology, 70(1), 293-300. https://doi.org/10.1128/Aem.70.1.293-300.2004

Broderick, N. A., Robinson, C. J., McMahon, M. D., Holt, J., Handelsman, J., & Raffa, K. F. (2009). Contributions of gut bacteria to Bacillus thuringiensis-induced mortality vary across a range of Lepidoptera. BMC Biology, 7(11). https://doi.org/Artn1110.1186/1741-7007-7-11

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. https://doi.org/10.1603/Ec09377

Chan, Y. A., Boyne, M. T., Podevels, A. M., Klimowicz, A. K., Handelsman, J., Kelleher, N. L., & Thomas, M. G. (2006). Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. Proceedings of the National Academy of Sciences of the United States of America, 103(39), 14349-14354. https://doi.org/10.1073/pnas.0603748103

Chen, J., Jacobson, L. M., Handelsman, J., & Goodman, R. M. (1996). Compatibility of systemic acquired resistance and microbial biocontrol for suppression of plant disease in a laboratory assay. Molecular Ecology, 5(1), 73-80. https://doi.org/10.1111/j.1365-294X.1996.tb00292.x

Chevrette, M. G. & Handelsman, J. (2020). From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome. Biochemistry, 59(6), 729-730.

Chevrette, M. G., Selem-Mojica, N., Aguilar, C., Labby, K., Bustos-Diaz, E. D., Handelsman, J., & Barona-Gómez, F. (2022). Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis. Methods in Molecular Biology, 2489, 129-155. doi.org/10.1007/978-1-0716-2273-5_8

Chevrette, M. G., Thomas, C. S., Hurley, A., Rosario-Meléndez, N., Sankaran, K., Tu, Y., Hall, A., Magesh, S., & Handelsman, J. (2022). Microbiome Composition Modulates Secondary Metabolism in a Multispecies Bacterial Community. PNAS, 119(42). https://doi.org/10.1073/pnas.2212930119

Cloud-Hansen, K. A., Peterson, S. B., Stabb, E. V., Goldman, W. E., McFall-Ngai, M. J., & Handelsman, J. (2006). Breaching the great wall: peptidoglycan and microbial interactions. Nature Reviews Microbiology, 4(9), 710-716. https://doi.org/10.1038/nrmicro1486

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. https://doi.org/10.1007/s10529-011-0693-6

Delalibera, I., Handelsman, J., & Raffa, K. F. (2005). Contrasts in cellulolytic activities of gut microorganisms between the wood borer, Saperda vestita (Coleoptera: Cerambycidae), and the bark beetles, Ips pini and Dendroctonus frontalis (Coleoptera: Curculionidae). Environmental Entomology, 34(3), 541-547. https://doi.org/10.1603/0046-225x-34.3.541

Delalibera, I., Vasanthakumar, A., Burwitz, B. J., Schloss, P. D., Klepzig, K. D., Handelsman, J., & Raffa, K. F. (2007). Composition of the bacterial community in the gut of the pine engraver, Ips pini (Say) (Coleoptera) colonizing Red Pine. Symbiosis, 43(2), 97-104.

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. https://doi.org/10.1128/Aem.01763-09

Dunn, A. K., & Handelsman, J. (1999). A vector for promoter trapping in Bacillus cereus. Gene, 226(2), 297-305. https://doi.org/10.1016/S0378-1119(98)00544-7

Dunn, A. K., & Handelsman, J. (2002). Toward an understanding of microbial communities through analysis of communication networks. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 81(1-4), 565-574. https://doi.org/10.1023/A:1020565807627

Dunn, A. K., Klimowicz, A. K., & Handelsman, J. (2003). Use of a promoter trap to identify Bacillus cereus genes regulated by tomato seed exudate and a rhizosphere resident, Pseudomonas aureofaciens. Applied and environmental microbiology, 69(2), 1197-1205. https://doi.org/10.1128/Aem.69.2.1197-1205.2003

Emmert, E. A. B., & Handelsman, J. (1999). Biocontrol of plant disease: a (Gram-) positive perspective. FEMS Microbiology Letters, 171(1), 1-9.

Emmert, E. A. B., Milner, J. L., Lee, J. C., Pulvermacher, K. L., Olivares, H. A., Clardy, J., & Handelsman, J. (1998). Effect of canavanine from alfalfa seeds on the population biology of Bacillus cereus. Applied and Environmental Microbiology, 64(12), 4683-4688.

Emmert, E. A., Klimowicz, A. K., Thomas, M. G., & Handelsman, J. (2004). Genetics of zwittermicin a production by Bacillus cereus. Applied and Environmental Microbiology, 70(1), 104-113. https://doi.org/10.1128/aem.70.1.104-113.2004

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. https://doi.org/10.7554/eLife.18855

Gilbert, G. S., Clayton, M. K., Handelsman, J., & Parke, J. L. (1996). Use of cluster and discriminant analyses to compare rhizosphere bacterial communities following biological perturbation. Microbial Ecology, 32(2), 123-147.

Gilbert, G. S., Handelsman, J., & Parke, J. L. (1990). Role of ammonia and calcium in lysis of zoospores of Phytophthora cactorum by Bacillus cereus strain UW85. Experimental Mycology, 14(1), 1-8. https://doi.org/10.1016/0147-5975(90)90081-4

Gilbert, G. S., Handelsman, J., & Parke, J. L. (1994). Root camouflage and disease control. Phytopathology, 84(3), 222-225.

Gilbert, G. S., Parke, J. L., Clayton, M. K., & Handelsman, J. (1993). Effects of an introduced bacterium on bacterial communities on roots. Ecology, 74(3), 840-854. https://doi.org/10.2307/1940810

Gillespie, D. E., Brady, S. F., Bettermann, A. D., Cianciotto, N. P., Liles, M. R., Rondon, M. R., Clardy, J., Goodman, R. M., Handelsman, J. (2002). Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Applied and Environmental Microbiology, 68(9), 4301-4306. https://doi.org/10.1128/Aem.68.9.4301-4306.2002

Gillespie, D., Rondon, M. R., & Handelsman, J. (2005). Metagenomic libraries from uncultured microorganisms. In: A. M. Osborn & C. J Smith (Eds.), Molecular Microbial Ecology (pp. 261-279). BIOS Scientific.

Goodman, R. M., Bintrim, S. B., Handelsman, J., Quirino, B. F., Rosas, J. C., Simon, H. M., & Smith, K. P. (1998). A dirty look: Soil microflora and rhizosphere microbiology. In: H. E. Flores, J. P. Lynch, & D. Eissenstat (Eds.), Radical Biology: Advances and Perspectives on the Function of Plant Roots, (pp. 219-231). American Society of Plant Physiologists.

Guan, C. H., Ju, J. J., Borlee, B. R., Williamson, L. L., Shen, B., Raffa, K. F., & Handelsman, J. (2007). Signal mimics derived from a metagenomic analysis of the gypsy moth gut microbiota. Applied and environmental microbiology, 73(11), 3669-3676. https://doi.org/10.1128/Aem.02617-06

Halverson, L. J., & Handelsman, J. (1991). Enhancement of soybean nodulation by Bacillus cereus UW85 in the field and in a growth chamber. Applied and Environmental Microbiology, 57(9), 2767-2770. https://doi.org/10.1128/Aem.57.9.2767-2770.1991

Halverson, L. J., Clayton, M. K., & Handelsman, J. (1993a). Population biology of Bacillus cereus UW85 in the rhizosphere of field-grown soybeans. Soil Biology & Biochemistry, 25(4), 485-493. https://doi.org/10.1016/0038-0717(93)90074-L

Halverson, L. J., Clayton, M. K., & Handelsman, J. (1993b). Variable stability of antibiotic-resistance markers in Bacillus cereus UW85 in the soybean rhizosphere in the field. Molecular Ecology, 2(2), 65-78. https://doi.org/10.1111/j.1365-294X.1993.tb00001.x

Handelsman, J. (2000). Antagonism. In: O.C. Maloy & T.D. Murray (Eds.), Encyclopedia of Plant Pathology. John Wiley.

Handelsman, J. (2004a). Metagenomics: Application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669. https://doi.org/10.1128/Mmbr.68.4.669-685.2004

Handelsman, J. (2004b). Soils – the metagenomics approach. In: A. T. Bull (Ed.), Microbial Diversity Bioprospecting, (pp. 109-119). American Society for Microbiology Press.

Handelsman, J. (2005a). How to find new antibiotics. Scientist, 19(19), 20-21.
Handelsman, J. (2005b). Metagenomics or megagenomics? Nature Reviews Microbiology, 3, 457-458.

Handelsman, J. (2005c). Sorting out metagenomes. Nature Biotechnology, 23(1), 38-39. https://doi.org/10.1038/nbt0105-38

Handelsman, J. (2007). Metagenomics and microbial communities. In: Encyclopedia of the Life Sciences. John Wiley and Sons, Ltd.

Handelsman, J. (2009). Metagenetics: spending our inheritance on the future. Microbial Biotechnology, 2(2), 138-139. https://doi.org/10.1111/j.1751-7915.2009.00090_8.x

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. https://doi.org/10.1128/9781555816841.ch25

Handelsman, J. 2002. Future trends in biocontrol. In: S.S. Gnanamanickam (Ed.), Biological Control of Crop Diseases (pp. 443-448). Marcel Dekker, Inc.,

Handelsman, J., & Brill, W. J. (1985). Erwinia herbicola isolates from alfalfa plants may play a role in nodulation of alfalfa by Rhizobium meliloti. Applied and Environmental Microbiology, 49(4), 818-821.

Handelsman, J., Elgin, S., Estrada, M., Hays, S., Johnson, T., Miller, S., Mingo, V., Shaffer, C., & Williams, J. (2022). Achieving STEM diversity: Fix the classrooms. Science, 376(6597), 1057-1059. https://doi.org/10.1126/science.abn9515

Handelsman, J., & Parke, J. L. (1989). Mechanisms of biocontrol of soilborne plant pathogens. In: T. Kosuge & E. W. Nester (Eds.), Plant Microbe Interactions Volume 3 (pp. 27-61). McGraw Hill.

Handelsman, J., & Smalla, K. (2003). Conversations with the silent majority. Current Opinion in Microbiology, 6(3), 271-273. https://doi.org/10.1016/S1369-5274(03)00062-6

Handelsman, J., & Stabb, E. V. (1996). Biocontrol of soilborne plant pathogens. Plant Cell, 8(10), 1855-1869. https://doi.org/10.2307/3870235

Handelsman, J., & Wackett, L. P. (2002). Ecology and industrial microbiology: Microbial diversity – sustaining the Earth and industry. Current Opinion in Microbiology, 5(3), 237-239. https://doi.org/10.1016/s1369-5274(02)00331-4

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

Handelsman, J., Liles, M., Mann, D., Riesenfeld, C., & Goodman, R. M. (2002). Cloning the metagenome: Culture-independent access to the diversity and functions of the uncultivated microbial world. Functional Microbial Genomics, 33, 241-255.

Handelsman, J., Mester, E. H., Wunderlich, L., & Grau, C. (1988). Rapid screening of bacteria for biocontrol of Phytophthora damping off of alfalfa. Biological and Cultural Tests for Control of Plant Disease, 3, 60.

Handelsman, J., Nesmith, W. S., & Raffel, S. J. (1991). Microassay for biological and chemical control of infection of tobacco by Phytophthora parasitica var. nicotianae. Current Microbiology, 22(5), 317-319. https://doi.org/10.1007/Bf02091961

Handelsman, J., Raffel, S. J., & Sequeira, L. (1990). Biological control of damping-off of alfalfa seedlings with Bacillus cereus UW85. Applied and Environmental Microbiology, 56(3), 713-718.

Handelsman, J., Raffel, S. J., & Sequeira, L. (1990). Monoclonal-antibodies against Agrobacterium tumefaciens strain C58. Current Microbiology, 21(3), 181-185. https://doi.org/10.1007/Bf02092119

Handelsman, J., Robinson, C.J., & Raffa, K. (2005). Microbial communities in lepidopteran guts: from models to metagenomics. In: M. J. McFall-Ngai, B. Henderson, & E.G. Ruby (Eds.), The Influence of Cooperative Bacteria on Animal Host Biology (pp. 143-168). Cambridge University Press.

Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., & Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chemistry & Biology, 5(10), R245-R249. https://doi.org/10.1016/S1074-5521(98)90108-9

Handelsman, J., Ugalde, R. A., & Brill, W. J. (1984). Rhizobium meliloti competitiveness and the alfalfa agglutinin. Journal of Bacteriology, 157(3), 703-707. https://doi.org/10.1128/Jb.157.3.703-707.1984&quot

He, H. Y., Silosuh, L. A., Handelsman, J., & Clardy, J. (1994). Zwittermicin A, an antifungal and plant protection agent from Bacillus cereus. Tetrahedron Letters, 35(16), 2499-2502. https://doi.org/10.1016/S0040-4039(00)77154-1

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. https://doi.org/10.1128/Iai.02442-14

Hurley, A., Chevrette, M. G., Acharya, D. D., Lozano, G. L., Garavito, M., Heinritz, J., Balderrama, L., Beebe, M., DenHartog, M. L., Corinaldi, K., Engels, R., Gutierrez, A., Jona, O., Putnam, J. H. I., Rhodes, B., Tsang, T., Hernandez, S., Bascom-Slack, C., Blum, J. E., Price, P. A., Davis, D., Klein, J., Pultorak, J., Sullivan, N. L., Mouncey, N. J., Dorrestein. P. C., Miller, S., Broderick, N. A., and Handelsman, J. (2021). Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery. mBio, 12:e03432-20. https://doi.org/10.1128/mBio.03432-20

Isenbarger, T. A., Finney, M., Rios-Velazquez, C., Handelsman, J., & Ruvkun, G. (2008). Miniprimer PCR, a new lens for viewing the microbial world. Applied and environmental microbiology, 74(3), 840-849. https://doi.org/10.1128/Aem.01933-07

Kazmar, E. R., Goodman, R. M., Grau, C. R., Johnson, D. W., Nordheim, E. V., Undersander, D. J., & Handelsman, J. (2000). Regression analyses for evaluating the influence of Bacillus cereus on alfalfa yield under variable disease intensity. Phytopathology, 90(6), 657-665. https://doi.org/10.1094/Phyto.2000.90.6.657

Klepzig, K. D., Adams, A. S., Handelsman, J., & Raffa, K. F. (2009). Symbioses: A key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans. Environmental Entomology, 38(1), 67-77. https://doi.org/10.1603/022.038.0109

Klimowicz, A. K., Benson, T. A., & Handelsman, J. (2010). A quadruple-enterotoxin-deficient mutant of Bacillus thuringiensis remains insecticidal. Microbiology-Sgm, 156, 3575-3583. https://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. https://doi.org/10.1128/Aem.00323-10

Lauffer, S. & Handelsman, J. (2004). A new generation of scientific teachers. Focus on Microbiology Education, 10, 4-6.
Liles, M. R., Manske, B. F., Bintrim, S. B., Handelsman, J., & Goodman, R. M. (2003). A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Applied and Environmental Microbiology, 69(5), 2684-2691. https://doi.org/10.1128/Aem.69.5.2684-2691.2003

Liles, M. R., Williamson, L. L., Rodbumrer, J., Torsvik, V., Goodman, R. M., & Handelsman, J. (2008). Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms. Applied and Environmental Microbiology, 74(10), 3302-3305. https://doi.org/10.1128/Aem.02630-07

Liles, M.R., Williamson, L.L., Handelsman, J., & Goodman, R.M. (2004). Isolation of high molecular weight genomic DNA from soil bacteria for genomic library construction. In: G.G. Kowalchuk, F.J. de Bruijn, I.M. Head, A.D. Akkermans, & J.D. van Elsas (Eds.), Molecular Microbial Ecology Manual, (2nd ed., pp. 839-852). Kluwer Academic Publishers.

Little, A. E. F., Robinson, C. J., Peterson, S. B., Raffa, K. E., & Handelsman, J. (2008). Rules of engagement: Interspecies interactions that regulate microbial communities. Annual Review of Microbiology, 62, 375-401. https://doi.org/10.1146/annurev.micro.030608.101423

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). https://doi.org/ARTN e00570-1710.1128/genomeA.00570-17

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). https://doi.org/ARTN e02846-1810.1128/mBio.02846-18

Lozano, G. L., Guan, C., Cao, Y., Borlee, B. R., Broderick, N. A., Stabb, E. V., Handelsman, J. (2020). A Chemical Counterpunch: Chromobacterium violaceum ATCC 31532 Produces Violacein in Response to Translation-Inhibiting Antibiotics. mBio, 11(3), e00948-20. https://mbio.asm.org/content/11/3/e00948-20

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). https://doi.org/10.1128/genomeA.00910-16

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). https://doi.org/UNSP e03058-1810.1128/AEM.03058-18

Magesh, S., Hurley, A. I., Nepper, J. F., Chevrette, M. G., Schrope, J. H., Li, C., Beebe, D. J., Handelsman, J. (2024). Surface colonization by Flavobacterium johnsoniae promotes its survival in a model microbial community. mBio, e03428-23. https://doi.org/10.1128/mbio.03428-23

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). https://doi.org/ARTN e00065-1110.1128/mBio.00065-11

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. https://doi.org/10.1128/AEM.00044-12

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

Milner, J. L., Araujo, R. S., & Handelsman, J. (1992). Molecular and symbiotic characterization of exopolysaccharide-deficient mutants of Rhizobium tropici strain CIAT899. Molecular Microbiology, 6(21), 3137-3147. https://doi.org/10.1111/j.1365-2958.1992.tb01770.x

Milner, J. L., Raffel, S. J., Lethbridge, B. J., & Handelsman, J. (1995). Culture conditions that influence accumulation of zwittermicin A by Bacillus cereus UW85. Applied Microbiology and Biotechnology, 43(4), 685-691.

Milner, J. L., Silo-Suh, L., Lee, J. C., He, H. Y., Clardy, J., & Handelsman, J. (1996). Production of kanosamine by Bacillus cereus UW85. Applied and Environmental Microbiology, 62(8), 3061-3065. https://doi.org/10.1128/Aem.62.8.3061-3065.1996

Milner, J. L., Stohl, E. A., & Handelsman, J. (1996). Zwittermicin A resistance gene from Bacillus cereus. Journal of Bacteriology, 178(14), 4266-4272. https://doi.org/10.1128/jb.178.14.4266-4272.1996

Milner, J., Silo-Suh, L., Goodman, R. M., & Handelsman, J. (1997). Antibiosis and beyond: Genetic diversity, microbial communities, and biological control. In: D. A. Andow, D. W. Ragsdale, & R. F. Nyvall (Eds.), Ecological Interactions and Biological Control (pp. 107-127). CRC Press.
O’Connell, K. P., & Handelsman, J. (1989). chvA locus may be involved in export of neutral cyclic ?-1,2-linked D-glucan from Agrobacterium tumefaciens. Molecular Plant Microbe Interactions, 2(1), 11-16.

O’Connell, K. P., Raffel, S. J., Saville, B. J., & Handelsman, J. (1998). Mutants of Rhizobium tropici strain CIAT899 that do not induce chlorosis in plants. Microbiology, 144(9), 2607-2617. https://doi.org/10.1099/00221287-144-9-2607

O’Connell, K. P., & Handelsman, J. (1993). Foliar chlorosis in symbiotic host and non-host plants induced by Rhizobium tropici type B strains. Applied Environmental Microbiology, 59(7), 2184-2189.

O’Connell, K. P., Araujo, R. S., & Handelsman, J. (1990). Exopolysaccharide-deficient mutants of Rhizobium sp. strain CIAT899 induce chlorosis in common bean Phaseolus vulgaris. Molecular Plant Microbe Interactions, 3(6), 424-428. https://doi.org/10.1094/Mpmi-3-424

OConnell, K. P., Goodman, R. M., & Handelsman, J. (1996). Engineering the rhizosphere: Expressing a bias. Trends in Biotechnology, 14(3), 83-88. https://doi.org/10.1016/0167-7799(96)80928-0

Osburn, R. M., Milner, J. L., Oplinger, E. S., Smith, R. S., & Handelsman, J. (1995). Effect of Bacillus cereus UW85 on the yield of soybean at two field sites in Wisconsin. Plant Disease, 79(6), 551-556. https://doi.org/10.1094/Pd-79-0551

Peterson, S. B., Dunn, A. K., Klimowicz, A. K., & Handelsman, J. (2006). Peptidoglycan from Bacillus cereus mediates commensalism with rhizosphere bacteria from the Cytophaga-Flavobacterium group. Applied and Environmental Microbiology, 72(8), 5421-5427. https://doi.org/10.1128/Aem.02928-05

Raffel, S. J., Kazmar, E. R., Winberg, R., Oplinger, E. S., Handelsman, J., Goodman, R. M., & Grau, C. R. (1999). First report of root rot of soybeans caused by Corynespora cassiicola in Wisconsin. Plant Disease, 83(7), 696. https://doi.org/10.1094/PDIS.1999.83.7.696B

Raffel, S. J., Stabb, E. V., Milner, J. L., & Handelsman, J. (1996). Genotypic and phenotypic analysis of zwittermicin A-producing strains of Bacillus cereus. Microbiology, 142, 3425-3436. https://doi.org/10.1099/13500872-142-12-3425

Riesenfeld, C. S., Goodman, R. M., & Handelsman, J. (2004). Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environmental Microbiology, 6(9), 981-989. https://doi.org/10.1111/j.1462-2920.2004.00664.x

Riesenfeld, C. S., Schloss, P. D., & Handelsman, J. (2004). Metagenomics: Genomic analysis of microbial communities. Annual Review of Genetics, 38, 525-552. https://doi.org/10.1146/annurev.genet.38.072902.091216

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. http://doi.org/10.1007/s00248-009-9595-8

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). https://doi.org/ARTN 018204310.1371/journal.pone.0182043

Rondon, M. R., August, P. R., Bettermann, A. D., Brady, S. F., Grossman, T. H., Liles, M. R., Loiacono, K. A., Lynch, B. A., MacNeil, I. A., Minor, C., Tiong, C. L.,
Gilman, M, Osburne, M. S., Clardy, J., Handelsman, J., & Goodman, R. M. (2000). Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Applied and Environmental Microbiology, 66(6), 2541-2547. https://doi.org/10.1128/Aem.66.6.2541-2547.2000

Rondon, M. R., Goodman, R. M., & Handelsman, J. (1999). The Earth’s bounty: assessing and accessing soil microbial diversity. Trends in Biotechnology, 17(10), 403-409. doi.org/10.1016/S0167-7799(99)01352-9

Rondon, M. R., Raffel, S. J., Goodman, R. M., & Handelsman, J. (1999). Toward functional genomics in bacteria: Analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proceedings of the National Academy of Sciences of the United States of America, 96(11), 6451-6455. doi.org/10.1073/pnas.96.11.6451

Rosas, J. C., Castro, J. A., Robleto, E. A., & Handelsman, J. (1998). A method for screening Phaseolus vulgaris L. germplasm for preferential nodulation with a selected Rhizobium etli strain. Plant and Soil, 203(1), 71-78. https://doi.org/10.1023/A:1004346114558

Sabree, Z. L., Bergendahl, V., Liles, M. R., Burgess, R. R., Goodman, R. M., & Handelsman, J. (2006). Identification and characterization of the gene encoding the Acidobacterium capsulatum major sigma factor. Gene, 376(1), 144-151. https://doi.org/10.1016/j.gene.2006.02.033

Sabree, Z. L., Rondon, M. R., & Handelsman, J. (2009). Metagenomics. In M. Schaechter (Ed.), Encyclopedia of Microbiology (2nd ed., pp. 622-632). Academic Press.

Safdar, N., Handelsman, J., & D.G. Maki. (2004). Does combination antimicrobial therapy reduce mortality in gram-negative bacteraemia? A meta-analysis. The Lancet – Infectious Diseases. 4(8): 519-27. https://doi.org/10.1016/S1473-3099(04)01108-9

Schloss, P. D., & Handelsman, J. (2003). Biotechnological prospects from metagenomics. Current Opinion in Biotechnology, 14(3), 303-310. https://doi.org/10.1016/S0958-1669(03)00067-3

Schloss, P. D., & Handelsman, J. (2004). Status of the microbial census. Microbiology and Molecular Biology Reviews, 68(4), 686. https://doi.org/10.1128/Mmbr.68.4.686-691.2004

Schloss, P. D., & Handelsman, J. (2005a). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and environmental microbiology, 71(3), 1501-1506. https://doi.org/10.1128/Aem.71.3.1501-1506.2005

Schloss, P. D., & Handelsman, J. (2005b). Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biology, 6(8). https://doi.org/ARTN 22910.1186/gb-2005-6-8-229

Schloss, P. D., & Handelsman, J. (2006a). Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Applied and Environmental Microbiology, 72(10), 6773-6779. https://doi.org/10.1128/Aem.00474-06

Schloss, P. D., & Handelsman, J. (2006b). Toward a census of bacteria in soil. Plos Computational Biology, 2(7), 786-793. https://doi.org/ARTN e92

Schloss, P. D., & Handelsman, J. (2006c). Introducing TreeClimber, a test to compare microbial community structures. Applied and Environmental Microbiology, 72(4), 2379-2384. https://doi.org/10.1128/AEM.72.4.2379-2384.2006

Schloss, P. D., & Handelsman, J. (2007). The last word: Books as a statistical metaphor for microbial communities. Annual Review of Microbiology, 61(1), 23-34. https://doi.org/10.1146/annurev.micro.61.011507.151712

Schloss, P. D., & Handelsman, J. (2008). A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics, 9, 34. https://doi.org/10.1186/1471-2105-9-34

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. http://doi.org/10.1089/dna.2010.1020

Schloss, P. D., Delalibera, I., Handelsman, J., & Raffa, K. F. (2006). Bacteria associated with the guts of two wood-boring beetles: Anoplophora glabripennis and Saperda vestita (Cerambycidae). Environmental Entomology, 35(3), 625-629. https://doi.org/10.1603/0046-225x-35.3.625

Schloss, P. D., Larget, B. R., & Handelsman, J. (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Applied and Environmental Microbiology, 70(9), 5485-5492. https://doi.org/10.1128/Aem.70.9.5485-5492.2004

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

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. https://doi.org/10.1038/ismej.2013.54

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. https://doi.org/10.1111/j.1462-2920.2012.02817.x

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). https://doi.org/ARTN e01371-1410.1128/mBio.01371-14

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. https://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). https://doi.org/ARTN e00602-1210.1128/mBio.00602-12

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. https://doi.org/ARTN 41710.3389/fmicb.2012.00417

Shang, H. Z., Chen, J. J., Handelsman, J., & Goodman, R. M. (1999). Behavior of Pythium torulosum zoospores during their interaction with tobacco roots and Bacillus cereus. Current Microbiology, 38(4), 199-204. https://doi.org/10.1007/Pl00006787

Shaska, J., Gursoy, M. C., Ross, T. D., Cheng, Y. -Y., Krieger, A., Thairu, M., Venturelli, O. S., Boedicker J., Handelsman, J., Mitra, U. (2023). Microbes as Communication & Decision-Making Networked Communities. IEEE Nanotechnology Magazine, 1(10). https://doi.org/10.1109/MNANO.2023.3262431

Silo-Suh, L. A., Lethbridge, B. J., Raffel, S. J., He, H., Clardy, J., & Handelsman, J. (1994). Biological activities of two fungistatic antibiotics produced by Bacillus cereus UW85. Applied and Environmental Microbiology, 60(6), 2023-2030.

Silo-Suh, L. A., Stabb, E. V., Raffel, S. J., & Handelsman, J. (1998). Target range of zwittermicin A, an aminopolyol antibiotic from Bacillus cereus. Current Microbiology, 37(1), 6-11.

Simon, H. M., Smith, K. P., Dodsworth, J. A., Guenthner, B., Handelsman, J., & Goodman, R. M. (2001). Influence of tomato genotype on growth of inoculated and indigenous bacteria in the spermosphere. Applied and Environmental Microbiology, 67(2), 514-520. https://doi.org/10.1128/Aem.67.2.514-520.2001

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. https://doi.org/10.1534/g3.118.200928

Smith, K. P., Handelsman, J., & Goodman, R. M. (1997). Modeling dose-response relationships in biological control: Partitioning host responses to the pathogen and biocontrol agent. Phytopathology, 87(7), 720-729. https://doi.org/10.1094/Phyto.1997.87.7.720

Smith, K. P., Handelsman, J., & Goodman, R. M. (1999). Genetic basis in plants for interactions with disease-suppressive bacteria. Proceedings of the National Academy of Sciences of the United States of America, 96(9), 4786-4790. https://doi.org/10.1073/pnas.96.9.4786

Smith, K. P., Havey, M. J., & Handelsman, J. (1993). Suppression of cottony leak of cucumber with Bacillus cereus strain UW85. Plant Disease, 77(2), 139-142. https://doi.org/10.1094/Pd-77-0139

Stabb, E. V., & Handelsman, J. (1998). Genetic analysis of zwittermicin A resistance in Escherichia coli: Effects on membrane potential and RNA polymerase. Molecular Microbiology, 27(2), 311-322. https://doi.org/10.1046/j.1365-2958.1998.00678.x

Stabb, E. V., Jacobson, L. M., & Handelsman, J. (1994). Zwittermicin A-producing strains of Bacillus cereus from diverse soils. Applied and Environmental Microbiology, 60(12), 4404-4412. https://doi.org/10.1128/Aem.60.12.4404-4412.1994

Stohl, E. A., Brady, S. F., Clardy, J., & Handelsman, J. (1999). ZmaR,
a novel and widespread antibiotic resistance determinant that acetylates zwittermicin A. Journal of Bacteriology, 181(17), 5455-5460. https://doi.org/10.1128/Jb.181.17.5455-5460.1999

Stohl, E. A., Milner, J. L., & Handelsman, J. (1999). Zwittermicin A biosynthetic cluster. Gene, 237(2), 403-411. https://doi.org/10.1016/S0378-1119(99)00315-7

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. https://doi.org/10.3389/fmicb.2016.00573

Triplett, E. W., Roberts, G. P., Ludden, P. W., & Handelsman, J. (1989). What’s new in nitrogen fixation. American Society for Microbiology News, 55, 15-21.

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. https://doi.org/10.1073/pnas.1409836111

Ugalde, R. A., Handelsman, J., & Brill, W. J. (1986). Role of galactosyltransferase activity in phage sensitivity and nodulation competitiveness of Rhizobium meliloti. Journal of Bacteriology, 166(1), 148-154.

Vasanthakumar, A., Delalibera, I., Jr., Handelsman, J., Klepzig, K. D., Schloss, P. D., & Raffa, K. F. (2006). Characterization of gut-associated bacteria in larvae and adults of the Southern Pine Beetle, Dendroctonus frontalis Zimmermann. Environmental Entomology, 35(6), 1710-1717. https://doi.org/10.1093/ee/35.6.1710

Vasanthakumar, A., Handelsman, J., Schloss, P. D., Bauer, L. S., & Raffa, K. F. (2008). Gut Microbiota of an invasive subcortical beetle, Agrilus planipennis Fairmaire, across various life stages. Environmental Entomology, 37(5), 1344-1353. https://doi.org/10.1603/0046-225x(2008)37[1344:Gmoais]2.0.Co;2

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

Williamson, L. L., Borlee, B. R., Schloss, P. D., Guan, C. H., Allen, H. K., & Handelsman, J. (2005). Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Applied and Environmental Microbiology, 71(10), 6335-6344. https://doi.org/10.1128/Aem.71.10.6335-6344.2005

Wood, W. B., & Handelsman, J. (2004). Meeting report: the 2004 National Academies Summer Institute on Undergraduate Education in Biology. Cell Biology Education, 3(4), 215-217. https://doi.org/10.1187/cbe.04-07-0057