Jeremiah Minich

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Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin. mSystems. 2023 02 23; 8(1):e0092222. Melnik AV, Callewaert C, Dorrestein K, Broadhead R, Minich JJ, Ernst M, Humphrey G, Ackermann G, Gathercole R, Aksenov AA, Knight R, Dorrestein PC. PMID: 36722970; PMCID: PMC9948701.

View in: PubMed Mentions: 1 Fields:
Mic Microbiology
Translation:Humans Cells
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nat Microbiol. 2022 12; 7(12):2128-2150. Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R, Earth Microbiome Project 500 (EMP500) Consortium. PMID: 36443458; PMCID: PMC9712116.

View in: PubMed Mentions: 10 Fields:
Mic Microbiology Par Parasitology Vir Virology
Translation:Animals
Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nat Commun. 2022 11 17; 13(1):6978. Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, Kunselman E, Shane MA, Perry DS, Gonzalez A, McDonald D, Knight R, Michael TP, Allen EE. PMID: 36396943; PMCID: PMC9671965.

View in: PubMed Mentions: 5 Fields:
Bio Biology Sci Science
Translation:Animals
A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Biotechniques. 2022 06; 73(1):34-46. Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R. PMID: 35713407; PMCID: PMC9361692.

View in: PubMed Mentions: 9 Fields:
Bio Biotechnology
Translation:Humans Cells
Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes. Anim Microbiome. 2022 May 23; 4(1):33. Sparagon WJ, Gentry EC, Minich JJ, Vollbrecht L, Laurens LML, Allen EE, Sims NA, Dorrestein PC, Kelly LW, Nelson CE. PMID: 35606844; PMCID: PMC9128220.

View in: PubMed Mentions: 6
Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound. Microbiol Spectr. 2022 06 29; 10(3):e0198221. Kunselman E, Minich JJ, Horwith M, Gilbert JA, Allen EE. PMID: 35536036; PMCID: PMC9241838.

View in: PubMed Mentions: 1 Fields:
Mic Microbiology
Translation:Animals Cells
Clean room microbiome complexity impacts planetary protection bioburden. Microbiome. 2021 12 04; 9(1):238. Hendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran K. PMID: 34861887; PMCID: PMC8643001.

View in: PubMed Mentions: 4 Fields:
Gen Genetics Mic Microbiology
Translation:Cells
Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi. Front Mar Sci. 2021 May; 8. Minich JJ, Nowak B, Elizur A, Knight R, Fielder S, Allen EE. PMID: 36248701; PMCID: PMC9563383.

View in: PubMed Mentions: 6
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. Biotechniques. 2021 03; 70(3):149-159. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. PMID: 33512248; PMCID: PMC7931620.

View in: PubMed Mentions: 9 Fields:
Bio Biotechnology
Translation:Humans Animals Cells
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome. 2021 01 22; 9(1):25. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 33482920; PMCID: PMC7821463.

View in: PubMed Mentions: 8 Fields:
Gen Genetics Mic Microbiology
Translation:Humans Cells
Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere. 2021 May; 271:129450. Petras D, Minich JJ, Cancelada LB, Torres RR, Kunselman E, Wang M, White ME, Allen EE, Prather KA, Aluwihare LI, Dorrestein PC. PMID: 33460888; PMCID: PMC7969459.

View in: PubMed Mentions: 10 Fields:
Bio Biology Che Chemistry Env Environmental Health
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. bioRxiv. 2020 Nov 14. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. PMID: 33200135; PMCID: PMC7668742.

View in: PubMed Mentions: 2
The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment. Front Microbiol. 2020; 11:2015. Minich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B, Allen EE. PMID: 32983024; PMCID: PMC7476325.

View in: PubMed Mentions: 4
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Res Sq. 2020 Aug 18. Minich J, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32839765; PMCID: PMC7444291.

View in: PubMed Mentions:
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. medRxiv. 2020 Aug 13. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert JA, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32511552; PMCID: PMC7274233.

View in: PubMed Mentions: 1
Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation. mSystems. 2020 Jul 28; 5(4). Malli Mohan GB, Parker CW, Urbaniak C, Singh NK, Hood A, Minich JJ, Knight R, Rucker M, Venkateswaran K. PMID: 32723791; PMCID: PMC7394354.

View in: PubMed Mentions: 4 Fields:
Mic Microbiology
Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Appl Environ Microbiol. 2020 06 02; 86(12). Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, Allen EE. PMID: 32303543; PMCID: PMC7267192.

View in: PubMed Mentions: 26 Fields:
Mic Microbiology
Translation:Animals PHPublic Health
Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus. mSphere. 2020 05 20; 5(3). Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen EE. PMID: 32434844; PMCID: PMC7380571.

View in: PubMed Mentions: 12 Fields:
Mic Microbiology Par Parasitology
Translation:Animals
Visualizing 'omic feature rankings and log-ratios using Qurro. NAR Genom Bioinform. 2020 Jun; 2(2):lqaa023. Fedarko MW, Martino C, Morton JT, González A, Rahman G, Marotz CA, Minich JJ, Allen EE, Knight R. PMID: 32391521; PMCID: PMC7194218.

View in: PubMed Mentions: 61
Atlantic Salmon (Salmo salar L., 1758) Gut Microbiota Profile Correlates with Flesh Pigmentation: Cause or Effect? Mar Biotechnol (NY). 2020 Dec; 22(6):786-804. Nguyen CDH, Amoroso G, Ventura T, Minich JJ, Elizur A. PMID: 31942646.

View in: PubMed Mentions: 10 Fields:
Bio Biology Bio Biotechnology
Translation:Animals Cells PHPublic Health
Home chemical and microbial transitions across urbanization. Nat Microbiol. 2020 01; 5(1):108-115. McCall LI, 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 OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG. PMID: 31686026; PMCID: PMC7895447.

View in: PubMed Mentions: 35 Fields:
Mic Microbiology Par Parasitology Vir Virology
Translation:Humans Animals Cells PHPublic Health
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 2019 10 31; 20(1):226. Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. PMID: 31672156; PMCID: PMC6822431.

View in: PubMed Mentions: 23 Fields:
Gen Genetics
Translation:Humans Animals
Quantifying and Understanding Well-to-Well Contamination in Microbiome Research. mSystems. 2019 Jun 25; 4(4). Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. PMID: 31239396; PMCID: PMC6593221.

View in: PubMed Mentions: 71 Fields:
Mic Microbiology
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Microbiome. 2019 04 08; 7(1):50. Checinska Sielaff A, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, Minich J, McDonald D, Mayer T, Knight R, Karouia F, Fox GE, Venkateswaran K. PMID: 30955503; PMCID: PMC6452512.

View in: PubMed Mentions: 87 Fields:
Gen Genetics Mic Microbiology
Translation:Humans Animals Cells PHPublic Health
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol. 2019 02; 27(2):105-117. Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. PMID: 30497919.

View in: PubMed Mentions: 316 Fields:
Mic Microbiology
Translation:Humans
High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. mSystems. 2018 Nov-Dec; 3(6). Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R. PMID: 30417111; PMCID: PMC6222042.

View in: PubMed Mentions: 31 Fields:
Mic Microbiology
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019 01; 17(2):218-230. Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R. PMID: 30240894; PMCID: PMC6391518.

View in: PubMed Mentions: 103 Fields:
Gas Gastroenterology
Translation:Humans
Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). Microbiologyopen. 2018 12; 7(6):e00716. Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. PMID: 30168288; PMCID: PMC6291788.

View in: PubMed Mentions: 9 Fields:
Mic Microbiology
Translation:Animals Cells
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018 May-Jun; 3(3). Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R. PMID: 29577086; PMCID: PMC5864415.

View in: PubMed Mentions: 65 Fields:
Mic Microbiology
Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. PLoS One. 2018; 13(2):e0192772. Minich JJ, Morris MM, Brown M, Doane M, Edwards MS, Michael TP, Dinsdale EA. PMID: 29474389; PMCID: PMC5825054.

View in: PubMed Mentions: 34 Fields:
Med Medicine (General)Sci Science
Translation:Animals PHPublic Health
From Sample to Multi-Omics Conclusions in under 48 Hours. mSystems. 2016 Mar-Apr; 1(2). Quinn RA, Navas-Molina JA, Hyde ER, Song SJ, Vázquez-Baeza Y, Humphrey G, Gaffney J, Minich JJ, Melnik AV, Herschend J, DeReus J, Durant A, Dutton RJ, Khosroheidari M, Green C, da Silva R, Dorrestein PC, Knight R. PMID: 27822524; PMCID: PMC5069746.

View in: PubMed Mentions: 26 Fields:
Mic Microbiology
Improved multiple displacement amplification (iMDA) and ultraclean reagents. BMC Genomics. 2014 Jun 06; 15:443. Motley ST, Picuri JM, Crowder CD, Minich JJ, Hofstadler SA, Eshoo MW. PMID: 24906487; PMCID: PMC4061449.

View in: PubMed Mentions: 24 Fields:
Gen Genetics
Translation:Humans