Publications – Tabs no Loop Grid – The Ley Lab

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

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

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

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

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

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

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

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).

DOI: https://doi.org/10.1186/s40168-016-0171-4

Crossover control study of the effect of personal care products containing triclosan on the microbiome.

Poole AC, Pischel L, Ley C, Suh G, Goodrich JK, Taggerty TD, Ley RE and Parsonnet J.

mSphere.

1:e00056-15.

(2016).

DOI: https://doi.org/10.1128/msphere.00056-15

Genetic determinants of the gut microbiome in UK twins.

Goodrich JK, Davenport ER, Jackson MA, Beaumont M, Knight R, Spector TD, Bell JT, Clark AG and Ley RE.

Cell Host & Microbe.

19:731-743.

(2016).

DOI: https://doi.org/10.1016/j.chom.2016.04.017

Proton pump inhibitors alter the composition of the gut microbiota.

Jackson MA, Goodrich JK, Maxan ME, Fredberg DE, Abrams JA, Poole AC, Sutter JL, Welter D, Ley RE, Bell JT, Spector TD and Steves CJ.

Gut.

65:749-756.

(2016).

DOI: http://dx.doi.org/10.1136/gutjnl-2015-310861

Cross-species comparisons of host genetic associations with the microbiome.

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

Science.

352:532-535.

(2016).

DOI: https://doi.org/10.1126/science.aad9379

Epithelial Sel1L is required for the maintenance of intestinal homeostasis.

Sun S, Lourie R, Cohen SB, Ji Y, Goodrich JK, Poole AC, Ley RE, Denkers EY, McGuckin MA, Long Q, Duhamel GE, Simpson KW and Qi L.

Molecular Biology of the Cell.

27:483-90.

(2016).

DOI: https://doi.org/10.1091/mbc.e15-10-0724

Prevotella in the gut: choose carefully.

Ley RE.

Nature reviews: Gastroenterology & Hepatology.

13:9–70.

(2016).

DOI: https://doi.org/10.1038/nrgastro.2016.4

Signatures of early frailty in the gut microbiota.

Jackson M, Jeffrey IB, Beaumont M, Bell JT, Clark AG, Ley RE, O’Toole PW, Spector TD and Steves CJ.

Genome Medicine.

8:8. .

(2016).

DOI: https://doi.org/10.1186/s13073-016-0262-7

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

Friedman ES, McPhillips LE, Werner JJ, Poole AC, Ley RE, Walter MT and Angenent LT.

Frontiers in Microbiology.

6:1523.

(2016).

DOI: https://doi.org/10.3389/fmicb.2015.01523

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.

82:1050-1059.

(2015).

DOI: https://doi.org/10.1128/AEM.03074-15

TGR5 contributes to glucoregulatory improvements after vertical sleeve gastrectomy in mice.

McGavigan AK, Garibay D, Henseler ZM, Chen J, Bettaieb A, Haj FG, Ley RE, Chouinard ML and Cummings BP.

Gut.

66:226-234.

(2015).

DOI: http://dx.doi.org/10.1136/gutjnl-2015-309871

Host genetic variation impacts microbiome composition across human body sites.

Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D and Clark AG.

Genome Biology.

16:191.

(2015).

DOI: https://doi.org/10.1186/s13059-015-0759-1

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

Barrios C, Beaumont M, Palmister T, Villar J, Goodrich JK, Clark A, Pascual J, Ley RE, Spector TD, Bell JT and Menni C.

PLoS One.

10:e0134311.

(2015).

DOI: https://doi.org/10.1371/journal.pone.0134311

Microbiota and host nutrition across plant and animal kingdoms.

Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S, McHardy AC, Dangl JL, Knight R, Ley RE and Schulze-Lefert P.

Cell Host & Microbe.

17:603-616.

(2015).

DOI: https://doi.org/10.1016/j.chom.2015.04.009

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.

(2015).

DOI: https://doi.org/10.1038/ismej.2014.196

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

Chassaing B, Koren O, Goodrich J, Poole A, Srinivasan S, Ley RE and Gewirtz AT.

Nature.

519:92-96.

(2015).

DOI: https://doi.org/10.1038/nature14232

The gene-microbe link.

Ley RE.

Nature.

518:S7.

(2015).

DOI: https://doi.org/10.1038/518S7a

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

Kumar H, Lund R, Laiho A, Lundelin K, Ley RE, Isolauri E and Salminen S.

MBio.

5:e02113-14.

(2014).

DOI: https://doi.org/10.1128/mbio.02113-14

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

Leifer CA, McConkey C, Li S, Chassaing B, Gewirtz AT and Ley RE.

Immunology Letters.

162: 3-9.

(2014).

DOI: https://doi.org/10.1016/j.imlet.2014.07.017

Intestinal epithelial cell toll-like receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice.

Chassaign B, Ley RE and Gewirtz AT.

Gastroenterology.

147:1363-1377.

(2014).

DOI: https://doi.org/10.1053/j.gastro.2014.08.033

Human genetics shape the gut microbiome.

Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG and Ley RE.

Cell.

159: 789-799.

(2014).

DOI: https://doi.org/10.1016/j.cell.2014.09.053

Advancing the microbiome research community.

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.

159: 227-230.

(2014).

DOI: https://doi.org/10.1016/j.cell.2014.09.022

Conducting a microbiome study.

Goodrich JK, Di Renzi SC, Poole AC, Koren O, Walters WA, Caporaso G, Knight R and Ley RE.

Cell.

17: 250-262.

(2014).

DOI: https://doi.org/10.1016/j.cell.2014.06.037

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

Ji Y, Sun S, Goodrich JK, Kim H, Poole AC, Duhamel GE, Ley RE and Qi L.

Cell Reports.

10: 137-149.

(2014).

DOI: https://doi.org/10.1016/j.celrep.2014.05.040

Discordance between changes in the microbiota and pathogenicity in a mouse model of spontaneous colotis.

Perez-Munoz M, Bergstrom K, Peng V, Schmaltz R, Jimenez-Cardona R, Marsteller N, McGee S, Clavel T, Ley RE, Xia L and Peterson D.

Gut Microbes.

5:286-295.

(2014).

DOI: https://doi.org/10.4161/gmic.28622

Harnessing microbiota to kill a pathogen: the sweet tooth of Clostridium difficile.

Ley RE.

Nature Medicine.

20:248-249.

(2014).

DOI: https://doi.org/10.1038/nm.3494

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.

14:571-581.

(2013).

DOI: https://doi.org/10.1016/j.chom.2013.10.009

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

Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF and Ley RE.

eLife.

2:e01102.

(2013).

DOI: https://doi.org/10.7554/elife.01102

Exploring the maize rhizosphere microbiome in the field: a glimpse into a highly complex system.

Peiffer JA and Ley RE.

Communicative Integrative Biology.

6:e25177.

(2013).

DOI: https://doi.org/10.4161/cib.25177

Diversity and heritability of the maize rhizosphere microbiome under field conditions.

Peiffer J, Spor A, Jin Z, Koren O, Tringe SG, Dangl JL, Buckler ES and Ley RE.

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

110:6548-6553.

(2013).

DOI: https://doi.org/10.1073/pnas.1302837110

When guests turn hostile.

Ley RE.

Nature.

494:437-438.

(2013).

DOI: https://doi.org/10.1038/494437a

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.

Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C and Ley RE.

PLoS Computational Biology.

9:e1002863.

(2013).

DOI: https://doi.org/10.1371/journal.pcbi.1002863

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

Brook SM, van Coeverden de Groot P, Scott C, Boag P, Long B, Ley RE, Reischer GH, Williams AC, Mahood SP, Minh Hien T, Polet G, Cox N and Thanh Hai B.

Biological Conservation.

155:59-67.

(2012).

DOI: https://doi.org/10.1016/j.biocon.2012.06.008

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice.

Carvalho FA, Koren O, Johansson M, Nalbantoglu I, Aitken JD, Su Y, Walters WA, González Peña A, Clemente JC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE and Gewirtz AT.

Cell Host Microbe.

12:139-152.

(2012).

DOI: https://doi.org/10.1016/j.chom.2012.07.004

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.

Cell.

150:1-11.

(2012).

DOI: https://doi.org/10.1016/j.cell.2012.07.008

Defining the core arabidopsis thaliana root microbiome.

Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrekston A, Kunin V, del Rio TG, Edgar R, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG and Dangl JL.

Nature.

488:86-90.

(2012).

DOI: https://doi.org/10.1038/nature11237

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88.

Larsson E, Tremaroli V, Lee YS, Koren O, Fricker A, Nookaew I, Nielsen J, Ley RE and Bäckhed F.

Gut.

61:1124-1131.

(2012).

DOI: https://doi.org/10.1136/gutjnl-2011-301104

A framework for human microbiome research.

The human microbiome project consortium.

Nature.

486: 215-221.

(2012).

DOI: https://doi.org/10.1038/nature11209

Structure, function and diversity of the healthy human microbiome.

The human microbiome project consortium.

Nature.

486:207-214.

(2012).

DOI: https://doi.org/10.1038/nature11234

Responses of gut microbiota to weight loss in obese and lean mice.

Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE and Leibel RL.

Obesity.

20:738-747.

(2012).

DOI: https://doi.org/10.1038/oby.2011.111

Interleukin-1β (IL-1β) promotes susceptibility of toll-like receptor 5 (TLR5) deficient mice to colitis.

Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M and Gewirtz AT.

Gut.

61:373-384.

(2012).

DOI: https://doi.org/10.1136/gut.2011.240556

Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys.

Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R and Ley RE.

The ISME Journal.

6:94-103.

(2012).

DOI: https://doi.org/10.1038/ismej.2011.82

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

Ran-Ressler RR, Khailova L, Arganbright KM, Adkins-Rieck CK, Jouni ZE, Koren O, Ley RE, Brenna JT and Dvorak B.

PLoS One.

6:e29032.

(2011).

DOI: https://doi.org/10.1371/journal.pone.0029032

The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine.

Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley RE, Wakeland EK and Hooper LV.

Science.

334:255-258.

(2011).

DOI: https://doi.org/10.1126/science.1209791

The human gut microbiome: ecology and recent evolutionary changes.

Walter J and Ley RE.

Annual Reviews of Microbiology.

65:411-429.

(2011).

DOI: https://doi.org/10.1146/annurev-micro-090110-102830

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, the MIMARKS consortium.

Nature Biotechnology.

29:415-420.

(2011).

DOI: https://doi.org/10.1038/nbt.1823

Development of the human gastrointestinal microbiota and insights from high-throughput sequencing.

Dominguez-Bello MG, Blaser MJ, Ley RE and Knight R.

Gastroenterology.

140:1713-1719.

(2011).

DOI: https://doi.org/10.1053/j.gastro.2011.02.011

Supervised classification of microbiota mitigates mislabeling errors.

Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ and Kelley ST.

The ISME Journal.

5:570-573.

(2011).

DOI: https://doi.org/10.1038/ismej.2010.148

Unravelling the effects of the environment and host genotype on the gut microbiome.

Spor A, Koren O and Ley RE.

Nature Reviews Microbiology.

9:279-290.

(2011).

DOI: https://doi.org/10.1038/nrmicro2540

Succession of microbial consortia in the developing infant gut microbiome.

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.

108 Suppl1:4578-4585.

(2011).

DOI: https://doi.org/10.1073/pnas.1000081107

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.

108 Suppl 1:4592-4598.

(2011).

DOI: https://doi.org/10.1073/pnas.1011383107

QIIME allows analysis of high-throughput community sequencing data.

Caporaso JG, Kaczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello E, Fierer N, Gonzales Pena A, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone C, McDonald D, Muegge B, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, van Treuren W, Walters WA, Widmann J, Yatsunenko T, Zaneveld J and Knight R.

Nature Methods.

7:335-336.

(2010).

DOI: https://doi.org/10.1038/nmeth.f.303

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

Vijay-Kumar M, Aitken JD, Carvalho FA, Mwangi S, Srinivasa S, Sitaraman SV, Cullender T, Knight R, Ley RE and Gewirtz AT.

Science.

328:228-231.

(2010).

DOI: https://doi.org/10.1126/science.1179721

Direct sequencing of the human microbiome readily reveals community differences.

Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley S, Ley RE, Gordon JI and Knight R.

Genome Biology.

5:210-219.

(2010).

DOI: https://doi.org/10.1186/gb-2010-11-5-210

Obesity and the human microbiome.

Ley RE.

Current Opinion in Gastroenterology.

26:5-11.

(2010).

DOI: https://doi.org/10.1097/MOG.0b013e328333d751

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.

Nature.

457:480-484.

(2009).

DOI: https://doi.org/10.1038/nature07540

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.

Nature.

455:1109-1113.

(2008).

DOI: https://doi.org/10.1038/nature07336

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.

74:5905-5912.

(2008).

DOI: https://doi.org/10.1128/AEM.00574-08

Worlds within worlds: evolution of the vertebrate gut microbiota.

Ley RE, Lozupone CA, Hamady M, Knight R and Gordon JI.

Nature Reviews Microbiology.

6:776-788.

(2008).

DOI: https://doi.org/10.1038/nrmicro1978

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.

Science.

320:1647-1651.

(2008).

DOI: https://doi.org/10.1126/science.1155725

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.

(2008).

DOI: https://doi.org/10.1016/j.cbpa.2008.01.015

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.

74:329-332.

(2008).

DOI: https://doi.org/10.1128/AEM.01448-07

The human microbiome project.

Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett C, Knight R and Gordon JI.

Nature.

449:804-810.

(2007).

DOI: https://doi.org/10.1038/nature06244

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.

PLoS Biology.

5:e156.

(2007).

DOI: https://doi.org/10.1371/journal.pbio.0050156

The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology.

Ley RE, Knight RD and Gordon JI.

Environmental Microbiology.

9:3-4.

(2007).

DOI: https://doi.org/10.1111/j.1462-2920.2006.01222_3.x

Microbial ecology: human gut microbes associated with obesity.

Ley RE, Turnbaugh P, Klein S and Gordon JI.

Nature.

444:1022-1023.

(2006).

DOI: https://doi.org/10.1038/4441022a

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

Turnbaugh PJ, Ley RE, Mahowald M, Magrini V, Mardis ER and Gordon JI.

Nature.

444:1027-1031.

(2006).

DOI: https://doi.org/10.1038/nature05414

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

Rawls JF, Mahowald MM, Ley RE and Gordon JI.

Cell.

127:423-433.

(2006).

DOI: https://doi.org/10.1016/j.cell.2006.08.043

The human intestinal microbiota and its relationship to energy balance.

Bäckhed FR, Ley RE, Sonnenburg JL and Gordon JI.

Scandinavian Journal of Food and Nutrition.

50:121-123.

(2006).

DOI: https://doi.org/10.3402/fnr.v50i0.1586

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.

Applied and Environmental Microbiology.

72:3685-3695.

(2006).

DOI: https://doi.org/10.1128/AEM.72.5.3685-3695.2006

Ecological and evolutionary forces shaping microbial diversity in the human intestine.

Ley RE, Peterson DA and Gordon JI.

Cell.

124:837-848.

(2006).

DOI: https://doi.org/10.1016/j.cell.2006.02.017

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

Gordon JI, Ley RE, Wilson R, Mardis E, Xu J, Fraser CM and Relman DA.

NHGRI White paper (prioritized).

(2006).

Obesity alters gut microbial ecology.

Ley RE, Bäckhed F, Turnbaugh P, Lozupone C, Knight R and Gordon JI.

Proceedings of the National Academy of Sciences USA.

31:11070-11075.

(2005).

DOI: https://doi.org/10.1073/pnas.0504978102

Host-bacterial mutualism in the human intestine.

Bäckhed FR, Ley RE, Sonnenburg JL, Peterson DA and Gordon JI.

Science.

307:1915-1920.

(2005).

DOI: https://doi.org/10.1126/science.1104816

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

Cleveland CC, Townsend AR, Constance BC, Ley RE and Schmidt SK.

Biotropica.

36:184-195.

(2004).

DOI: https://doi.org/10.1111/j.1744-7429.2004.tb00311.x

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

Schmidt SK, Lipson DA, Ley RE, Fisk MC and West AE.

Biogeochemistry.

69:1-17.

(2004).

DOI: https://doi.org/10.1023/B:BIOG.0000031028.53116.9b

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

Ley RE, Williams MW and Schmidt SK.

Biogeochemistry.

68:313-335.

(2004).

DOI: https://doi.org/10.1023/B:BIOG.0000031032.58611.d0

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

Jakosky BM, Nealson KH, Bakermans C, Ley RE and Mellon MT.

Astrobiology.

3:343-350.

(2003).

DOI: https://doi.org/10.1089/153110703769016433

Complexity in natural microbial ecosystems: the Guerrero Negro experience.

Spear JS, Ley RE, Berger AB and Pace NR.

Biological Bulletin.

204:168-173.

(2003).

DOI: https://doi.org/10.2307/1543553

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

Ley RE and Schmidt SK.

Soil Biology and Biochemistry.

34:989-995.

(2002).

DOI: https://doi.org/10.1016/S0038-0717(02)00032-9

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

Mack MA, D'Antonio CM and Ley RE.

Ecological Applications.

11:1323-1335.

(2001).

DOI: https://doi.org/10.2307/3060923

Soil ecological interactions: comparisons between tropical and subalpine forests.

Gonzalez G, Ley RE, Schmidt SK, Zou X and Seastedt TR.

Oecologia.

128:549-556.

(2001).

DOI: https://doi.org/10.1007/s004420100685

Microbial biomass levels in barren and vegetated high altitude talus soils.

Ley RE, Lipson DA and Schmidt SK.

Soil Science Society of America Journal.

65:111-117.

(2001).

DOI: https://doi.org/10.2136/sssaj2001.651111x

Exotic grass invasion alters potential rates of N fixation in Hawaiian woodlands.

Ley RE and D'Antonio CM.

Oecologia.

113:179-187.

(1998).

DOI: https://doi.org/10.1007/s004420050366

Ongoing research into revegetation of degraded dry forest in Hawai’i.

D'Antonio CM, Tunison JT, Ley RE and Loh R.

Restoration and Management Notes, Winter.

(1994).

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Department of Microbiome Science

Max Planck Institute for Biology Tübingen

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