Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Last Name
Institution

Matthew Raymond Olm

TitleAssistant Professor
InstitutionUniversity of Colorado Boulder
DepartmentIntegrative Physiology

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Deng L, Taelman S, Olm MR, Toe LC, Balini E, Ou?draogo LO, Bastos-Moreira Y, Argaw A, Tesfamariam K, Sonnenburg ED, Hanley-Cook GT, Ou?draogo M, Ganaba R, Van Criekinge W, Huybregts L, Stock M, Kolsteren P, Sonnenburg JL, Lachat C, Dailey-Chwalib?g T. Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial. Nat Commun. 2025 Mar 18; 16(1):2683. PMID: 40102379.
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    2. Olm MR, Spencer SP, Takeuchi T, Silva EL, Sonnenburg JL. Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut. Nat Microbiol. 2025 Jan; 10(1):112-125. PMID: 39747692.
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    3. Qian J, Yeo EN, Olm MR. Hospitalization throws the preterm gut microbiome off-key. Cell Host Microbe. 2024 Oct 09; 32(10):1651-1653. PMID: 39389029.
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    4. Olm MR, Mueller NT. Milk to mucus: How B.?fragilis colonizes the gut. Cell Host Microbe. 2024 Feb 14; 32(2):149-150. PMID: 38359795.
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    5. Gerrick ER, Zlitni S, West PT, Carter MM, Mechler CM, Olm MR, Caffrey EB, Li JA, Higginbottom SK, Severyn CJ, Kracke F, Spormann AM, Sonnenburg JL, Bhatt AS, Howitt MR. Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition. Cell. 2024 01 04; 187(1):62-78.e20. PMID: 38096822.
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    6. Olm MR, Spencer SP, Silva EL, Sonnenburg JL. Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome. bioRxiv. 2023 Nov 21. PMID: 38045399.
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    7. Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice. Cell Rep. 2023 11 28; 42(11). PMID: 38510311.
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    8. Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell. 2023 07 06; 186(14):3111-3124.e13. PMID: 37348505.
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    9. Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice. bioRxiv. 2023 Mar 09. PMID: 36945614.
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    10. Lou YC, Hoff J, Olm MR, West-Roberts J, Diamond S, Firek BA, Morowitz MJ, Banfield JF. Using strain-resolved analysis to identify contamination in metagenomics data. Microbiome. 2023 03 02; 11(1):36. PMID: 36864482.
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    11. Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes. bioRxiv. 2022 Oct 06. PMID: 36238714.
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    12. Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng X, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science. 2022 06 10; 376(6598):1220-1223. PMID: 35679413.
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    13. Carter MM, Olm MR, Sonnenburg ED. Microbiome assembly in The Gambia. Nat Microbiol. 2022 01; 7(1):18-19. PMID: 34972823.
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    14. Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, R?hlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021 11; 27(11):1885-1892. PMID: 34789871.
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    15. Lou YC, Olm MR, Diamond S, Crits-Christoph A, Firek BA, Baker R, Morowitz MJ, Banfield JF. Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition. Cell Rep Med. 2021 09 21; 2(9):100393. PMID: 34622230.
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    16. West PT, Peters SL, Olm MR, Yu FB, Gause H, Lou YC, Firek BA, Baker R, Johnson AD, Morowitz MJ, Hettich RL, Banfield JF. Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics. Microbiome. 2021 06 21; 9(1):142. PMID: 34154658.
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    17. Olm MR, Sonnenburg JL. Ancient human faeces reveal gut microbes of the past. Nature. 2021 06; 594(7862):182-183. PMID: 34007025.
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    18. Matheus Carnevali PB, Lavy A, Thomas AD, Crits-Christoph A, Diamond S, M?heust R, Olm MR, Sharrar A, Lei S, Dong W, Falco N, Bouskill N, Newcomer ME, Nico P, Wainwright H, Dwivedi D, Williams KH, Hubbard S, Banfield JF. Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale. Microbiome. 2021 05 22; 9(1):121. PMID: 34022966.
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    19. Crits-Christoph A, Kantor RS, Olm MR, Whitney ON, Al-Shayeb B, Lou YC, Flamholz A, Kennedy LC, Greenwald H, Hinkle A, Hetzel J, Spitzer S, Koble J, Tan A, Hyde F, Schroth G, Kuersten S, Banfield JF, Nelson KL. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio. 2021 01 19; 12(1). PMID: 33468686.
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    20. Olm MR, Crits-Christoph A, Bouma-Gregson K, Firek BA, Morowitz MJ, Banfield JF. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol. 2021 06; 39(6):727-736. PMID: 33462508.
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    21. Crits-Christoph A, Bhattacharya N, Olm MR, Song YS, Banfield JF. Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome Res. 2021 Feb; 31(2):239-250. PMID: 33361114.
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    22. Crits-Christoph A, Olm MR, Diamond S, Bouma-Gregson K, Banfield JF. Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J. 2020 07; 14(7):1834-1846. PMID: 32327732.
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    23. Sher Y, Olm MR, Raveh-Sadka T, Brown CT, Sher R, Firek B, Baker R, Morowitz MJ, Banfield JF. Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut. PLoS One. 2020; 15(3):e0229537. PMID: 32130257.
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    24. Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, M?heust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JHD, Santini JM, Banfield JF. Clades of huge phages from across Earth's ecosystems. Nature. 2020 02; 578(7795):425-431. PMID: 32051592.
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    25. Olm MR, Crits-Christoph A, Diamond S, Lavy A, Matheus Carnevali PB, Banfield JF. Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries. mSystems. 2020 Jan 14; 5(1). PMID: 31937678.
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    26. Olm MR, Bhattacharya N, Crits-Christoph A, Firek BA, Baker R, Song YS, Morowitz MJ, Banfield JF. Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. Sci Adv. 2019 12; 5(12):eaax5727. PMID: 31844663.
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    27. Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF. Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun. 2019 03 26; 10(1):1451. PMID: 30914645.
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    28. Bouma-Gregson K, Olm MR, Probst AJ, Anantharaman K, Power ME, Banfield JF. Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. ISME J. 2019 06; 13(6):1618-1634. PMID: 30809011.
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    29. Olm MR, West PT, Brooks B, Firek BA, Baker R, Morowitz MJ, Banfield JF. Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms. Microbiome. 2019 02 15; 7(1):26. PMID: 30770768.
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    30. Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF. Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun. 2019 01 28; 10(1):463. PMID: 30692531.
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    31. Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat Microbiol. 2019 04; 4(4):693-700. PMID: 30692672.
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    32. Brooks B, Olm MR, Firek BA, Baker R, Geller-McGrath D, Reimer SR, Soenjoyo KR, Yip JS, Dahan D, Thomas BC, Morowitz MJ, Banfield JF. The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms. Microbiome. 2018 06 20; 6(1):112. PMID: 29925423.
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    33. Brown CT, Xiong W, Olm MR, Thomas BC, Baker R, Firek B, Morowitz MJ, Hettich RL, Banfield JF. Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. mBio. 2018 04 10; 9(2). PMID: 29636439.
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    34. Rahman SF, Olm MR, Morowitz MJ, Banfield JF. Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. mSystems. 2018 Jan-Feb; 3(1). PMID: 29359195.
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    35. Brooks B, Olm MR, Firek BA, Baker R, Thomas BC, Morowitz MJ, Banfield JF. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun. 2017 11 27; 8(1):1814. PMID: 29180750.
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    36. Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017 12; 11(12):2864-2868. PMID: 28742071.
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    37. Olm MR, Butterfield CN, Copeland A, Boles TC, Thomas BC, Banfield JF. The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis. mBio. 2017 02 21; 8(1). PMID: 28223457.
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    38. Olm MR, Brown CT, Brooks B, Firek B, Baker R, Burstein D, Soenjoyo K, Thomas BC, Morowitz M, Banfield JF. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res. 2017 04; 27(4):601-612. PMID: 28073918.
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    39. Brown CT, Olm MR, Thomas BC, Banfield JF. Measurement of bacterial replication rates in microbial communities. Nat Biotechnol. 2016 Dec; 34(12):1256-1263. PMID: 27819664.
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    40. Dedrick RM, Mavrich TN, Ng WL, Cervantes Reyes JC, Olm MR, Rush RE, Jacobs-Sera D, Russell DA, Hatfull GF. Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. Mol Microbiol. 2016 08; 101(4):625-44. PMID: 27146086.
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    41. Pope WH, Anders KR, Baird M, Bowman CA, Boyle MM, Broussard GW, Chow T, Clase KL, Cooper S, Cornely KA, DeJong RJ, Delesalle VA, Deng L, Dunbar D, Edgington NP, Ferreira CM, Weston Hafer K, Hartzog GA, Hatherill JR, Hughes LE, Ipapo K, Krukonis GP, Meier CG, Monti DL, Olm MR, Page ST, Peebles CL, Rinehart CA, Rubin MR, Russell DA, Sanders ER, Schoer M, Shaffer CD, Wherley J, Vazquez E, Yuan H, Zhang D, Cresawn SG, Jacobs-Sera D, Hendrix RW, Hatfull GF. Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes. J Virol. 2014 Mar; 88(5):2461-80. PMID: 24335314.
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