Publications
Link to google scholar
Carter* M.M., Olm* M.R., Merrill* B.D., Dahan D., Tripathi S., Spencer S.P., Yu F.B., Jain S., Neff N., Jha A.R., Sonnenburg E.D., Sonnenburg J.L.
Gellman R.H., Olm M.R., Terrapon N., Enam F., Higginbottom S.K., Sonnenburg J.L., Sonnenburg E.D.
Lou Y.C., Hoff J., Olm M.R., West-Roberts J., Diamond S., Firek B.A., Morowitz M.J., Banfield J.F.
Olm* M.R., Dahan* D., Carter M.M., Merrill B.D., Yu F.B., Jain S., Meng X., Tripathi S., Wastyk H., Neff N., Holmes S., Sonnenburg E.D., Jha A.R., Sonnenburg J.L.
Carter M.M., Olm M.R., Sonnenburg E.D.
Mirzayi C., Renson A., Furlanello C., Sansone S., Zohra F., Elsafoury S., Geistlinger L., Kasselman L.J., Eckenrode K., van d.W.J., Loughman A., Marques F.Z., MacIntyre D.A., Arumugam M., Azhar R., Beghini F., Bergstrom K., Bhatt A., Bisanz J.E., Braun J., Bravo H.C., Buck G.A., Bushman F., Casero D., Clarke G., Collado M.C., Cotter P.D., Cryan J.F., Demmer R.T., Devkota S., Elinav E., Escobar J.S., Fettweis J., Finn R.D., Fodor A.A., Forslund S., Franke A., Furlanello C., Gilbert J., Grice E., Haibe-Kains B., Handley S., Herd P., Holmes S., Jacobs J.P., Karstens L., Knight R., Knights D., Koren O., Kwon D.S., Langille M., Lindsay B., McGovern D., McHardy A.C., McWeeney S., Mueller N.T., Nezi L., Olm M., Palm N., Pasolli E., Raes J., Redinbo M.R., Rühlemann M., Balfour S.R., Schloss P.D., Schriml L., Segal E., Shardell M., Sharpton T., Smirnova E., Sokol H., Sonnenburg J.L., Srinivasan S., Thingholm L.B., Turnbaugh P.J., Upadhyay V., Walls R.L., 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 C.E., Mercer T.R., Sansone S., Scherer A., Shi L., Thakkar S., Tong W., Wolfinger R., Hunter C., Segata N., Huttenhower C., Dowd J.B., Jones H.E., Waldron L., Genomic S.C., Massive A.a.Q.C.S.
Bouma‐Gregson K., Crits‐Christoph A., Olm M.R., Power M.E., Banfield J.F.
Lou Y.C., Olm M.R., Diamond S., Crits-Christoph A., Firek B.A., Baker R., Morowitz M.J., Banfield J.F.
West P.T., Peters S.L., Olm M.R., Yu F.B., Gause H., Lou Y.C., Firek B.A., Baker R., Johnson A.D., Morowitz M.J., Hettich R.L., Banfield J.F.
Olm M.R., Crits-Christoph A., Bouma-Gregson K., Firek B.A., Morowitz M.J., Banfield J.F.
Matheus C.P.B., Lavy A., Thomas A.D., Crits-Christoph A., Diamond S., Méheust R., Olm M.R., Sharrar A., Lei S., Dong W., Falco N., Bouskill N., Newcomer M.E., Nico P., Wainwright H., Dwivedi D., Williams K.H., Hubbard S., Banfield J.F.
Olm M.R., Sonnenburg J.L.
Crits-Christoph A., Kantor R.S., Olm M.R., Whitney O.N., Al-Shayeb B., Lou Y.C., Flamholz A., Kennedy L.C., Greenwald H., Hinkle A., Hetzel J., Spitzer S., Koble J., Tan A., Hyde F., Schroth G., Kuersten S., Banfield J.F., Nelson K.L.
Crits-Christoph A., Bhattacharya N., Olm M.R., Song Y.S., Banfield J.F.
Crits-Christoph A., Olm M.R., Diamond S., Bouma-Gregson K., Banfield J.F.
Sher Y., Olm M.R., Raveh-Sadka T., Brown C.T., Sher R., Firek B., Baker R., Morowitz M.J., Banfield J.F.
Olm M.R., Crits-Christoph A., Diamond S., Lavy A., Carnevali P.B.M., Banfield J.F.
Al-Shayeb B., Sachdeva R., Chen L., Ward F., Munk P., Devoto A., Castelle C.J., Olm M.R., Bouma-Gregson K., Amano Y., He C., Méheust R., Brooks B., Thomas A., Lavy A., Matheus-Carnevali P., Sun C., Goltsman D.S.A., Borton M.A., Sharrar A., Jaffe A.L., Nelson T.C., Kantor R., Keren R., Lane K.R., Farag I.F., Lei S., Finstad K., Amundson R., Anantharaman K., Zhou J., Probst A.J., Power M.E., Tringe S.G., Li W., Wrighton K., Harrison S., Morowitz M., Relman D.A., Doudna J.A., Lehours A., Warren L., Cate J.H.D., Santini J.M., Banfield J.F.
Olm M.R., Bhattacharya N., Crits-Christoph A., Firek B.A., Baker R., Song Y.S., Morowitz M.J., Banfield J.F.
Devoto A.E., Santini J.M., Olm M.R., Anantharaman K., Munk P., Tung J., Archie E.A., Turnbaugh P.J., Seed K.D., Blekhman R., Aarestrup F.M., Thomas B.C., Banfield J.F.
Bouma-Gregson K., Olm M.R., Probst A.J., Anantharaman K., Power M.E., Banfield J.F.
Olm* M.R., West* P.T., Brooks B., Firek B.A., Baker R., Morowitz M.J., Banfield J.F.
Carnevali P.B.M., Schulz F., Castelle C.J., Kantor R.S., Shih P.M., Sharon I., Santini J.M., Olm M.R., Amano Y., Thomas B.C., Anantharaman K., Burstein D., Becraft E.D., Stepanauskas R., Woyke T., Banfield J.F.
Rahman S.F., Olm M.R., Morowitz M.J., Banfield J.F.
Brooks B., Olm M.R., Firek B.A., Baker R., Geller-McGrath D., Reimer S.R., Soenjoyo K.R., Yip J.S., Dahan D., Thomas B.C., Morowitz M.J., Banfield J.F.
Brown C.T., Xiong W., Olm M.R., Thomas B.C., Baker R., Firek B., Morowitz M.J., Hettich R.L., Banfield J.F.
Rahman S.F., Olm M.R., Morowitz M.J., Banfield J.F.
Brooks B., Olm M.R., Firek B.A., Baker R., Thomas B.C., Morowitz M.J., Banfield J.F.
Brown C.T., Olm M.R., Thomas B.C., Banfield J.F.
Olm M.R., Brown C.T., Brooks B., Banfield J.F.
Olm M.R., Brown C.T., Brooks B., Firek B., Baker R., Burstein D., Soenjoyo K., Thomas B.C., Morowitz M., Banfield J.F.
Olm M.R., Butterfield C.N., Copeland A., Boles T.C., Thomas B.C., Banfield J.F.
Dedrick R.M., Mavrich T.N., Ng W.L., Reyes J.C.C., Olm M.R., Rush R.E., Jacobs‐Sera D., Russell D.A., Hatfull G.F.
Pope W.H., Anders K.R., Baird M., Bowman C.A., Boyle M.M., Broussard G.W., Chow T., Clase K.L., Cooper S., Cornely K.A., DeJong R.J., Delesalle V.A., Deng L., Dunbar D., Edgington N.P., Ferreira C.M., Hafer K.W., Hartzog G.A., Hatherill J.R., Hughes L.E., Ipapo K., Krukonis G.P., Meier C.G., Monti D.L., Olm M.R., Page S.T., Peebles C.L., Rinehart C.A., Rubin M.R., Russell D.A., Sanders E.R., Schoer M., Shaffer C.D., Wherley J., Vazquez E., Yuan H., Zhang D., Cresawn S.G., Jacobs-Sera D., Hendrix R.W., Hatfull G.F.
Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes - Cell (2023)
Carter* M.M., Olm* M.R., Merrill* B.D., Dahan D., Tripathi S., Spencer S.P., Yu F.B., Jain S., Neff N., Jha A.R., Sonnenburg E.D., Sonnenburg J.L.
Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice - bioRxiv (2023)
Gellman R.H., Olm M.R., Terrapon N., Enam F., Higginbottom S.K., Sonnenburg J.L., Sonnenburg E.D.
Using strain-resolved analysis to identify contamination in metagenomics data - Microbiome (2023)
Lou Y.C., Hoff J., Olm M.R., West-Roberts J., Diamond S., Firek B.A., Morowitz M.J., Banfield J.F.
Robust variation in infant gut microbiome assembly across a spectrum of lifestyles - Science (2022)
Olm* M.R., Dahan* D., Carter M.M., Merrill B.D., Yu F.B., Jain S., Meng X., Tripathi S., Wastyk H., Neff N., Holmes S., Sonnenburg E.D., Jha A.R., Sonnenburg J.L.
Microbiome assembly in The Gambia - Nature Microbiology (2021)
Carter M.M., Olm M.R., Sonnenburg E.D.
Reporting guidelines for human microbiome research: the STORMS checklist - Nature Medicine (2021)
Mirzayi C., Renson A., Furlanello C., Sansone S., Zohra F., Elsafoury S., Geistlinger L., Kasselman L.J., Eckenrode K., van d.W.J., Loughman A., Marques F.Z., MacIntyre D.A., Arumugam M., Azhar R., Beghini F., Bergstrom K., Bhatt A., Bisanz J.E., Braun J., Bravo H.C., Buck G.A., Bushman F., Casero D., Clarke G., Collado M.C., Cotter P.D., Cryan J.F., Demmer R.T., Devkota S., Elinav E., Escobar J.S., Fettweis J., Finn R.D., Fodor A.A., Forslund S., Franke A., Furlanello C., Gilbert J., Grice E., Haibe-Kains B., Handley S., Herd P., Holmes S., Jacobs J.P., Karstens L., Knight R., Knights D., Koren O., Kwon D.S., Langille M., Lindsay B., McGovern D., McHardy A.C., McWeeney S., Mueller N.T., Nezi L., Olm M., Palm N., Pasolli E., Raes J., Redinbo M.R., Rühlemann M., Balfour S.R., Schloss P.D., Schriml L., Segal E., Shardell M., Sharpton T., Smirnova E., Sokol H., Sonnenburg J.L., Srinivasan S., Thingholm L.B., Turnbaugh P.J., Upadhyay V., Walls R.L., 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 C.E., Mercer T.R., Sansone S., Scherer A., Shi L., Thakkar S., Tong W., Wolfinger R., Hunter C., Segata N., Huttenhower C., Dowd J.B., Jones H.E., Waldron L., Genomic S.C., Massive A.a.Q.C.S.
Microcoleus (Cyanobacteria) form watershed wide populations without strong gradients in population structure - Molecular Ecology (2021)
Bouma‐Gregson K., Crits‐Christoph A., Olm M.R., Power M.E., Banfield J.F.
Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition - Cell Reports Medicine (2021)
Lou Y.C., Olm M.R., Diamond S., Crits-Christoph A., Firek B.A., Baker R., Morowitz M.J., Banfield J.F.
Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics - Microbiome (2021)
West P.T., Peters S.L., Olm M.R., Yu F.B., Gause H., Lou Y.C., Firek B.A., Baker R., Johnson A.D., Morowitz M.J., Hettich R.L., Banfield J.F.
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains - Nature Biotechnology (2021)
Olm M.R., Crits-Christoph A., Bouma-Gregson K., Firek B.A., Morowitz M.J., Banfield J.F.
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale - Microbiome (2021)
Matheus C.P.B., Lavy A., Thomas A.D., Crits-Christoph A., Diamond S., Méheust R., Olm M.R., Sharrar A., Lei S., Dong W., Falco N., Bouskill N., Newcomer M.E., Nico P., Wainwright H., Dwivedi D., Williams K.H., Hubbard S., Banfield J.F.
Ancient human faeces reveal gut microbes of the past - Nature (2021)
Olm M.R., Sonnenburg J.L.
Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants - mBio (2021)
Crits-Christoph A., Kantor R.S., Olm M.R., Whitney O.N., Al-Shayeb B., Lou Y.C., Flamholz A., Kennedy L.C., Greenwald H., Hinkle A., Hetzel J., Spitzer S., Koble J., Tan A., Hyde F., Schroth G., Kuersten S., Banfield J.F., Nelson K.L.
Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity - Genome Research (2021)
Crits-Christoph A., Bhattacharya N., Olm M.R., Song Y.S., Banfield J.F.
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow - The ISME Journal (2020)
Crits-Christoph A., Olm M.R., Diamond S., Bouma-Gregson K., Banfield J.F.
Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut - Plos one (2020)
Sher Y., Olm M.R., Raveh-Sadka T., Brown C.T., Sher R., Firek B., Baker R., Morowitz M.J., Banfield J.F.
Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries - mSystems (2020)
Olm M.R., Crits-Christoph A., Diamond S., Lavy A., Carnevali P.B.M., Banfield J.F.
Clades of huge phages from across Earth’s ecosystems - Nature (2020)
Al-Shayeb B., Sachdeva R., Chen L., Ward F., Munk P., Devoto A., Castelle C.J., Olm M.R., Bouma-Gregson K., Amano Y., He C., Méheust R., Brooks B., Thomas A., Lavy A., Matheus-Carnevali P., Sun C., Goltsman D.S.A., Borton M.A., Sharrar A., Jaffe A.L., Nelson T.C., Kantor R., Keren R., Lane K.R., Farag I.F., Lei S., Finstad K., Amundson R., Anantharaman K., Zhou J., Probst A.J., Power M.E., Tringe S.G., Li W., Wrighton K., Harrison S., Morowitz M., Relman D.A., Doudna J.A., Lehours A., Warren L., Cate J.H.D., Santini J.M., Banfield J.F.
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria - Science advances (2019)
Olm M.R., Bhattacharya N., Crits-Christoph A., Firek B.A., Baker R., Song Y.S., Morowitz M.J., Banfield J.F.
Megaphages infect Prevotella and variants are widespread in gut microbiomes - Nature Microbiology (2019)
Devoto A.E., Santini J.M., Olm M.R., Anantharaman K., Munk P., Tung J., Archie E.A., Turnbaugh P.J., Seed K.D., Blekhman R., Aarestrup F.M., Thomas B.C., Banfield J.F.
Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network - The ISME Journal (2019)
Bouma-Gregson K., Olm M.R., Probst A.J., Anantharaman K., Power M.E., Banfield J.F.
Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms - Microbiome (2019)
Olm* M.R., West* P.T., Brooks B., Firek B.A., Baker R., Morowitz M.J., Banfield J.F.
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria - Nature Communications (2019)
Carnevali P.B.M., Schulz F., Castelle C.J., Kantor R.S., Shih P.M., Sharon I., Santini J.M., Olm M.R., Amano Y., Thomas B.C., Anantharaman K., Burstein D., Becraft E.D., Stepanauskas R., Woyke T., Banfield J.F.
Functional potential of bacterial strains in the premature infant gut microbiome is associated with gestational age - bioRxiv (2019)
Rahman S.F., Olm M.R., Morowitz M.J., Banfield J.F.
The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms - Microbiome (2018)
Brooks B., Olm M.R., Firek B.A., Baker R., Geller-McGrath D., Reimer S.R., Soenjoyo K.R., Yip J.S., Dahan D., Thomas B.C., Morowitz M.J., Banfield J.F.
Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles - mBio (2018)
Brown C.T., Xiong W., Olm M.R., Thomas B.C., Baker R., Firek B., Morowitz M.J., Hettich R.L., Banfield J.F.
Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome - mSystems (2018)
Rahman S.F., Olm M.R., Morowitz M.J., Banfield J.F.
Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome - Nature Communications (2017)
Brooks B., Olm M.R., Firek B.A., Baker R., Thomas B.C., Morowitz M.J., Banfield J.F.
Measurement of bacterial replication rates in microbial communities - Nature Biotechnology (2017)
Brown C.T., Olm M.R., Thomas B.C., Banfield J.F.
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication - The ISME Journal (2017)
Olm M.R., Brown C.T., Brooks B., Banfield J.F.
Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates - Genome Research (2017)
Olm M.R., Brown C.T., Brooks B., Firek B., Baker R., Burstein D., Soenjoyo K., Thomas B.C., Morowitz M., Banfield J.F.
The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis - mBio (2017)
Olm M.R., Butterfield C.N., Copeland A., Boles T.C., Thomas B.C., Banfield J.F.
Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems - Molecular Microbiology (2016)
Dedrick R.M., Mavrich T.N., Ng W.L., Reyes J.C.C., Olm M.R., Rush R.E., Jacobs‐Sera D., Russell D.A., Hatfull G.F.
Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotypes - Journal of Virology (2014)
Pope W.H., Anders K.R., Baird M., Bowman C.A., Boyle M.M., Broussard G.W., Chow T., Clase K.L., Cooper S., Cornely K.A., DeJong R.J., Delesalle V.A., Deng L., Dunbar D., Edgington N.P., Ferreira C.M., Hafer K.W., Hartzog G.A., Hatherill J.R., Hughes L.E., Ipapo K., Krukonis G.P., Meier C.G., Monti D.L., Olm M.R., Page S.T., Peebles C.L., Rinehart C.A., Rubin M.R., Russell D.A., Sanders E.R., Schoer M., Shaffer C.D., Wherley J., Vazquez E., Yuan H., Zhang D., Cresawn S.G., Jacobs-Sera D., Hendrix R.W., Hatfull G.F.