1. Fareed S, Sarode N, Stewart FJ, Malik A, Laghale E, Khizer S, Yan F, Pratte Z, Lewis J Immergluck I. 2018. Applying fecal microbiota transplantation (FMT) to treat recurrent Clostridium difficile infections (rCDI) in children. PeerJ. In press.
  2. Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Woyke T, Ulloa O, Konstantinidis KK, Thamdrup B, Stewart FJ. 2018. Genomic evidence for the use of alternative nitrogen substrates by anammox bacteria. The ISME Journal. In press.
  3. Patin NV, Pratte ZA, Regensburger M, Hall E, Gilde K, Dove ADM, Stewart FJ. 2018. Microbiome dynamics in a large artificial seawater aquarium. Applied and Environmental Microbiology. In press.  Online version.
  4. Pratte ZA, Besson M, Hollman RD, Stewart FJ. 2018. The gills of reef fish support a distinct microbiome influenced by host-specific factors.  Applied and Environmental Microbiology. 84: e00063-18..
  5. Beatty DS, Clements CS, Stewart FJ, Hay ME. 2018. Inter-generational effects of macroalgal reef dominance on coral: major declines in survival of coral larvae but subtle changes in microbiomes. Marine Ecology Progress Series. 589: 97-114Online version.
  6. Sharp KH, Pratte ZA, Kerwin AH, Rotjan RD, Stewart FJ. 2017. Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. Microbiome. 5:120.  Open Access Copy.
  7. Pratte ZA Longo GO, Burns AS, Hay ME, Stewart FJ. 2017. Contact with turf algae alters the coral microbiome: contact versus systemic impacts.  Coral Reefs. 37:1-13.  doi:10.1007/s00338-017-1615-4
  8. Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. 2017. Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column. Environmental Microbiology. 19: 4392-4416.  DOI: 10.1111/1462-2920.13879
  9. Hay ME, Beatty DS, Stewart FJ. 2017. Chemical ecology: the language of microbiomes.  In: Exploring the Chemistry of Microbiomes.  National Academies Proceedings Series.
  10. Garcia-Robledo E, Padilla CC, Aldunate M, Paulmier A, Gregori G, Stewart FJ, Ulloa O, Revsbech NP. 2017. Cryptic oxygen cycling in anoxic marine zones. Proceedings of the National Academy of Sciences of the USA. 114: 8319-8324. doi: 10.1073/pnas.1619844114
  11. Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, Stewart FJ, Sullivan MB. 2017. Putative Archaeal viruses from the mesopelagic ocean. PeerJ. 5:e3428. Open Access Copy.
  12. Bray MS, Wu J, Reed BC, Kretz CB, Stewart FJ, DiChristina TJ, Brandes JA, Fowle DA, Crowe SA, Glass JB. 2017.  Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment communities.  Geobiology. 15: 678-689.  DOI: 10.1111/gbi.12239
  13. Padilla CC, Bertagnolli AD, Bristow LA, Sarode N, Glass JB, Thamdrup B, Stewart FJ. 2017. Metagenomic binning recovers a transcriptionally active Gammaproteobacterium linking methanotrophy to partial denitrification in an anoxic oxygen minimum zone. Frontiers in Marine Science.  4:23. Open Access Copy.
  14. Parris DJ, Brooker RM, Morgan MA, Dixson DL, Stewart FJ. 2016. Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement.  PeerJ. 4:e2412  Open Access Copy
  15. Tsementzi D, Wu J, Deutsch S, Nath N, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ. 2016. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. 536:179-183. doi:10.1038/nature19068  A view only version is available here.
  16. Seston SL, Beinart R, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ. 2016. Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes. Frontiers in Microbiology. 7:1074. Open Access Copy.
  17. Larsen M, Lehner P, Borisov SM, Klimant I, Fischer J, Stewart FJ, Canfield DE, Glud RN. 2016. In situ quantification of ultra-low O2 concentrations in oxygen minimum zones. Limnology & Oceanography Methods. doi:10.1002/lom3.10126
  18. Beckler JS, Kiriazis N, Rabouille C, Stewart FJ, Taillefert M. 2016. Importance of microbial iron reduction in deep sediments of river-dominated continental margins.  Marine Chemistry. 178:22-34.
  19. Padilla CC, Bristow LA, Sarode N, Garcia-Robledo E, Gomez Ramirez E, Benson CR, Bourbonnais A, Altabet MA, Girguis PR, Thamdrup B, Stewart FJ. 2016. NC10 bacteria in marine oxygen minimum zones. The ISME Journal. 10:2067-2071.
  20. Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WL, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Stewart FJ. 2015. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones. Frontiers in Microbiology. Open Access copy.
  21. Bristow LA, Sarode N, Cartee J, Caro-Quintero A, Thamdrup B, Stewart FJ. 2015. Biogeochemical and metagenomic analysis of nitrite accumulation in the Gulf of Mexico hypoxic zone. Limnology & Oceanography. 60:1733-1750.
  22. Padilla CC, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ. 2015. Standard filtration practices may significantly distort planktonic microbial diversity estimates. Frontiers in Microbiology. 6:547.
    PubMed PDF
  23. Duret MT, Pachiadaki MG, Stewart FJ, Sarode N, Christaki U, Monchy S, Edgcomb VP. 2015. Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone. FEMS Microbiology Ecology. 91. fiv037.
    PubMed Abstract.
  24. Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ. 2015. Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. The ISME Journal. 9: 2682-2696.
    PubMed PDF
  25. Sarode N, Parris DJ, Ganesh S, Seston SL, Stewart FJ. 2015. Generation and analysis of microbial metatranscriptomes. Manual of Environmental Microbiology, Fourth Edition.
  26. Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ. 2014. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile. Frontiers in Microbiology. 5:543.
    PubMed PDF
  27. Dalsgaard T, Stewart FJ, Thamdrup B, De Brabandere L, Revsbech NP, Ulloa O, Canfield DE, DeLong EF. 2014. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression of anammox and denitrification in the oxygen minimum zone off northern Chile. mBio, 5(6), e01966-14.
    PubMed PDF
  28. Dmytrenko O, Russel SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. 2014. The genome of the intracellular bacterium of the coastal bivalve Solemya velum: A blueprint for thriving in and out of symbiosis. BMC Genomics. 15:924.
    PubMed PDF
  29. Lee FJ, Rusch D, Stewart FJ, Mattila HR, Newton ILG. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environmental Microbiology. 17:796-815.
    PubMed PDF
  30. Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G. 2014. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Research. 42:7473-7485.
    PubMed PDF
  31. Stewart FJ, Ulloa O. 2014. Microbial metagenomics of oxygen minimum zones. Marco D (ed.) Metagenomics of the Microbial Nitrogen Cycle: Current innovations and future trends. Horizon Scientific Press.
    Book access
  32. Ganesh S, Parris DJ, DeLong EF, Stewart FJ. 2014. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. The ISME Journal. 8:187-211.
    PubMed PDF
  33. Stewart FJ. 2013. Where the genes flow. Nature Geoscience. 6:688-690.
    Open Access
  34. Stewart FJ. 2013. Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. Methods in Enzymology. 531:187-218.
  35. Cavanaugh, CM, McKiness ZP, Newton ILG, Stewart FJ. 2013. Marine chemosynthetic symbioses. In: Rosenberg et al. (eds). The Prokaryotes. 1:579-607. Springer-Verlag, New York.
    Book Access
  36. Sanders JG, Beinart RA, Stewart FJ, DeLong EF, Girguis PR. 2013. Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts. The ISME Journal. 7:1556-1567.
    Open Access PubMed
  37. Dimond JL, Kerwin AH, Rotjan R, Sharp K, Stewart FJ, Thornhill DJ. 2013. A simple temperature-based model predicts the upper latitudinal limit of the temperate coral Astrangia poculata. Coral Reefs. 32:401-409.
  38. Ulloa O, Canfield DE, DeLong EF, Letelier RM, Stewart FJ. 2012. Perspective: Microbial oceanography of anoxic oxygen minimum zones. Proceedings of the National Academy of Sciences of the USA. 109:15996-16003.
    Open Access PubMed
  39. Stewart FJ, Dalsgaard T, Thamdrup B, Revsbech NP, Ulloa O, Canfield DE, and DeLong EF. Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton. PLoS ONE. 7:e37118.
    Open Access PubMed
  40. Bryant JA, Stewart FJ, Eppley JM, and DeLong EF. 2012. Microbial community phylogenetic and trait diversity decline steeply with depth in a marine oxygen minimum zone. Ecology. 93:1659-1673.
    Journal PubMed
  41. Stewart FJ, Ulloa O, DeLong EF. 2012. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environmental Microbiology. 14:23-40.
    PubMed PDF
  42. Stewart FJ, 2011. Dissimilatory sulfur cycling in oxygen minimum zones: an emerging metagenomics perspective. Biochemical Society Transactions. 39:1859-11863.
    PubMed PDF
  43. Stewart FJ, Dmytrenko O, DeLong EF, Cavanaugh CM. 2011. Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of Solemya velum. Frontiers in Microbiology. 2:134.
    PubMed PDF
  44. Stewart FJ, Cavanaugh CM. Pyrosequencing analysis of endosymbiont diversity. 2011. In: de Bruijn FJ (ed.). Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. Wiley-Blackwell.
    Book Access
  45. Stewart FJ, Sharma AK, Bryant JA, Eppley JM, DeLong EF. 2011. Community transcriptomics reveals universal patterns of protein sequence conservation in microbial communities. Genome Biology. 12:R26.
    Open Access PubMed
  46. Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, DeLong EF, Revsbech NP, Ulloa O. 2010. A cryptic sulfur cycle in oxygen-minimum zone waters off the Chilean Coast. Science. 330:1375-1378.
    PubMed PDF Perspectives Article (A. Teske) PDF
  47. Stewart FJ, Ottesen EA, DeLong EF. 2010. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. The ISME Journal. 4:896-907.
    PubMed PDF Protocol
  48. Roeselers G, Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson P, Barry K, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2010. Complete genome sequence of Candidatus Ruthia magnifica. Standards in Genomics Sciences. 3:163-173.
    PMC full text
    PubMed PDF
  49. Stewart FJ, Baik AHY, Cavanaugh CM. 2009. Genetic subdivision of chemosynthetic endosymbionts of Solemya velum along the southern New England coast. Applied and Environmental Microbiology. 75:6005-6007.
    PubMed PDF
  50. Stewart FJ, Cavanaugh CM. 2009. Pyrosequencing analysis of endosymbiont population structure: co-occurrence of divergent symbiont lineages in a single vesicomyid host clam. Environmental Microbiology. 11:2136-2147.
    PubMed PDF
  51. Stewart FJ, Young CR, Cavanaugh CM. 2009. Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Molecular Biology and Evolution. 26:1391-1404.
    PubMed PDF
  52. Fritsen CH, Memmott JC, Stewart FJ. 2008. Inter-annual sea ice dynamics and micro-algal biomass in winter pack ice: Marguerite Bay, Antarctica. Deep-Sea Res. Pt II. 55:2059-2067.
    Journal PDF
  53. Stewart FJ, Young CR, Cavanaugh CM. 2008. Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Molecular Biology and Evolution. 25:673-687.
    PubMed PDF
  54. Stewart FJ, Cavanaugh CM. 2007. Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in Bacteria. Journal of Molecular Evolution. 65:44-67.
    PubMed PDF
  55. Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science. 315:998-1000.
    PubMed PDF
  56. Stewart FJ, Cavanaugh CM. 2006. Bacterial endosymbioses in Solemya (Mollusca, Bivalvia): model systems for studies of symbiont-host adaptation. Antonie van Leeuwenhoek Journal. 90:343-360.
    PubMed PDF
  57. Cavanaugh CM, McKiness ZP, Newton ILG, Stewart FJ. 2006. Marine chemosynthetic symbioses. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds.). The Prokaryotes. Third Edition. Springer, New York.
    Book Access PDF
  58. Mix LJ, Armstrong JC, Mandell AM, Mosier AC, Raymond J, Raymond SN, Stewart FJ, von Braun K, Zhaxybayeva O (eds.). 2006. The Astrobiology Primer: An outline of general knowledge. Astrobiology. 6(5):735-813.
    PubMed PDF
  59. Stewart FJ, Cavanaugh CM. 2005. Symbiosis of thioautotrophic bacteria with Riftia pachyptila. In: Overmann, J. (ed.). Molecular Basis of Symbiosis. Prog. Mol. Subcell. Biol. vol-41. Springer Berlin Heidelberg. p.197-225.
    Book Access PubMed PDF
  60. Stewart FJ, Newton ILG, Cavanaugh CM. 2005. Chemosynthetic endosymbioses: adaptations to oxic-anoxic interfaces. Trends in Microbiology. 13:439-448.
    PubMed PDF
  61. Stewart FJ, Fritsen CH, Garrison DL. 2005. Bacteria-algae associations in the sea ice and upper water column of the Ross Sea in late austral summer. Antarctic Journal of the Unites States. 33:38-41.
  62. Stewart FJ, Fritsen CH. 2004. Bacteria-algae relationships in Antarctic sea ice. Antarctic Science. 16:143-156.