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Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients.
Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV. Cox MJ, et al. Among authors: daly ra. PLoS One. 2010 Jun 23;5(6):e11044. doi: 10.1371/journal.pone.0011044. PLoS One. 2010. PMID: 20585638 Free PMC article.
A functional microbiome catalogue crowdsourced from North American rivers.
Borton MA, McGivern BB, Willi KR, Woodcroft BJ, Mosier AC, Singleton DM, Bambakidis T, Pelly A, Daly RA, Liu F, Freiburger A, Edirisinghe JN, Faria JP, Danczak R, Leleiwi I, Goldman AE, Wilkins MJ, Hall EK, Pennacchio C, Roux S, Eloe-Fadrosh EA, Good SP, Sullivan MB, Wood-Charlson EM, Miller CS, Ross MRV, Henry CS, Crump BC, Stegen JC, Wrighton KC. Borton MA, et al. Among authors: daly ra. Nature. 2025 Jan;637(8044):103-112. doi: 10.1038/s41586-024-08240-z. Epub 2024 Nov 20. Nature. 2025. PMID: 39567690 Free PMC article.
Polyphenol rewiring of the microbiome reduces methane emissions.
McGivern BB, Ellenbogen JB, Hoyt DW, Bouranis JA, Stemple BP, Daly RA, Bosman SH, Sullivan MB, Hagerman AE, Chanton JP, Tfaily MM, Wrighton KC. McGivern BB, et al. Among authors: daly ra. bioRxiv [Preprint]. 2024 Oct 22:2024.10.22.619724. doi: 10.1101/2024.10.22.619724. bioRxiv. 2024. PMID: 39484614 Free PMC article. Preprint.
Gut microbiota carbon and sulfur metabolisms support Salmonella infections.
Leleiwi I, Kokkinias K, Kim Y, Baniasad M, Shaffer M, Sabag-Daigle A, Daly RA, Flynn RM, Wysocki VH, Ahmer BMM, Borton MA, Wrighton KC. Leleiwi I, et al. Among authors: daly ra. ISME J. 2024 Jan 8;18(1):wrae187. doi: 10.1093/ismejo/wrae187. ISME J. 2024. PMID: 39404095 Free PMC article.
Time resolved multi-omics reveals diverse metabolic strategies of Salmonella during diet-induced inflammation.
Kokkinias K, Sabag-Daigle A, Kim Y, Leleiwi I, Shaffer M, Kevorkian R, Daly RA, Wysocki VH, Borton MA, Ahmer BMM, Wrighton KC. Kokkinias K, et al. Among authors: daly ra. bioRxiv [Preprint]. 2024 Feb 4:2024.02.03.578763. doi: 10.1101/2024.02.03.578763. bioRxiv. 2024. Update in: mSphere. 2024 Oct 29;9(10):e0053424. doi: 10.1128/msphere.00534-24 PMID: 38352409 Free PMC article. Updated. Preprint.
Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection.
Leleiwi I, Kokkinias K, Kim Y, Baniasad M, Shaffer M, Sabag-Daigle A, Daly RA, Flynn RM, Wysocki VH, Ahmer BMM, Borton MA, Wrighton KC. Leleiwi I, et al. Among authors: daly ra. bioRxiv [Preprint]. 2024 Jan 19:2024.01.16.575907. doi: 10.1101/2024.01.16.575907. bioRxiv. 2024. Update in: ISME J. 2024 Jan 8;18(1):wrae187. doi: 10.1093/ismejo/wrae187 PMID: 38293109 Free PMC article. Updated. Preprint.
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