Microbiology Publications in 2000s


Sabree, Z.L., M.R. Rondon, and J. Handelsman. 2009. Metagenomics. In: Encyclopedia of Microbiology (Third Edition). Academic Press, pp. 622-632.

Handelsman, J. 2009. Metagenetics: spending our inheritance on the future. Microbial Biotechnology 2(2): 138-139.

Broderick, N.A., C.J. Robinson, M.D. McMahon, J. Holt, J. Handelsman and K.F. Raffa. 2009. Contributions of gut bacteria to Bacillus thuringiensis-induced mortality vary across a range of Lepidoptera. BMC Biology 7: 11-20.

Klepzig, K.D., A. S. Adams, J. Handelsman, and K. F. Raffa. 2009. Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans. Environ. Entomol. 38(1): 67-77.

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


Vasanthakumar, A., Handelsman, J., Schloss, P.D., and Raffa, K. F. 2008. Gut microbiota of an invasive subcortical beetle, Agrilus planipennis Fairmaire, across various life stages. Environ. Entomol. 37(5): 1344-1353.

Allen, H. K., Moe, L. A., Rodbumrer, J., Gaarder, A., and Handelsman, J. 2008. Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil. ISME Journal. 3: 243–251.

Little, A. E. F., Robinson, C., Peterson, S. B., Raffa, K. F., and Handelsman, J. 2008. Rules of engagement: Interspecies interactions that regulate microbial communities. Annu. Rev. Microbiol. 62: 375-401.

Borlee, B. R., Geske, G.D., Robinson, C.R., Blackwell, H., and Handelsman, J. 2008. Quorum-sensing signals in the microbial community of the cabbage white butterfly larval midgut. ISME Journal 2: 1101-1111.

Liles, M.R., Williamson, L.L., Rodbumrer, J., Torsvik, V., Goodman, R.M., and Handelsman, J. 2008. Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms. Appl. Environ. Microbiol. 74(10): 3302-3305.

Isenbarger, T. A., Finney, M., Rios-Velazquez, C., Handelsman, J., and Ruvkun, G. 2008. Miniprimer PCR, a new lens for viewing the microbial world. Appl. Environ. Microbiol. 74(3): 840-849.

Schloss, P.D., Handelsman, J. 2008. The Last Word: Books as a statistical metaphor for microbial communities. Annu. Rev. Microbiol. 61: 23-24.

Schloss, P.D. and Handelsman, J. 2008. A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities. BMC Bioinformatics 9: 34.


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

Delalibera, I. Vasanthakumar, A., Burwitz, B.J., Schloss, P.D., Klepzig, K.D., Handelsman, J. and 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: 97-104.

Guan, C., Ju, J., Borlee, B.R., Williamson, L.L., Shen, B., Raffa, K.F., and Handelsman, J. 2007. Signal mimics derived from a metagenomic analysis of gypsy moth gut microbiota. Appl. Environ. Microbiol. 73(11): 3669-3676.


Vasanthakumar, A, Delalibera Jr. I., Handelsman, J., Klepzig, K.D., P. Schloss, P., and Raffa, K.F. 2006. Characterization of gut-associated microorganisms in larvae and adults of the southern pine beetle, Dendroctonus frontalis Zimmerman. Environ. Entomol. 35: 1710-1717.

Broderick, N.A., Raffa, KR., and Handelsman, J. 2006. Midgut bacteria required for Bacillus thuringiensis insecticidal activity. Proc. Natl. Acad. Sci. USA. 103(41): 15196-15199.

Chan, Y.A., Boyne, M.T., Podevels, A.M., Klimowicz, A.K., Handelsman, J., Kelleher, N.L., and Thomas, M.G. 2006. Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. Proc. Natl. Acad. Sci. USA. 103(39): 14349-14354.

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: 144-151.

Peterson, S.B., Dunn, A.K., Klimowicz, A.K., and Handelsman, J. 2006. Peptidoglycan from Bacillus cereus mediates commensalism with rhizosphere bacteria from the Cytophaga-Flavobacterium group. Applied and Environmental Microbiology 72: 5421-5427.

Schloss, P.D., I. Delalibera, J. Handelsman, K. F. Raffa. 2006. Bacteria associated with the guts of two wood-boring beetles: Anoplophora glabripennis and Saperda vestita (Cerambycidae). Environ. Entomol. 35: 625-629.

Schloss, P.D. and Handelsman, J. 2006. Introducing TreeClimber, a tool for phylogeny of microbial communities. Appl. Environ. Microbiol. 72: 2379-2384.

Schloss, P.D. and Handelsman, J. 2006. Introducing SONS, A tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl. Environ. Microbiol. 72(10): 6773-6779.

Schloss, P.D. and Handelsman, J. 2006. Toward a census of bacteria in soil. PLoS Computational Biology 2: e92.

Handelsman, J. 2006. Metagenomics or megagenomics? Nature Rev. Microbiol. 3: 457-458.

Cloud-Hansen, K.A., S. B. Peterson, E.V. Stabb, W.E. Goldman, M.J. McFall-Ngai, and J. Handelsman. 2006. Breaching the great wall: Peptidoglycan and microbial interactions. Nature Rev. Microbiol. 4: 710-716.


Gillespie, D., Rondon, M.R., and Handelsman, J. 2005. Metagenomic libraries from uncultured microorganisms. In: Molecular Microbial Ecology. A.M. Osborn and C. J. Smith, eds. Bios Sci. Pub.: 261-279.

Williamson, L.L., Borlee, B.R., Schloss, P.D., Guan, C., Allen, H.K., and Handelsman, J. 2005. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl. Environ. Microbiol. 71: 6335-6344.

Handelsman, J. 2005. How to find new antibiotics. The Scientist 19: 20.

Schloss, P.D. and J. Handelsman. 2005. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biology 6:229.

Delalibera, I., K. Raffa, and J. Handelsman. 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). Environ. Entomol. 34: 541-547.

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

Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and species richness. Appl. Environ. Microbiol. 71(3): 1501-1506.

Handelsman, J. 2005. Sorting out metagenomes. Nature Biotechnology. 23(1): 38-39.


Schloss, P. D., and J. Handelsman. 2004. Status of the microbial census. Microbiol. Molec. Biol. Rev. 68(4): 686-691.

Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Molec. Biol. Rev. 68(4): 669-685.

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

Safdar, N., J. Handelsman, and 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.

Schloss, P. D., B. R. Larget, and J. Handelsman. 2004. Integration of microbial ecology and statistics: A test to compare gene libraries. Appl. Environ Microbiol. 70(9): 5485-92.

Riesenfeld, C.R., Schloss, P.D., and Handelsman, J. 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genetics. 38: 525-52.

Riesenfeld, C.R., Goodman, R.M., and Handelsman, J. 2004. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6(9): 981-989.

Emmert, E.A.B., Klimowicz, A.K., Thomas, M.G., and Handelsman, J. 2004. Genetics of zwittermicin A production in Bacillus cereus. Appl. Environ. Microbiol. 70: 104-113.

Broderick, N.A., Raffa, K., Goodman, R.M., and Handelsman, J. 2004. Census of the bacterial community of the gypsy moth larval midgut using culturing and culture-independent methods. Appl. Environ. Microbiol. 70: 293-300.

Handelsman, J. 2004. Soils – the metagenomics approach. In: Microbial Diversity Bioprospecting. Alan T. Bull, ed. American Society for Microbiology Press, pp. 109-119.


Handelsman, J., and Smalla, K. 2003. Conversations with the silent majority. Current Op. Micro. 6: 271-273.

Schloss, P.D., and Handelsman, J. 2003. Biotechnological prospects from metagenomics. Current Op. Biotech. 14: 303-310.

Liles, M.R., Manske, B.F., Bintrim, S.B., Handelsman, J., and Goodman, R.M. 2003. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl. Environ. Microbiol. 69: 2684-2691

Dunn, A.K., Klimowicz, A.K., and Handelsman, J. 2003. Use of a promoter trap to identify Bacillus cereus genes regulated by tomato seed exudate and a rhizosphere resident, Pseudomonas aureofaciens. Appl. Environ. Microbiol. 69: 1197-205.

Broderick, N.A., Goodman, R.M., Handelsman, J., and 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. Environ. Entomol. 32: 387-391.


Handelsman, J., and Wackett, L.P. 2002. Ecology and industrial microbiology: Microbial diversity – sustaining the Earth and industry, editorial overview. Curr. Opin. Microbiol. 5: 237-239.

Gillespie, D.E., Brady, S.F., Bettermann, A.D., Cianciotto, N.P., Liles, M.R., Rondon, M.R., Clardy, J., Goodman, R.M., and Handelsman, J. 2002. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68: 4301-4306.

Dunn, A.K., and Handelsman, J. 2002. Toward an understanding of microbial communities through analysis of communication networks. ISME 9 Antonie von Leewenhoek 81: 565-574.

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

Handelsman, J., Liles, M., Mann, D., Riesenfeld, C., and Goodman, R.M. 2002. Cloning the metagenome: culture-independent access to the diversity and functions of the uncultivated microbial world. In: Methods in Microbiology – Functional Microbial Genomics. Academic Press, pp. 241-255.


Brady, S.F., Chao, C.J., Handelsman, J., and Clardy, J. 2001. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Organic Letters 3: 1981-1984.

Simon, H.M., Smith, K.P., Dodsworth, J.A., Guenthner, B., Handelsman, J., and Goodman, R.M. 2001. Influence of tomato genotype on growth of inoculated and indigenous bacteria in the spermosphere. Appl. Environ. Microbiol. 67: 514-520.


Bittinger, M.A., Gross, J.A., Widom, J., Clardy, J., and Handelsman, J. 2000. Rhizobium etli CE3 carries vir gene homologs on a self-transmissible plasmid. Molec. Plant-Microbe Interact. 13: 1019-1021.

Handelsman, J. 2000. Antagonism. In: Encyclopedia of Plant Pathology. O.C. Maloy and T.D. Murray, eds. New York: John Wiley.

Kazmar, E.R., Goodman, R.M., Grau, C.R., Johnson, D.W., Nordheim, E.V., Undersander, D.J., and Handelsman, J. 2000. Regression analyses for evaluating the influence of Bacillus cereus on alfalfa yield under variable disease intensity. Phytopathology 90: 657-665.

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., and Goodman, R.M. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541-2547.

Bittinger, M.A., and Handelsman, J. 2000. Identification of genes in the RosR regulon of Rhizobium etli. J. Bacteriol. 182: 1706-1713.

Broderick, N.A., Goodman, R.M., Raffa, K.F., and Handelsman, J. 2000. Synergy between zwittermicin A and Bacillus thuringiensis subsp. kurstaki against gypsy moth (Lepidoptera: Lymantriidae). Environ. Entomol. 29: 101-107.