Publications – The Ley Lab

2025

Clinical translation of microbiome research

Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K and Knight R.

Nature Medicine.

(2025).

DOI: https://doi.org/10.1038/s41591-025-03615-9

Cross-kingdom-mediated detection of intestinal protozoa through NLRP6.

Winsor NJ, Bayer G, Singh O, Chan JK, Li LY, Lieng BY, Foerster E, Popovic A, Tsankov BK, Maughan H, Lemire P, Tam E, Streutker C, Chen L, Heaver SL, Ley RE, Parkinson J, Montenegro-Burke JR, Birchenough GMH, Philpott DJ and Girardin SE.

Cell Host & Microbe.

In press.

(2025).

DOI: https://doi.org/10.1016/j.chom.2025.02.008

In vitro microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier.

Rytter H, Naimi S, Wu G, Lewis J, Duquesnoy M, Vigué L, Tenaillon O, Belda E, Vazquez-Gomez M, Touly N, Arnone D, Hao F, Ley RE, Clément K, Peyrin-Biroulet L, Patterson AD, Gewirtz AT and Chassaing B.

Gut.

Online ahead of print.

(2025).

DOI: https://gut.bmj.com/content/early/2025/01/13/gutjnl-2024-333925

Medication use is associated with distinct microbial features in anxiety and depression.

Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP and Knight R; Alzheimer Gut Microbiome Project Consortium.

Molecular Psychiatry.

Epub ahead of print.

(2025).

DOI: https://doi.org/10.1038/s41380-024-02857-2

2024

Prevention and cure of murine C. difficile infection by a Lachnospiraceae strain

Noriega Tejada J, Walters WA, Wang Y, Kordahi M, Chassaing B, Pickard J, Nunez G, Ley RE and Gewirtz AT

Gut Microbes.

Article: 2392872.

(2024).

DOI: https://doi.org/10.1080/19490976.2024.2392872

Stress-sensitive neural circuits change the gut microbiome via duodenal glands

Chang H, Perkins MH, Novaes LS, Qian F, Zhang T, Neckel PH, Scherer S, Ley RE, Han W and de Araujo IE

Cell.

187:1-20.

(2024).

DOI: https://doi.org/10.1016/j.cell.2024.07.019

Gut bacterial metabolism produces neuroactive steroids in pregnant women.

Huus KE and Ley RE.

Life Metabolism.

Accepted manuscript.

(2024).

DOI: https://doi.org/10.1093/lifemeta/loae030

Gut microbiome diversity within Clostridia is negatively associated with human obesity.

Salazar-Jaramillo L, de la Cuesta-Zuluaga J, Chica LA, Cadavid M, Ley RE, Reyes A and Escobar JS

mSystems.

0:e00627-24.

(2024).

DOI: https://doi.org/10.1128/msystems.00627-24

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution.

Enav H, Paz I and Ley RE.

Nature Biotechnology.

(2024).

DOI: https://doi.org/10.1038/s41587-024-02276-2

Tracking gene order provides a new perspective on intraspecific evolution in microbiotas.

Enav H and Ley RE.

Nature Biotechnology.

(2024).

DOI: https://doi.org/10.1038/s41587-024-02277-1

Spatially resolved lipidomics shows conditional transfer of lipids produced by Bacteroides thetaiotaomicron into the mouse gut.

Mirretta Barone C, Heaver SL, Gruber L, Zundel F, Vu DL and Ley RE.

Cell Host & Microbe.

32:1025-1036.

(2024).

DOI: https://doi.org/10.1016/j.chom.2024.04.021

Integrating research on bacterial pathogens and commensals to fight infections—an ecological perspective.

Maier L, Stein-Thoeringer C, Ley RE, Brötz-Oesterhelt H, Link H, Ziemert N, Wagner S and Peschel A.

The Lancet Microbe.

In press, corrected proof.

(2024).

DOI: https://doi.org/10.1016/S2666-5247(24)00049-1

The keystone gut species Christensenella minuta boosts gut microbial biomass and voluntary physical activity in mice.

Akbuğa-Schön T, Suzuki T, Jakob D, Vu DL, Waters JL and Ley RE.

mBIO.

15:e02836-23.

(2024).

DOI: https://doi.org/10.1128/mbio.02836-23

Human intestinal microbiome determines individualized inflammatory response to dietary emulsifier carboxymethylcellulose consumption.

Daniel N, Wu GD, Walters W, Compher C, Ni J, Delaroque C, Albenberg L, Ley RE, Patterson AD, Lewis JD, Gewirtz AT and Chassaing B.

Cellular and Molecular Gastroenterology and Hepatology.

17:315-318.

(2024).

DOI: https://doi.org/10.1016/j.jcmgh.2023.11.001

A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the USA.

Walters WA, Ley C, Hastie T, Ley RE and Parsonnet J.

BMC Medical Research Methodology.

24:27.

(2024).

DOI: https://doi.org/10.1186/s12874-024-02145-1

2023

An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter.

Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dräger A, Ley RE, Marcellin E, Angenent LT and Molitor B.

iScience.

26:108016.

(2023).

DOI: https://doi.org/10.1016/j.isci.2023.108016

Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy.

de la Cuesta-Zuluaga J, Huus KE, Youngblut ND, Escobar JS and Ley RE.

Gut Microbes.

15:2246634.

(2023).

DOI: https://doi.org/10.1080/19490976.2023.2246634

The sound of silence.

Clasen S.

Science.

381:37-38.

(2023).

DOI: https://doi.org/10.1126/science.adi6265

Toward microbiome engineering: Expanding the repertoire of genetically tractable members of the human gut microbiome.

Marsh JW, Kirk C and Ley RE.

Annual Review of Microbiology.

77:427-449.

(2023).

DOI: https://doi.org/10.1146/annurev-micro-032421-112304

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.

Mineeva O, Danciu D, Schölkopf B, Ley RE, Rätsch G, Youngblut ND.

PLoS Computational Biology.

19:e1011001.

(2023).

DOI: https://doi.org/10.1371/journal.pcbi.1011001

Psyllium fiber protects against colitis via activation of bile acid sensor FXR.

Bretin A, Zou J, Yeoh BS, Ngo VL, Winer S, Winer DA, Reddivari L, Pellizzon M, Walters WA, Patterson AD, Ley RE, Chassaing B, Vijay-Kumar M and Gewirtz AT.

Cellular and Molecular Gastroenterology and Hepatology.

15:1421-1442.

(2023).

DOI: https://doi.org/10.1016/j.jcmgh.2023.02.007

Longitudinal comparison of the developing gut virome in infants and their mothers.

Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J and Chiu CY.

Cell Host & Microbe.

31:187–198.

(2023).

DOI: https://doi.org/10.1016/j.chom.2023.01.003

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.

Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M and Walter J.

Nature.

613:639-649.

(2023).

DOI: https://doi.org/10.1038/s41586-022-05546-8

Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis.

Pinto Y, Frishman S, Turjeman S, Eshel A, Nuriel-Ohayon M, Shrossel O, Ziv O, Walters W, Parsonnet J, Ley C, Johnson EL, Kumar K, Schweitzer R, Khatib S, Magzal F, Muller E, Tamir S, Tenenbaum-Gavish K, Rautava S, Salminen S, Isolauri E, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Borenstein E, Ley RE, Schwartz B, Louzoun Y, Hadar E and Koren O.

Gut.

5:918-928.

(2023).

DOI: http://dx.doi.org/10.1136/gutjnl-2022-328406

Silent recognition of flagellins from human gut commensal bacteria by toll-like receptor 5.

Clasen SJ, Bell MEW, Borbón A, Lee DH, Henseler ZM, de la Cuesta-Zuluaga J, Parys K, Zou J, Wang Y, Altmannova V, Youngblut ND, Weir JR, Gewirtz AT, Belkhadir Y and Ley RE.

Science Immunology.

8:eabq7001.

(2023).

DOI: https://doi.org/10.1126/sciimmunol.abq7001

2022

Interpreting tree ensemble machine learning models with endoR.

Ruaud A, Pfister N, Ley RE and Youngblut ND.

PLoS Computational Biology.

18:e1010714.

(2022).

DOI: https://doi.org/10.1371/journal.pcbi.1010714

Codiversification of gut microbiota with humans.

Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Mbong Ngwese M, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Song LH, Spector TD, Muehlbauer AL, Marchi N, Kang H, Maier L, Blekhman R, Ségurel L, Ko G, Youngblut ND, Kremsner P and Ley RE.

Science.

377:1328-1332.

(2022).

DOI: https://doi.org/10.1126/science.abm7759

Characterization of inositol lipid metabolism in gut-associated Bacteroidetes.

Heaver SL, Le HH, Tang P, Baslé A, Mirretta Barone C, Vu DL, Waters JL, Marles-Wright J, Johnson EL, Campopiano DJ and Ley RE.

Nature Microbiology.

7:986–1000.

(2022).

DOI: https://doi.org/10.1038/s41564-022-01152-6

The developing infant gut microbiome: A strain-level view.

Enav H, Bäckhed F and Ley RE.

Cell Host & Microbe.

30:627-638.

(2022).

DOI: https://doi.org/10.1016/j.chom.2022.04.009

Randomized controlled-feeding study of dietary emulsifier carboxymethylcellulose reveals detrimental impacts on the gut microbiota and metabolome.

Chassaing B, Compher C, Bonhomme B, Liu Q, Tian Y, Walters W, Nessel L, Delaroque C, Hao F, Gershuni V, Chau L, Ni J, Bewtra M, Albenberg L, Bretin A, McKeever L, Ley RE, Patterson AD, Wu GD, Gewirtz AT and Lewis JD

Gastroenterology.

162:743–756.

(2022).

DOI: https://doi.org/10.1053/j.gastro.2021.11.006

Microbiome engineering: Taming the untractable.

Marsh JW and RE Ley.

Cell.

185:416-418.

(2022).

DOI: https://doi.org/10.1016/j.cell.2021.12.034

Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes.

Youngblut ND, de la Cuesta-Zuluaga J and Ley RE.

Environmental Microbiology.

24:3966-3984.

(2022).

DOI: https://doi.org/10.1111/1462-2920.15910

Microbes set the (woodrat) menu: Host genetics control diet-specific gut microbes.

Suzuki TA and Ley RE.

Proceedings of the National Academy of Sciences, USA.

119:e2120125118.

(2022).

DOI: https://doi.org/10.1073/pnas.2120125118

2021

Vertebrate host phylogeny influences gut archaeal diversity.

Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, Stalder G, Farnleitner AH and Ley RE.

Nature Microbiology.

6:1443–1454.

(2021).

DOI: https://doi.org/10.1038/s41564-021-00980-2

Blowing hot and cold: body temperature and the microbiome.

Huus KE and Ley RE.

mSystems.

6:e00707-21.

(2021).

DOI: https://doi.org/10.1128/msystems.00707-21

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets.

Youngblut ND and Ley RE.

PeerJ.

9:e12198.

(2021).

DOI: https://doi.org/10.7717/peerj.12198

MicroRNAs and extracellular vesicles in the gut: new host modulators of the microbiome.

Du X, Ley R and Buck AH.

Microlife.

2:uqab010.

(2021).

DOI: https://doi.org/10.1093/femsml/uqab010

Informative regions in viral genomes.

Moreno-Gallego JL and Reyes A.

Viruses.

13:1164.

(2021).

DOI: https://doi.org/10.3390/v13061164

The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil.

Di Rienzi S, Johnson E, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT and Ley RE.

The Journal of Nutritional Biochemistry.

97:108808.

(2021).

DOI: https://doi.org/10.1016/j.jnutbio.2021.108808

Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb.nov. based on whole genome analysis.

Liu X, Sutter JS, de la Cuesta-Zuluaga J, Waters JL, Youngblut ND and Ley RE.

International Journal of Systematic and Evolutionary Microbiology.

71:004774.

(2021).

DOI: https://doi.org/10.1099/ijsem.0.004774

Free-living psychrophilic bacteria of the genus Psychrobacter are descendents of pathobionts.

Welter DK, Ruaud A, Henseler ZM, de Jong HN, van Coerverden de Groot P, Michaux J, Goermezano L, Waters JL, Youngblut ND and Ley RE.

mSystems.

6:e00258-21.

(2021).

DOI: https://doi.org/10.1128/msystems.00258-21

Genomic insights into adaptations of trimethylamine-utilizing methanogens to diverse habitats, including the human gut.

de la Cuesta-Zuluaga J, Spector TD, Youngblut ND and Ley RE.

mSystems.

6:e00939-20.

(2021).

DOI: https://doi.org/10.1128/msystems.00939-20

2020

The role of the microbiota in human genetic adaptation.

Suzuki TA and Ley RE.

Science.

370:eaaz6827.

(2020).

DOI: https://doi.org/10.1126/science.aaz6827

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity.

Youngblut ND, de la Cuesta-Zuluaga J, Reischer GH, Dauser S, Schuster N, Walzer C, Stalder G, Farnleitner A and Ley RE.

mSystems.

5:e01045-20.

(2020).

DOI: https://doi.org/10.1128/mSystems.01045-20

Strain-level analysis of Bifidobacterium spp. from gut microbiomes of adults of differing lactase persistence genotypes.

Schmidt V, Enav H, Spector T, Youngblut ND and Ley RE.

mSystems.

5:e00911-20.

(2020).

DOI: https://doi.org/10.1128/mSystems.00911-20

Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler’s diarrhea.

Walters WA, Reyes F, Soto GM, Reynolds ND, Fraser JA, Aviles R, Tribble DR, Irvin AP, Loughnane NK, Gutierrez RL, Riddle MS, Ley RE and Goodson MS.

PLoS One.

15:e0236703.

(2020).

DOI: https://doi.org/10.1371/journal.pone.0236703

Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels.

Johnson EL, Heaver SL, Waters JL, Kim BI, Bretin A, Goodman AL, Gewirtz AT, Worgall TS and Ley RE.

Nature Communications.

11:2471.

(2020).

DOI: https://doi.org/10.1038/s41467-020-16274-w

DeepMAsED: Evaluating the quality of metagenomics assemblies.

Mineeva O, Rojas-Carulla M, Ley RE, Schoelkopf B and Youngblut ND.

Bioinformatics.

36:3011-3017.

(2020).

DOI: https://doi.org/10.1093/bioinformatics/btaa124

Struo: a pipeline for building custom databases for common metagenome profilers.

de la Cuesta-Zuluaga J, Ley RE and Youngblut ND.

Bioinformatics.

36:2314-2315.

(2020).

DOI: https://doi.org/10.1093/bioinformatics/btz899

Syntrophy via interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut.

Ruaud A, Esquivel-Elizondo S, de la Cuesta-Zuluaga J, Waters JL, Angenent LT, Youngblut ND and Ley RE.

mBio.

11:e03235-19.

(2020).

DOI: https://doi.org/10.1128/mbio.03235-19

Iron deficiency causes wrinkles in host-commensal relationships.

Clasen S and Ley RE.

Cell Metabolism.

31:8-10.

(2020).

DOI: https://doi.org/10.1016/j.cmet.2019.12.003

2019

Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases.

Tran HQ, Ley RE, Gewirtz AT and Chassaing B.

Nature Communications.

10:5650.

(2019).

DOI: https://doi.org/10.1038/s41467-019-13538-y

Interactions between the gut microbiome and mucosal immunoglobulins A, M, and G in the developing infant gut.

Janzon A, Goodrich JK, Koren O, TEDDY Study Group, Waters JL and Ley RE.

mSystems.

4:e00612-19.

(2019).

DOI: https://doi.org/10.1128/msystems.00612-19

The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health.

Waters JL and Ley RE.

BMC Biology.

17:83.

(2019).

DOI: https://doi.org/10.1186/s12915-019-0699-4

Expanding the scope and scale of microbiome research.

Knight R, Ley RE, Raes J and Grice EA.

Genome Biology.

20:191.

(2019).

DOI: https://doi.org/10.1186/s13059-019-1804-2

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR et al.

Nature Biotechnology.

37:852-857.

(2019).

DOI: https://doi.org/10.1038/s41587-019-0209-9

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades.

Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE and Farnleitner AH.

Nature Communications.

10:2200.

(2019).

DOI: https://doi.org/10.1038/s41467-019-10191-3

Age- and sex-dependent patterns of gut microbial diversity in human adults.

De la Cuesta Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R and Thackray VG.

mSystems.

4:e00261-19.

(2019).

DOI: https://doi.org/10.1128/msystems.00261-19

Human salivary amylase gene copy number impacts oral and gut microbiomes.

Poole AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG and Ley RE.

Cell Host & Microbe.

25:553-564.

(2019).

DOI: https://doi.org/10.1016/j.chom.2019.03.001

Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins.

Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector T, Bell JT, Youngblut ND, Hewson I, Reyes A and Ley RE.

Cell Host & Microbe.

25:261-272.

(2019).

DOI: https://doi.org/10.1016/j.chom.2019.01.019

Murine methyl donor deficiency impairs early growth in association with dysmorphic small intestinal crypts and reduced gut microbial diversity.

Alves da Silva AV, Oliveira SB, DiRienzi SC, Dehan LM, Rood JK, Carreira VS, Le H, Maier EA, Betz KJ, Aihara E, Ley RE, Preidis GE, Shen L and Moore SR.

Current Developments in Nutrition.

3;nzy070 .

(2019).

DOI: https://doi.org/10.1093/cdn/nzy070

2018

Large-scale replicated field study of maize rhizosphere identifies heritable microbes.

Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi Q, Knight R, Glavina del Rio T, Tringe SG, Buckler ES, Dangl JL and Ley RE.

Proceedings of the National Academy of Sciences of the United States of America.

115:7368-7373.

(2018).

DOI: https://doi.org/10.1073/pnas.1800918115

American gut: an open platform for citizen science microbiome research.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzales A, et al.

mSystems.

3:e00031-18.

(2018).

DOI: https://doi.org/10.1128/msystems.00031-18

Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids.

Di Rienzi SC, Jacobson J, Kennedy EA, Bell ME, Shi Q, Waters JL, Lawrence P, Brenna JT, Britton RA, Walter J and Ley RE.

eLife.

7:e32581.

(2018).

DOI: https://doi.org/10.7554/eLife.32581

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hatori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Othman H, O'Toole PW, Quince C, Reman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R and Bork P.

Nature Microbiology.

3:8-16.

(2018).

DOI: https://doi.org/10.1038/s41564-017-0072-8

Sphingolipids in host-microbial interactions.

Heaver SL, Johnson EL and Ley RE.

Current Opinion in Microbiology.

43:92-99.

(2018).

DOI: https://doi.org/10.1016/j.mib.2017.12.011

2017

Genomic features of bacterial adaptation to plants.

Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, Devescoyvi G, Stillman K, Monteiro F, Rangel Alvarez B, Lundberg DS, Lu TY, Lebens S, Jin Z, McDonald M, Klein AP, Fletcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Bringe SG, Wolke T and Dang JL.

Nature Genetics.

50:138-150.

(2017).

DOI: https://doi.org/10.1038/s41588-017-0012-9

The relationship between the human genome and microbiome comes into view.

Goodrich JK, Davenport ER, Clark AG and Ley RE.

Annual Review of Genetics.

51:413-433.

(2017).

DOI: https://doi.org/10.1146/annurev-genet-110711-155532

Alterations to the gut microbiome impair bone strength and tissue material properties.

Guss JD, Horsfield MW, Fontenele FF, Sandoval TN, Luna M, Apoorva F, Lima SF, Bicalho RC, Singh A, Ley RE, van der Meulen MC, Goldring SR and Hernandez CJ.

Journal of Bone and Mineral Research.

32:1343-1353.

(2017).

DOI: https://doi.org/10.1002/jbmr.3114

Vertical sleeve gastrectomy reduces blood pressure and hypothalamic endoplasmic reticulum stress in mice.

McGavigan AK, Henseler ZM, Garibay D, Butler SD, Jayasinghe S, Ley RE, Davisson RL and Cummings BP.

Disease Models & Mechanisms.

10:235-243.

(2017).

DOI: https://doi.org/10.1242/dmm.027474

2016

Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes.

Johnson EL, Heaver SL, Walters WA and Ley RE.

Journal of Molecular Medicine (Berl).

95:1-8.

(2016).

DOI: https://doi.org/10.1007/s00109-016-1492-2

ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.

Davenport ER, Goodrich JK, Bell JT, Spector TD, Ley RE and Clark AG.

BMC Genomics.

17:941.

(2016).

DOI: https://doi.org/10.1186/s12864-016-3290-1

Heritbale components of the human fecal microbiome are associated with visceral fat.

Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD and Bell JT.

Genome Biology.

17:189.

(2016).

DOI: https://doi.org/10.1186/s13059-016-1052-7

Corralling flagellated microbiota.

Ley RE and Gewirtz AT.

The New England Journal of Medicine.

375:85-87.

(2016).

DOI: https://doi.org/10.1056/NEJMcibr1604801

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome.

Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE and Hanson MR.

Microbiome.

4:30.

(2016).

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Genome Medicine.

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Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics.

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Frontiers in Microbiology.

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Novel rhizosphere soil alleles for the enzyme 1-aminocyclopropane-1-carboxylate deaminase queried for function with an in vivo competition assay.

Jin Z, Di Renzi SC, Janzon A, Werner JJ, Angenent LT, Fowler DM, Dangl JL and Ley RE.

Applied and Environmental Microbiology.

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66:226-234.

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Genome Biology.

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Gut-microbiota-metabolite axis in early renal function decline.

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PLoS One.

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Microbiota and host nutrition across plant and animal kingdoms.

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Cell Host & Microbe.

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Selection on plant microbiomes reveals reproducible impacts on plant function.

Panke-Buisse K, Poole AC, Goodrich JK, Ley RE and Kao-Kniffin J.

ISME Journal.

9:980-989.

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Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome.

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Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis.

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Linking genetic variation in toll-like receptor 5 genes to the gut microbiome’s potential to cause inflammation.

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Gastroenterology.

147:1363-1377.

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Human genetics shape the gut microbiome.

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Cell.

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Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Marhurkar A, Ravel J and White O.

Cell.

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Cell.

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Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice.

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Cell Reports.

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Nature Medicine.

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2013

Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut.

Cullender TC, Chassaing B, Janzon A, Kumar K, Muller C, Werner JJ, Angenent LT, Bell ME, Hay AG, Peterson DA, Walter J, Vijay-Kumar M, Gewirtz AT and Ley RE.

Cell Host Microbe.

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The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.

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Proceedings of the National Academy of Sciences of the United States of America.

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Integrated and novel survey methods for rhinoceros populations confirm the extinction of Rhinoceros sondaicus annamiticus from Vietnam.

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Host remodeling of the gut microbiome and metabolic changes during pregnancy.

Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed H, Gonzalez A, Werner JJ, Angenent LT, Knight R, Bäckhed F Isolauri E, Salminen S and Ley RE.

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Defining the core arabidopsis thaliana root microbiome.

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Branched chain fatty acids reduce the incidence of necrotizing enterocolitis and alter gastrointestinal microbial ecology in a neonatal rat model.

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Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT and Ley RE.

Proceedings of the National Academy of Sciences USA.

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Human oral, gut, and plaque microbiota in patients with atherosclerosis.

Koren O, Spor A, Felin J, Fak F, Stombaugh J, Tremaroli V, Behre CB, Knight R, Fagerberg B, Ley RE and Bäckhed F.

Proceedings of the National Academy of Sciences USA.

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2010

QIIME allows analysis of high-throughput community sequencing data.

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Metabolic syndrome and altered gut microbiota in mice lacking toll-like receptor 5.

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Genome Biology.

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2009

A core gut microbiome in obese and lean twins.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R and Gordon JI.

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Innate immunity and intestinal microbiota in the development of type 1 diabetes.

Wen L, Volchkov P, Ley RE, Stranges P, Avanesyan L, Stonebraker A, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI and Chervonsky AV.

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Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird.

Godoy-Vitorino F, Ley RE, Gao Z, Pei Z, Ortiz-Zuazaga H, Pericchi LR, Garcia-Amado MA, Michelangeli F, Blaser MJ, Gordon JI and Dominguez-Bello MG.

Applied and Environmental Microbiology.

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Worlds within worlds: evolution of the vertebrate gut microbiota.

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Evolution of mammals and their gut microbes.

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R and Gordon JI.

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Host-bacterial coevolution and the search for new drug targets.

Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI and Knight R.

Current Opinion in Chemical Biology.

12:109-114.

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Eucaryotic diversity in a hypersaline microbial mat.

Feazel LM, Spear JR, Berger AB, Harris JK, Frank DN, Ley RE and Pace NR.

Applied and Environmental Microbiology.

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The human microbiome project.

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Evolution of symbiotic bacteria in the distal human intestine.

Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD and Gordon JI.

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Microbial ecology: human gut microbes associated with obesity.

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An obesity-associated gut microbiome with increased capacity for energy harvest.

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Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection.

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The human intestinal microbiota and its relationship to energy balance.

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Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat.

Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin M and Pace NR.

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Extending our view of self: the Human Gut Microbiome Initiative (HGMI).

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Obesity alters gut microbial ecology.

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Soil microbial dynamics in Costa Rica: seasonal and biogeochemical constraints.

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Impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils.

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Microbial population dynamics in an extreme environment: controlling factors in unvegetated talus soils at 3750m in the Colorado Rocky Mountains.

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Sub-freezing activity of microorganisms and the potential habitability of Mars’ polar regions.

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Fungal and bacterial responses to amino acid and phenolic compound additions in high altitude barren soil.

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Alteration of ecosystem nitrogen dynamics by exotic plants: a case study of C4 grasses in Hawai’i.

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Characterization and description of Clostridium filamentum ETTB, a novel gut bacterium with TLR5 modulating properties.

Makki K, Martino ME, Alberdi A, Aizpurua O, Quagliariello A, Olsson L, Clasen S, Jönsson J, Brolin H, Dwibedi C, Yang G, Favero C, Bergh P-O, Schnupf P, Ley RE, Khan M-T, Tremaroli V and Bäckhed F.

bioRxiv.

2025.02.28.640726 .

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DOI: https://doi.org/10.1101/2025.02.28.640726

Flagellin in the human gut microbiome is a diet-adjustable adjuvant for vaccination.

Huus KE, uHEAT Clinical Study Group, Tan YH, Abo H, Keller R, Atay E, Vu DL, Dauser S, Prokipchuk A, Tyakht A, Youngblut N, Chassaing B, Kang S-M, Parsonnet J, Kremsner PG, Maier L, Gewirtz AT, Esen M and Ley RE.

bioRxiv.

2025.02.21.639485.

(2025).

DOI: https://doi.org/10.1101/2025.02.21.639485

Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.

Ngwese MM, Adegbite BR, Zinsou JF, Fitzstevens JL, Schmidt VT, Moure PAN, Maloum MN, Tyakht AV, Huus KE, Youngblut ND, Kremsner PG, Akim AA and Ley RE.

bioRxiv.

2025.01.23.634469.

(2025).

DOI: https://doi.org/10.1101/2025.01.23.634469

Selection and transmission of the gut microbiome alone shifts mammalian behavior.

Suzuki TA, Akbuga-Schoen T, Waters JL, Jakob D, Vu DL, Ballinger MA, Di Rienzi SC, Chang H, de Araujo IE, Tyakht AV and Ley RE.

bioRxiv.

2025.01.21.634013.

(2025).

DOI: https://doi.org/10.1101/2025.01.21.634013

Kinetic and structure-based comparisons of silent and stimulatory flagellin interactions with TLR5.

Bell MEW, Haag M, Clasen SJ, Boecker MA, Maksymenko K, Koch I, Hipp K, Hartmann M, Weir JR, Merino F and Ley RE.

bioRxiv.

2024.12.09.627598.

(2024).

DOI: https://doi.org/10.1101/2024.12.09.627598

Medication use is associated with distinct microbial features in anxiety and depression.

Hazel Dilmore A, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, Mahmoudian Dehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R, Alzheimer Gut Microbiome Project Consortium.

bioRxiv.

2024.03.19.585820.

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DOI: https://doi.org/10.1101/2024.03.19.585820

ResMiCo: Increasing the Quality of Metagenome-Assembled Genomes with Deep Learning.

Mineeva O, Danciu D, Schoelkopf B, Ley RE, Raetsch G and Youngblut ND.

bioRxiv.

2022.06.23.497335.

(2022).

DOI: https://doi.org/10.1101/2022.06.23.497335

Silent recognition of flagellins from human gut commensal bacteria by toll-like receptor 5.

Clasen SJ, Bell MEW, Lee D-H, Henseler ZM, Borbón A, de la Cuesta-Zuluaga J, Parys K, Zou J, Youngblut ND, Gewirtz AT, Belkhadir Y and Ley RE.

bioRxiv.

2022.04.12.488020.

(2022).

DOI: https://doi.org/10.1101/2022.04.12.488020

Interpreting tree ensemble machine learning models with endoR.

Ruaud A, Pfister N, Ley RE and Youngblut ND.

bioRxiv.

2022.01.03.474763v1 .

(2022).

DOI: https://doi.org/10.1101/2022.01.03.474763

SynTracker: a synteny-based tool for tracking microbial strains.

Enav H and Ley RE.

bioRxiv.

(2021).

DOI: https://doi.org/10.1101/2021.10.06.463341

Codiversification of gut microbiota with humans.

Suzuki TA, Fitzstevens L, Schmidt VT, Enav H, Huus K, Mbong M, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Huu Song L, Spector TD, Muehlbauer AL, Marchi N, Blekhman R, Segurel L, Youngblut ND, Kremsner P and Ley RE.

bioRxiv.

2021.10.12.462973.

(2021).

DOI: https://doi.org/10.1101/2021.10.12.462973

First trimester gut microbiome induces Inflammation-dependent gestational diabetes phenotype in mice.

Pinto Y, Frishman S, Turjeman S , Eshel A, Nuriel-Ohayon M, Ziv O, Walters W, Parsonnet J, Ley C, Johnson E, Schweitzer R, Khatib S, Magzal F, Tamir S, Tenenbaum Gavish K, Rautava S, Salminen S, Isolauri E, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Ley R, Schwartz B, Hadar E, Louzoun Y, Koren O.

medRxiv.

2021.09.17.21262268.

(2021).

DOI: https://doi.org/10.1101/2021.09.17.21262268

Inositol lipid synthesis is widespread in host-associated Bacteroidetes.

Heaver SL , Le HH, Tang P, Baslé A, Marles-Wright J, Johnson EL, Campopiano DJ and Ley RE.

bioRxiv.

(2021).

DOI: https://doi.org/10.1101/2021.04.26.441525

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets.

Youngblut ND and RE Ley.

bioRxiv.

(2021).

DOI: https://doi.org/10.1101/2021.02.10.430604

High-resolution QTL mapping with Diversity Outbred mice identifies genetic variants that impact gut microbiome composition.

Schlamp F, Zhang DY, Cosgrove E, Simecek P, Edwards M, Goodrich JK, Ley RE, Churchill GA, and Clark AG.

bioRxiv.

(2021).

DOI: https://doi.org/10.1101/722744

Strong influence of vertebrate host phylogeny on gut archaeal diversity.

Youngblut ND, Reischer GH, Dauser S, Walzer C, Stalder G, Farnleitner AH and Ley RE

bioRxiv.

(2020).

DOI: https://doi.org/10.1101/2020.11.10.376293

Free-living psychrophilic bacteria of the genus Psychrobacter are descendents of pathobionts.

Welter DK, Ruaud A, Henseler ZM, de Jong HN, van Coerverden de Groot P, Michaux J, Goermezano L, Waters JL, Youngbluy ND and Ley RE.

bioRxiv.

(2020).

DOI: https://doi.org/10.1101/2020.10.23.352302

Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb.nov. based on whole genome analysis.

Liu X, Sutter JS, de la Cuesta-Zuluaga J, Waters JL, Youngblut ND and Ley RE.

bioRxiv.

2020.09.21.306662.

(2020).

DOI: https://doi.org/10.1101/2020.09.21.306662

Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut.

de la Cuesta-Zuluaga J, Spector TD, Youngblut ND and Ley RE.

bioRxiv.

(2020).

DOI: https://doi.org/10.1101/2020.09.17.302828

The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil.

Di Rienzi S, Johnson E, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT and RE Ley.

bioRxiv.

2020.09.03.281626.

(2020).

DOI: https://doi.org/10.1101/2020.09.03.281626

Strain-level analysis of Bifidobacterium spp. from gut microbiomes of adults of differing lactase persistence genotypes.

Schmidt V, Enav H, Spector T, Youngblut ND and RE Ley.

bioRxiv.

2020.07.16.207811.

(2020).

DOI: https://doi.org/10.1101/2020.07.16.207811

Incorporating genome-based phylogeny and trait similarity into diversity assessments helps to resolve a global collection of human gut metagenomes.

Youngblut ND, de la Cuesta-Zuluaga J and RE Ley.

bioRxiv.

2020.07.16.207845.

(2020).

DOI: https://doi.org/10.1101/2020.07.16.207845

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity.

Youngblut ND, de la Cuesta-Zuluaga J, Reischer GH, Dauser S, Schuster N, Walzer C, Stalder G, Farnleitner A and Ley RE.

bioRxiv.

135962.

(2020).

DOI: https://doi.org/10.1101/2020.06.05.135962

Syntrophy via interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut.

Ruaud A, Esquivel-Elizondo S, de la Cuesta-Zuluaga J, Waters JL, Angenent LT, Youngblut ND, and Ley RE.

bioRxiv.

872333.

(2019).

DOI: https://doi.org/10.1101/872333

Struo: a pipeline for building custom databases for common metagenome profilers.

de la Cuesta-Zuluaga J, Ley RE and Youngblut ND.

bioRxiv.

774372.

(2019).

DOI: https://doi.org/10.1101/774372

DeepMAsED: Evaluating the quality of metagenomic assemblies.

Rojas-Carulla M, Ley RE, Schoelkopf B and Youngblut ND.

bioRxiv.

(2019).

DOI: https://www.biorxiv.org/content/10.1101/763813v1

Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut.

Janzon A, Goodrich JK, Koren O, the TEDDY study group, Waters J and Ley R.

bioRxiv.

637959.

(2019).

DOI: https://doi.org/10.1101/637959

Sphingolipid production by gut Bacteroidetes regulates glucose homeostasis.

Johnson EL, Heaver SL, Waters JL, Kim BI, Bretin A, Goodman AL, Gewirtz AT, Worgall TS and Ley RE.

bioRxiv.

632877.

(2019).

DOI: https://doi.org/10.1101/632877

GeNet: Deep representations for metagenomics.

Rojas-Carulla M, Tolstikhin I, Luque G, Youngblut N, Ley R and Schölkopf B.

arXiv.

(2019).

DOI: https://arxiv.org/pdf/1901.11015

Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins.

Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector T, Bell JT, Youngblut N, Hewson I, Reyes A and Ley RE.

bioRxiv.

(2019).

DOI: https://doi.org/10.1101/509273

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, et al.

PeerJ Preprints.

6:e27295v2.

(2018).

DOI: https://doi.org/10.7287/peerj.preprints.27295v2

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades.

Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE and Farnleitner AH.

bioRxiv.

484006.

(2018).

DOI: https://doi.org/10.1101/484006

Human salivary amylase gene copy number impacts oral and gut microbiomes.

Poole AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG and Ley RE.

bioRxiv.

359737.

(2018).

DOI: https://doi.org/10.1101/359737

Wie der Toll-like-Rezeptor 5 die Immunantwort umgeht

Clasen S and Ley RE.

Biospektrum.

19 Oct 2023

https://link.springer.com/article/10.1007/s12268-023-2017-5/

Like genes, your gut microbes pass from one generation to the next

Suzuki T and Ley R.

Salon.

30 Sep 2022

https://www.salon.com/2022/09/30/like-genes-your-gut-microbes-pass-from-one-generation-to-the-next-_partner/

The African microbiome: Clues of human adaptation and population history.

Schmidt VT and Ley RE.

Kems Verlag, Tübingen, Germany. In book: Modern human origins and dispersal, Sahle Y, Reyes-Centeno H and Bentz C (Eds.).

1 May 2019

Women in metabolism: Part IV.

Ley RE.

Cell Metabolism Voices. 24:767-770.

13 Dec 2016

https://doi.org/10.1016/j.cmet.2016.11.014

The human intestinal microbiota and microbiome.

Koren O and Ley RE.

Textbook of Gastroenterology, Sixth edition.

27 Nov 2015

https://doi.org/10.1002/9781118512074.ch32

Probiotics, prebiotics, and the host microbiome: the science of translation.

Petschow B, Doré J, Hibberd P, Dinan T, Reid G, Blaser M, Cani PD, Degnan FH, Foster J, Gibson G, Hutton J, Klaenhammer TR, Ley RE, Nieuwdorp M, Pot B, Relman D, Serafijn A and Sanders ME.

Annals of the New York Academy of Sciences. 1306:1-17.

1 Dec 2013

https://doi.org/10.1111/nyas.12303

The human intestinal microbiota and microbiome.

Ley RE and Gordon JI.

Textbook of Gastroenterology. Fifth edition (Dr. Tadataka Yamada, Ed.). Blackwell Publishing.

1 Oct 2011

In Person: Breaking all the rules.

Ley RE.

Science Career Magzine.

29 May 2009

https://www.science.org/content/article/person-breaking-all-rules

Profile: Ruth Ley. Gut reactions.

Pennisi E.

Science. 324:1136-1137.

29 May 2009

https://leylab.com/wp-content/uploads/2024/03/Gut-Reactions.pdf

Microbial competition and soil structure limit the expression of allelochemicals in nature.

Schmidt SK and Ley RE.

Principles and Practices in Plant Ecology: Alleochemical Interactions. (S.Inderjit, Ed.). CRC Press, p. 339-351.

2 Jan 1999

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