Paperbase

Jonathon Baker

Baker Jonathon

ORCID: 0000-0001-5378-322X

A Modified Chromogenic Assay for Determination of the Ratio of Free Intracellular NAD+/NADH in Streptococcus mutans 10.21769/bioprotoc.1902

Acid-adaptive Responses ofStreptococcus Mutans, and Mechanisms of Integration With Oxidative Stress 10.1002/9781119004813.ch88

Acid-adaptive mechanisms ofStreptococcus mutans-the more we know, the more we don't 10.1111/omi.12162

Loss of NADH Oxidase Activity in Streptococcus mutans Leads to Rex-Mediated Overcompensation in NAD+Regeneration by Lactate Dehydrogenase 10.1128/jb.00383-15

Transcriptional profile of glucose-shocked and acid-adapted strains ofStreptococcus mutans 10.1111/omi.12110

Streptococcus mutans NADH Oxidase Lies at the Intersection of Overlapping Regulons Controlled by Oxygen and NAD+ Levels 10.1128/jb.01542-14

Characterization of the Trehalose Utilization Operon in Streptococcus mutans Reveals that the TreR Transcriptional Regulator Is Involved in Stress Response Pathways and Toxin Production 10.1128/jb.00057-18

Development and comparison of a quantitative TaqMan-MGB real-time PCR assay to three other methods of quantifying vaccinia virions 10.1016/j.jviromet.2013.10.026

Host Factor SAMHD1 Restricts DNA Viruses in Non-Dividing Myeloid Cells 10.1371/journal.ppat.1003481

Ecology of the Oral Microbiome: Beyond Bacteria 10.1016/j.tim.2016.12.012

Exploiting the Oral Microbiome to Prevent Tooth Decay: Has Evolution Already Provided the Best Tools? 10.3389/fmicb.2018.03323

KlebsiellaandProvidenciaemerge as lone survivors following long-term starvation of oral microbiota 10.1073/pnas.1820594116

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease 10.1128/mbio.00321-19

Cariogenic Streptococcus mutans produces strain-specific antibiotics that impair commensal colonization 10.1101/755025

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules 10.1101/804443

Precision Reengineering of the Oral Microbiome for Caries Management 10.1177/0022034519877386

Cariogenic Streptococcus mutans Produces Tetramic Acid Strain-Specific Antibiotics That Impair Commensal Colonization 10.1021/acsinfecdis.9b00365

Streptococcus mutans SpxA2 relays the signal of cell envelope stress from LiaR to effectors that maintain cell wall and membrane homeostasis 10.1111/omi.12282

Development of a Bacteriophage Cocktail to Constrain the Emergence of Phage-Resistant Pseudomonas aeruginosa. 10.3389/fmicb.2020.00327

Caries-Associated Biosynthetic Gene Clusters in Streptococcus mutans 10.1177/0022034520914519

Composite Long- and Short-Read Sequencing Delivers a Complete Genome Sequence of B04Sm5, a Reutericyclin- and Mutanocyclin-Producing Strain of Streptococcus mutans 10.1128/MRA.01067-20

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules 10.1101/gr.265645.120

Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle 10.1101/2021.05.28.446221

Complete Genome Sequence of Strain JB001, a Member of Saccharibacteria Clade G6 (“ Candidatus Nanogingivalaceae”) 10.1128/MRA.00517-21

Complete Genomes of Clade G6 Saccharibacteria Suggest a Divergent Ecological Niche and Lifestyle 10.1128/mSphere.00530-21

Márcia Botelho Dinis

Botelho Dinis Márcia / Márcia Dinis

ORCID: 0000-0001-8734-4276

Lollipop containing Glycyrrhiza uralensis extract reduces Streptococcus mutans colonization and maintains oral microbial diversity in Chinese preschool children. 10.1371/journal.pone.0221756

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease. 10.1128/mBio.00321-19

Group A Streptococcus emm3 strains induce early macrophage cell death. 10.1093/femspd/ftv124

AMA1-deficient Toxoplasma gondii parasites transiently colonize mice and trigger an innate immune response that leads to long-lasting protective immunity. 10.1128/IAI.02606-14

The innate immune response elicited by Group A Streptococcus is highly variable among clinical isolates and correlates with the emm type. 10.1371/journal.pone.0101464

Molecular epidemiology of sil locus in clinical Streptococcus pyogenes strains. 10.1128/JCM.00290-14

Extracellular nucleotide catabolism by the Group B Streptococcus ectonucleotidase NudP increases bacterial survival in blood. 10.1074/jbc.M113.545632

rEnolase maternal immunization confers caries protection on offspring. 10.1177/0022034510391793

Oral therapeutic vaccination with Streptococcus sobrinus recombinant enolase confers protection against dental caries in rats. 10.1086/594372

Leukocyte populations and cytokine expression in the mammary gland in a mouse model of Streptococcus agalactiae mastitis. 10.1099/jmm.0.007385-0

Identification of immunoreactive extracellular proteins of Streptococcus agalactiae in bovine mastitis. 10.1139/w08-083

Adult rabbits acquire resistance to lethal calicivirus infection by adoptive transfer of sera from infected young rabbits. 10.1016/j.vetimm.2007.09.005

Enolase from Streptococcus sobrinus is an immunosuppressive protein. 10.1046/j.1462-5822.2003.00344.x

Identification of NAD+ synthetase from Streptococcus sobrinus as a B-cell-stimulatory protein. 10.1128/JB.186.2.419-426.2004

Therapeutic vaccine against Streptococcus sobrinus-induced caries. 10.1177/154405910408300416

Omics and interspecies interaction. 10.1111/prd.12354

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules. 10.1101/gr.265645.120

Gajender Aleti

Aleti Gajender

ORCID: 0000-0002-1867-9758

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease 10.1128/mbio.00321-19

Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage 10.1038/s41598-017-02314-x

Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review 10.1016/j.scitotenv.2018.02.037

The draft genome sequence of Paenibacillus polymyxa strain CCI-25 encompasses high potential for secondary metabolite production 10.1128/genomeA.00366-16

Wake-up-call, a lin-52 paralogue, and Always early, a lin-9 homologue physically interact, but have opposing functions in regulating testis-specific gene expression 10.1016/j.ydbio.2011.04.030

Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis 10.3389/fimmu.2019.02602

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/j.foodchem.2019.125290

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity 10.1371/journal.pone.0198107

Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus 10.1111/1462-2920.13405

Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults 10.1016/j.bbi.2020.02.004

Correction: Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity(PLoS ONE (2018) 13:6 (e0198107) DOI: 10.1371/journal.pone.0198107) 10.1371/journal.pone.0201624

Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes 10.1016/j.csbj.2015.03.003

A community resource for paired genomic and metabolomic data mining. 10.1038/s41589-020-00724-z

Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma. 10.1007/s00248-020-01596-5

ReDU: a framework to find and reanalyze public mass spectrometry data. 10.1038/s41592-020-0916-7

Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides 10.1101/2021.08.10.21255754

Anna Edlund

Edlund Anna

ORCID: 0000-0002-3394-4804

https://www.linkedin.com/in/anna-edlund-7ba5646/

Discovery of a Novel Periodontal Disease-Associated Bacterium 10.1007/s00248-018-1200-6

Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation 10.1186/s40168-018-0591-4

Establishing microbial composition measurement standards with reference frames. 10.1038/s41467-019-10656-5

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease. 10.1128/mBio.00321-19

Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota. 10.1073/pnas.1820594116

Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x. 10.3389/fmicb.2018.02049

Exploiting the Oral Microbiome to Prevent Tooth Decay: Has Evolution Already Provided the Best Tools? 10.3389/fmicb.2018.03323

Correction for Morton et al., "Uncovering the Horseshoe Effect in Microbial Analyses". 10.1128/mSystems.00006-18

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules. 10.1128/mSystems.00058-17

Uncovering the Horseshoe Effect in Microbial Analyses. 10.1128/mSystems.00166-16

The Denture-Associated Oral Microbiome in Health and Stomatitis. 10.1128/mSphere.00215-16

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen. 10.1128/mSystems.00139-16

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. 10.1038/nbt.3597

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles. 10.1371/journal.pcbi.1004991

High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model. 10.1128/genomeA.01684-15

Draft Genome Sequence of "Candidatus Bacteroides periocalifornicus," a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients. 10.1128/genomeA.01485-15

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism. 10.1038/ismej.2015.72

Bacteria-mediated effects of antibiotics on Daphnia nutrition. 10.1021/acs.est.5b00833

Bacteriophage and their potential roles in the human oral cavity. 10.3402/jom.v7.27423

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. 10.1073/pnas.1419038112

An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome. 10.1186/2049-2618-1-25

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. 10.1073/pnas.1219809110

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. 10.1101/gr.150433.112

Observing the invisible through imaging mass spectrometry, a window into the metabolic exchange patterns of microbes. 10.1016/j.jprot.2012.05.036

Antibiotic-induced change of bacterial communities associated with the copepod Nitocra spinipes. 10.1371/journal.pone.0033107

Microdiversity and evidence for high dispersal rates in the marine actinomycete 'Salinispora pacifica'. 10.1111/j.1462-2920.2011.02641.x

Geographic distribution of secondary metabolite genes in the marine actinomycete Salinispora arenicola. 10.1128/AEM.00611-11

Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments. 10.1111/j.1574-6941.2008.00513.x

Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. 10.1111/j.1462-2920.2008.01624.x

Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments. 10.1128/AEM.00971-06

Microbial community structure in polluted Baltic Sea sediments. 10.1111/j.1462-2920.2005.00887.x

Cariogenic Streptococcus mutans Produces Tetramic Acid Strain-Specific Antibiotics That Impair Commensal Colonization 10.1021/acsinfecdis.9b00365

Caries-Associated Biosynthetic Gene Clusters in Streptococcus mutans 10.1177/0022034520914519

Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore 10.1128/mSystems.00161-20

Composite Long- and Short-Read Sequencing Delivers a Complete Genome Sequence of B04Sm5, a Reutericyclin- and Mutanocyclin-Producing Strain of Streptococcus mutans 10.1128/MRA.01067-20

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules 10.1101/gr.265645.120

The Oral Host–Microbial Interactome: An Ecological Chronometer of Health? 10.1016/j.tim.2020.11.004

A community resource for paired genomic and metabolomic data mining. 10.1038/s41589-020-00724-z

Xiaoyu Tang

Tang Xiaoyu

ORCID: 0000-0002-7855-5984

Minimization of the Thiolactomycin Biosynthetic Pathway Reveals that the Cytochrome P450 Enzyme TlmF Is Required for Five-Membered Thiolactone Ring Formation 10.1002/cbic.201700090

Back Cover: Minimization of the Thiolactomycin Biosynthetic Pathway Reveals that the Cytochrome P450 Enzyme TlmF Is Required for Five-Membered Thiolactone Ring Formation (ChemBioChem 12/2017) 10.1002/cbic.201700270

Enzymatic C-H Oxidation-Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity. 10.1002/anie.201705239

Broad-Host-Range Expression Reveals Native and Host Regulatory Elements That Influence Heterologous Antibiotic Production in Gram-Negative Bacteria. 10.1128/mbio.01291-17

A two-step sulfation in antibiotic biosynthesis requires a type III polyketide synthase. 10.1038/nchembio.1310

Identification of mureidomycin analogues and functional analysis of an N-acetyltransferase in napsamycin biosynthesis. 10.1002/cbic.201300287

The biosynthesis of caprazamycins and related liponucleoside antibiotics: new insights. 10.1515/hsz-2012-0274

Engineering Salinispora tropica for heterologous expression of natural product biosynthetic gene clusters 10.1007/s00253-018-9283-z

KlebsiellaandProvidenciaemerge as lone survivors following long-term starvation of oral microbiota 10.1073/pnas.1820594116

Genetic platforms for heterologous expression of microbial natural products 10.1039/C9NP00025A

Direct cloning and heterologous expression of natural product biosynthetic gene clusters by transformation-associated recombination. 10.1016/bs.mie.2019.02.026

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease. 10.1128/mBio.00321-19

Identification of a napsamycin biosynthesis gene cluster by genome mining. 10.1002/cbic.201000460

Biochemical properties and potential applications of a solvent-stable protease from the high-yield protease producer Pseudomonas aeruginosa PT121. 10.1007/s12010-009-8665-1

Screening and isolation of an organic solvent-tolerant bacterium for high-yield production of organic solvent-stable protease. 10.1016/j.biortech.2008.01.030

Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining. 10.1021/acschembio.5b00658

Pass-back chain extension expands multimodular assembly line biosynthesis 10.1038/s41589-019-0385-4

Cariogenic Streptococcus mutans Produces Tetramic Acid Strain-Specific Antibiotics That Impair Commensal Colonization 10.1021/acsinfecdis.9b00365

Grincamycins P–T: Rearranged Angucyclines from the Marine Sediment-Derived Streptomyces sp. CNZ-748 Inhibit Cell Lines of the Rare Cancer Pseudomyxoma Peritonei 10.1021/acs.jnatprod.1c00179

Nini Tran

Tran Nini / Thawinee Chaichanasakul

ORCID: 0000-0003-1716-4995

Osteogenic potential of mandibular vs. Long-bone marrow stromal cells 10.1177/0022034510378427

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation 10.1177/0022034517707512

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease 10.1128/mBio.00321-19

Periapical disease and bisphosphonates induce osteonecrosis of the jaws in mice 10.1002/jbmr.1894

Effectiveness of the GumChucks flossing system compared to string floss for interdental plaque removal in children: a randomized clinical trial 10.1038/s41598-020-59705-w

Diverse osteoclastogenesis of bone marrow from mandible versus long bone 10.1902/jop.2013.130376

Corrigendum to " Modified bacterial artificial chromosomes for zebrafish transgenesis" Methods 39 (2006) 183-188 10.1016/j.ymeth.2010.11.001

Microbiome Associated with Severe Caries in Canadian First Nations Children. 10.1177/0022034517718819

Modified bacterial artificial chromosomes for zebrafish transgenesis. 10.1016/j.ymeth.2006.04.011

Oral colonization of Candida albicans and Streptococcus mutans in children with or without fixed orthodontic appliances: A pilot study 10.1016/j.jds.2021.07.026

Omics and interspecies interaction. 10.1111/prd.12354

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules. 10.1101/gr.265645.120