49. Probst AJ, Ping H, Sun CL, Dubinsky EA, Sieber CMK, Banfield JB, and Gary L Andersen (2017). Strain variants and population structure during the Deepwater Horizon oil spill. PNAS, published ahead of print Oct 10 2017

48. Sieber CMK, Probst AJ, Sharon I, Sharrar A, Thomas BC, Hess M, Tringe SG, and Banfield JB (2016). Recovery of genomes from metagenoms via a dereplication aggregation and scoring strategy. bioRxiv, 107789

47. Finstad KM, Probst AJ, Thomas BC, Andersen GL, Piceno YM, Demergasso C, Amundson RG, and Banfield JB (2016). A fog-derived moisture gradient shapes halophilic microbial communities of the hyperarid Atacama Desert, Chile. Frontiers in Microbiol, Vol. 8 1435

46. Hu P, Dubinksy EA, Probst AJ, Wang J, Sieber MKC, Tom LM, Gardinali P, Banfield JF, and Andersen GL (2016). Experimental reproduction of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon-degraders. PNAS, Vol. 114 (28):7432–7437

45. Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst AJ, Burstein D, Thomas BC, and Banfield JF (2017). Potential for microbial H2 and metal transformations in deep terrestrial subsurface sediments: relevance for nuclear waste disposal. ISME J, Vol. 11 1915–1929

44. Moissl-Eichinger C, Probst AJ, Birarda G, Auerbach A, Koskinen K, Wolf P, and Holman H-Y (2017). Human age and skin physiology shape diversity and abundance of Archaea on skin. Scientific Reports, 7, 4039

43. Burstein D*, Harrington LB*, Strutt SC*, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, and Banfield JB (2017). New CRISPR-Cas systems from uncultivated microbes. Nature, 237-241, Vol. 524(7640) – * authors contributed equally


42. Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, and Banfield JF (2016). Proteomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ, e2687, Vol. 4

41. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, and Banfield JF (2016). Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Commun, 13219, Vol. 7

40. Bird JT, Baker BJ, Probst AJ, Podar M, and Lloyd KG (2016). Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Frontiers in Microbiol, 1221, Vol. 7

39. Probst AJ, Castelle C, Singh A, Brown CT, Anantharaman K, Sharon I, Hug LA, Emerson JB, Thomas BC, and Banfield JF (2016). Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Env Microbiol, 459-474, Vol. 19(2)

38. Tischler C, Weikl F, Probst AJ, Stnadl M, Heinrich J, and Pritsch K (2016). Urban dust microbiome: Impact on later atopy and wheezing. Environmental Health Perspectives, Epub ahead of print

37. Mayer T*, Blachowicz A*, Probst AJ, Vaishampayan P, Checkinska A, Swarmer T, de Leon P, and Venkateswaran K (2016). Microbial succession in an inflated Lunar/Mars analog habitat during a 30-day occupation by student astronauts. Microbiome, 22, Vol. 4 – *authors contributed equally

36. Weikl F, Tischer C, Probst AJ, Heinrich J, Pritsch K (2016). Fungal and bacterial communities in indoor dust follow different environmental determinants. PLoS One, e0154131

35. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman D, Finstad KM, Amundson R, Thomas BC, and Banfield JF (2015). A new view of the tree of life. Nature Microbiol, ArtNo 16048

34. Burstein D, Sun CL, Brown CT, Sharon I, Anantharaman K, Probst AJ, Thomas BC, and Banfield FJ (2016). Major bacterial lineages are essentially devoid of CRISPR-Cas viral defense systems. Nature Commun, 10613, Vol. 7

33. Anantharaman K, Brown CT, Burstein D, Castelle CJ, Probst AJ, Thomas BC, Kenneth WH, Banfield JF (2016). Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. PeerJ, e1607


32. Weinmaier  T*, Probst AJ*, LaDuc MT, Ciobanu D, Cheng J-F, Ivanova N, Rattei T, Vaishampayan P (2015). A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. Microbiome, 62, Vol. 3 – *authors contributed equally

31. Checinska A, Probst AJ, Vaishampayan P, White JR, Kumar D, Stepanov VG, Fox GE, Nilsson HR, Pierson DL, Perry J, Venkateswaran K (2015). Microbiomes of the dust particles collected from the international space station and spacecraft assembly facilities. Microbiome, 50, Vol. 3

30. Mahnert A, Vaishampayan P, Probst AJ, Moissl-Eichinger C, Venkateswaran K, and Berg G (2015). Cleanroom maintenance significantly reduces abundance but not diversity of indoor microbiomes. PLoS One, e0134848

29. Perras AK, Daum B, Ziegler C, Takahashi LK, Ahmed M, Wanner G, Klingl A, Leitinger G, Kolb-Lenz D, Gribarldo S, Auerbach A, Mora M, Probst AJ, Bellack A, Moissl-Eichinger C (2015). S-layer at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence. Frontiers in Microbiol, 543, Vol. 6

28. Probst AJ and Moissl-Eichinger C (2015). “Altiarchaeales”: Uncultivated Archaea from the Subsurface. Life, pp. 1381–1395, Vol 5

27. Andrade K, Logemann J, Heidelberg KB, Emerson JB, Comolli LR, Hug LA, Probst AJ, Keillar A, Thomas BC, Miller CS, Allen EE, Moreau JW, Brocks JJ, and Banfield JF (2015). Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME J, doi:10.1038

26. Probst AJ*, Weinmaier T*, DeSantis TZ, SantoDomingo J, and Ashbolt N (2015). New perspectives on microbial community distortion after whole-genome amplification. PLoS One, e0124158 – *authors contributed equally

25. Moissl-Eichinger C, Auerbach AK, Probst AJ, Mahnert A, Tom L, Piceno Y, Andersen GL, Venkateswaran K, Rettberg P, Barczyk S, Pukall R, Berg G (2015). Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments. Scientific Reports, 9156, Vol. 5

24. Probst AJ, Lum PY, John B, Dubinsky EA, Piceno YM, Tom LM, Andersen GL, and DeSantis TZ (2015). Microarray of 16S rRNA gene probes for quantifying population differences across microbiome samples. In: Microarrays: Current Technology, Innovations and Applications. Editor: Zhili He, Horizon Scientific Press and Caister Academic Press, Chapter 5, pp. 99–119

23. Probst AJ (2015). Neue Archaeen aus der Tiefe setzen Treibhausgas um. BioSpektrum, p. 351, Vol 21


22. Probst AJ, Weinmaier T, Raymann K, Perras A, Emerson JB, Rattei T, Wanner G, Klingl A, Berg IA, Yoshinaga M, Viehweger B, Hinrichs K-U, Thomas BC, Meck S, Auerbach AK, Heise M, Schintlmeister A, Schmid M, Wagner M, Gribaldo S, Banfield JF*, and Moissl-Eichinger C* (2014). Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nature Commun, 5497, Vol 5 – *co-corresponding authors

21. Perras AK, Wanner G, Klingl A, Mora M, Auerbach AK, Heinz V, Probst AJ, Huber H, Rachel R, Meck S, Moissl-Eichinger C (2014). Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm. Frontiers in Microbiol, 397, Vol. 5

20. Probst AJ*, Birarda B*, Holman H-YN, DeSantis TZ, Wanner G, Andersen GL, Perras AK, Meck S, Völkel J, Bechtel HA, Wirth R, and Moissl-Eichinger C (2014). Coupling genetic and chemical microbiome profiling reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms that are Dominated by the Same Archaeal Species. PLoS One, e99801, Vol. 9 – *authors contributed equally

19. Miezeiewski M, Schnaufer T, Muravsky M, Wang S, Caro-Aguilar I, Secore S, Thiriot DS, Hsu C, Rogers I, DeSantis TZ, Kuczynski J, Probst AJ, Chehoud C, Steger R, Warrington J, Bodmer J-L, Hinrichs JH (2014). An in virto culture model to study the dynamics of colonic microbiota in syrian golden hamster and their susceptibility to infection with Clostridium difficile. ISME J, 321–332, Vol. 9, No. 2

18. Bauermeister A, Mahnert A, Auerbach A, Böker A, Flier N, Weber C, Probst AJ, Moissl-Eichinger C, Haberer K (2014). Quantification of encapsulated bioburden in spacecraft polymer materials by cultivation-dependent and molecular methods. PLoS One, e94265, Vol. 9

17. Krebs JE*, Vaishampayan P*, Probst AJ*, Tom LM, Marteinsson VT, Andersen GL, and Venkateswaran K (2014). Microbial community structures of novel icelandic hot spring systems revealed by PhyloChip G3 analysis. Astrobiology, pp. 220-240, Vol. 14, No. 3 – *authors contributed equally


16. Moissl-Eichinger C, Pukall R, Probst AJ, Stieglmeier M, Schwendner P, Mora M, Barczyk S, Bohmeier M, and Rettberg P (2013). Lessons Learned from the Microbial Analysis of the Herschel Spacecraft during Assembly, Integration, and Test Operations. Astrobiology, pp. 1125–1139, Vol. 13, No. 12.

15. Probst AJ, Auerbach AK, and Moissl-Eichinger C (2013). Archaea on human skin. PLoS One, e65388, Vol. 8

14. Probst AJ, Holman H-YN, DeSantis TZ, Andersen GL, Bechtel HA, Sonnleitner M, Venkateswaran K, and Moissl-Eichinger C (2013). Tackling the minority: Sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. ISME J, pp. 635–651, Vol. 7


13. Vaishampayan P*, Probst AJ*, LaDuc MT*, Bargoma E, Bernadini JN, Andersen GL, Venkateswaran K (2012). New perspectives on viable microbial communities in low-biomass cleanroom environments. ISME J, pp. 312–324, Vol. 7 – *authors contributed equally

12. Probst A, Mahnert A, Weber C, Haberer K, and Moissl-Eichinger C (2012). Detecting inactivated endospores in fluorescence microscopy using propidium monoazide. Int J Astrobiol, p. 117–123, Vol. 11, No. 2

11. Weiner A, Schopf S, Wanner G, Probst A, and Wirth R (2012). Positive, neutral and negative interactions in cocultures between Pyrococcus furiosus and different methanogenic Archaea. Microbiol Insights, pp. 1–10, Vol. 4

10. Venkateswaran K*, LaDuc MT*, Vaishampayan P*, Osman S, Kwan K, Bargoma E, Probst A, Cooper M, Benardini JN, and Spry JA (2012). Genetic Inventory Task: Final Report, Volume 2, JPL Publication 12-12, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA – *main contributors


9. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Eddy SR, Arkin A, Knight R, and Hugenholtz P (2011). An Improved Greengenes Taxonomy for Bacteria and Archaea with explicit ranks. ISME J, pp. 610–618, Vol., No. 3

 8. Cooper M, LaDuc MT, Probst A, Vaishampayan P, Stam C, Benardini JN, Piceno YM, Andersen GL, and Venkateswaran K (2011). Comparison of Innovative Molecular Approaches and Standard Spore Assays for Assessment of Surface Cleanliness. Appl Environ Microbiol, pp. 5438–5444, Vol. 77, No. 15

 7. Probst A, Facius R, Wirth R, Wolf M, and Moissl-Eichinger C (2011). Recovery of Bacillus spores from rough surfaces: A challenge to cleanliness control of space missions. Appl Environ Microbiol, pp. 1628–37, Vol. 77, No. 5

 6. Wirth R, Bellack A, Bertl M, Bilek Y, Heimerl T, Herzog B, Leisner M, Probst A, Rachel R, Sarbu C, Schopf S, and Wanner G (2011). The Mode of Cell Wall Growth in Selected Archaea Follows the General Mode of Cell Wall Growth in Bacteria — An Analysis using Fluorescent Dyes. Appl Environ Microbiol, pp. 1556–1562, Vol. 77, No. 5


5. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JR, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad MS, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal RL, D'haeseleer P, Holman H-YN, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, and Mason OU (2010). Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria. Science, pp. 204–208, Vol. 330, No. 6001

 4. Probst A, Facius R, Wirth R, and Moissl-Eichinger C (2010). Validation of the Nylon-Flocked Swab for Efficient Recovery of Bacterial Spores from Smooth and Rough Surfaces. Appl Environ Microbiol, pp. 5148–5158, Vol. 76, No. 15

 3. Probst A, Vaishampayan P, Osman S, Moissl-Eichinger C, Andersen G, and Venkteswaran K (2010). Diversity of Anaerobic Microbes in Spacecraft Assembly Clean Rooms. Appl Environ Microbiol, pp. 2837–2845, Vol. 76, No. 9

 2. Vaishampayan P, Probst A, Krishnamurthi S, Ghosh S, Osman S, McDowall A, Ruckmani A, Mayilraj S, and Venkateswaran K (2010). Bacillus horneckiae sp. nov., isolated from a spacecraft assembly clean room. Int J Syst Evol Microbiol, pp. 1031–1037, Vol. 60

1. Venkateswaran K, Probst A, Vaishampayan PA, and Ghosh S (2010). NASA New Technology Report: Isolation of Resistance-bearing Microorganisms. NASA Tech Briefs, 03/2010