2024

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). 

SynTracker differentiates evolution via point mutation or structural changes on a per-species basis in complex microbiomes.

Enav H, Paz I and Ley RE.

Nature Biotechnology. 

In press. 

(2024). 

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). 

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.

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). 

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). 

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). 

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). 

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). 

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). 

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). 

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). 

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). 

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). 

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.

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.

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.

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). 

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.

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). 

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). 

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). 

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). 

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). 

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

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

bioRxiv. 

774372. 

(2019). 

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). 

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). 

Gut microbiota influence B cell function in a TLR5-dependent manner.

Li S, Walters W, Chassaing B, Zhang B, Shi Q, Waters J, Gewirtz AT, Leifer CA and Ley RE.

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.

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). 

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). 

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).