Mathew R Olm

Affiliations

Plant and Microbial Ecology Department, University of California, Berkeley, California, USA.

Publications (27)

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow.

The ISME journal

Avec: Alexander Crits-Christoph , Matthew R Olm , Spencer Diamond , Keith Bouma-Gregson , Jillian F Banfield

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut.

PloS one

Avec: Yonatan Sher , Matthew R Olm , Tali Raveh-Sadka , Christopher T Brown , Ruth Sher , Brian Firek , Robyn Baker , Michael J Morowitz , Jillian F Banfield

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale.

Microbiome

Avec: Paula B Matheus Carnevali , Adi Lavy , Alex D Thomas , Alexander Crits-Christoph , Spencer Diamond , Raphaël Méheust , Matthew R Olm , Allison Sharrar , Shufei Lei , Wenming Dong , Nicola Falco , Nicholas Bouskill , Michelle E Newcomer , Peter Nico , Haruko Wainwright , Dipankar Dwivedi , Kenneth H Williams , Susan Hubbard , Jillian F Banfield

Using strain-resolved analysis to identify contamination in metagenomics data.

Microbiome

Avec: Yue Clare Lou , Jordan Hoff , Matthew R Olm , Jacob West-Roberts , Spencer Diamond , Brian A Firek , Michael J Morowitz , Jillian F Banfield

Hadza

bioRxiv : the preprint server for biology

Avec: Rebecca H Gellman , Matthew R Olm , Nicolas Terrapon , Fatima Enam , Steven K Higginbottom , Justin L Sonnenburg , Erica D Sonnenburg

Hadza

Cell reports

Avec: Rebecca H Gellman , Matthew R Olm , Nicolas Terrapon , Fatima Enam , Steven K Higginbottom , Justin L Sonnenburg , Erica D Sonnenburg

Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.

Nature communications

Avec: Paula B Matheus Carnevali , Frederik Schulz , Cindy J Castelle , Rose S Kantor , Patrick M Shih , Itai Sharon , Joanne M Santini , Matthew R Olm , Yuki Amano , Brian C Thomas , Karthik Anantharaman , David Burstein , Eric D Becraft , Ramunas Stepanauskas , Tanja Woyke , Jillian F Banfield

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms.

Microbiome

Avec: Matthew R Olm , Patrick T West , Brandon Brooks , Brian A Firek , Robyn Baker , Michael J Morowitz , Jillian F Banfield

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles.

Science (New York, N.Y.)

Avec: Matthew R Olm , Dylan Dahan , Matthew M Carter , Bryan D Merrill , Feiqiao B Yu , Sunit Jain , Xiandong Meng , Surya Tripathi , Hannah Wastyk , Norma Neff , Susan Holmes , Erica D Sonnenburg , Aashish R Jha , Justin L Sonnenburg

Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome.

bioRxiv : the preprint server for biology

Avec: Matthew R Olm , Sean P Spencer , Evelyn Lemus Silva , Justin L Sonnenburg

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries.

mSystems

Avec: Matthew R Olm , Alexander Crits-Christoph , Spencer Diamond , Adi Lavy , Paula B Matheus Carnevali , Jillian F Banfield

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.

Nature communications

Megaphages infect Prevotella and variants are widespread in gut microbiomes.

Nature microbiology

Avec: Audra E Devoto , Joanne M Santini , Matthew R Olm , Karthik Anantharaman , Patrick Munk , Jenny Tung , Elizabeth A Archie , Peter J Turnbaugh , Kimberley D Seed , Ran Blekhman , Frank M Aarestrup , Brian C Thomas , Jillian F Banfield

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition.

Cell

Avec: Elias R Gerrick , Soumaya Zlitni , Patrick T West , Matthew M Carter , Claire M Mechler , Matthew R Olm , Elisa B Caffrey , Jessica A Li , Steven K Higginbottom , Christopher J Severyn , Frauke Kracke , Alfred M Spormann , Justin L Sonnenburg , Ami S Bhatt , Michael R Howitt

Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure.

Molecular ecology

Avec: Keith Bouma-Gregson , Alexander Crits-Christoph , Mathew R Olm , Mary E Power , Jillian F Banfield

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.

Nature biotechnology

Avec: Matthew R Olm , Alexander Crits-Christoph , Keith Bouma-Gregson , Brian A Firek , Michael J Morowitz , Jillian F Banfield

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants.

mBio

Avec: Alexander Crits-Christoph , Rose S Kantor , Matthew R Olm , Oscar N Whitney , Basem Al-Shayeb , Yue Clare Lou , Avi Flamholz , Lauren C Kennedy , Hannah Greenwald , Adrian Hinkle , Jonathan Hetzel , Sara Spitzer , Jeffery Koble , Asako Tan , Fred Hyde , Gary Schroth , Scott Kuersten , Jillian F Banfield , Kara L Nelson

Necrotizing enterocolitis is preceded by increased gut bacterial replication,

Science advances

Avec: Matthew R Olm , Nicholas Bhattacharya , Alexander Crits-Christoph , Brian A Firek , Robyn Baker , Yun S Song , Michael J Morowitz , Jillian F Banfield

Clades of huge phages from across Earth's ecosystems.

Nature

Avec: Basem Al-Shayeb , Rohan Sachdeva , Lin-Xing Chen , Fred Ward , Patrick Munk , Audra Devoto , Cindy J Castelle , Matthew R Olm , Keith Bouma-Gregson , Yuki Amano , Christine He , Raphaël Méheust , Brandon Brooks , Alex Thomas , Adi Lavy , Paula Matheus-Carnevali , Christine Sun , Daniela S A Goltsman , Mikayla A Borton , Allison Sharrar , Alexander L Jaffe , Tara C Nelson , Rose Kantor , Ray Keren , Katherine R Lane , Ibrahim F Farag , Shufei Lei , Kari Finstad , Ronald Amundson , Karthik Anantharaman , Jinglie Zhou , Alexander J Probst , Mary E Power , Susannah G Tringe , Wen-Jun Li , Kelly Wrighton , Sue Harrison , Michael Morowitz , David A Relman , Jennifer A Doudna , Anne-Catherine Lehours , Lesley Warren , Jamie H D Cate , Joanne M Santini , Jillian F Banfield

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.

The ISME journal

Avec: Keith Bouma-Gregson , Matthew R Olm , Alexander J Probst , Karthik Anantharaman , Mary E Power , Jillian F Banfield

Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition.

Cell reports. Medicine

Avec: Yue Clare Lou , Matthew R Olm , Spencer Diamond , Alexander Crits-Christoph , Brian A Firek , Robyn Baker , Michael J Morowitz , Jillian F Banfield

Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity.

Genome research

Avec: Alexander Crits-Christoph , Nicholas Bhattacharya , Matthew R Olm , Yun S Song , Jillian F Banfield

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics.

Microbiome

Avec: Patrick T West , Samantha L Peters , Matthew R Olm , Feiqiao B Yu , Haley Gause , Yue Clare Lou , Brian A Firek , Robyn Baker , Alexander D Johnson , Michael J Morowitz , Robert L Hettich , Jillian F Banfield

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes.

bioRxiv : the preprint server for biology

Avec: Bryan D Merrill , Matthew M Carter , Matthew R Olm , Dylan Dahan , Surya Tripathi , Sean P Spencer , Brian Yu , Sunit Jain , Norma Neff , Aashish R Jha , Erica D Sonnenburg , Justin L Sonnenburg

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.

Cell

Avec: Matthew M Carter , Matthew R Olm , Bryan D Merrill , Dylan Dahan , Surya Tripathi , Sean P Spencer , Feiqiao B Yu , Sunit Jain , Norma Neff , Aashish R Jha , Erica D Sonnenburg , Justin L Sonnenburg

Milk to mucus: How B. fragilis colonizes the gut.

Cell host & microbe

Avec: Matthew R Olm , Noel T Mueller

Hospitalization throws the preterm gut microbiome off-key.

Cell host & microbe

Avec: Jing Qian , Emily N Yeo , Matthew R Olm

Réseau de co-auteurs

Matthew R Olm 26 collaborations

Jillian F Banfield 18 collaborations

Alexander Crits-Christoph 9 collaborations

Michael J Morowitz 7 collaborations

Justin L Sonnenburg 7 collaborations

Brian A Firek 6 collaborations

Spencer Diamond 5 collaborations

Keith Bouma-Gregson 5 collaborations

Robyn Baker 5 collaborations

Erica D Sonnenburg 5 collaborations

Karthik Anantharaman 5 collaborations

Paula B Matheus Carnevali 4 collaborations

Yue Clare Lou 4 collaborations

Joanne M Santini 4 collaborations

Matthew M Carter 4 collaborations

Adi Lavy 3 collaborations

Steven K Higginbottom 3 collaborations

Cindy J Castelle 3 collaborations

Rose S Kantor 3 collaborations

Yuki Amano 3 collaborations

Brian C Thomas 3 collaborations

Patrick T West 3 collaborations

Dylan Dahan 3 collaborations

Bryan D Merrill 3 collaborations

Feiqiao B Yu 3 collaborations

Sunit Jain 3 collaborations

Surya Tripathi 3 collaborations

Norma Neff 3 collaborations

Aashish R Jha 3 collaborations

Sean P Spencer 3 collaborations

Mary E Power 3 collaborations

Raphaël Méheust 2 collaborations

Allison Sharrar 2 collaborations

Shufei Lei 2 collaborations

Rebecca H Gellman 2 collaborations

Nicolas Terrapon 2 collaborations

Fatima Enam 2 collaborations

Frederik Schulz 2 collaborations

Patrick M Shih 2 collaborations

Itai Sharon 2 collaborations

David Burstein 2 collaborations

Eric D Becraft 2 collaborations

Ramunas Stepanauskas 2 collaborations

Tanja Woyke 2 collaborations

Brandon Brooks 2 collaborations

Patrick Munk 2 collaborations

Basem Al-Shayeb 2 collaborations

Nicholas Bhattacharya 2 collaborations

Yun S Song 2 collaborations

Alexander J Probst 2 collaborations

Yonatan Sher 1 collaboration

Tali Raveh-Sadka 1 collaboration

Christopher T Brown 1 collaboration

Ruth Sher 1 collaboration

Brian Firek 1 collaboration

Alex D Thomas 1 collaboration

Wenming Dong 1 collaboration

Nicola Falco 1 collaboration

Nicholas Bouskill 1 collaboration

Michelle E Newcomer 1 collaboration

Peter Nico 1 collaboration

Haruko Wainwright 1 collaboration

Dipankar Dwivedi 1 collaboration

Kenneth H Williams 1 collaboration

Susan Hubbard 1 collaboration

Jordan Hoff 1 collaboration

Jacob West-Roberts 1 collaboration

Xiandong Meng 1 collaboration

Hannah Wastyk 1 collaboration

Susan Holmes 1 collaboration

Evelyn Lemus Silva 1 collaboration

Audra E Devoto 1 collaboration

Jenny Tung 1 collaboration

Elizabeth A Archie 1 collaboration

Peter J Turnbaugh 1 collaboration

Kimberley D Seed 1 collaboration

Ran Blekhman 1 collaboration

Frank M Aarestrup 1 collaboration

Elias R Gerrick 1 collaboration

Soumaya Zlitni 1 collaboration

Claire M Mechler 1 collaboration

Elisa B Caffrey 1 collaboration

Jessica A Li 1 collaboration

Christopher J Severyn 1 collaboration

Frauke Kracke 1 collaboration

Alfred M Spormann 1 collaboration

Ami S Bhatt 1 collaboration

Michael R Howitt 1 collaboration

Oscar N Whitney 1 collaboration

Avi Flamholz 1 collaboration

Lauren C Kennedy 1 collaboration

Hannah Greenwald 1 collaboration

Adrian Hinkle 1 collaboration

Jonathan Hetzel 1 collaboration

Sara Spitzer 1 collaboration

Jeffery Koble 1 collaboration

Asako Tan 1 collaboration

Fred Hyde 1 collaboration

Gary Schroth 1 collaboration

Scott Kuersten 1 collaboration

Kara L Nelson 1 collaboration

Rohan Sachdeva 1 collaboration

Lin-Xing Chen 1 collaboration

Fred Ward 1 collaboration

Audra Devoto 1 collaboration

Christine He 1 collaboration

Alex Thomas 1 collaboration

Paula Matheus-Carnevali 1 collaboration

Christine Sun 1 collaboration

Daniela S A Goltsman 1 collaboration

Mikayla A Borton 1 collaboration

Alexander L Jaffe 1 collaboration

Tara C Nelson 1 collaboration

Rose Kantor 1 collaboration

Ray Keren 1 collaboration

Katherine R Lane 1 collaboration

Ibrahim F Farag 1 collaboration

Kari Finstad 1 collaboration

Ronald Amundson 1 collaboration

Jinglie Zhou 1 collaboration

Susannah G Tringe 1 collaboration

Wen-Jun Li 1 collaboration

Kelly Wrighton 1 collaboration

Sue Harrison 1 collaboration

Michael Morowitz 1 collaboration

David A Relman 1 collaboration

Jennifer A Doudna 1 collaboration

Anne-Catherine Lehours 1 collaboration

Lesley Warren 1 collaboration

Jamie H D Cate 1 collaboration

Samantha L Peters 1 collaboration

Haley Gause 1 collaboration

Alexander D Johnson 1 collaboration

Robert L Hettich 1 collaboration

Brian Yu 1 collaboration

Noel T Mueller 1 collaboration

Jing Qian 1 collaboration

Emily N Yeo 1 collaboration