Publication List

* = equal contribution; ** = corresponding author(s); Bold Names = Dantas Lab Authors

[167]
Choi J*, Thänert R*, Reske KA., Nickel, K. B., Olsen, M. A., Hink, T. Thänert A, Wallace MA, Wang B, Cass C, Barlet MH, Struttmann EL, Iqbal ZH, Sax SR, Fraser VJ, Baker AW, Foy KR, Williams B, Xu B, Capocci-Tolomeo P, Lautenbach E, Burnham C-AD, Dubberke ER**, Dantas G**, Kwon JH**, on behalf of the CDC Prevention Epicenters Program. Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study. eClinicalMedicine, 2024 Apr;102490. doi: 10.1016/j.eclinm.2024.102490. [PDF]

[166]
Mahmud B*, Vargas RC*, Sukhum KV, Patel S, Liao J, Hall LR, Kesaraju A, Le T, Kitchner T, Kronholm E, Koshalek K, Bendixsen CG, VanWormer JJ, Shukla SK**, Dantas G**. Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes. Nat Microbiol. 2024 Apr;9(4):1007-1020. doi: 10.1038/s41564-024-01639-4. Epub 2024 Apr 3. PMID: 38570675. [PDF]

[165]
Blake KS*, Kumar H*, Loganathan A*, Williford EE*, Diorio-Toth L, Xue YP, Tang WK, Campbell TP, Chong DD, Angtuaco S, Wencewicz TA**, Tolia NH**, Dantas G**. Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes. Commun Biol. 2024 Mar 16;7(1):336. doi: 10.1038/s42003-024-06023-w. PMID: 38493211. [PDF]

[164]
Fishbein SRS*’ **, Evbuomwan EM*’ **, Dantas G. Conquering homocystinuria with engineered probiotics. Cell Host Microbe. 2024 Mar 13;32(3):298-300. doi: 10.1016/j.chom.2024.02.008. PMID: 38484708. [PDF]

[163]
Newcomer EP*, Fishbein SRS*, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Burnham C-AD, Dubberke ER**, Dantas G**. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. mBio. 2024 Feb 8:e0330023. doi: 10.1128/mbio.03300-23. Epub ahead of print. PMID: 38329369. [PDF]

[162]
Blake KS*, Schwartz DJ*, Paruthiyil S*, Wang B, Ning J, Isidean SD, Burns DS, Whiteson H, Lalani T, Fraser JA, Connor P, Troth T, Porter CK, Tribble DR, Riddle MS, Gutiérrez RL, Simons MP**, Dantas G**. Gut microbiome and antibiotic resistance effects during travelers' diarrhea treatment and prevention. mBio. 2023 Dec 12:e0279023. doi: 10.1128/mbio.02790-23. Epub ahead of print. PMID: 38085102. [PDF]

[161]
Amrofell MB*, Rengarajan S*, Vo ST, Ramirez Tovar ES, LoBello L, Dantas G, Moon TS**. Engineering E. coli strains using antibiotic-resistance-gene-free plasmids. Cell Rep Methods. 2023 Dec 3:100669. doi: 10.1016/j.crmeth.2023.100669. Epub ahead of print. PMID: 38086386. [PDF}

[160]
Zhang K*, Potter RF*, Marino J, Muenks CE, Lammers MG, Dien Bard J, Dingle TC, Humphries R, Westblade LF, Burnham C-AD**, Dantas G**. Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus. mSystems. 2023 Dec 5:e0069723. doi: 10.1128/msystems.00697-23. Epub ahead of print. PMID: 38051037. [PDF}

[159]
Sawhney SS*, Vargas RC*, Wallace MA, Muenks CE, Lubbers BV, Fritz SA, Burnham CD**, Dantas G**. Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms. Nat Commun. 2023 Nov 3;14(1):7065. doi: 10.1038/s41467-023-42694-5. PMID: 37923729; PMCID: PMC10624692. [PDF]

[158]
Schwartz DJ*, Langdon A*, Sun X, Langendorf C, Berthé F, Grais RF, Trehan I, Isanaka S, Dantas G**. Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial. Lancet Microbe. 2023 Nov;4(11):e931-e942. doi: 10.1016/S2666-5247(23)00213-6. Epub 2023 Oct 19. PMID: 37866373; PMCID: PMC10620469. [PDF]

[157]
Xu W**, Rustenhoven J, Nelson CA, Dykstra T, Ferreiro A, Papadopoulos Z, Burnham CD, Dantas G, Fremont DH, Kipnis J**. A novel immune modulator IM33 mediates a glia-gut-neuronal axis that controls lifespan. Neuron. 2023 Aug 7:S0896-6273(23)00543-3. doi: 10.1016/j.neuron.2023.07.010. Epub ahead of print. PMID: 37582366. [PDF]

[156]
Fishbein SRS*, Mahmud B*, Dantas G**. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol. 2023 Jul 25. doi: 10.1038/s41579-023-00933-y. Epub ahead of print. PMID: 37491458. [PDF]

[155]
Potter RF*, Zhang K*, Reimler B, Marino J, Muenks CE, Alvarado K, Wallace MA, Westblade LF, McElvania E, Yarbrough ML, Hunstad DA, Dantas G**, Burnham CD. Uncharacterized and lineage-specific accessory genes within the Proteus mirabilispan-genome landscape. mSystems. 2023 Jun 21:e0015923. doi: 10.1128/msystems.00159-23. Epub ahead of print. PMID: 37341494. [PDF]

[154]
Diorio-Toth L, Wallace MA, Farnsworth CW, Wang B, Gul D, Kwon JH, Andleeb S**, Burnham CD**, Dantas G**. Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids. mSystems. 2023 Jul 13:e0020623. doi: 10.1128/msystems.00206-23. Epub ahead of print. PMID: 37439570. [PDF]

[153]
DeVeaux A*, Ryou J*, Dantas G**, Warner BB**, Tarr PI**. Microbiome-targeting therapies in the neonatal intensive care unit: safety and efficacy. Gut Microbes. 2023 Jan-Dec;15(1):2221758. doi: 10.1080/19490976.2023.2221758. PMID: 37358104; PMCID: PMC10294772. [PDF]

[152]
Ferreiro AL, Choi J, Ryou J, Newcomer EP, Thompson R, Bollinger RM, Hall-Moore C, Ndao IM, Sax L, Benzinger TLS, Stark SL, Holtzman DM, Fagan AM, Schindler SE, Cruchaga C, Butt OH, Morris JC, Tarr PI, Ances BM**, Dantas G**. Gut microbiome composition may be an indicator of preclinical Alzheimer's disease. Sci Transl Med. 2023 Jun 14;15(700):eabo2984. doi: 10.1126/scitranslmed.abo2984. Epub 2023 Jun 14. PMID: 37315112. [PDF]

[151]
Choi J, Keen EC, Wallace MA, Fishbein S, Prusa J, Zimbric M, Mejia-Chew CR, Mehta SB, Bailey TC, Caverly LJ, Burnham CD**, Dantas G**. Genomic Analyses of Longitudinal Mycobacterium abscessus Isolates in a Multi-Center Cohort Reveal Parallel Signatures of In-Host Adaptation. J Infect Dis. 2023 May 31:jiad187. doi: 10.1093/infdis/jiad187. Epub ahead of print. PMID: 37254795. [PDF]

[150]
Tarlton NJ, Wallace MA, Potter RF, Zhang K, Dantas G, Dubberke ER, Burnham CD, Yarbrough ML**. Evaluation of the NG-Test CARBA 5 Lateral Flow Assay with an IMP-27-Producing Morganella morganii and Other Morganellaceae. Microbiol Spectr. 2023 May 18:e0079323. doi: 10.1128/spectrum.00793-23. Epub ahead of print. PMID: 37199652. [PDF]

[149]
Roell GW, Schenk C, Anthony WE, Carr RR, Ponukumati A, Kim J, Akhmatskaya E, Foston M, Dantas G, Moon TS**, Tang YJ**, García Martín H**. A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism. ACS Synth Biol. 2023 May 15. doi: 10.1021/acssynbio.2c00618. Epub ahead of print. PMID: 37186551. [PDF]

[148]
Schwartz DJ*, Shalon N*, Wardenburg K, DeVeaux A, Wallace MA, Hall-Moore C, Ndao IM, Sullivan JE, Radmacher P, Escobedo M, Burnham CD, Warner BB, Tarr PI, Dantas G**. Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Sci Transl Med. 2023 May 3;15(694):eadg5562. doi: 10.1126/scitranslmed.adg5562. Epub 2023 May 3. PMID: 37134153. [PDF]

[147]
Kumar H, Williford EE, Blake KS, Virgin-Downey B, Dantas G**, Wencewicz TA**, Tolia NH**. Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases. Commun Biol. 2023 Apr 17;6(1):423. doi: 10.1038/s42003-023-04792-4. PMID: 37062778; PMCID: PMC10106456. [PDF]

[146]
Williford EE, DeAngelo CM, Blake KS, Kumar H, Lam KK, Jones KV, Tolia NH**, Dantas G**, Wencewicz TA**. Structure-Based Design of Bisubstrate Tetracycline Destructase Inhibitors That Block Flavin Redox Cycling. J Med Chem. 2023 Mar 23;66(6):3917-3933. doi: 10.1021/acs.jmedchem.2c01629. Epub 2023 Mar 6. PMID: 36877173. [PDF]

[145]
Talat A, Blake KS, Dantas G, Khan AU. Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance. Microbiol Spectr. 2023 Feb 14:e0410222. doi: 10.1128/spectrum.04102-22. Epub ahead of print. PMID: 36786639. [PDF]

[144]
Kaur M, Ferreiro A, Hung CY, Dantas G, Ramasubramanian AK**. A low-cost, high-throughput microfluidic nano-culture platform for functional metagenomics. Biotechnol Prog. 2022 Dec 13:e3317. doi: 10.1002/btpr.3317. Epub ahead of print. PMID: 36514196. [PDF]

[143]
Zou Z, Potter RF, McCoy Th WH, Wildenthal JA, Katumba GL, Mucha PJ, Dantas G, Henderson JP**. Escherichia coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants. JCI Insight. 2022 Dec 13:e161461. doi: 10.1172/jci.insight.161461. Epub ahead of print. PMID: 36512427. [PDF]

[142]
Boolchandani M, Blake KS, Tilley DH, Cabada MM, Schwartz DJ, Patel S, Morales ML, Meza R, Soto G, Isidean SD, Porter CK, Simons MP**, Dantas G**. Impact of international travel and diarrhea on gut microbiome and resistome dynamics. Nat Commun. 2022 Dec 5;13(1):7485. doi: 10.1038/s41467-022-34862-w. PMID: 36470885. [PDF]

[141]
Mahmud B*, Boolchandani M*, Patel S*, Dantas G**. Functional Metagenomics to Study Antibiotic Resistance. Methods Mol Biol. 2023;2601:379-401. doi: 10.1007/978-1-0716-2855-3_21. PMID: 36445596. [PDF]

[140]
Calix JJ, de Almeida MCS, Potter RF, Wallace MA, Burnham CD, Dantas G**. Outpatient clonal propagation propelled rapid regional establishment of an emergent carbapenem-resistant Acinetobacter baumannii lineage ST499Pas. J Infect Dis. 2022 Oct 27:jiac427. doi: 10.1093/infdis/jiac427. Epub ahead of print. PMID: 36301240. [PDF]

[139]
Jean S*, Wallace MJ*, Dantas G, Burnham CD**. Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group. J Clin Microbiol. 2022 Sep 21;60(9):e0236120. doi: 10.1128/jcm.02361-20. Epub 2022 Jun 14. PMID: 35700139; PMCID: PMC9491163. [PDF]

[138]
Kwak S*, Crook N*, Yoneda A, Ahn N, Ning J, Cheng J, Dantas G**. Functional mining of novel terpene synthases from metagenomes. Biotechnol Biofuels Bioprod. 2022 Oct 8;15(1):104. doi: 10.1186/s13068-022-02189-9. PMID: 36209178. [PDF]

[137]
Bai W*, Anthony WE*, Hartline CJ, Wang S, Wang B, Ning J, Hsu FF, Dantas G**, Zhang F**. Engineering diverse fatty acid compositions of phospholipids in Escherichia coli. Metab Eng. 2022 Sep 1;74:11-23. doi: 10.1016/j.ymben.2022.08.011. Epub ahead of print. PMID: 36058465. [PDF]

[136]
Mahmud B, Wallace MA, Reske KA, Alvarado K, Muenks CE, Rasmussen DA, Burnham CD, Lanzas C**, Dubberke ER**, Dantas G**. Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli. mSystems. 2022 Aug 22:e0051922. doi: 10.1128/msystems.00519-22. Epub ahead of print. PMID: 35993734. [PDF]

[135]
Ransom EM, Sawhney SS, Dantas G, Burnham CD, Fishbein SRS**. Draft Genome Sequence of a Mycobacterium Strain Isolated from a Clinical Wound Sample. Microbiol Resour Announc. 2022 Jun 2:e0017022. doi: 10.1128/mra.00170-22. Epub ahead of print. PMID: 35652667. [PDF]

[134]
Sukhum KV*, Newcomer EP*, Cass C, Wallace MA, Johnson C, Fine J, Sax S, Barlet MH, Burnham CD**, Dantas G**, Kwon JH**. Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates. Commun Med (Lond). 2022 Jun 1;2:62. doi: 10.1038/s43856-022-00124-5. PMID: 35664456; PMCID: PMC9160058. [PDF]

[133]
Diorio-Toth L*, Irum S*, Potter RF, Wallace MA, Arslan M, Munir T, Andleeb S**, Burnham CD**, Dantas G**. Genomic Surveillance of Clinical Pseudomonas aeruginosa Isolates Reveals an Additive Effect of Carbapenemase Production on Carbapenem Resistance. Microbiol Spectr. 2022 May 31:e0076622. doi: 10.1128/spectrum.00766-22. Epub ahead of print. PMID: 35638817. [PDF]

[132]
Thänert R*, Sawhney SS*, Schwartz DJ*, Dantas G**. The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy. Cell Host Microbe. 2022 May 11;30(5):675-683. doi: 10.1016/j.chom.2022.03.013. PMID: 35550670. [PDF]

[131]
Thänert R*, Choi J*, Reske KA, Hink T, Thänert A, Wallace MA, Wang B, Seiler S, Cass C, Bost MH, Struttmann EL, Iqbal ZH, Sax SR, Fraser VJ, Baker AW, Foy KR, Williams B, Xu B, Capocci-Tolomeo P, Lautenbach E, Burnham CD, Dubberke ER**, Kwon JH**, Dantas G**; CDC Prevention Epicenters Program. Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements. Cell Host Microbe. 2022 May 9:S1931-3128(22)00214-1. doi: 10.1016/j.chom.2022.04.008. PMID: 35545083. [PDF]

[130]
Anthony WE, Wang B, Sukhum KV, D'Souza AW, Hink T, Cass C, Seiler S, Reske KA, Coon C, Dubberke ER, Burnham CD**, Dantas G**, Kwon JH**. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Rep. 2022 Apr 12;39(2):110649. doi: 10.1016/j.celrep.2022.110649. PMID: 35417701. [PDF]

[129]
Stogios PJ*, Bordeleau E*, Xu Z, Skarina T, Evdokimova E, Chou S, Diorio-Toth L, D'Souza AW, Patel S, Dantas G, Wright GD, Savchenko A**. Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family. Commun Biol. 2022 Mar 25;5(1):263. doi: 10.1038/s42003-022-03219-w. PMID: 35338238. [PDF]

[128]
Rottinghaus AG*, Ferreiro A*, Fishbein SRS, Dantas G**, Moon TS**. Genetically stable CRISPR-based kill switches for engineered microbes. Nat Commun. 2022 Feb 3;13(1):672. doi: 10.1038/s41467-022-28163-5. PMID: 35115506. [PDF]

[127]
Fishbein SR, Robinson JI, Hink T, Reske KA, Newcomer EP, Burnham CD, Henderson JP, Dubberke ER**, Dantas G**. Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis. Elife. 2022 Jan 27;11:e72801. doi: 10.7554/eLife.72801. PMID: 35083969. [PDF]

[126]
Wallace MJ*, Jean S*, Wallace MA, Burnham CD**, Dantas G**. Comparative Genomics of Bacteroides fragilis Group Isolates Reveals Species-Dependent Resistance Mechanisms and Validates Clinical Tools for Resistance Prediction. mBio 2022 Feb 22;13(1) doi: 10.1128/mbio.03603-21 [PDF]

[125]
Sawhney SS*, Ransom EM*, Wallace MA, Reich PJ, Dantas G**, Burnham CD**. Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit. mBio 2022 Feb 22;13(1) doi: 10.1128/mbio.03196-21 [PDF]

[124]
Adu-Oppong B*, Thänert R*, Wallace MA, Burnham CD**, Dantas G**. Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Microbiome. 2022 Jan 17;10(1):6. doi: 10.1186/s40168-021-01204-9. PMID: 35039079; PMCID: PMC8762997. [PDF]

[123]
Sawhney SS, Johnson C, Shupe A, Fine J, Dantas G, Burnham CD, Yarbrough ML**. Assessment of the Urinary Microbiota of MSM Using Urine Culturomics Reveals a Diverse Microbial Environment. Clin Chem. 2021 Dec 30;68(1):192-203. doi: 10.1093/clinchem/hvab199. PMID: 34969116. [PDF]

[122]
Kwak S*, Mahmud B*, Dantas G**. A Tunable and Expandable Transactivation System in Probiotic Yeast Saccharomyces boulardii. ACS Synth Biol. 2021 Dec 23. doi: 10.1021/acssynbio.1c00384. Epub ahead of print. PMID: 34939781. [PDF]

[121]
Marks, LR*, Calix, JJ*, Wildenthal, JA, Wallace, MA, Sawhney, SS, Ransom, EM, Durkin, MJ, Henderson, JP, Burnham CD**, Dantas G**. Staphylococcus aureus injection drug use-associated bloodstream infections are propagated by community outbreaks of diverse lineages. Communications Medicine. 2021 Nov 30;1(1):1-0. https://doi.org/10.1038/s43856-021-00053-9. [PDF]

[120]
Keen EC, Choi J, Wallace MA, Azar M, Mejia-Chew CR, Mehta SB, Bailey TC, Caverly LJ, Burnham CD**, Dantas G**. Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. mSystems. 2021 Oct 26;6(5):e0119421. doi: 10.1128/mSystems.01194-21. Epub 2021 Oct 19. PMID: 34665012; PMCID: PMC8525567. [PDF]

[119]
Wang GC*, Wallace MJ*, Krishnan G, Olson PD, Carlson AL, Dantas G**, Fleckenstein JM**. Spontaneous Bacterial Peritonitis Caused by Bordetella hinzii. Emerg Infect Dis. 2021 Nov;27(11):2966-2968. doi: 10.3201/eid2711.211428. Epub 2021 Aug 31. PMID: 34463239. [PDF]

[118]
Thänert R*, Thänert A*, Ou J*, Bajinting A, Burnham CD, Engelstad HJ, Tecos ME, Ndao IM, Hall-Moore C, Rouggly-Nickless C, Carl MA, Rubin DC, Davidson NO, Tarr PI, Warner BB, Dantas G**, Warner BW**. Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Gut Microbes. 2021 Jan-Dec;13(1):1940792. doi: 10.1080/19490976.2021.1940792. PMID: 34264786. [PDF]

[117]
D'Souza AW*, Boolchandani M*, Patel S, Galazzo G, van Hattem JM, Arcilla MS, Melles DC, de Jong MD, Schultsz C; COMBAT Consortium, Dantas G**, Penders J**. Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers. Genome Med. 2021 Jun 7;13(1):79. doi: 10.1186/s13073-021-00893-z. PMID: 34092249. [PDF]

[116]
Sukhum KV*, Vargas RC*, Boolchandani M, D'Souza AW, Patel S, Kesaraju A, Walljasper G, Hegde H, Ye Z, Valenzuela RK, Gunderson P, Bendixsen C, Dantas G**, Shukla SK**. Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil. mBio. 2021 May 11;12(3):e00798-21. doi: 10.1128/mBio.00798-21. PMID: 33975936. [PDF]

[115]
Langdon A*, Schwartz DJ*, Bulow C, Sun X, Hink T, Reske KA, Jones C, Burnham CD, Dubberke ER*, Dantas G**; CDC Prevention Epicenter Program. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. Genome Med. 2021 Feb 16;13(1):28. doi: 10.1186/s13073-021-00843-9. PMID: 33593430. [PDF]

[114]
Blake KS*, Choi J*, Dantas G**. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cell Mol Life Sci. 2021 Feb 13. doi: 10.1007/s00018-020-03717-2. Epub ahead of print. PMID: 33582841. [PDF]

[113]
Rebeck ON, Dantas G, Schwartz DJ**. Improving ICI outcomes with a little help from my microbial friends. Cell Host Microbe. 2021 Feb 10;29(2):155-157. doi: 10.1016/j.chom.2021.01.012. PMID: 33571442. [PDF]

[112]
Basak JM, Ferreiro A, Cohen LS, Sheehan PW, Nadarajah CJ, Kanan MF, Sukhum KV, Dantas G, Musiek ES**. Bacterial sepsis increases hippocampal fibrillar amyloid plaque load and neuroinflammation in a mouse model of Alzheimer's disease. Neurobiol Dis. 2021 Feb 5;152:105292. doi: 10.1016/j.nbd.2021.105292. Epub ahead of print. PMID: 33556539. [PDF]

[111]
Fishbein SRS, Hink T, Reske KA, Cass C, Struttmann E, Iqbal ZH, Seiler S, Kwon JH, Burnham CA, Dantas G**, Dubberke ER**. Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients. mSphere. 2021 Jan 13;6(1):e00936-20. doi: 10.1128/mSphere.00936-20. PMID: 33441409. [PDF]

[110]
Thänert R*, Keen EC*, Dantas G**, Warner BB**, Tarr PI**. Necrotizing enterocolitis and the microbiome: Current status and future directions. J Infect Dis. 2020 Dec 17:jiaa604. doi: 10.1093/infdis/jiaa604. Epub ahead of print. PMID: 33330904. [PDF]

[109]
Anthony WE, Burnham CD, Dantas G, Kwon JH**. The Gut Microbiome as a Reservoir for Antimicrobial Resistance. J Infect Dis. 2020 Dec 16:jiaa497. doi: 10.1093/infdis/jiaa497. Epub ahead of print. PMID: 33326581. [PDF]

[108]
Sukhum KV*, Jean S*, Wallace M, Anderson N, Burnham CA**, Dantas G**. Genomic characterization of emerging bacterial uropathogen Neisseria meningitidis misidentified as Neisseria gonorrhoeae by nucleic acid amplification testing. J Clin Microbiol. 2020 Nov 11:JCM.01699-20. doi: 10.1128/JCM.01699-20. Epub ahead of print. PMID: 33177123. [PDF]

[107]
Wallace MJ*, Fishbein SRS*, Dantas G**. Antimicrobial resistance in enteric bacteria: current state and next-generation solutions. Gut Microbes. 2020 Nov 9;12(1):1799654. doi: 10.1080/19490976.2020.1799654. PMID: 32772817. [PDF]

[106]
Vernier CL, Chin IM, Adu-Oppong B, Krupp JJ, Levine J, Dantas G, Ben-Shahar Y**. The gut microbiome defines social group membership in honey bee colonies. Science Advances. 2020 Oct 14;6(42):eabd3431. doi: 10.1126/sciadv.abd3431 . [PDF]

[105]
Schwartz DJ*, Langdon AE*, Dantas G**. Understanding the impact of antibiotic perturbation on the human microbiome. Genome Med. 2020 Sep 28;12(1):82. doi: 10.1186/s13073-020-00782-x. PMID: 32988391; PMCID: PMC7523053. [PDF]

[104]
Ransom EM*, Potter RF*, Dantas G, Burnham CD**. Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes! Clin Chem. 2020 Sep 12:hvaa172. doi: 10.1093/clinchem/hvaa172. Epub ahead of print. PMID: 32918462. [PDF]

[103]
Kwak S*, Choi J*, Hink T, Reske KA, Blount K, Jones C, Bost MH, Sun X, Burnham CD, Dubberke ER**, Dantas G** ; CDC Prevention Epicenter Program. Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial. Microbiome. 2020 Aug 31;8(1):125. doi: 10.1186/s40168-020-00907-9. PMID: 32862830; PMCID: PMC7457799. [PDF]

[102]
Wang HJ, Tatituri RVV, Goldner NK, Dantas G, Hsu FF**. Unveiling the biodiversity of lipid species in Corynebacteria- characterization of the uncommon lipid families in C. glutamicum and pathogen C. striatum by mass spectrometry. Biochimie. 2020 Jul 10:S0300-9084(20)30156-5. doi: 10.1016/j.biochi.2020.07.002. Epub ahead of print. PMID: 32659445. [PDF] [supplementary material]

[101]
Adu-Oppong B, Mangan SA, Stein C, Catano CP, Myers JA, Dantas G**. Prairie plants harbor distinct and beneficial root-endophytic bacterial communities. PLoS One. 2020 Jun 23;15(6):e0234537. doi: 10.1371/journal.pone.0234537. PMID: 32574172; PMCID: PMC7310688. [PDF] [supplementary material]

[100]
Gasparrini AJ, Markley JL, Kumar H, Wang B, Fang L, Irum S, Symister CT, Wallace M, Burnham CD, Andleeb S, Tolia NH**, Wencewicz TA**, Dantas G**. Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance. Communications Biology. 2020 May 15;3(1):241. Doi:10.1038/s42003-020-0966-5. PubMed: PMID: 32415166 PubMed Central: PMCID PMC7229144. [PDF] [supplementary material]

[99]
Crook N*, Ferreiro A*, Condiotte Z, Dantas G**. Transcript Barcoding Illuminates the Expression Level of Synthetic Constructs in E. coli Nissle Residing in the Mammalian Gut. ACS Synthetic Biology. 2020 May 15;9(5):1010-1021. doi: 10.1021/acssynbio.0c00040. Epub 2020 Apr 29. PubMed PMID: 32324995; PubMed Central PMCID: PMC7293544. [PDF]

[98]
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Campbell TP*, Sun X, Patel VH, Sanz C, Morgan D, Dantas G**. The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography. ISME Journal. 2020 Jun;14(6):1584-1599. doi: 10.1038/s41396-020-0634-2. Epub 2020 Mar 20. PubMed PMID: 32203121; PubMed Central PMCID: PMC7242348. [PDF] [supplementary material]

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Sun J*, Liao XP*, D'Souza AW*, Boolchandani M*, Li SH*, Cheng K, Luis Martínez J, Li L, Feng YJ, Fang LX, Huang T, Xia J, Yu Y, Zhou YF, Sun YX, Deng XB, Zeng ZL, Jiang HX, Fang BH, Tang YZ, Lian XL, Zhang RM, Fang ZW, Yan QL, Dantas G**, Liu YH**. Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms. Nature Communications. 2020 Mar 18;11(1):1427. doi: 10.1038/s41467-020-15222-y. PubMed PMID: 32188862; PubMed Central PMCID: PMC7080799. [PDF] [supplementary material]

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Keen E, Tasoff P, Hink T, Reske KA, Burnham CA, Kwon JH, Dubberke ER**, Dantas G**. Microbiome restoration by RBX2660 does not preclude recurrence of multidrug-resistant urinary tract infection following subsequent antibiotic exposure: A case report. Open Forum Infectious Diseases. 2020 Mar;7(3):ofaa042. doi: 10.1093/ofid/ofaa042. eCollection 2020 Mar. PubMed PMID: 32154322; PubMed Central PMCID: PMC7052748. [PDF]

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Gandra S**, Choi J, McElvania E, Green SJ, Harazin M, Thomson RB, Singh KS, Das S, Dantas G. Faropenem resistance causes in vitro cross resistance to carbapenems in ESBL- producing Escherichia coli. International Journal of Antimicrobial Agents. 2020 Mar;55(3):105902. doi: 10.1016/j.ijantimicag.2020.105902. Epub 2020 Jan 17. PubMed PMID: 31954833. [PDF]

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Yoneda A*, Thänert R*, Burnham CD**, Dantas G**. In vitro activity of meropenem/piperacillin/tazobactam triple combination therapy against clinical isolates of Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus pseudintermedius and vancomycin-resistant Enterococcus spp. International Journal of Antimicrobial Agents. 2020 Feb;55(2):105864. doi: 10.1016/j.ijantimicag.2019.105864. Epub 2019 Dec 20. PubMed PMID: 31870598. [PDF]

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Rafique M*, Potter RF*, Ferreiro A, Wallace MA, Rahim A, Malik AA, Siddique N, Abbas MA, D’Souza AW, Burnham CD, Ali N, Dantas G**. Genomic characterization of antibiotic resistant Escherichia coli isolated from domestic chickens in Pakistan. Frontiers in Microbiology. 2019; 10:3052. doi: 10.3389/fmicb.2019.03052. eCollection 2019. PubMed PMID: 32010104; PubMed Central PMCID: PMC6978674. [PDF]

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D'Souza AW*, Moodley-Govender E*, Berla B, Kelkar T, Wang B, Sun X, Daniels B, Coutsoudis A, Trehan I, Dantas G**. Cotrimoxazole prophylaxis increases resistance gene prevalence and α-diversity but decreases β-diversity in the gut microbiome of HIV-exposed, uninfected infants. Clinical Infectious Diseases. 2019 Dec 13;. doi: 10.1093/cid/ciz1186. PubMed PMID: 31832638. [PDF] [supplementary material]

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Yarbrough ML**, Wallace MA, Potter RF, D'Souza AW, Dantas G, Burnham CD. Breakpoint beware: reliance on historical breakpoints for Enterobacteriaceae leads to discrepancies in interpretation of susceptibility testing for carbapenems and cephalosporins and gaps in detection of carbapenem-resistant organisms. Eur J Clin Microbiol Infect Dis. 2020 Jan;39(1):187-195. doi: 10.1007/s10096-019-03711-y. Epub 2019 Nov 2. PubMed PMID: 31679102. [PDF]

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D'Souza AW*, Potter RF*, Wallace M, Shupe A, Patel S, Sun X, Gul D, Kwon JH, Andleeb S**, Burnham CD**, Dantas G**. Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces. Nature Communications. 2019 Oct 8;10(1):4569. doi: 10.1038/s41467-019-12563-1. PubMed PMID: 31594927; PubMed Central PMCID: PMC6783542. [PDF] [supplementary material]

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Wardenburg KE*, Potter RF*, D'Souza AW, Hussain T, Wallace MA, Andleeb S, Burnham CD**, Dantas G**. Phenotypic and genotypic characterization of linezolid-resistant Enterococcus faecium from the USA and Pakistan. Journal of Antimicrobial Chemotherapy. 2019 Dec 1;74(12):3445-3452. doi: 10.1093/jac/dkz367. PubMed PMID: 31504566; PubMed Central PMCID: PMC6857194. [PDF]

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Potter RF, Burnham CD**, Dantas G**. In Silico Analysis of Gardnerella Genomospecies Detected in the Setting of Bacterial Vaginosis. Clinical Chemistry. 2019 Nov; 65(11): 1375-1387 doi:10.1373/clinchem.2019.305474. Epub 2019 Aug 28. PubMed PMID: 31462445 PubMed Central PMCID: PMC7055668. [PDF]

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Thänert R, Reske KA, Hink T, Wallace MA, Wang B, Schwartz DJ, Seiler S, Cass C, Burnham CA, Dubberke ER**, Kwon JH**, Dantas G**. Comparative Genomics of Antiobiotic-Resistant Uropathogens Implicates Three Routes for Recurrence of Urinary Tract Infections. mBio. 2019 Aug 27;10(4). doi: 10.1128/mBio.01977-19. PubMed PMID: 31455657; PubMed Central PMCID: PMC6712402. [PDF]

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Posada-Perlaza CE, Ramírez-Rojas A, Porras P, Adu-Oppong B, Botero-Coy AM, Hernández F, Anzola JM, Díaz L, Dantas G, Reyes A**, Zambrano MM**. Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes. Scientific Reports. 2019 Aug 13;9(1):11764. doi:10.1038/s41598-019-48200-6. PubMed PMID: 31409850; PubMed Central PMCID: PMC6692338. [PDF]

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Schwartz DJ*, Rebeck ON*, Dantas G**. Complex interactions between the microbiome and cancer immune therapy. Critical Reviews in Clinical Laboratory Sciences. 2019 Dec;56(8):567-585. doi: 10.1080/10408363.2019.1660303. Epub 2019 Sep 17. PubMed PMID: 31526274; PudMed Central PMCID: PMC6776419. [PDF]

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Gasparrini AJ, Wang B, Sun X, Kennedy EA, Hernandez-Leyva A, Ndao IM, Tarr PI, Warner BB, Dantas G**. Persistent metagenomics signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nature Microbiology. 2019 Dec 4(12):2285-2297 doi: 10.1038/s41564-019-0550-2. Epub 2019 Sep 9. PubMed PMID: 31501537; PubMed Central PMCID: PMC6879825. [PDF] [supplementary material]

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Anthony WE**, Carr RR**, DeLorenzo DM, Campbell T, Shang Z, Foston M, Moon TS, Dantas G**. Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high value compounds. Biotechnology for Biofuels. 2019 Aug 5;12:192. doi:10.1186/s13068-019-1535-3. PubMed PMID: 31404385; PubMed Central: PMCID: PMC6683499. [PDF]

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Bailey AL*, Potter RF*, Wallace MA, Johnson C, Dantas G**, Burnham CA**. Genotypic and Phenotypic Characterization of Antimicrobial Resistance in Neisseria Gonorrhoeae: A Cross-Sectional Study of Isolates Recovered from Routine Urine Cultures in a High-Incidence Setting. mSphere. 2019 Jul 24;4(4). pii: e00373-19. doi: 10.1128/mSphere.00373-19. PubMed PMID: 31341071; PubMed Central PMCID: PMC6656870. [PDF]

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Roell GW, Carr RR, Campbell T, Shang Z, Henson WR, Czajka JJ, Martín HG, Zhang F, Foston M, Dantas G, Moon TS**, Tang YJ**. A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630. Metabolic Engineering. 2019 Sep;55:120-130. doi: 10.1016/j.ymben.2019.06.013. Epub 2019 Jul 2. PubMed PMID: 31271774. [PDF]

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Di Venanzio G, Flores-Mireles AL, Calix JJ, Haurat MF, Scott NE, Palmer LD, Potter RF, Hibbing ME, Friedman L, Wang B, Dantas G, Skaar EP, Hultgren SJ, Feldman MF**. Urinary tract colonization is enhanced by a plasmid that regulates uropathogenic Acinetobacter baumannii chromosomal genes. Nature Communications. 2019 Jun 24;10(1):2763. doi: 10.1038/s41467-019-10706-y. PubMed PMID: 31235751; PubMed Central PMCID: PMC6591400. [PDF]

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Sukhum KV*, Diorio-Toth L*, Dantas G**. Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance. Clinical Pharmacology & Therapeutics. 2019 Sep;106(3):512-524. doi: 10.1002/cpt.1535. Epub 2019 Jul 22. Review. PubMed PMID: 31172511; PubMed Central PMCID: PMC6692204. [PDF]

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Irum S, Potter RF, Kamran R, Mustafa Z, Wallace MA, Burnham CA, Dantas G, Andleeb S**. Draft Genome Sequence of a bla (NDM-1)- and bla (PME-1)-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan. Microbiology Resource Announcements. 2019 Apr 25;8(17). pii: e00107-19. doi: 10.1128/MRA.00107-19. PubMed PMID: 31023810; PubMed Central PMCID: PMC6486239. [PDF]

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Crook N*, Ferreiro A*, Gasparrini AJ, Pesesky MW, Gibson MK, Wang B, Sun X, Condiotte Z, Dobrowolski S, Peterson D, Dantas G**. Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut. Cell Host & Microbe. 2019 Apr 10;25(4):499-512.e8. doi: 10.1016/j.chom.2019.02.005. Epub 2019 Mar 26. PubMed PMID: 30926240; PubMed Central PMCID: PMC6487504. [PDF]

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Crofts TS**, Sontha P, King AO, Wang B, Biddy BA, Zanolli N, Gaumnitz J, Dantas G**. Discovery and Characterization of a Nitroreductase Capable of Conferring Bacterial Resistance to Chloramphenicol. Cell Chemical Biology. 2019 Apr 18;26(4):559-570.e6. doi: 10.1016/j.chembiol.2019.01.007. Epub 2019 Feb 21. PubMed PMID: 30799223; PubMed Central PMCID: PMC6474809. [PDF] [supplementary material]

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Markley JL, Fang L, Gasparrini AJ, Symister CT, Kumar H, Tolia NH**, Dantas G**, Wencewicz TA**. Semisynthetic Analogues of Anhydrotetracycline as Inhibitors of Tetracycline Destructase Enzymes. ACS Infect Dis. 2019 Apr 12; 5(4):618-633. doi: 10.1021/acsinfecdis.8b00349. Epub 2019 Mar 5 PubMed PMID: 30835428. [PDF] [supplementary material]

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Boolchandani M*, D'Souza AW*, Dantas G**. Sequencing-based methods and resources to study antimicrobial resistance. Nature Reviews Genetics. 2019 Mar 18. doi: 10.1038/s41576-019-0108-4. Epub 2019 Mar 18 Review. PubMed PMID: 30886350. [PDF]

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Ferreiro A, Dantas G, Ciorba MA**. Insights into How Probiotics Colonize the Healthy Human Gut. Gastroenterology. 2019 Jan 16. pii: S0016-5085(19)30043-5. doi: 10.1053/j.gastro.2019.01.022. Epub 2019 Jan 16 PubMed PMID: 30659834. [PDF]

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Di Venanzio G, Moon KH, Weber BS, Lopez J, Ly PM, Potter RF, Dantas G, Feldman MF**. Multidrug-resistant plasmids repress chromosomally encoded T6SS to enable their dissemination. Proceedings of the National Academy of Sciences USA. 2019 Jan 22;116(4):1378-1383. doi: 10.1073/pnas.1812557116. Epub 2019 Jan 9. PubMed PMID: 30626645; PubMed Central PMCID: PMC6347727. [PDF] [supplementary material]

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Henson WR, Hsu FF, Dantas G, Moon TS**, Foston M**. Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion. Biotechnology for Biofuels. 2018 Dec 28;11:339. doi: 10.1186/s13068-018-1337-z. eCollection 2018. PubMed PMID: 30607174; PubMed Central PMCID: PMC6309088. [PDF]

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Potter RF, Lainhart W, Twentyman J, Wallace MA, Wang B, Burnham CA**, Rosen DA**, Dantas G**. Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella variicola. mBio. 2018 Dec 18;9(6). pii: e02481-18. doi: 10.1128/mBio.02481-18. PubMed PMID: 30563902; PubMed Central PMCID: PMC6299229. [PDF] [supplementary material]

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Bulow C, Langdon A, Hink T, Wallace M, Reske KA, Patel S, Sun X, Seiler S, Jones S, Kwon JH, Burnham CA, Dantas G**, Dubberke ER**. Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential. mSphere. 2018 Nov 21;3(6). pii: e00588-18. doi: 10.1128/mSphereDirect.00588-18. PubMed PMID: 30463925; PubMed Central PMCID: PMC6249645. [PDF]

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Baumann-Dudenhoeffer AM, D'Souza AW, Tarr PI, Warner BB, Dantas G**. Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes. Nature Medicine. 2018 Dec;24(12):1822-1829. doi: 10.1038/s41591-018-0216-2. Epub 2018 Oct 29. PubMed PMID: 30374198; PubMed Central PMCID: PMC6294307. [PDF] [supplementary material]

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Quintanilla E**, Ramírez-Portilla C, Adu-Oppong B, Walljasper G, Glaeser SP, Wilke T, Muñoz AR, Sánchez JA. Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease. Scientific Reports. 2018 Oct 2;8(1):14636. doi: 10.1038/s41598-018-33007-8. PubMed PMID: 30279438; PubMed Central PMCID: PMC6168572. [PDF]

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Goldner NK*, Bulow C*, Cho K, Wallace M, Hsu FF, Patti GJ, Burnham CA, Schlesinger P, Dantas G**. Mechanism of High-Level Daptomycin Resistance in Corynebacterium striatum. mSphere. 2018 Aug 8;3(4). pii: e00371-18. doi: 10.1128/mSphereDirect.00371-18. PubMed PMID: 30089649; PubMed Central PMCID: PMC6083094. [PDF]

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Potter RF*, D'Souza AW*, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Beatty W, Andleeb S, Burnham CD**, Dantas G**. Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum β-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces. Frontiers in Microbiology. 2018 Jul 20;9:1629. doi: 10.3389/fmicb.2018.01629. eCollection 2018. PubMed PMID: 30079059; PubMed Central PMCID: PMC6062592. [PDF]

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Henson WR*, Campbell T*, DeLorenzo DM*, Gao Y, Berla B, Kim SJ, Foston M, Moon TS**, Dantas G**. Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus. Metabolic Engineering. 2018 Sep;49:69-83. doi: 10.1016/j.ymben.2018.06.009. Epub 2018 Jul 27. PubMed PMID: 30059786. [PDF]

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Tsukayama P*, Boolchandani M*, Patel S, Pehrsson EC, Gibson MK, Chiou KL, Jolly CJ, Rogers J, Phillips-Conroy JE, Dantas G**. Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes. mSystems. 2018 Jun 26;3(3). pii: e00016-18. doi: 10.1128/mSystems.00016-18. eCollection 2018 May-Jun. PubMed PMID: 29963641; PubMed Central PMCID: PMC6020475. [PDF]

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Keen EC, Dantas G**. Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity. Trends Microbiol. 2018 Nov;26(11):943-954. doi: 10.1016/j.tim.2018.05.009. Epub 2018 Jun 13. Review. PubMed PMID: 29909042. [PDF]

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Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G**. Shared strategies for β-lactam catabolism in the soil microbiome. Nature Chemical Biology. 2018 Jun;14(6):556-564. doi: 10.1038/s41589-018-0052-1. Epub 2018 Apr 30. Erratum in: Nat Chem Biol. 2019 Feb;15(2):206. PubMed PMID: 29713061; PubMed Central PMCID: PMC5964007. [PDF] [supplementary material]

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Keen EC*, Crofts TS*, Dantas G**. Checkpoint Checkmate: Microbiota Modulation of Cancer Immunotherapy. Clinical Chemistry. 2018 Sep;64(9):1280-1283. doi: 10.1373/clinchem.2017.286229. Epub 2018 Apr 24. PubMed PMID: 29691222. [PDF]

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Ferreiro A*, Crook N*, Gasparrini AJ*, Dantas G**. Multiscale Evolutionary Dynamics of Host-Associated Microbiomes. Cell. 2018 Mar 8;172(6):1216-1227. doi: 10.1016/j.cell.2018.02.015. Review. PubMed PMID: 29522743; PubMed Central PMCID: PMC5846202. [PDF]

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Potter RF, Wallace MA, McMullen AR, Prusa J, Stallings CL, Burnham CD**, Dantas G**. (bla)IMP-27 on transferable plasmids in Proteus mirabilis and Providencia rettgeri. Clinical Microbiology and Infection. 2018 Sep;24(9):1019.e5-1019.e8. doi: 10.1016/j.cmi.2018.02.018. Epub 2018 Mar 1. PMID: 29496594; PMCID: PMC6105362. [PDF]

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Gonzalez-Zapata FL, Bongaerts P, Ramírez-Portilla C, Adu-Oppong B, Walljasper G, Reyes A, Sanchez JA**. Holobiont Diversity in a Reef-Building Coral over Its Entire Depth Range in the Mesophotic Zone. Frontiers in Marine Science. 2018 Feb 7;5:29. doi: 10.3389/fmars.2018.00029. [PDF]

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Keen EC, Bliskovsky VV, Adhya SL, Dantas G**. Draft Genome Sequence of the Naturally Competent Bacillus simplex Strain WY10. Genome Announcements. 2017 Nov 16;5(46). pii: e01295-17. doi: 10.1128/genomeA.01295-17. PubMed PMID: 29146837; PubMed Central PMCID: PMC5690344. [PDF]

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Gul D, Potter RF, Riaz H, Ashraf ST, Wallace MA, Munir T, Ali A, Burnham CA, Dantas G, Andleeb S**. Draft Genome Sequence of a Salmonella enterica Serovar Typhi Strain Resistant to Fourth-Generation Cephalosporin and Fluoroquinolone Antibiotics. Genome Announcements. 2017 Oct 19;5(42). pii: e00850-17. doi: 10.1128/genomeA.00850-17. PubMed PMID: 29051234; PubMed Central PMCID: PMC5646387. [PDF]

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Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G**. Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria. Genome Announcements. 2017 Aug 10;5(32). pii: e00653-17. doi: 10.1128/genomeA.00653-17. PubMed PMID: 28798166; PubMed Central PMCID: PMC5552975. [PDF]

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Xu Z, Stogios PJ, Quaile AT, Forsberg KJ, Patel S, Skarina T, Houliston S, Arrowsmith C, Dantas G, Savchenko A. Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes. ACS Infectious Diseases. 2017 Sep 8;3(9):653-665. doi: 10.1021/acsinfecdis.7b00068. Epub 2017 Aug 16. PubMed PMID: 28756664. [PDF] [supplementary material]

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Potter RF*, D'Souza AW*, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Andleeb S, Burnham CA, Dantas G**. Draft Genome Sequence of the bla(OXA-436)- and bla(NDM-1)-Harboring Shewanella putrefaciens SA70 Isolate. Genome Announcements. 2017 Jul 20;5(29). pii: e00644-17. doi: 10.1128/genomeA.00644-17. PubMed PMID: 28729267; PubMed Central PMCID: PMC5522934. [PDF]

[50]
Park J*, Gasparrini AJ*, Reck MR, Symister CT, Elliott JL, Vogel JP, Wencewicz TA**, Dantas G**, Tolia NH**. Plasticity, dynamics, and inhibition of emerging tetracycline resistance enzymes. Nature Chemical Biology. 2017 May 8. doi: 10.1038/nchembio.2376. PMID: 28481346. [PDF] [supplementary material]

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Crofts TS*, Gasparrini AJ*, Dantas G**. Next-generation approaches to understand and combat the antibiotic resistome. Nature Reviews Microbiology. 2017 Apr 10. doi: 10.1038/nrmicro.2017.28. PMID: 28392565. [PDF]

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Pesesky MW, Hussain T, Wallace M, Patel S, Andleeb S, Burnham CD, Dantas G**. Evaluation of Machine Learning and Rules-Based Approaches for Predicting Antimicrobial Resistance Profiles in Gram-negative Bacilli from Whole Genome Sequence Data. Frontiers in Microbiology. 2016 Nov 28;7:1887. PubMed PMID: 27965630; PubMed Central PMCID: PMC5124574. [PDF]

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Potter RF*, D'Souza AW*, Dantas G**. The rapid spread of carbapenem-resistant Enterobacteriaceae. Drug Resistance Updates. 2016 Nov;29:30-46. doi: 10.1016/j.drup.2016.09.002. Review. PubMed PMID: 27912842; PubMed Central PMCID: PMC5140036. [PDF]

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Díaz-Muñoz SL, Boddy AM, Dantas G, Waters CM, Bronstein JL. Contextual organismality: Beyond pattern to process in the emergence of organisms. Evolution. 2016 Dec;70(12):2669-2677. doi: 10.1111/evo.13078. PubMed PMID: 27704542; PubMed Central PMCID: PMC5132100. [PDF]

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Boolchandani M*, Patel S*, Dantas G**. Functional Metagenomics to Study Antibiotic Resistance. Methods in Molecular Biology. 2017;1520:307-329. PubMed PMID: 27873261. [PDF]

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Adu-Oppong B*, Gasparrini AJ*, Dantas G**. Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes. Annals of the New York Academy of Sciences. 2016 Oct 21. doi: 10.1111/nyas.13257. [Epub ahead of print] PubMed PMID: 27768825. [PDF]

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Gasparrini AJ*, Crofts TS*, Gibson MK, Tarr PI, Warner BB, Dantas G**. Antibiotic perturbation of the preterm infant gut microbiome and resistome. Gut Microbes. 2016 Sep 2;7(5):443-449. doi: 10.1080/19490976.2016.1218584. PubMed PMID: 27472377; PubMed Central PMCID: PMC5154371. [PDF]

[42]
Yoneda A, Wittmann BJ, King JD, Blankenship RE**, Dantas G**. Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410. Photosynthesis Research. 2016 Aug;129(2):171-182. doi: 10.1007/s11120-016-0279-1. PubMed PMID: 27276888. [PDF] [supplementary material 1] [supplementary material 2]

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Pehrsson EC*, Tsukayama P*, Patel S, Mejía-Bautista M, Sosa-Soto G, Navarrete KM, Calderon M, Cabrera L, Hoyos-Arango W, Bertoli MT, Berg DE, Gilman RH, Dantas G**. Interconnected microbiomes and resistomes in low-income human habitats. Nature. 2016 May 12;533(7602):212-216. doi: 10.1038/nature17672. PubMed PMID: 27172044; PubMed Central PMCID: PMC4869995. [PDF] [supplementary material 1] [supplementary material 2]

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Langdon A*, Crook N*, Dantas G**. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med. 2016 Apr 13;8(1):39. doi: 10.1186/s13073-016-0294-z. PubMed PMID: 27074706; PubMed Central PMCID: PMC4831151. [PDF]

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Gibson MK, Wang B, Ahmadi S, Burnham CA, Tarr PI, Warner BB, Dantas G**. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nature Microbiology. 2016 Mar 7;1:16024. doi: 10.1038/nmicrobiol.2016.24. PubMed PMID: 27572443; PubMed Central PMCID: PMC5031140. [PDF] [supplementary material 1] [supplementary material 2] [supplementary material 3] [supplementary material 4]

[38]
Yoneda A*, Henson WR*, Goldner NK, Park KJ, Forsberg KJ, Kim SJ, Pesesky MW, Foston M, Dantas G**, Moon TS**. Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Research. 2016 Mar 18;44(5):2240-2254. doi: 10.1093/nar/gkw055. Epub 2016 Feb 2. PMID: 26837573. [PDF] [supplementary material 1] [supplementary material 2]

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Krueger AS*, Munck C*, Dantas G, Church GM, Galagan J, Lehár J, Sommer MO. Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis. PLoS One. 2016 Jan 28;11(1):e0147651. doi: 10.1371/journal.pone.0147651. eCollection 2016. PMID: 26821252; PMCID: PMC4731467. [PDF]

[36]
Kaminski J*, Gibson MK*, Franzosa EA, Segata N, Dantas G**, Huttenhower C**. High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PLoS Computational Biology. 2015 Dec 18;11(12):e1004557. doi: 10.1371/journal.pcbi.1004557. eCollection 2015 Dec. PMID: 26682918; PMCID: PMC4684307. [PDF] [supplementary material]

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Forsberg KJ, Patel S, Witt E, Wang B, Ellison TD, Dantas G**. Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes. Applied and Environmental Microbiology. 2015 Nov 6;82(2):528-537. doi: 10.1128/AEM.02838-15. PMID: 26546427; PMCID: PMC4711125. [PDF] [supplementary material]

[34]
Gonzales PR, Pesesky MW, Bouley R, Ballard A, Biddy BA, Suckow MA, Wolter WR, Schroeder VA, Burnham CA, Mobashery S, Chang M, Dantas G**. Synergistic, collaterally sensitive β-lactam combinations suppress resistance in MRSA. Nature Chemical Biology. 2015 Nov;11(11):855-861. doi: 10.1038/nchembio.1911. Epub 2015 Sep 14. PMID: 26368589; PMCID: PMC4618095. [PDF] [supplementary material]

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Gibson MK*, Crofts TS*, Dantas G**. Antibiotics and the developing infant gut microbiota and resistome. Current Opinion in Microbiology. 2015 Oct;27:51-56. doi: 10.1016/j.mib.2015.07.007. Epub 2015 Aug 1. PMID: 26241507; PMCID: PMC4659777. [PDF]

[32]
Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao IM, Deych E, Shannon W, Tarr PI, Warner BB, Dantas G**. Gut resistome development in healthy twin pairs in the first year of life. Microbiome. 2015 Jun 25;3:27. doi: 10.1186/s40168-015-0090-9. eCollection 2015. PMID: 26113976; PMCID: PMC4480905. [PDF]. [supplementary materials]

[31]
Forsberg KJ, Patel S, Wencewicz TA, Dantas G**. The Tetracycline Destructases: A Novel Family of Tetracycline-Inactivating Enzymes. Chemistry & Biology. 2015 Jun 18. pii: S1074-5521(15)00202-1. doi: 10.1016/j.chembiol.2015.05.017. [Epub ahead of print] PMID: 26097034. [PDF] [supplementary materials]

[30]
Pesesky MW*, Hussain T*, Wallace M, Wang B, Andleeb S, Burnham CA, Dantas G**. KPC and NDM-1 genes in related Enterobacteriaceae strains and plasmids from Pakistan and the United States. Emerging Infectious Diseases. 2015 Jun;21(6):1034-1037. doi: 10.3201/eid2106.141504. PMID: 25988236; PMCID: PMC4451916. [PDF] [supplementary materials]

[29]
Clemente JC*, Pehrsson EC*, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG**. The microbiome of uncontacted Amerindians. Science Advances. 2015 Apr 3;1(3). pii: e1500183. PMID: 26229982; PMCID: PMC4517851. [PDF] [supplementary materials]

[28]
Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, Desai MM**. Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics. PLoS One. 2015 Mar 25;10(3):e0069533. doi: 10.1371/journal.pone.0069533. eCollection 2015. PMID: 25807523; PMCID: PMC4373940. [PDF] [supplementary material]

[27]
Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA**. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014 Aug 29;345(6200):1048-1052. doi: 10.1126/science.1254529. PMID: 25170151; PMCID: PMC4337996. [PDF] [supplementary materials]

[26]
Gibson MK, Forsberg KJ, Dantas G**. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME Journal. 2015 Jan;9(1):207-216. doi: 10.1038/ismej.2014.106. Epub 2014 Jul 8. PMID: 25003965; PMCID: PMC4274418. [PDF] [supplementary materials]

[25]
Gibson MK*, Pesesky MW*, Dantas G**. The yin and yang of bacterial resilience in the human gut microbiota. Journal of Molecular Biology. 2014 Nov 25;426(23):3866-3876. doi: 10.1016/j.jmb.2014.05.029. Epub 2014 Jun 6. Review. PMID: 24911583; PMCID: PMC4252752. [PDF]

[24]
Forsberg KJ*, Patel S*, Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G**. Bacterial phylogeny structures soil resistomes across habitats. Nature. 2014 May 29;509(7502):612-616. doi: 10.1038/nature13377. Epub 2014 May 21. PMID: 24847883; PMCID: PMC4079543. [PDF] [supplementary materials]

[23]
Dantas G**, Sommer MOA**, How to fight back against antibiotic resistance. American Scientist. 2014; 102: 42. doi: 10.1511/2014.106.42. [PDF]

[22]
Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, Qin X, Tarr PI, Dantas G**. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One. 2013 Nov 13;8(11):e78822. doi: 10.1371/journal.pone.0078822. eCollection 2013. PMID: 24236055; PMCID: PMC3827270. [PDF] [supplementary materials]

[21]
Dantas G, Sommer MOA, Degnan PH, Goodman AL, Experimental approaches for defining functional roles of microbes in the human gut. Annual Review of Microbioly. 2013;67:459-475. doi: 10.1146/annurev-micro-092412-155642. Review. PubMed PMID: 24024637. [PDF]

[20]
Pehrsson EC, Forsberg KJ, Gibson MK, Ahmadi S, Dantas G**. Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs. Frontiers in Microbiology. 2013 Jun 7;4:145. doi: 10.3389/fmicb.2013.00145. eCollection 2013. PMID: 23760651; PMCID: PMC3675766. [PDF]

[19]
Dantas G**, Sommer MOA**. Ecological and clinical consequences of antibiotic subsistence by environmental microbes. In: Keen PL, Montforts MHMM, eds., Antimicrobial resistance in the environment. Hoboken: John Wiley & Sons, Inc., 2012:29-42. [PDF]

[18]
Dantas G**, Sommer MO**. Context matters - the complex interplay between resistome genotypes and resistance phenotypes. Current Opinion in Microbiology. 2012 Oct;15(5):577-582. doi: 10.1016/j.mib.2012.07.004. Epub 2012 Sep 3. Review. PMID: 22954750. [PDF]

[17]
Forsberg KJ*, Reyes A*, Wang B, Selleck EM, Sommer MO**, Dantas G**. The shared antibiotic resistome of soil bacteria and human pathogens. Science. 2012 Aug 31;337(6098):1107-1111. doi: 10.1126/science.1220761. PMID: 22936781; PMCID: PMC4070369. [PDF] [supplementary materials]

[16]
Bush K, Courvalin P, Dantas G, Davies J, Eisenstein B, Huovinen P, Jacoby GA, Kishony R, Kreiswirth BN, Kutter E, Lerner SA, Levy S, Lewis K, Lomovskaya O, Miller JH, Mobashery S, Piddock LJV, Projan S, Thomas CM, Tomasz A, Tulkens PM, Walsh TR, Watson, JD, Witkowski J, Witte W, Wright G, Yeh P, Zgurskaya HI, Tackling antibiotic resistance. Nature Reviews Microbiology 2011 Nov 2;9(12):894-896. doi:10.1038/nrmicro2693. PMID: 22048738; PMCID: PMC4206945. [PDF]

[15]
Moore AM*, Munck C*, Sommer MO**, Dantas G**. Functional metagenomic investigations of the human intestinal microbiota. Frontiers in Microbiology. 2011 Oct 17;2:188. doi: 10.3389/fmicb.2011.00188. eCollection 2011. PMID: 22022321; PMCID: PMC3195301. [PDF]

[14]
Sommer MO**, Dantas G**. Antibiotics and the resistant microbiome. Current Opinion in Microbiology. 2011 Oct;14(5):556-563. doi: 10.1016/j.mib.2011.07.005. Epub 2011 Jul 27. Review. PMID: 21802347.  [PDF]

[13]
Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, Gordon JI**. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proceedings of the National Academy of Sciences USA. 2011 Apr 12;108(15):6252-6257. doi: 10.1073/pnas.1102938108. Epub 2011 Mar 21. PMID: 21436049; PMCID: PMC3076821. [PDF] [supplementary materials]

[12]
Sommer MO, Church GM, Dantas G**. The human microbiome harbors a diverse reservoir of antibiotic resistance genes. Virulence. 2010 Jul-Aug;1(4):299-303. doi: 10.4161/viru.1.4.12010. PMID: 21178459. [PDF]

[11]
Sommer MO, Church GM, Dantas G**. A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Molecular Systems Biology. 2010 Apr 13;6:360. doi:10.1038/msb.2010.16. PMID: 20393580; PMCID: PMC2872612. [PDF] [supplementary materials]

[10]
Sommer MO**, Dantas G**, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science. 2009 Aug 28;325(5944):1128-1131. doi: 10.1126/science.1176950. PMID: 19713526. [PDF] [supplementary materials]

[9]
Dantas G*, Sommer MO*, Oluwasegun RD, Church GM. Bacteria subsisting on antibiotics. Science. 2008 Apr 4;320(5872):100-103. doi: 10.1126/science.1155157. PMID: 18388292. [PDF]  [supplementary materials]

[8]
Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D**. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. Journal of Molecular Biology. 2007 Mar 2;366(4):1209-1221. Epub 2006 Dec 2. PMID: 17196978; PMCID: PMC3764424.  [PDF]

[7]
Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D**. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of Molecular Biology. 2006 Oct 6;362(5):1004-1024. Epub 2006 Aug 4. PMID: 16949611. [PDF]

[6]
Dobson N, Dantas G, Baker D, Varani G**. High-resolution structural validation of the computational redesign of human U1A protein. Structure. 2006 May;14(5):847-856. PMID: 16698546. [PDF]

[5]
Dobson N, Dantas G, Varani G**. 1H, 13C and 15N resonance assignments of URNdesign, a computationally redesigned RRM protein. Journal of Biomolecular NMR. 2005 Oct;33(2):135. PMID: 16258832. [PDF]

[4]
Bradley P, Kuhlman B, Dantas G, Baker D**, Predicting protein structures accurately. Science 2004: 304:1597-1599. [PDF]

[3]
Kuhlman B*, Dantas G*, Ireton GC, Varani G, Stoddard BL, Baker D**. Design of a novel globular protein fold with atomic-level accuracy. Science. 2003 Nov 21;302(5649):1364-1368. PMID: 14631033. [PDF] [supplementary materials]

[2]
Dantas G*, Kuhlman B*, Callender D, Wong M, Baker D**. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. Journal of Molecular Biology. 2003 Sep 12;332(2):449-460. PMID: 12948494. [PDF]

[1]
Hoye RC**, Richman JE, Dantas G, Lightbourne MF, Shinneman LS. Synthesis of polyazamacrocyclic compounds via modified Richman-Atkins cyclization of beta-trimethylsilylethanesulfonamides. Journal of Organic Chemistry. 2001 Apr 20;66(8):2722-2725. PMID: 11304193. [PDF]

Preprints in Review

* = equal contribution; ** = corresponding author(s); Bold Names = Dantas Lab Authors

Patents

Bold Names = Dantas Lab Authors

[4]
Dantas, G., Kwak, S., Herbert, V. “Engineered Microorganisms and Methods of Making and Using Same.” WIPO Patent Application WO/2020/061389, filed 20 September, 2019

[3]
Tolia, J., Dantas, G., Wencewicz, T., Park, J., Gasparrini, A., Forsberg, K., Vogel, J. “Inhibition and Diagnostics of Emerging Tetracycline Resistance Enzymes.” U.S. Patent Application No. 62/354,404, filed 24 June, 2016.

[2]
Dantas, G., Gonzales, P., Forsberg, K., Pesesky, M., Chang, M., Mobashery, S. “Compositions and Methods of Use of Antibacterial Drug Combinations.” U.S. Patent Application No. 62/190,588, filed 9 July, 2015.

[1]
Agresti, J., Chu, L., Weitz, D.A., Kim, J., Rowat, A., Sommer, M., Dantas, G., Church, G. “Assays and Other Reactions Involving Droplets.” US Patent Application No. 12/529,926, filed 7 March, 2008.