Publications (reverse chronological order; *denotes publication of particular interest; #denotes pending):
#37. Tang, J., Baker, J.L. The salivary virome during childhood dental caries. Manuscript in submission. Preprint available on bioRxiv
36. Hirose, Y., Zielenski, D.C., Poudel, S., Rychel, K., Baker, J.L., Toya, Y., Heinken, A., Thiele, I., Kawabata, S., Palsson, B.O., Nizet, V. A genome-scale metabolic model of a globally disseminated
hyperinvasive M1 strain of Streptococcus pyogenes. mSystems 2024 August 19; doi: 10.1128/msystems.00736-24
35. Liu, J., Spencer, N., Utter, D.R., Grossman, A., Santos, N.C.D., Shi, W., Baker, J.L., Hasturk, H., He, X., Bor, B. Persistent enrichment of Klebsiella in oral and nasal microbiome community under long-term starvation. Microbiome 2024 July 20; doi: 10.1186/s40168-024-01854-5
34. Bjånes, E., Stream, A., Gibson, P.S., Bravo., A.M., Dahesh, S., Baker, J.L., Varble, A., Nizet, V., Veening, J.W. An efficient in vivo-inducible CRISPR interference system for group A Streptococcus genetic analysis and pathogenesis studies. mBio 2024 July 2; doi: 10.1128/mbio.00840-24
33. Brar, N.K., Dhariwal, A., Åmdal, H.A., Junges, R., Salvadori, G., Baker, J.L., Edlund, A., Petersen, F.C. Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. npj Biofilms and Microbiomes. 2024 April 2; 10:37; doi:10.1038/s41522-024-00507-7
32. Baker, J.L. The Baker Lab at the OHSU School of Dentistry: leveraging bioinformatics and molecular biology to discover how the bacteria that live in our mouth impact human health and disease. OHSU School of Dentistry Anthology. 2023 December 19; 1(1):3-11;doi:10.6083/bpxhc42395
31. Baker, J.L., Mark Welch, J.L., Kauffman, K., McLean, J.S., He, X. The oral microbiome: diversity, biogeography and human health. Nature Reviews Microbiology. 2023 September 12; doi:10.1038/s41579-023-00963-6
30. Baker, J.L. Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research. FEMS Microbiology Reviews. 2023 September 4; doi: 10.1093/femsre/fuad051
*29. Baker, J.L. Using nanopore sequencing to obtain complete genomes from saliva samples. mSystems.. 2022 Aug 22:e0049122. doi: 10.1128/msystems.00491-22.
28. Baker, J.L., Tang, X., LaBonte, S., Uranga, C., Edlund, A. mucG, mucH, and mucI modulate production of mutanocyclin and reutericyclins in Streptococcus mutans B04Sm5. Journal of Bacteriology. 2022 April 11; doi: 10.1128/jb.00042-22
27. Baker, J.L. Complete genome sequence of Candidatus Nanosynbacter strain HMT-348_TM7c-JB, a member of Saccharibacteria Clade G1. Microbiology Resource Announcements. 2022 April 11; doi: 10.1128/mra.00023-22
*26. Tinder, E.L., Faustoferri, R.C., Buckley, A.A., Quivey, Jr., R.G., Baker, J.L. Analysis of the Streptococcus mutans proteome during acid and oxidative stress reveals modules of co-expression and an expanded role for the TreR transcriptional regulator. mSystems. 2022 March 15; doi: 10.1128/msystems.01272-21
25. Uranga, C., Nelson, K.E., Edlund, A., Baker, J.L. Tetramic acids mutanocyclin and reutericyclin-A, produced by Streptococcus mutans strain B04Sm5, modulate the ecology of an in vitro oral biofilm. Frontiers in Oral Health. 2022 January 6; 2:796140; doi: 10.3389/froh.2021796140
24. Silveira, C.B., Cobian-Guemes, A.G., Uranga, C., Baker, J.L., Edlund, A., Rohwer, F., Conrad, D. Multi-omics study of keystone bacterial species in a cystic fibrosis lung microbiome. International Journal of Molecular Sciences. 2021 November 7; 22, 12050; doi: 10.3390/ijms222112050
23. Baker, J.L. Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle. mSphere. 2021 Aug 11; e00530-21. doi: https://doi.org/10.1128/mSphere.00530-21
22. Baker, J.L. A complete genome sequence of strain JB001, a member of Saccharibacteria clade G6 (“Ca. Nanogingivalaceae”). Microbiology Resource Announcements. 2021 Jun;10(23):e0051721 doi: 10.1128/MRA.00517-21
*21. Baker, J.L., Morton, J.T., Dinis, M., Alvarez, R., Tran, N.C., Knight, R., Edlund, A. Deep metagenomic sequencing examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules. Genome Research. 2021 January; 31(1):64-74. doi: 10.1101/gr.265645.120
20. Baker, J.L., Edlund, A. Identification of bacterial biosynthetic gene clusters associated with caries. In Adami, G., (ed), The Oral Microbiome: Methods and Protocols. Springer Science+Business Media, LLC. 2021. IBSN: 978-1-0716-1517-1
19. Baker, J.L., Edlund, A. Composite long- and short-read sequencing delivers a complete genome sequence of B04Sm5, a reutericyclin- and mutanocyclin-producing strain of Streptococcus mutans. Microbiology Resource Announcements. 2020 Nov; 9:e01067-20. doi:10.1128/MRA.01067-20
18. Momeni, S., Beno, S., Baker, J.L., Edlund, A., Ghazal, T., Wu, H., Childers, N.K. Caries-associated biosynthetic gene clusters of Streptococcus mutans. Journal of Dental Research. 2020 July; 99(8):969-976; doi:10.1177/0022034520914519
17. Yang, Y., Shen, W., Zhong, Q., He, X., Baker, J.L., Xiong, K., Jin, X., Wang, J., Hu, F., Le, S. Development of a bacteriophage cocktail to constrain the emergence of phage-resistant Pseudomonas aeruginosa. Frontiers in Microbiology. 2020 March 4; 11:327; doi:10.339/fmicb.2020.00327
16. Baker, J.L., Saputo, S., Faustoferri, R., Quivey Jr., R.G. Streptococcus mutans SpxA2 relays the signal of cell envelope stress from LiaR to effectors that maintain cell wall and membrane homeostasis. Molecular Oral Microbiology. 2020 June; 35(3): 118-128; doi:10.1111/omi.12282
*15. Tang, X., Kudo, Y., Baker, J.L., LaBonte, S., Jordan, P.A., Huan, T., KcKinnie, S.M.K., Guo, J., Huan, T., Moore, B.S., Edlund, A. Cariogenic Streptococcus mutans produces tetramic acid strain-specific antibiotics that impair commensal colonization. ACS Infectious Diseases. 2020 April; 6(4):563-571; doi:10.1021/acsinfecdis.9b00365
*14. Baker, J.L., Hendrickson, E.L., Tang, X., Lux, R., He, X., Edlund, A., McLean, J.S., Shi, W. Klebsiella and Providencia emerge as lone survivors following long-term starvation of the oral microbiota. PNAS.. 2019 April 23; 116(17):8499-8504; doi: https://doi.org/10.1073/pnas.1820594116
*13. Aleti, G., Baker, J.L., Tang, X., Alvarez, R., Denis, M., Tran, N.C., Melnik, A.V., Zhong, C., Ernst, M., Dorrestein, P.C., Edlund, A. Identification of the biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease. mBio.. 2019 April 16;doi: https://doi.org/10.1128/mBio.00321-19
12. Baker, J.L., He, X., Shi, W. Precision reengineering of the oral microbiome for caries management. Advances in Dental Research.. 2019 October 21; 30(2), 34-39; doi: https://doi.org/10.1177/0022034519877386
11. Baker, J.L., Edlund, A. Exploiting the oral microbiome to prevent tooth decay: has evolution already provided the best tools? Frontiers in Microbiology.. 2019 Jan 11; 9:3323; doi: 10.3389/fmicb2018.03323
10. Baker, J.L., Lindsay, E.L., Faustoferri, R.C., To, T.T., Hendrickson, E.L., He, X., Shi, W., McLean, J.S., Quivey Jr., R.G. Characterization of the trehalose utilization operon in Streptococcus mutans reveals that the TreR transcriptional regulator is involved in stress response pathways and toxin production. Journal of Bacteriology.. 2018 May 24;200(12): pii: JB.00057-18. doi: 10.1128/JB.00057-18.
9. Baker, J.L., Bor, B., Agnello, M., Shi, W., He, X. Ecology of the oral microbiome: beyond bacteria. Trends in Microbiology.. 2017 May; 25(5): 362-374. doi: 10.1016/j.tim.2016.12.012
8. Baker, J.L., Faustoferri, R.C., Quivey, Jr., R.G. Acid-adaptive mechanisms of Streptococcus mutans—the more we know, the more we don’t. Molecular Oral Microbiology.. 2017 Apr; 32(2): 107-117. doi: 10.1111/omi.12162
7. Baker, J.L., Faustoferri, R.C., Quivey, Jr., R.G. A modified chromogenic assay for determination of free intracellular NAD+/NADH in Streptococcus mutans. Bio-Protocol.. 2016 Aug; 6(16). Pii: e1902. doi: 10.21769/BioProtoc.1902.
6. Faustoferri, R.C., Santiago, B., Baker, J.L., Cross, B., Xiao, J., Quivey Jr., R.G. Acid adaptive responses of S. mutans, and mechanisms of integration with oxidative stress. In de Bruijn, F. (ed), Stress and Environmental Control of Gene Expression in Bacteria, 1st Edition. John Wiley & Sons, Inc. 2016 Aug; ISBN: 9781119004882
*5. Baker, J.L., Derr, A.D., Faustoferri, R.C., Quivey Jr., R.G., Loss of NADH oxidase activity in Streptococcus mutans leads to Rex-mediated overcompensation of NAD+ regeneration by lactate dehydrogenase. Journal of Bacteriology.. 2015 Dec; 197(23):3645-57. doi: 10.1128/JB.00383-15.
4. Baker, J.L., Abranches, J.A., Faustoferri, R.C., Hubbard, C.J., Lemos, J.A., Courtney, M.A., Quivey Jr., R.G. Transcriptional profile of glucose-shocked and acid-adapted strains of Streptococcus mutans. Molecular Oral Microbiology.. 2015 Dec; 30(6):496-517.
3. Baker, J.L., Derr, A.M., Karuppiah, K., MacGilvray, M.E., Kajfasz, J.K., Faustoferri, R.C., Rivera-Ramos, I., Bitoun, J.P., Lemos, J.A., Wen, Z.T., Quivey Jr., R.G. Streptococcus mutans NADH oxidase lies at the intersection of overlapping regulons controlled by oxygen and NAD+ Levels. Journal of Bacteriology.. 2014 June; 196(12):2166-2177.
2. Baker, J.L., Ward, B.M.** Development and comparison of a quantitative TaqMan-MGB real-time PCR assay to three other methods of quantifying vaccinia virions. Journal of Virological Methods. 2014. 196:126-132.
*1. Hollenbaugh,,J.A., Gee, P., Baker, J., Daly, M.B., Amie, S.M., Tate, J., Kasai, N., Kanemura, Y., Kim, D., Ward, B.M., Koyanagi, Y., Kim, B. 2013. Host Factor SAMHD1 Restricts DNA Viruses in Non-Dividing Myeloid Cells. PLOS Pathogens. 9(6) e1003481.