Baker Lab members displayed in bold in the author lines.
2025
Β
Comparative characterization reveals conserved and divergent ecological traits of oral corynebacteria
Burnside, M., Helliwell, E., Treerat, P., Rozendal, T., Merritt, J., Baker, J.L., Kreth, J.
- Isolation, characterization, and genome analysis of two new strains of Corynebacterium.
- C. durum forms robust biofilms while C. argentoratense produces thin biofilms.
- Pangenomics identifies differences in nitrate reductase genes across the species, correlating with ability to grow anerobically.
π Microbiology Spectrum, 2025 Dec 22 | π Google Scholar | π doi:10.1128/spectrum.02973-25
Β
Multi-omics profiling reveals atypical sugar utilization and identifies a key membrane composition regulator in Streptococcus pneumoniae
de Bakker, V., Liu, X., Tang, J., Barbisan, M., Baker, J.L., Veening, J.W.
- Multi-omics analysis reveals novel metabolic pathways in Streptococcus pneumoniae.
- Identifies key regulators of membrane composition critical for pathogenesis.
- Integrates genomics, transcriptomics, and proteomics to elucidate bacterial physiology.
π Nature Communications, 2025 Nov 21 | π Google Scholar | π doi:10.1038/s41467-025-66611-0
Β
The salivary virome during childhood dental caries
Tang, J., Baker, J.L.
- Showed for the first time the oral virome of children with childhood dental caries is different from those with healthy dentition.
- Identified a total of 1,865 unique species-level viral OTUs (vOTUs), of which 478 appeared to be novel.
- Several vOTUs predicted to infect Haemophilus and Neisseria were strongly correlated with health, while 5 vOTUs predicted to infect Saccharibacteria, Prevotella and Veillonella were correlated with caries.
π mSphere, 2025 July 28 | π Google Scholar | π doi:10.1128/msphere.00198-25
Β
The Effect of Beta vulgaris on an in vitro oral microbiome of electronic cigarette users
Staton, D.V., Tang, J., Barbisan, M., Nussbaum, J., Baker, J.L.
- The saliva of e-cigarette users had a lower pH and was depleted of Neisseria spp.
- The impacts of e-cigarette usage and beetroot supplementation were somewhat limited, with beetroot juice extract supplementation having a significant impact on diversity according to some, but not all, diversity metrics examined.
- This study suggests that beetroot juice extract supplementation may impact the microbiota of e-cigarette users and adds to contemporary research paving the way for more in-depth studies examining the role of nitrate-rich supplements as prebiotics to promote oral health.
π Journal of Oral Microbiology, 2025 May 25 | π Google Scholar | π doi:10.1080/20002297.2025.2509669
Β
Shining Light on Oral Biofilm Fluorescent in situ Hybridization (FISH): Probing the accuracy of in situ biogeography studies
Burnside, M., Tang, J., Baker, J.L., Merritt, J., Kreth, J.
- The specificity of several commonly used FISH probes is compromised, with cross-species hybridization being more common than previously assumed.
- Some biogeographical associations within in situ biofilms may need to be reassessed with more specific probes using the latest genomic data
π Molecular Oral Microbiology, 2025 April 11 | π Google Scholar | π doi:10.1111/omi.12494
2024
Β
A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes
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.
- We present the first genome-scale model (GEM) for a highly virulent Streptococcus pyogenes serotype M1.
- The GEM achieved high accuracy in predicting gene essentiality.
- This model should provide useful insights for rational drug design against S. pyogenes.
π mSystems, 2024 August 19 | π Google Scholar | π doi:10.1128/msystems.00736-24
Β
Persistent enrichment of Klebsiella in oral and nasal microbiome community under long-term starvation
Liu, J., Spencer, N., Utter, D.R., Grossman, A., Santos, N.C.D., Shi, W., Baker, J.L., Hasturk, H., He, X., Bor, B.
- When Klebsiella pneumoniae and Klebsiella aerogenes were present in a human nasal or oral sample, these two species came to dominate the community during in vitro starvation conditions.
- These Klebsiella were resistant to multiple classes of antibiotics.
- This further supports our earlier work suggesting the Klebsiella win out versus other oral bacteria when the community is starved, possibly contributing to dissemination via hospital sinks and drains.
π Microbiome, 2024 July 20 | π Google Scholar | π doi:10.1186/s40168-024-01854-5
Β
An efficient in vivo-inducible CRISPR interference system for group A Streptococcus genetic analysis and pathogenesis studies
BjΓ₯nes, E., Stream, A., Gibson, P.S., Bravo., A.M., Dahesh, S., Baker, J.L., Varble, A., Nizet, V., Veening, J.W.
- We report the first development of a CRISPRi system in Streptococcus pyogenes.
- This system enables construction of a gene knockdown strain in just two days, as opposed to several weeks with earlier technologies.
- The tools and methodologies described in this work are poised to facilitate fundamental research in Streptococcus pyogenes, contributing to vaccine development and the discovery of novel antibiotic targets.
π mBio, 2024 July 2 | π Google Scholar | π doi:10.1128/mbio.00840-24
Β
Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome
Brar, N.K., Dhariwal, A., Γ
mdal, H.A., Junges, R., Salvadori, G., Baker, J.L., Edlund, A., Petersen, F.C.
- We used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability
- Even low concentrations of ampicillin could shift the taxonomic profile and and enhance biofilm viability.
- Ampicillin caused an increase of antibiotic resistance genes in Streptococcus mitis, which is known to transfer these genes to the pathogen, Streptococcus pneumoniae.
π npj Biofilms and Microbiomes, 2024 April 2; 10:37 | π Google Scholar | π doi:10.1038/s41522-024-00507-7
2023
Β
Β
The oral microbiome: diversity, biogeography and human health
Baker, J.L., Mark Welch, J.L., Kauffman, K., McLean, J.S., He, X.
- This review highlights recent advances in our understanding of the human oral microbiome and its impact on human health
- There is a special focus on non-canonical members, such as fungi, viruses, ultrasmall bacteria.
- The impact of hte oral microbiome on human health beyond the oral cavity is also reviewed in detail.
π Nature Reviews Microbiology, 2023 September 12 | π Google Scholar | π doi:10.1038/s41579-023-00963-6
Β
2022
Β
*Publication of particular interest
Β
mucG, mucH, and mucI modulate production of mutanocyclin and reutericyclins in Streptococcus mutans B04Sm5
Baker, J.L., Tang, X., LaBonte, S., Uranga, C., Edlund, A.
- This study elucidates the function of mucG and mucH transcriptional regulators and the mucI transporter in reutericyclin and mutanocyclin production in Streptococcus mutans strain B04Sm5.
- This study also provides a pangenome of Streptococcus mutans.
π Journal of Bacteriology, 2022 April 11 | π Google Scholar | π doi:10.1128/jb.00042-22
Β
2021
Β
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
Tinder, E.L., Faustoferri, R.C., Buckley, A.A., Quivey, Jr., R.G., Baker, J.L.
- This study reports changes in the Streptococcus mutans proteome during acid and oxidative stresses
- This dataset provides oral health researchers with a proteome atlas that will enable a more complete understanding of the Streptococcus mutans stress responses that are required for pathogenesis, and will facilitate the development of new and improved therapeutic approaches for dental caries.
- This study explains the oxygen-sensitive phenotype of the treR deletion strain, which stems from lowered expression of the mutanobactin biosynthetic gene cluster.
π mSystems, 2022 March 15 | π Google Scholar | π doi:10.1128/msystems.01272-21
*Publication of particular interest
Β
Tetramic acids mutanocyclin and reutericyclin-A, produced by Streptococcus mutans strain B04Sm5, modulate the ecology of an in vitro oral biofilm
Uranga, C., Nelson, K.E., Edlund, A., Baker, J.L.
- Using an in vitro biofilm model, we demonstrated that mutanobactin and reutericyclin, produced by Streptococcus mutans UA159, can modulate community ecoogy.
- Mutanocyclin specifically reduced Limosilactobaciullus fermentum.
- Muatnocyclin and reutericyclin appeared to inhibit the ability of S. mutans to engraft in an oral community.
π Frontiers in Oral Health, 2022 January 6; 2:796140 | π Google Scholar | π doi:10.3389/froh.2021.796140
Β
Multi-omics study of keystone bacterial species in a cystic fibrosis lung microbiome
Silveira, C.B., Cobian-Guemes, A.G., Uranga, C., Baker, J.L., Edlund, A., Rohwer, F., Conrad, D.
- This study follows the sputum microbiome of a cystic fibrosis patient during several rounds of antibiotic treatment using multiomics.
- During periods of rapid lung function loss, the patientβs lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera.
- This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions.
π International Journal of Molecular Sciences, 2021 November 7; 22, 12050 | π Google Scholar | π doi:10.3390/ijms222112050
Β
Β
Β
Deep metagenomic sequencing examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules
Baker, J.L., Morton, J.T., Dinis, M., Alvarez, R., Tran, N.C., Knight, R., Edlund, A.
- This landmark study examined the oral microbiome of children with severe dental caries versus those with healthy teeth.
- This study showed the children with caries had a distinct microbiome, enriched in Prevotella and depleted of Rothia, Neisseria, and Haemophilus.
- This study also identified the first genomes of 42 novel taxa, and co-analysis with salivary immunological markers provided an atlas of microbe-host factor co-occurrences.
π Genome Research, 2021 January; 31(1):64-74 | π Google Scholar | π doi:10.1101/gr.265645.120
*Publication of particular interest
Β
2020
Β
Β
Caries-associated biosynthetic gene clusters of Streptococcus mutans
Momeni, S., Beno, S., Baker, J.L., Edlund, A., Ghazal, T., Wu, H., Childers, N.K.
- This study examined Streptococcus mutans biosynthetic gene clusters with elevated transcription during dental caries across a large epidemiological study.
- 3 butyrolactone and ladderane-type biosynthetic clusters were identified.
- Strains encoding these gene clusters appeared to have increased acid production, suggesting increased virulence.
π Journal of Dental Research, 2020 July; 99(8):969-976 | π Google Scholar | π doi:10.1177/0022034520914519
Β
Development of a bacteriophage cocktail to constrain the emergence of phage-resistant Pseudomonas aeruginosa
Yang, Y., Shen, W., Zhong, Q., He, X., Baker, J.L., Xiong, K., Jin, X., Wang, J., Hu, F., Le, S.
- Using phage training, we developed a a phage able to infect Pseudomonas aeruginosa mutants with a truncated O-antigen.
- We then developed a phage cocktail that was effective against diverse isolates of P. aeruginosa and in the short term constrained evolution of phage resistance
- This study provides an alternative strategy for designing phage cocktails for phage therapy.
π Frontiers in Microbiology, 2020 March 4; 11:327 | π Google Scholar | π doi:10.3389/fmicb.2020.00327
Β
Streptococcus mutans SpxA2 relays the signal of cell envelope stress from LiaR to effectors that maintain cell wall and membrane homeostasis
Baker, J.L., Saputo, S., Faustoferri, R., Quivey Jr., R.G.
- Deletion of the SpxA2 regulator in Streptococcus mutans results in increased unsaturated fatty acids, and altered transcription of fabT and fabM.
- Expression of spxA2 was dependent on the liaR component of the LiaFSR system, known to sense membrane stress in other Gram positive bacteria.
- Overall, the results of this study indicate that SpxA2 serves a crucial role in transmitting the signal of cell wall/membrane damage from the LiaFSR sensor to downstream effectors in the SpxA2 regulon which restore and maintain membrane and cell wall homeostasis.
π Molecular Oral Microbiology, 2020 June; 35(3): 118-128 | π Google Scholar | π doi:10.1111/omi.12282
Β
Cariogenic Streptococcus mutans produces tetramic acid strain-specific antibiotics that impair commensal colonization
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.
- Streptococcus mutans strain B04Sm5 produces multiple tetramic acids using a novel PKS/NRPS-type biosyntheic gene cluster.
- This gene cluster, which we designate muc produces at least three types of reutericyclins and a novel unacylated tetramic acid which we are naming mutanocyclin.
- B04Sm5 was able to use reutericyclin to inhibit the growth of neighboring commensals, suggesting a role in virulence.
- The mucF gene was identified as a novel class of acylase, which appears to be broadly distributed and have an HXXEE domain.
π ACS Infectious Diseases, 2020 April; 6(4):563-571 | π Google Scholar | π doi:10.1021/acsinfecdis.9b00365
*Publication of particular interest
2019
Β
Klebsiella and Providencia emerge as lone survivors following long-term starvation of the oral microbiota
Baker, J.L., Hendrickson, E.L., Tang, X., Lux, R., He, X., Edlund, A., McLean, J.S., Shi, W.
- We observed the salivary microbiome through a starvation phase in sterile-filtered saliva for 100 days.
- The only surviving and transcriptionally active species were Klebsiella and Providencia.
- The isolates accumulated single nucleotide polymorphisms in known growth advantage in stationary phase alleles and produced natural products closely resembling antimicrobial cyclic depsipeptides.
- This study suggests that pathogenic Enterobacteriaceae persist much longer than their more benign neighbors in the salivary microbiome when faced with starvation. This is particularly significant, given that hospital surfaces contaminated with oral fluids, especially sinks and drains, are well-established sources of outbreaks of drug-resistant Enterobacteriaceae.
π PNAS, 2019 April 23; 116(17):8499-8504 | π Google Scholar | π doi:10.1073/pnas.1820594116
*Publication of particular interest
Β
Identification of the biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease
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.
- We mined for biosynthetic gene clusters across 461 genomes from oral bacteria, identifying 4,915 such clusters.
- These were cross-referenced across 254 metagenomes and metatranscriptomes from individuals with healthy teeth, dental caries, or periodontitis, identifying 2,473 differentially represented clusters.
- Confirmatory mass spectrometry of a novel set of saliva samples from caries versus health identifed several compounds with homology to the predicted BGC products.
- These findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the worldβs most common chronic diseases.
π mBio, 2019 April 16 | π Google Scholar | π doi:10.1128/mBio.00321-19
*Publication of particular interest
Β
Precision reengineering of the oral microbiome for caries management
Baker, J.L., He, X., Shi, W.
- This review discusses advances in precision approaches to combat dental caries, especially highlighting specifically targeted antimicrobial peptides (STAMPs).
- C16G2 is a STAMP synthesized by combining the Streptococcus mutans pheromone, CSP, with a a killing domain from the antimicrobial novispirin.
- C16G2 was able to selectively remove S. mutans from biofilms, representing a promising novel therapeutic against dental caries.
π Advances in Dental Research, 2019 October 21; 30(2), 34-39 | π Google Scholar | π doi:10.1177/0022034519877386
Β
Exploiting the oral microbiome to prevent tooth decay: has evolution already provided the best tools?
Baker, J.L., Edlund, A.
- This article reviews approaches to combat dental caries, including diet modifications, probiotics, fluoride, polyol gums, vaccines, and novel antimicrobials including STAMPs and phage .
- We make the argument that the oral microbiome has likely evolved many antimicrobials that can eliminate pathogenic bacteria that lead to dysbiosis and ultimately dental caries.
π Frontiers in Microbiology, 2019 Jan 11; 9:3323 | π Google Scholar | π doi:10.3389/fmicb.2018.03323
2018
Β
Characterization of the trehalose utilization operon in Streptococcus mutans reveals that the TreR transcriptional regulator is involved in stress response pathways and toxin production
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.
- This study characterized the trehalose utiliztion operon in Streptococcus mutans.
- The operon was required for growth on trehalose, and unexpectedly the TreR regulator was required for tolerance of oxidative stress.
- RNA-seq also identified the treR was involved in regulation of mutacin production and competence, suggesting a role in competative fitness.
π Journal of Bacteriology, 2018 May 24; 200(12) | π Google Scholar | π doi:10.1128/JB.00057-18
2017
Β
Ecology of the oral microbiome: beyond bacteria
Baker, J.L., Bor, B., Agnello, M., Shi, W., He, X.
- This article reviews the current understanding of the oral microbiome, especially regarding noncanonical members such as fungi, viruses, and ultrasmall bacteria.
- Recently discovered ultrasmall Saccharibacteria are essentially tiny parasitic bacteria dependent on physical association with a host bacterium, and appear to be involved in oral inflammation.
- The fungus Candida albicans is increasingly recognized to have different mechanistic associations with various oral bacteria, and can both be proinflammatory and increase caries pathogenesis.
π Trends in Microbiology, 2017 May; 25(5): 362-374 | π Google Scholar | π doi:10.1016/j.tim.2016.12.012
Β
Acid-adaptive mechanisms of Streptococcus mutansβthe more we know, the more we don't
Baker, J.L., Faustoferri, R.C., Quivey, Jr., R.G.
- This review discusses the diverse acid tolerance mechanisms of Streptococcus mutans, which enable it to cause disease.
- Mechanisms reviewed include unsaturated fatty acid biosynthesis, glucan production, ATPase activity, agmatine deiminase, malolactic fermentation, BCAA biosynthesis, ion transport, alteration of sugar import, alteration of glycolytic end-products, DNA-repair, and protein fate.
- What is known about regulation and scope of the acid-tolerance response at the transcriptional level is also reviewed.
π Molecular Oral Microbiology, 2017 Apr; 32(2): 107-117 | π Google Scholar | π doi:10.1111/omi.12162
2016
Β
Β
Acid adaptive responses of S. mutans, and mechanisms of integration with oxidative stress
Faustoferri, R.C., Santiago, B., Baker, J.L., Cross, B., Xiao, J., Quivey Jr., R.G.
- This textbook chapter discusses the diverse acid tolerance mechanisms of Streptococcus mutans, which enable it to cause disease.
- The acid tolerance response is also intimately linked and overlapping with the oxidative stress response.
π Stress and Environmental Control of Gene Expression in Bacteria, 1st Edition, 2016 Aug | π Google Scholar | π doi:10.1002/9781119004813.ch88
2015
Β
*Publication of particular interest
Β
Transcriptional profile of glucose-shocked and acid-adapted strains of Streptococcus mutans
Baker, J.L., Abranches, J.A., Faustoferri, R.C., Hubbard, C.J., Lemos, J.A., Courtney, M.A., Quivey Jr., R.G.
- This study characterized the transcriptional response of Streptococcus mutans through a glucose shock and resulting pH drop within a continuous culture bioreactor..
- A fabM mutant, which as highly acid-sensitive and could not produce unsaturated fatty acids was also examined.
- This study defines both an immediate transcriptional response to pH drop, and the response during long-term growth in acidic conditions, which is important for S. mutans virulence.
π Molecular Oral Microbiology, 2015 Dec; 30(6):496-517 | π Google Scholar | π doi:10.1111/omi.12150
2014
Β
Streptococcus mutans NADH oxidase lies at the intersection of overlapping regulons controlled by oxygen and NAD+ Levels
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.
- This study illustrates that Streptococcus mutans nox is regulated by the SpxA1 and Rex transcriptional regulators.
- RNA-seq identifed the large-scale transcriptional response to either addition of oxygen to the culture, or deletion of nox.
- These data suggest a regulatory loop in which the roles of nox in reduction of oxygen and regeneration of NAD+ affect the activity levels of Spx and Rex, respectively, and their regulons, which control several genes, including nox, crucial to growth of S. mutans under conditions of oxidative stress.
π Journal of Bacteriology, 2014 June; 196(12):2166-2177 | π Google Scholar | π doi:10.1128/JB.01542-14
2013
Β
Β
Host Factor SAMHD1 Restricts DNA Viruses in Non-Dividing Myeloid Cells
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.
- SAMHD1 restricts vaccinia and HSV 1 replication in non dividing myeloid cells by depleting intracellular dNTP pools.
- Viral replication is even more impaired when viral dNTP metabolism genes such as thymidine kinase are absent.
- The study positions SAMHD1 as a broadly acting innate antiviral factor against multiple DNA viruses in macrophages.
π PLOS Pathogens, 2013; 9(6):e1003481 | π Google Scholar | π doi:10.1371/journal.ppat.1003481