2025

22. Kelliher JM, Mirzayi C, Bordenstein SR, Oliver A, Kellogg CA, Hatcher EL, Berg M, Baldrian P, Aljumaah M, Miller CML, Mungall C, Novak V, Palucki A, Smith E, Tabassum N, Bonito G, Brister JR, Chain PSG, Chen M, Degregori S, Dundore-Arias JP, Emerson JB, Fernandes VMC, Flores R, Gonzalez A, Hansen ZA, Jackson SA, Moustafa AM, Northern TR, Pariente N, Pett-Ridge J, Record S, Reji L, Reysenbach AL, Rich VI, Richardson L, Roux S, Schriml LM, Shabman RS, Sierra MA, Sullivan MB, Sundaramurthy P, Thibault KM, Thompson LR, Tighe S, Vereen E, STREAMS Consortium, Eloe-Fadrosh EA. STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies. Nature Microbiology. [link]

21. Feeser K*, Longley R*, Gallegos-Graves LV, Albright M, Shakya M. Recovering new viruses from New Mexico soils. Microbiology Resource Announcements. [link]

20. Bonito G, Miyauchi S, Hayes RD, Tan H, Kuo A, Robinson A, Wang X, Van Wyk J, Kohler A, Fauchery L, Drula E, Benucci GMN, Morin E, Ryberg M, Khan FK, Cravero M, Longley R, Barry K, Clum A, Duffy K, Lipzen A, LaButti K, Riley R, Singan V, Steindorff A, Wang J, Bruns T, Maurice S, Clowez P, Bindschedler S, Junier P, Chain P, Grigoriev IV, Martin FM. Pangeneric analyses reveal the divergent genome evolution and ecologies between morels and truffles in the Morchellaceae. Current Biology. [link]

19. Kelliher JM, Johnson LYD, Rodriguez FE, Saunder JK, Kroeger ME, Hanson B, Robinson AJ, Anthony WE, Van Goethem MW, Kiledal A, Shibi AA, Serrao de Andrade AA, Ettinger CL, Gupta CL, Robinson CRP, Zuniga C, Sprockett D, Machado DT, Skoog EJ, Oduwole I, Rothman JA, Prime K, Lane KR, Nascimento L, Karstens L, McCauley M, Seyoum MM, Elmassry MM, Guzel M, Longley R, Roux S, Pitot TM, Eloe-Fadrosh EA. A cost and community perspective on the barriers to microbiome data reuse. Frontiers in Bioinformatics.[link]

18. Kelliher JM, Rodriguez FE, Johnson LYD, Roux S, Smith M, Clum A, Lynch W, Bias CH, Finks SS, Keenum I, Kiledal EA, Lin, HA, Longley R, McDonald R, Pitot TM, Rodriguez-Ramos J, Shen J, Sprockett DD, Swift J, Yadav A, Eloe-Fadrosh EA. Quantifying the impact of workshops promoting microbiome data standards and data stewardship. Scientific Reports. [link]

2024
17. Longley R, Robinson AJ, Asher OA, Middlebrook E, Bonito G, Chain PSG. Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes. Msphere. [link]

16. Kelliher JM, Johnson LY, Robinson AJ, Longley R, Hanson BT, Cailleau G, Bindschedler S, Junier P, Chain PS. Fabricated Devices for Performing Bacterial-Fungal Interaction Experiments across Scales. Frontiers in Microbiology. [link]

15. Kelliher JM, Johnson LYD, Robinson AJ, Palmieri I, Hanson BT, Longley R, Gallegos-Graves LV, Prime K, Cailleau G, Bindschedler S, Chain PSG, Junier P. Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates. Journal of Visualized Experiments (JoVE). [link]

14. Longley R, Benucci GMN, Pochon X, Bonito G, Bonito V. Species-specific coral microbiome assemblages support host bleaching resistance during an extreme marine heatwave. Science of the Total Environment. [link]

2023
13. Sultaire SM, Benucci GMN, Longley R, Kroll AJ, Verschuyl J, Bonito G, Roloff GJ. Using high-throughput sequencing to investigate summer truffle consumption by chipmunks in relation to retention forestry. Forest Ecology and Management. [link]

12. Longley R, Robinson A, Liber JA, Bryson AE, Morales DP, LaButti K, Riley R, Mondo SJ, Kuo A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Desirò A, Chain PSG, Bonito G. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Communications Biology. [link]

11. Szymanski S, Longley R, Hatlen RJ, Heger L, Sharma N, Bonito G, Miles TD. The blueberry fruit mycobiome varies by tissue type and fungicide treatment. Phytobiomes Journal. [link]

10. Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales DP, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. Microbiome. [link]

9. Robinson A, Babinski M, Xu Y, Kelliher J, Longley R, Chain P. A centralized resource for bacterial–fungal interactions research. Fungal Biology. [link]

2022
8. Noel ZA*, Longley R*, Benucci GMN, Trail F, Chilvers MI, Bonito G. Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management. ISME Communications. [link]

7. Liber JA, Minier DH, Stouffer-Hopkins A, Van Wyk J, Longley R, Bonito G. Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities. Peerj. [link]

2021
6. Chen KH, Longley R, Bonito G, Liao HL. A two-step PCR protocol enabling flexible primer choice and high sequencing yield for Illumina MiSeq meta-barcoding. Agronomy. [link]

2020
5. Longley R, Noel ZA, Benucci GMN, Chilvers MI, Trail F, Bonito G. Crop Management Impacts the Soybean (Glycine max) Microbiome. Frontiers in Microbiology. [link]

4. Miller SR, Longley R, Hutchins PR, Bauersachs. Cellular innovation of the cyanobacterial heterocyst by the adaptive loss of plasticity. Current Biology. [link]

2019
3. McCoy AG, Roth MG, Shay R, Noel ZA, Jayawardana, Longley RW, Bonito G, Chilvers MI. Identification of fungal communities within the tar spot complex of corn in Michigan via next-generation sequencing. Phytobiomes Journal. [link]

2. Benucci GMN*, Longley R*, Zhang P, Zhao Q, bonito G, Yu F.Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses. PeerJ. [link]

1. Longley R*, Benucci GMN*, Mills G, Bonito G. Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors. FEMS Microbiology Letters. [link]

(*) Designates equal contribution

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