Microbiology Publications in the 2000s


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. doi.org/10.1089/dna.2008.0812

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. doi.org/10.1038/ismej.2008.86

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). doi.org/Artn1110.1186/1741-7007-7-11

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

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. doi.org/10.1603/022.038.0109

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


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. doi.org/10.1038/ismej.2008.70

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. doi.org/10.1128/Aem.01933-07

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. doi.org/10.1128/Aem.02630-07

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. doi.org/10.1146/annurev.micro.030608.101423

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

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. doi.org/10.1603/0046-225x(2008)37[1344:Gmoais]2.0.Co;2


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.

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. doi.org/10.1128/Aem.02617-06

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

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. doi.org/10.1146/annurev.micro.61.011507.151712


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. doi.org/10.1073/pnas.0604865103

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. doi.org/10.1073/pnas.0603748103

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. doi.org/10.1038/nrmicro1486

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. doi.org/10.1128/Aem.02928-05

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. doi.org/10.1016/j.gene.2006.02.033

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. doi.org/10.1603/0046-225x-35.3.625

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. 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. 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. doi.org/10.1128/AEM.72.4.2379-2384.2006

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. doi.org/10.1093/ee/35.6.1710


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. doi.org/10.1603/0046-225x-34.3.541

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.

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. doi.org/10.1038/nbt0105-38

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.

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. 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). doi.org/ARTN 22910.1186/gb-2005-6-8-229

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. doi.org/10.1128/Aem.71.10.6335-6344.2005


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. doi.org/10.1128/Aem.70.1.293-300.2004

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

Handelsman, J. (2004a). Metagenomics: Application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669. 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.

Lauffer, S. & Handelsman, J. (2004). A new generation of scientific teachers. Focus on Microbiology Education, 10, 4-6.

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.

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. 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. doi.org/10.1146/annurev.genet.38.072902.091216

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. (2004). Status of the microbial census. Microbiology and Molecular Biology Reviews, 68(4), 686. doi.org/10.1128/Mmbr.68.4.686-691.2004

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. doi.org/10.1128/Aem.70.9.5485-5492.2004

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. doi.org/10.1187/cbe.04-07-0057


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. doi.org/10.1603/0046-225x-32.2.387

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. doi.org/10.1128/Aem.69.2.1197-1205.2003

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

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. doi.org/10.1128/Aem.69.5.2684-2691.2003

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


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. doi.org/10.1023/A:1020565807627

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. doi.org/10.1128/Aem.68.9.4301-4306.2002

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


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. doi.org/10.1021/ol015949k

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. doi.org/10.1128/Aem.67.2.514-520.2001


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. doi.org/10.1094/Mpmi.2000.13.9.1019

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

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. doi.org/10.1603/0046-225x-29.1.101

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

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. doi.org/10.1094/Phyto.2000.90.6.657

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. doi.org/10.1128/Aem.66.6.2541-2547.2000