Peer reviewed scientific papers

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2020 (in-prep)

Minich JJ*, Petras D, Kunselman E, White M, Allen EE, Aluwihare L, Rob Knight and Pieter C. Dorrestein P. Non-targeted metabolomics and 16S amplicon sequencing of molecular and microbial shifts in coastal sea water. (Microbiome, Ecology letters, or Environmental Science & Technology, in prep).

Melnik AV, Callewaert C, Dorrestein K, Aksenov A, Minich JJ, Humphrey G, Ackermann G, Knight R, and PC Dorrestein. You are what you wear, the impact of clothing on the human skin (in prep).

Pendergraft M*, Minich JJ*, Belda-Ferre P, Knight R, and Prather KA. Evaluation and optimization of sampling methods and time on characterization of sea-spray aersol microbiome. (in prep, Nature Microbiology)

Jones K, Minich JJ, Leizerowicz F, Knight R, Dorrestein P. Colgate tooth project: effects of microbes and metabolites on teeth staining

Sparagon W, Minich JJ, Vollbrecht L, Laurens L, Allen EE, Wegley L, Sims N, and C Nelson. Microbial communities exhibit fine spatial-scale succession in the gastrointestinal tract of herbivorous kyphosids. (in prep, Microbiome)

2020 (in-review)

Sauer JS, Minich JJ, Mayer KJ, Malfatti F, Santander MD, Pendergraft M, Mitts B, Wange X, Rico B, Knight R, Bertram TH, Prather KA. Production of Dimethyl Sulfide, Methanethiol, and Dimethyl Disulfide During Controlled Phytoplankton-Bacterial Mesocosm Experiments.. (in review, JBGS)

Petras D*, Minich JJ, Cancelada, LB, Torres RR, Kunselman E, Wang M, White M, Allen EE, Prather KA, Aluwihare L, Rob Knight and Pieter C. Dorrestein P. Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. (in review, Analytic Chemistry; ChemRxiv 9817133).

Minich JJ, Nowak B, Elizur A, Knight R, Fielder S, and Allen EE. Impacts of the marine hatchery built environment on mucosal microbiome colonization across ontogeny in yellowtail kingfish, Seriola lalandi (in review, Microbiome)

Hendrickson R, Urbaniak C, Minich JJ, Aronson H, Martion C, Stepanauskas R, Knight R, and Venkateswaran K. Assessment of the NASA standard spore assay in predicting bacterial populations of a Mars Mission Assembly Facility. (in review, Microbiome)


23. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter S, McDonald D, Gilbert JA, Allard SM, Allen EE, Knight R, Sweeney D, and Swafford A. Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs. (accepted, BMC Microbiome; medRxiv 2020.05.12.20073577)

22. Minich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B, and Allen EE. The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment. Front. Microbiol. 24 August 2020. Doi.10.3389/fmicb.2020.02015

21. Mohan GBM, Parker C, Urbaniak C, Singh NK, Hood A, Minich JJ, Knight R, Rucker M, and Venkateswaran K. Microbiome and metagenome analyses of a closed habitat during human occupation. mSystems.DOI: 10.1128/mSystems.00367-20

20. Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen E. Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus. (Msphere 5.3 (2020). Doi.10.1128/mSphere.00401-20

19. Fedarko MW, Martino C, Morton JT, Gonzalez A, Rahman G, Marotz CA, Minich JJ, Allen EE, and Rob Knight. Visualizing ‘omic feature rankings in tandem with sample abundances using Qurro. NAR Genomics and Bioinformatics 2.2 (2020): Iqaa023. Doi/10.1093/nargab/Iqaa023

18. Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, and Allen E. Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota. (Applied and Environmental Microbiology 2020. Doi.10.1128/AEM.00411-20)

17. Nguyen CDH, Amoroso G, Ventura T, Minich JJ, and A Elizur. Atlantic salmon (Salmo salar L., 1758) gut microbiota profile correlates with flesh pigmentation: cause or effect?. Marine Biotechnology, pp.1-19.


16. McCall Laura-Isobel, Callewaert C, Zhu Q, Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch O, Blaser MJ, Paulino LC, Dorrestein PC, Knight Rob, and Dominguez-Bello MG. Home chemical and microbial transitions across urbanization. Nature Microbiology. Doi.10.1038/s41564-019-0593-4

15. Sanders J, Nurk S, Salido RA, Minich JJ, Zhenjiang ZX, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr, L, Dorrestein PC, Pevzner PA, and Rob Knight. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biology 20 (1),1-14. Doi.10.1186/s13059-019-1834-910.

14. Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert J, and Knight R. Quantifying and understanding well-to-well contamination in microbiome research. mSystems (2019): e00186-19. Doi.10.1128/mSystems.00186-19

13. Sielaff AC, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, Minich JJ, McDonald D, Mayer T, Knight R, Karouia F, Fox G, and K Venkateswaran. Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Microbiome 2019 7:50. Doi.10.1186/s40168-019-0666-x.


12. Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, and Weyrich LS. Contamination in low-biomass microbiome studies: issues and recommendations. Trends in Microbiology (2018). Doi:10.1016/j.tim.2018.11.003

11. Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R. High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity. mSystems 3 (6) (2018): e00166-18. Doi.10.1128/mSystems.00166-18

10. Allaband C, McDonald D, Vazquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, and Knight R. Microbiome 101: Studying, analyzing, and interpreting gut microbiome data for clinicians. Clinical Gastroenterology and Hepatology (2018). Doi: 10.1016/j.cgh.2018.09.017

9. Minich JJ, Zhu Q, Zech X, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, and Knight R. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish, (Clarias gariepinus). MicrobiologyOpen (2018) e00716. Doi: 10.1002/mbo3.716

8. Minich JJ, Zhu Q, Janssen S, Hendrickson R, Benardini J, Amir A, Vetter R, Hyde J, Doty M, Stillwell K, Kim J, Allen EE, Knight R, and Venkateswaran K. KatharoSeq enables high-throughput microbiome analysis from low-biomass samples. mSystems 3 (3) (2018): e00218-17. Doi: 10.1128/mSystems.00218-17

7. Minich, J.J., Morris, M.M., Brown, M., Doane, M., Edwards, M.S., Michael, T.P. and Dinsdale, E.A., 2018. Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruptionPloS one13(2), p.e0192772.


6. Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., Prill, R.J., Tripathi, A., Gibbons, S.M., Ackermann, G. and Navas-Molina, J.A., 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature551(7681).


5. Quinn, R.A., Navas-Molina, J.A., Hyde, E.R., Song, S.J., Vázquez-Baeza, Y., Humphrey, G., Gaffney, J., Minich, J.J., Melnik, A.V., Herschend, J. and DeReus, J., 2016. From sample to multi-omics conclusions in under 48 hoursMSystems1(2), pp.e00038-16.


4. Motley, S.T., Picuri, J.M., Crowder, C.D., Minich, J.J., Hofstadler, S.A. and Eshoo, M.W., 2014. Improved multiple displacement amplification (iMDA) and ultraclean reagentsBMC genomics15(1), p.443.

3. Minich, J. and Dinsdale, E.A., 2015. Experimental metagenomics: influence of pulses of carbon dioxide on Kelp forest microbial ecologyEncyclopedia of Metagenomics: Environmental Metagenomics, pp.176-182.


2. Robertson, K.M., Minich, J., Bowman, A.J. and Morin, P.A., 2013. A thin soup: extraction and amplification of DNA from DMSO and ethanol used as preservative for cetacean tissue samplesConservation Genetics Resources5(4), pp.929-933.

1. Kellar, N.M., Trego, M.L., Chivers, S.J., Archer, F.I., Minich, J.J. and Perryman, W.L., 2013. Are there biases in biopsy sampling? Potential drivers of sex ratio in projectile biopsy samples from two small delphinidsMarine Mammal Science29(4), pp.E366-E389.

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