Publications

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Early Career

2025

Dietary fat disrupts a commensal-host lipid network that functions to promote metabolic health

Klag KA, Ott D, Tippets T, Nicolson R, Tatum S, Bauer KM, Victor-Stephens E, Weis AM, Bell R, Weagley J, Maschek JA, O’Connell RM, Holland W, Summers S, Stephens WZ, and Round JL.  

In press, Cell Metabolism 2025

A capsular polysaccharide from a healthy human microbiota member activates a Lag-3-NK cell axis to restrain colon cancer and augment immunotherapy

Weis AM, Bauer K, Tang WW, Stephen-Victor E, Bell R, Brown DG, Ekiz HA, Tran V, Klag KA, Swanson EA, Greenewood M, Barrios L, Hill JH, Ost KS, Gigic B, Schneider M, Ose J, Hardikar S, Toriola AT, Shibata D, Li CI, Figueiredo JC, Byrd DA, Siegel EM, Ulrich CM, Stephens WZ, Round JL.

Cell Reports 2025 Aug 23;44(9):116172

Neonatal fungi promote lifelong metabolic health through macrophage-dependent β cell development

Hill JH, Bell R, Barrios L, Baird H, Ost K, Greenewood M, Monts JK, Tracy E, Meili CH, Chiaro TR, Weis AM, Guillemin K, Beaudin AE, Murtaugh LC, Stephens WZ, Round JL.

Science 387 (6738), eadn0953

A microRNA-regulated transcriptional state defines intratumoral CD8+ T cells that respond to immunotherapy

Tang WW, Battistone B, Bauer KM, Weis AM, Barba C, Fadlullah MZH, Ghazaryan A, Tran VB, Lee SH, Agir ZB, Nelson MC, Victor ES, Thibeaux A, Hernandez C, Tantalla J, Tan AC, Rao D, Williams M, Drummond MJ, Beswick EJ, Round JL, Ekiz HA, Voth WP, O'Connell RM.

Cell Reports 44 (2)

Clec12a controls colitis by tempering inflammation and restricting expansion of specific commensals

Chiaro TR*, Greenewood M*, Bauer KM, Ost KS, Stephen-Victor E, Murphy M, Weis AM, Nelson MC, Hill JH, Bell R, Voth W, Jackson T, Klag K, O’Connell RM, Stephens WZ, Round JL.

Cell Host & Microbe 33 (1), 89-103. e7

Draft genome of a human gut-derived Blautia sp. that ameliorates colitis and colitis-associated sociability deficits in mice

Murphy M, Brown D, Bell R, Weis AM, Barrios L, Stephens WZ, Round JL

Microbiology Resource Announcements 14 (1), e00726-24

2024

Draft Turicibacter sp. genome isolated from a spore-forming community in mice

Weis AM*, Klag KA*, Stephens WZ, Round JL.

Microbiology Resource Announcements 13 (8), e00385-24

Genomes of diverse Clostridia isolated from a spore forming community in mice that were associated with protection against metabolic syndrome and obesity

Weis AM*, Klag KA*, Bell R, Stephens WZ, Round JL.

Microbiology Resource Announcements 13 (7), e00351-24

Colitis reduces active social engagement in mice and is ameliorated by supplementation with human microbiota members

Brown DG, Murphy M, Caddedu R, Bell R, Weis AM, Chiaro T, Klag KA, Morgan J, Coon H, Stephens WZ, Bortolato M, Round JL.

Nature Communications 15 (1), 2769

Draft genome of a human-derived pks+ E. coli that caused spontaneous disseminated infection in a mouse

Weis AM, Matthews OJ, Mulvey MA, Round JL.

Microbiology Resource Announcements 13 (7), e00387-24

2022

CD11c+ myeloid cell exosomes reduce intestinal inflammation during colitis

Bauer KM, Nelson MC, Tang WW, Chiaro TR, D. Brown DG, Ghazaryan A, Lee S, Weis AM, Hill JH, Ramstead A, Monts J, Marvin J, Alexander M, Voth WP, Stephens WZ, Ward D, Petrey A, Round JL and O’Connell RM.

JCI insight 7 (19), e159469

2021

Epithelial-myeloid exchange of MHC class II constrains immunity and microbiota composition

Stephens WZ, Kubinak JL, Ghazaryan A, Bauer KM, Bell R, Buhrke K, Chiaro TR, Weis AM, Tang WW, Monts JK, Soto R, Ekiz HA, O’Connell RM, Round JL.

Cell reports 37 (5)

Microbiota-antibody interactions that regulate gut homeostasis

AM Weis, JL Round

Cell host & microbe 29 (3), 334-346

2018

Commensal regulation of T cell survival through Erdr1

Weis AM, Soto R, Round JL.

2018. Gut Microbes. Mar 15:1-17. PMID: 29543554

Graduate Work

Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data

Miller JJ, Weimer BC, Timme R, Lüdeke CHM, Pettengill JB, Bandoy DD, Weis AM, Kaufman J, Huang BC, Payne J, Strain E, Jones JL.

Appl Environ Microbiol. 2021 Jan 15;87(3). Print 2021 Jan 15. PubMed PMID: 33187991; PubMed Central PMCID: PMC7848924.

Insular Microbiogeography: Three Pathogens as Exemplars

Kaufman JH, Elkins CA, Davis M, Weis AM, Huang BC, Mammel MK, Patel IR, Beck KL, Edlund S, Chambliss D, Douglas J, Bianco S, Kunitomi M, Weimer BC.

Curr Issues Mol Biol. 2020;36:89-108. Epub 2019 Oct 9. PubMed PMID: 31596250.

Low heterozygosity is associated with vector-borne disease in crows. Ecosphere

Townsend A, Taff C, Wheeler S, Weis A, Hinton M, Jones M, Logsdon R, Reisen W, Freund D, Sehgal R, Saberi M, Suh Y, Hurd J, Boyce W.

2018 October; 9(10):e02407. doi: 2150-8925.

Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing

Lawton SJ, Weis AM, Byrne BA, Fritz H, Taff CC, Townsend AK, Weimer BC, Mete A, Wheeler S, Boyce WM.

J Vet Diagn Invest. 2018 May;30(3):354-361. Epub 2018 Mar 12. PubMed PMID: 29528812; PubMed Central PMCID: PMC6505823.

Commensal regulation of T cell survival through Erdr1

Weis AM, Soto R, Round JL.Gut Microbes. 2018;9(5):458-464.

Epub 2018 Apr 11. Review. PubMed PMID: 29543554; PubMed Central PMCID: PMC6219650.

Draft Genome Sequences of 1,183 Salmonella Strains from the 100K Pathogen Genome Project

Kong N, Davis M, Arabyan N, Huang BC, Weis AM, Chen P, Thao K, Ng W, Chin N, Foutouhi S, Foutouhi A, Kaufman J, Xie Y, Storey DB, Weimer BC.

Genome Announc. 2017 Jul 13;5(28). PubMed PMID: 28705963; PubMed Central PMCID: PMC5511902.

Implication of Sialidases in Salmonella Infection: Genome Release of Sialidase Knockout Strains from Salmonella enterica Serovar Typhimurium LT2

Arabyan N, Weis AM, Huang BC, Weimer BC.

Genome Announc. 2017 May 11;5(19). PubMed PMID: 28495784; PubMed Central PMCID: PMC5427219.

Shigella Draft Genome Sequences: Resources for Food Safety and Public Health

Weis AM, Gilpin B, Huang BC, Kong N, Chen P, Weimer BC.

Genome Announc. 2017 Apr 20;5(16). PubMed PMID: 28428292; PubMed Central PMCID: PMC5399251.

Draft Genome Sequence of Multidrug-Resistant Abortive Campylobacter jejuni from Northern California

Weis AM, Clothier KA, Huang BC, Kong N, Weimer BC.

Genome Announc. 2017 Apr 13;5(15). PubMed PMID: 28408683; PubMed Central PMCID: PMC5391421.

Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

Kong N, Ng W, Thao K, Agulto R, Weis A, Kim KS, Korlach J, Hickey L, Kelly L, Lappin S, Weimer BC.

Stand Genomic Sci. 2017;12:27. eCollection 2017. PubMed PMID: 28344744; PubMed Central PMCID: PMC5363030.

Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains

Draper JL, Hansen LM, Bernick DL, Abedrabbo S, Underwood JG, Kong N, Huang BC, Weis AM, Weimer BC, van Vliet AH, Pourmand N, Solnick JV, Karplus K, Ottemann KM.

mBio. 2017 Feb 21;8(1). PubMed PMID: 28223462; PubMed Central PMCID: PMC5358919.

Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project

Weis AM, Huang BC, Storey DB, Kong N, Chen P, Arabyan N, Gilpin B, Mason C, Townsend AK, Smith WA, Byrne BA, Taff CC, Weimer BC.

Genome Announc. 2017 Jan 5;5(1). PubMed PMID: 28057746; PubMed Central PMCID: PMC5255908.

Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock

Weis AM, Storey DB, Taff CC, Townsend AK, Huang BC, Kong NT, Clothier KA, Spinner A, Byrne BA, Weimer BC.

Appl Environ Microbiol. 2016 Dec 15;82(24):7165-7175. Print 2016 Dec 15. PubMed PMID: 27736787; PubMed Central PMCID: PMC5118927.

Draft Genome Sequences of Campylobacter jejuni Strains That Cause Abortion in Livestock

Weis AM, Clothier KA, Huang BC, Kong N, Weimer BC.

Genome Announc. 2016 Dec 1;4(6). PubMed PMID: 27908990; PubMed Central PMCID: PMC5137404.

Influence of Host Ecology and Behavior on Campylobacter jejuni Prevalence and Environmental Contamination Risk in a Synanthropic Wild Bird Species

Taff CC, Weis AM, Wheeler S, Hinton MG, Weimer BC, Barker CM, Jones M, Logsdon R, Smith WA, Boyce WM, Townsend AK.

Appl Environ Microbiol. 2016 Aug 1;82(15):4811-20. Print 2016 Aug 1. PubMed PMID: 27260356; PubMed Central PMCID: PMC4984290.

Salmonella Degrades the Host Glycocalyx Leading to Altered Infection and Glycan Remodeling

Arabyan N, Park D, Foutouhi S, Weis AM, Huang BC, Williams CC, Desai P, Shah J, Jeannotte R, Kong N, Lebrilla CB, Weimer BC.

Sci Rep. 2016 Jul 8;6:29525. PubMed PMID: 27389966; PubMed Central PMCID: PMC4937416.

Prevalence and pathogenic potential of campylobacter isolates from free-living, human-commensal american crows 

Weis AM, Miller WA, Byrne BA, Chouicha N, Boyce WM, Townsend AK.

Appl Environ Microbiol. 2014 Mar;80(5):1639-44. Epub 2013 Dec 27. PubMed PMID: 24375131; PubMed Central PMCID: PMC3957608.

Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome

Dahlem TJ, Hoshijima K, Jurynec MJ, Gunther D, Starker CG, Locke AS, Weis AM, Voytas DF, Grunwald DJ.

PLoS Genet. 2012;8(8):e1002861. Epub 2012 Aug 16. PubMed PMID: 22916025; PubMed Central PMCID: PMC3420959.

C. elegans BLOC-1 functions in trafficking to lysosome-related gut granules

Hermann GJ, Scavarda E, Weis AM, Saxton DS, Thomas LL, Salesky R, Somhegyi H, Curtin TP, Barrett A, Foster OK, Vine A, Erlich K, Kwan E, Rabbitts BM, Warren K.

PLoS One. 2012;7(8):e43043. Epub 2012 Aug 15. PubMed PMID: 22916203; PubMed Central PMCID: PMC3419718.

glo-3, a novel Caenorhabditis elegans gene, is required for lysosome-related organelle biogenesis

Rabbitts BM, Ciotti MK, Miller NE, Kramer M, Lawrenson AL, Levitte S, Kremer S, Kwan E, Weis AM, Hermann GJ.

Genetics. 2008 Oct;180(2):857-71. Epub 2008 Sep 9. PubMed PMID: 18780725; PubMed Central PMCID: PMC2567386.