Berkeley Lab

m-CAFEs

Publications

BOLD: Impact Factor >8.0 or ** of outstanding interest

2024

  1. Adler, B.A.; M.I. Trinidad, D. Bellieny-Rabelo, E. Zhang, H.M. Karp, P. Skopintsev, B.W. Thornton, R.F. Weissman, P.H. Yoon, L. Chen, T. Hessler, A.R. Eggers, D. Colognori, R. Boger, E.E. Doherty, C.A. Tsuchida, R.V. Tran, L. Hofman, H. Shi, K.M. Wasko, Z. Zhou, C. Xia, M.J. Al-Shimary, J.R. Patel, V.C.J.X. Thomas, R. Pattali, M.J. Kan, A. Vardapetyan, A. Yang, A. Lahiri, M.F. Maxwell, A.G. Murdock, G.C. Ramit, H.R. Henderson, R.W. Calvert, R.S. Bamert, G.J. Knott, A. Lapinaite, P. Pausch, J.C. Cofsky, E.J. Sontheimer, B. Wiedenheft, P.C. Fineran, S.J.J. Brouns, D.G. Sashital, B.C. Thomas, C.T. Brown, D.S.A. Goltsman, R. Barrangou, V. Siksnys, J.F. Banfield, D.F. Savage and J.A. Doudna (2023) CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Research. [doi]:10.1093/nar/gkad890 {PMID}:37889041 OSTI:2203961
  2. Chen, M.; S.M. Acharya, M.O. Yee, K.G.M. Cabugao and R. Chakraborty (2024) Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture. Frontiers in Microbiology. [doi]:10.3389/fmicb.2024.1401794
  3. Enriquez-Felix, E.E.; C. Pérez-Salazar, J.G. Rico-Ruiz, A. Calheiros de Carvalho, P. Cruz-Morales, J.M. Villalobos-Escobedo and A. Herrera-Estrella (2024) Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Microbiology spectrum. [doi]:10.1128/spectrum.03165-23 {PMID}:38441469 OSTI:2318771
  4. Hessler, T.; R.J. Huddy, R. Sachdeva, S. Lei, S.T.L. Harrison, S. Diamond and J.F. Banfield (2023) Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms. Nature Communications. [doi]:10.1038/s41467-023-40360-4 {PMID}:37553333 PMCID:PMC10409787 https://rdcu.be/diOIu OSTI:1995510
  5. Lin, H.-H.; M. Torres, C.A. Adams, P.F. Andeer, T.K. Owens, K. Zhalnina, L.K. Jabusch, H.K. Carlson, J. Kuehl, A.M. Deutschbauer, T. Northen, N.L. Glass and J.C. Mortimer (2023) Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem. Phytobiomes Journal. [doi]:10.1094/PBIOMES-06-23-0050-R OSTI: 2203547
  6. Liu, Y.; X. Zhao, F. Gan, X. Chen, K. Deng, S.A. Crowe, G.A. Hudson, M.S. Belcher, M. Schmidt, M.C.T. Astolfi, S.M. Kosina, B. Pang, M. Shao, J. Yin, S. Sirirungruang, A.T. Iavarone, J. Reed, L.B.B. Martin, A. El-Demerdash, S. Kikuchi, R.C. Misra, X. Liang, M.J. Cronce, X. Chen, C. Zhan, R. Kakumanu, E.E.K. Baidoo, Y. Chen, C.J. Petzold, T.R. Northen, A. Osbourn, H. Scheller and J.D. Keasling (2024) Complete biosynthesis of QS-21 in engineered yeast. Nature. [doi]:10.1038/s41586-024-07345-9
  7. Morgan, C.J. ; E. Enustun, E.G. Armbruster, E.A. Birkholz, A. Prichard, T. Forman, A. Aindow, W. Wannasrichan, S. Peters, K. Inlow, I.L. Shepherd, A. Razavilar, V. Chaikeeratisak, B.A. Adler, B.F. Cress, J.A. Doudna, K. Pogliano, E. Villa, K.D. Corbett and J. Pogliano (2024) An essential and highly selective protein import pathway encoded by nucleus-forming phage. Proceedings of the National Academy of Sciences of the United States of America. [doi]:10.1073/pnas.2321190121 {PMID}:38687783
  8. Song, Y.; S. Yao, X. Li, T. Wang, X. Jiang, N. Bolan, C.R. Warren, T.R. Northen and S.X. Chang (2024) Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems. Eco-Environment & Health. [doi]:https://doi.org/10.1016/j.eehl.2024.03.001
  9. Villalobos-EscobedoJ.M.,; M.B. Mercado-Esquivias, C. Adams, W.B. Kauffman, R.R. Malmstrom, A.M. Deutschbauer and N.L. Glass (2023) Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites. PLoS Genetics. [doi]: 10.1371/journal.pgen.1010909 {PMID}:37651474 OSTI: 2004597
  10. Wu, M.; T.R. Northen and Y. Ding (2023) Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses. Frontiers in Plant Science. [DOI]:10.3389/fpls.2023.1272363 OSTI:2205612

2023

  1. Acharya, S.M.; M.O. Yee, S. Diamond, P.F. Andeer, N.F. Baig, O.T. Aladesanmi, T.R. Northen, J.F. Banfield, R. Chakraborty (2023) Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in young Brachypodium plant roots. ISME Communications. [doi]:10.1038/s43705-023-00265-1 PMCID: PMC10244434 OSTI: 1983999
  2. Hessler, T.; R.J. Huddy, R. Sachdeva, S. Lei, S.T.L. Harrison, S. Diamond and J.F. Banfield (2023) Vitamin interdependencies predicted by metagenomics-informed network analyses validated in microbial community microcosms. BioRxiv. [doi]:10.1038/s41467-023-40360-4 {PMID}:37553333 PMCID:PMC10409787 OSTI: 1995510
  3. Hu, Y.; P.F. Andeer, Q. Zheng, S.M. Kosina, K.J. Jardine, L.Z. Han, Y. Gao, B.P. Bowen, R. Sibout, D. Laudencia-Chingcuanco, J. Mortimer, J.P. Vogel, T.R. Northen (2023) Plants uptake diverse metabolites from exudates. Nature Communications. In revision. 
  4. Jo, C.; D.B. Bernstein, N. Vaisman, H.M. Frydman and D. Segrè (2023) Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions. mSystems. [doi]:10.1128/msystems.00017-21 {PMID}:36802169 OSTI: 1958538
  5. Jo, C.; C. Jo, J. Zhang, J.M. Tam, G.M. Church, A.S. Khalil, D. Segrè and T.-C. Tang (2023) Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Materials Today. Bio. [doi]:10.1016/j.mtbio.2023.100560 {PMID}:36756210 PMCID:PMC9900623 OSTI: 1958544
  6. McLaughlin, S.; K. Zhalnina, S. Kosina, T.R. Northen and J. Sasse (2023) The core metabolome and root exudation dynamics of three phylogenetically distinct plant species. Nature Communications. [doi]:10.1038/s41467-023-37164-x {PMID}:36964135 PMCID:PMC10039077 OSTI: 1963348
  7. Silverstein, M.; D. Segrè and J.M. Bhatnagar (2023) Environmental microbiome engineering for the mitigation of climate change. Global Change Biology. [doi]:10.1111/gcb.16609 {PMID}:36661406 OSTI: 1958537
  8. Villalobos Escobedo, J.M.: M.B. Mercado-Esquivias, C.A. Adams, A.M. Deutschbauer and N. L. Glass (2023) Genome-wide fitness profiling reveals molecular mechanisms that rhizobacteria use to interact with Trichoderma atroviride metabolites. PLoS Genetics. [doi]: 10.1371/journal.pgen.1010909 {PMID}:37651474 OSTI: 2004597

2022

  1. Adler, B.A.; T. Hessler, B.F. Cress, V.K. Mutalik, R. Barrangou, J.F. Banfield, J.A. Doudna (2022) RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity. Nature Microbiology [DOI]:10.1038/s41564-022-01258-x OSTI: 1896705
  2. Baker, N., Zhalnina, K., Yuan, M., Herman, D., Ceja-Navarro, J., Sasse, J., Jordan, J.,  Bowen, B., Wu, L., Fossum, C., Chew, A., Fu, Y., Saha, M., Zhoug, J., Pett-Ridgei, J., Northen, T., Firestone, M. (2022) Nutrient and moisture limitation reveal keystone metabolites that link switchgrass rhizosphere metabolome and microbiome dynamics. bioRxiv [doi]:10.1101/2022.06.20.496911v1
  3. Coker, J.; K. Zhalnina, C. Marotz, D. Thiruppathy, M. Tjuanta, G. D’Elia, R. Hailu, T. Mahosky, M. Rowan, T.R. Northen and K. Zengler (2022) A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology. mSystems. [DOI]:10.1128/msystems.00951-22 {PMID}:36472419 PMCID:PMC9765266 OSTI: 1902465
  4. Conway, J. M.; Walton, W. G.; Salas-González, I.; Law, T. F.; Lindberg, C. A.; Crook, L. E.; Kosina, S. M.; Fitzpatrick, C.R.; Lietzan, A. D.; Northen, T. R.; Jones, C. D.; Finkel, O. M.; Redinbo, M. R.; Dangl, J. L. Nature Microbiology 2022, 1–17. [DOI]:10.1038/s41564-022-01244-3
  5. Forchielli*, E.; T. Wang*, M. Thommes*, I.C. Paschalidis, D. Segrè (2022) Prediction of representative phenotypes using multi-output subset selection. bioRxiv [doi]:10.1101/2022.06.20.496733 Nature submitted
  6. Golden, A.; I. Dukovski, D. Segrè, K.S. Korolev (2022) Growth instabilities shape morphology and genetic diversity of microbial colonies. Phys Biol. 2022 Jul 28; [DOI]: 10.1088/1478-3975/ac8514 {PMID}: 35901792
  7. Goldford, J.E.; A.B. George, A.I. Flamholz and D. Segrè (2021) Protein cost minimization promotes the emergence of coenzyme redundancy. Proceedings of the National Academy of Sciences of the United States of America. [DOI]:10.1073/pnas.2110787119 {PMID}:35344442
  8. Huang, C.J.; B.A. Adler and J.A. Doudna (2022) A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression. Molecular Cell. 2022 Jun; 82(11) 2148-2160.e4 [DOI]: 10.1016/j.molcel.2022.04.020
  9. Jo, C., Bernstein, D. B., Vaisman, N., Frydman, H. M., & Segrè, D. (2021). A co-culture microplate for real-time measurement of microbial interactions. bioRxiv [doi]:10.1101/2021.01.07.425753
  10. Kishore, D., Birzu, G., Hu, Z., DeLisi, C., Korolev, K. S., & Segrè, D. (2020). Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation. bioRxiv [doi]:10.1101/2020.09.23.309781
  11. Nethery, M; C. Hidalgo-Cantabrana, A. Roberts R. Barrangou (2022) CRISPR-based engineering of phages for in situ bacterial base editing. PNAS [DOI]:10.1073/pnas.2206744119 OSTI:1897669
  12. Pacheco, A.R.; C. Pauvert, D. Kishore, and D. Segrè (2022) Toward FAIR representations of microbial interactions, Perspective article. mSystems [DOI]:10.1128/msystems.00659-22 OSTI: 1883414
  13. Pacheco, A.R.; and D. Segrè (2021) An evolutionary algorithm for designing microbial communities via environmental modification. Journal of the Royal Society, Interface. [doi]:10.1098/rsif.2021.0348 {PMID}:34157894 PMCID:PMC8220269 OSTI: 1889427
  14. Quintin, M.; I. Dukovski, J. Bhatnagar and D. Segrè (2022) Optimality of extracellular enzyme production and activity in dynamic flux balance modeling bioRxiv [doi]:10.1101/2021.11.01.466736
  15. Roberts, A.; M.A. Nethery and R. Barrangou (2022) Functional characterization of diverse type I-F CRISPR-associated transposons. Nucleic Acids Research. [doi]:10.1093/nar/gkac985 {PMID}:36384163 PMCID:PMC9723613 OSTI: 1958536
  16. Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Smock DC, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA, Species- and site-specific genome editing in complex bacterial communities. Nat Biotechnol [DOI]: 10.1038/s41564-021-01014-7 {PMID}: 34873292 OSTI:1835956
  17. Wang, Y.; Wilhelm, R. C.; Swenson, T. L.; Silver, A.; Andeer, P.; Golini, A.; Kosina, S. M.; Bowen, B. P.; Buckley, D. H.; Northen, T. R., Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies. Front. Microbiol., 09 June 2022, [DOI]:10.3389/fmicb.2022.914472 OSTI:1889858
  18. York, L. M., Cumming, J. R., Trusiak, A., Bonito, G., von Haden, A. C., Kalluri, U. C.,  Tiemann, L. K., Andeer, P. F., Blanc-Betes, E., Diab, J. H., Favela, A., Germon, A., Gomez-Casanovas, N., Hyde, C. A., Kent, A. D., Ko, D. K., Lamb, A., Missaoui, A., Northen, T. R., Pu, Y., Ragauskas, A. J., Raglin, S., Scheller, H. V., Ware, A., Washington, L., Yang, W. H. (2022). Bioenergy Underground: challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production. The Plant Phenome Journal. 5: e20028. [DOI]:10.1002/ppj2.20028
  19. Zomorrodi, A.R; C. Hemez, P. Arranz-Gibert, T. Wu, F.J. Isaacs and D. Segrè (2022) Computational design and construction of an Escherichia coli strain engineered producing the non-standard amino acid para-aminophenylalanine. iScience [DOI]:10.1016/j.isci.2022.104562 OSTI:1889425

2021

  1. Barrangou, R. The CRISPR Chronicles and the Power of Storytelling (2021) Apr 2021.158-159. [doi]:10.1089/crispr.2021.29126.rba
  2. Bernstein, D.B.; S. Sulheim, E. Almaas, D. Segrè (2021) Addressing uncertainty in genome-scale metabolic model reconstruction and analysis, Genome Biology (2021) 22, 64. [doi]:10.1186/s13059-021-02289-z  OSTI:1812364
  3. Chiniquy, D., Barnes, E. M., Zhou, J., Hartman, K., Li, X., Sheflin, A., Pella, A., Marsh, E., Prenni, J., Deutschbauer, A. M., Schachtman, D. P., & Tringe, S. G. (2021). Microbial community field surveys reveal abundant pseudomonas population in sorghum rhizosphere composed of many closely related phylotypes. Frontiers in Microbiology, 12, 598180. [doi]:10.3389/fmicb.2021.598180 PMID: 33767674, PMCID: PMC7985074 OSTI:1774893
  4. Ding Y, Northen TR, Khalil A, Huffaker A, Schmelz EA (2021) Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience. Curr Opin Biotechnol. 2021 Jun 11; 70 174-186 [doi]:10.1016/j.copbio.2021.05.010 PMID:34129999 OSTI:1812518
  5. Dukovski, I.; D. Bajić, J.M. Chacón, M. Quintin, J.C.C. Vila, S. Sulheim, A.R. Pacheco, D.B. Bernstein, W.J. Riehl, K.S. Korolev, A. Sanchez, W.R. Harcombe, D. Segrè (2021), A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS), Nature Protocols [doi] 10.1038/s41596-021-00593-3 OSTI:1825266
  6. Jabusch, L.K.; Kim, P.W.; Chiniquy, D.; Zhao, Z.; Wang, B.; Bowen, B.; Kang, A.J.; Yoshikuni, Y.; Deutschbauer, A.M.; Singh, A.K.; Northen, T.R. Microfabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant–Microbe Interactions. Int. J. Mol. Sci. 2021, 22, 7880. PMID: 34360661 PMCID: PMC8348081 [doi]:10.3390/ijms22157880 OSTI:1812357
  7. Pacheco, A. R., Osborne, M. L., & Segrè, D. (2021). Non-additive microbial community responses to environmental complexity. Nature Communications, 12(1), 2365. [doi]:10.1038/s41467-021-22426-3 PMID: 33888697, PMCID: PMC8062479 OSTI:1812365
  8. Pacheco, A. R., & Segrè, D. (2021). An evolutionary algorithm for designing microbial communities via environmental modification. Journal of the Royal Society Interface. [doi]:10.1098/rsif.2021.0348
  9. Qiao, L., Lan, C., Capriotti, L., Ah-Fong, A., Nino Sanchez, J., Hamby, R., Heller, J., Zhao, H., Glass, N. L., Judelson, H. S., Mezzetti, B., Niu, D., & Jin, H. (2021). Spray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake. Plant Biotechnology Journal. [doi]:10.1111/pbi.13589 PMID: 33774895 OSTI:1784294
  10. Singer E, Vogel JP, Northen T, Mungall CJ, Juenger ET. (2021) Novel and emerging capabilities that can provide a holistic understanding of the plant root microbiome”Phytobiomes Journal. [doi]:10.1094/PBIOMES-05-20-0042-RVW OSTI:1827329
  11. Yee, M.O., Kim, P.W., Li, Y., Singh, A.K, Northen, T.R., Chakraborty, R., Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions. Front. Microbiol., 26 March 2021. [doi]:10.3389/fmicb.2021.625752 PMID: 33841353, PMCID: PMC8032546 OSTI:1889431
  12. Zhalnina, K., Hawkes, C., Shade, A., Firestone, M. K., Pett-Ridge, J. (2021) Managing Plant Microbiomes for Sustainable Biofuel Production. Phytobiomes J.5: 3-13 [doi]: 10.1094/PBIOMES-12-20-0090-E OSTI:1826906

2020

  1. Barrangou, R. (2020). Ushering in the next CRISPR decade. The CRISPR Journal, 3(1), 2. [doi]:10.1089/crispr.2020.29085.rba
  2. Hidalgo-Cantabrana, C., & Barrangou, R. (2020). Characterization and applications of Type I CRISPR-Cas systems. Biochemical Society Transactions, 48(1), 15–23. [doi]:10.1042/BST20190119
  3. Sasse, J., Kosina, S. M., de Raad, M., Jordan, J. S., Whiting, K., Zhalnina, K., & Northen, T. R. (2020). Root morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyon. Plant Direct, 4(7), e00207. [doi]:10.1002/pld3.207
  4. Wang, B., Zhao, Z., Jabusch, L. K., Chiniquy, D. M., Ono, K., Conway, J. M., Zhang, Z., Wang, G., Robinson, D., Cheng, J.-F., Dangl, J. L., Northen, T. R., & Yoshikuni, Y. (2020). CRAGE-Duet Facilitates Modular Assembly of Biological Systems for Studying Plant-Microbe Interactions. ACS Synthetic Biology [Electronic Resource], 9(9), 2610–2615. [doi]:10.1021/acssynbio.0c00280

2019

  1. Barrangou, R. (2019). Partnering with bioRxiv. The CRISPR Journal, 2(6), 342. [doi]:10.1089/crispr.2019.29076.rba
  2. Sasse, J.; Kant, J.; Cole, B. J., Klein, A. P., Arsova, B.; Schlaepfer, P.; Gao, J.; Lewald, K.; Zhalnina, K.; Kosina, S.; Bowen, B. P., Treen, D.; Vogel, J.; Visel, A.; Watt, M.; Dangl, J. L. and Northen, T. R. (2019) Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. New Phytol, 222: 1149-1160. [doi]:10.1111/nph.15662
  3. Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR. (2019) EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nat Methods. 16(7):567-571. [doi]:10.1038/s41592-019-0465-0
  4. Zhalnina, K, Newman D, Zengler K, Northen TR. (2019) Need for laboratory ecosystems to unravel the structure and function of microbial communities mediated by chemistry. mBio. e01175-18. [doi]: 10.1128/mBio.01175-18

2018

  1. Gao J, Sasse J, Lewald KM, Zhalnina K, Cornmesser LT, Duncombe TA, Yoshikuni Y, Vogel JP, Firestone MK, Northen TR. Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions. J Vis Exp. 2018;(134):e57170. [doi]:10.3791/57170
  2. Sasse J, Martinoia E, Northen T. Feed your friends: do plant exudates shape the root microbiome? (2018) Trends Plant Sci. 2018;23(1):25-41. [doi]:10.1016/j.tplants.2017.09.003
  3. Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Cho H, Karaoz U, Loqué D, Bowen BP, Firestone MK, Northen TR, Brodie EL. (2018) Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3(4):470-480. [doi]:10.1038/s41564-018-0129-3
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