Skip to main content



Divangahi, M., Aaby, P., Abdul Khader, S., … & Netea, M.G. (2021). Trained immunity, tolerance, priming and differentiation: distinct immunological processes. Nat Immunol. 10.1038/s41590-020-00845-6

Patrick, D.M., Van Beusecum, J.P. & Kirabo, A. (2021). The role of inflammation in hypertension: novel concepts. Curr Opin Physiol. 10.1016/j.cophys.2020.09.016


Altman, M.C., Beigelman, A., Ciaccio, C., … & Peebles R.S. Jr. (2020). Evolving concepts in how viruses impact asthma: a work group report of the microbes in allergy committee of the American Academy of Allergy, Asthma & Immunology. J Allergy Clin Immunol. 10.1016/j.jaci.2019.12.904

Anderson, D.M., Sheedlo, M.J., Jensen, J.L. & Lacy, D.B. (2020). Structural insights into the transition of Clostridioides difficile binary toxin from prepore to pore. Nat Microbiol. 10.1038/s41564-019-0601-8

Anderson, E.J., Lopman, B., Yi, J., … & Edwards, K. (2020). Effect of concomitant antibiotic and vaccine administration on serologic responses to Rotavirus vaccine. J Pediatric Infect Dis Soc. 10.1093/jpids/piz044

Aronoff, D.M. & Blaser, M.J. (2020). Disturbing the neonatal microbiome is a small price to pay for preventing early-onset neonatal group B streptococcus disease: AGAINST: Against relying on antibiotics to prevent early-onset neonatal group B streptococcus disease. BJOG. 10.1111/1471-0528.15988

Balachandran, M., Cross, K.L. & Podar, M. (2020). Single-cell genomics and the oral microbiome. J Dent Res. 10.1177/0022034520907380

Banerjee, A., Herring, C.A., Chen, B., … & Lau, K.S. (2020). Succinate produced by intestinal microbes promotes specification of Tuft cells to suppress ileal inflammation. Gastroenterology. 10.1053/j.gastro.2020.08.029

Byndloss, M.X. (2020). Microbial management. Science. 10.1126/science.abc5619

Chambers, S.A. & Townsend, S.D. (2020). Like mother, like microbe: human milk oligosaccharide mediated microbiome symbiosis. Biochem Soc Trans. 10.1042/BST20191144

Chen, S., Jiang, P.P., Yu, D., … & Zhu, H.L. (2020). Effects of probiotic supplementation on serum trimethylamine-N-oxide level and gut microbiota composition in young males: a double-blinded randomized controlled trial. Eur J Nutr. doi: 10.1007/s00394-020-02278-1

Curci, J.A. (2020). A model platform for studies of the microbiome on vascular injury response. J Vasc Surg. 10.1016/j.jvs.2019.07.065

Dosoky, N.S., May-Zhang, L.S. & Davies, S.S. (2020). Engineering the gut microbiota to treat chronic diseases. Appl Microbiol Biotechnol. 10.1007/s00253-020-10771-0

Elijovich, F., Laffer, C.L., Sahinoz, M., Pitzer, A., Ferguson, J.F. & Kirabo, A. (2020). The gut microbiome, inflammation, and salt-sensitive hypertension. Curr Hypertens Rep. 10.1007/s11906-020-01091-9

Engevik, M.A., Danhof, H.A., Auchtung, J., … & Versalovic, J. (2020). Fusobacterium nucleatum adheres to Clostridioides difficile via the RadD adhesin to enhance biofilm formation in intestinal mucus. Gastroenterology. 10.1053/j.gastro.2020.11.034

Engevik, M.A., Engevik, A.C., Engevik, K.A., … & Versalovic, J. (2020). Mucin-degrading microbes release monosaccharides that chemoattract Clostridiodes difficile and facilitate colonization of the human intestinal mucus layer. ACS Infect Dis. 10.1021/acsinfecdis.0c00634

Ferguson, J. Maternal microbial molecules affect offspring health. (2020). Science. 10.1126/science.aba7673

Hawkins, K.G., Casolaro, C., Brown, J.A., Edwards, D.A. & Wikswo, J.P. (2020). The microbiome and the gut-liver-brain axis for central nervous system clinical pharmacology: challenges in specifying and integrating in vitro and in silico models. Clin Pharmacol Ther. 10.1002/cpt.1870

Hosgood, H.D., Cai, Q., Hua, X., … & Lan, Q. (2020). Variation in oral microbiome is associated with future risk of lung cancer among never-smokers. Thorax. 10.1136/thoraxjnl-2020-215542

Lemon, A., Bordenstein, S.R. & Bordenstein, S.R. (2020). Discover the Microbes Within! The Wolbachia project: citizen science and student-based discoveries for 15 years and counting. Genetics. 10.1534/genetics.120.303649

Le Sage, E.H., LaBumbard, B.C., Reinert, L.K., … & Rollins-Smith, L.A. (2020).Preparatory immunity: Seasonality of mucosal skin defences and Batrachochytrium infections in Southern leopard frogs. J Anim Ecol. 10.1111/1365-2656.13386

Lim. S.J. & Bordenstein S.R. (2020). An introduction to phylosymbiosis. Proc Biol Sci. 10.1098/rspb.2019.2900

Loo, E.X.L., Zain, A., Yap, G.C., … & Lee, W.B. (2020). Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema. BMC Infect Dis. 10.1186/s12879-020-05000-y

Lopez, C.A., McNeely, T.P., Nurmakova, K., Beavers, W.N. & Skaar, E.P. (2020). Clostridioides difficile proline fermentation in response to commensal clostridia. Anaerobe. 10.1016/j.anaerobe.2020.102210

Macedonia, M.C., Drewes, J.L., Markham, N.O., … & Lau, K.S. (2020). Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms. NPJ Biofilms Microbiomes. 10.1038/s41522-020-00143-x

Martiny, J.B.H., Whiteson, K.L., Bohannan, B.J.M., … & Sachs, J.L. (2020). The emergence of microbiome centres. Nat Microbiol. 10.1038/s41564-019-0644-x

Maseda, D., Zackular, J.P. & Aronoff, D.M. (2020). Reply to Noori et al., “A complex scenario of nonsteroidal anti-inflammatory drugs induced prostaglandin E2 production and gut microbiota alteration in Clostridium difficile-infected mice”. mBio. 10.1128/mBio.03142-19

McGenity, T.J., Gessesse, A., Hallsworth, J.E., … & Timmis, K. (2020). Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes. Microb Biotechnol. 10.1111/1751-7915.13576

Nicholson, M.R., Mitchell, P.D., Alexander, E., … & Kahn, S.A. (2020). Efficacy of fecal microbiota transplantation for Clostridium difficile infection in children. Clin Gastroenterol Hepatol. 10.1016/j.cgh.2019.04.037

Ormseth, M.J., Wu, Q., Zhao, S., … & Stein, C.M. (2020). Circulating microbial small RNAs are altered in patients with rheumatoid arthritis. Ann Rheum Dis. 10.1136/annrheumdis-2020-217589

Perlmutter, J.I. & Bordenstein, S.R. (2020). Microorganisms in the reproductive tissues of arthropods. Nat Rev Microbiol. 10.1038/s41579-019-0309-z

Perlmutter, J.I., Myers, J.E. & Bordenstein S.R. (2020). Transgenic testing does not support a role for additional candidate genes in Wolbachia male killing or cytoplasmic incompatibility. mSystems. 5(1):e00658-19

Pulley, J.M., Rhoads, J.P., Jerome, R.N., … & Aronoff, D.M. (2020). Using what we already have: uncovering new drug repurposing strategies in existing omics data. Annu Rev Pharmacol Toxicol. 10.1146/annurev-pharmtox-010919-023537

Rajagopala, S.V., Singh, H., Yu, Y., … & Nelson, K.E. (2020). Persistent gut microbial dysbiosis in children with Acute Lymphoblastic Leukemia (ALL) during chemotherapy. Microb Ecol. 10.1007/s00248-019-01448-x

Renson, A., Mullan Harris, K., Dowd., J.B., … & Aiello, A.E. (2020). Early signs of gut microbiome aging: biomarkers of inflammation, metabolism, and macromolecular damage in young adulthood. J Gerontol A Biol Sci Med Sci. 10.1093/gerona/glaa122

Rollins-Smith, L.A., Smith, P.B., Ledeczi, A.M., Rowe, J.M. & Reinert, L.K. (2020). Caerin 1 antimicrobial peptides that inhibit HIV and Neisseria may spare protective Lactobacilli. Antibiotics (Basel). 10.3390/antibiotics9100661

Rosas-Salazar, C. & Hartert, T.V. (2020). New insights into the role of antibiotic use in infancy and the upper airway microbiome in childhood asthma development. Clin Infect Dis. 10.1093/cid/ciaa266

Ruocco, C., Ragni, M., Rossi, F., … & Nisoli, E. (2020). Manipulation of dietary amino acids prevents and reverses obesity in mice through multiple mechanisms that modulate energy homeostasis. (2020). Diabetes. 10.2337/db20-0489

Rustgi, S.D., Kayal, M. & Shah, S.C. (2020). Sex-based differences in inflammatory bowel diseases: a review. Therap Adv Gastroenterol. 10.1177/1756284820915043

Shah, R.D., Tang, Z.Z., Chen, G., Huang, S. & Ferguson, J.F. (2020). Soy food intake associates with changes in the metabolome and reduced blood pressure in a gut microbiota dependent manner. Nutr Metab Cardiovasc Dis. 10.1016/j.numecd.2020.05.001

Shelton, C.D. & Byndloss, M.X. (2020). Gut epithelial metabolism as key driver of intestinal dysbiosis associated with noncommunicable diseases. Infect Immunol. 10.1128/IAI.00939-19

Shilts, M.H., Rosas-Salazar, C., Lynch, C.E., … & Das, S.R. (2020). Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes. Sci Rep. 10.1038/s41598-020-77289-3

Shiroda, M., Aronoff, D.M., Gaddy, J.A. & Manning, S.D. (2020). The impact of Lactobacillus on group B streptococcal interactions with cells of the extraplacental membranes. Microb Pathog. 10.1016/j.micpath.2020.104463

Shropshire, J.D., Kalra, M. & Bordenstein, S.R. (2020).Evolution-guided mutagenesis of the cytoplasmic incompatibility proteins: Identifying CifA’s complex functional repertoire and new essential regions in CifB. PLoS Pathog. 10.1371/journal.ppat.1008794

Shropshire, J.D., Leigh, B. & Bordenstein, S.R. (2020). Symbiont-mediated cytoplasmic incompatibility: what have we learned in 50 years?. Elife. 10.7554/eLife.61989

Tucker, M.D. & Rini, B.I. (2020). Predicting response to immunotherapy in metastatic renal cell carcinoma. Cancers (Basel). 10.3390/cancers12092662

Woodhams, D.C., Rollins-Smith, L.A., Reinert, L.K., … & Bigler, L. (2020). Probiotics modulate a novel amphibian skin defense peptide that is antifungal and facilitates growth of antifungal bacteria. Microb Ecol. doi: 10.1007/s00248-019-01385-9

Yan, F. (2020). Mechanistic understanding of the symbiotic relationship between the gut microbiota and the host: an avenue toward therapeutic applications. Cell Mol Gastroenterol Hepatol. 10.1016/j.jcmgh.2020.05.003

Yan, F. & Polk, D.B. (2020). Probiotics and probiotic-derived functional factors – mechanistic insights into applications for intestinal homeostasis. Front Immunol. 10.3389/fimmu.2020.01428

Yang, J.J, Yu, D., Xiang, Y.B., … & Shu, X.O. (2020). Association of dietary fiber and yogurt consumption with lung cancer risk: a pooled analysis. JAMA Oncol. 10.1001/jamaoncol.2019.4107

Yang, Y., Zheng, W., Cai, Q. … & Long, J. (2020). Reply to Kenyon, “Are differences in the oral microbiome due to ancestry or socioeconomics?”. mSystems. 10.1128/mSystems.00891-19

Yu, D., Shu, X.O., Howard, E.F., Long, J., English, W.J. & Flynn, C.R. (2020).
Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery. Surg Obes Relat Dis. 10.1016/j.soard.2020.06.032


Anderson, D.M., Sheedlo, M.J., Jensen, J.L., & Lacy, D.B. (2019). Structural insights into the transition of Clostridioides difficile binary toxin from prepore to pore . Nat Microbiol. 10.1038/s41564-019-0601-8.

Aronoff, D.M., Blaser, M.J. (2019). Disturbing the neonatal microbiome is a small price to pay for preventing early onset neonatal GBS disease: AGAINST: Against relying on antibiotics to prevent GBS EOD. BJOG. 10.1111/1471-0528.15988.

Banerjee, A., Herring, C.A., Kim, H., Chen, B., Simmons, A.J., Southward-Smith A.N.,… & Lau, K.S. (2019). Commensal-derived succinate enhances tuft cell specification and suppresses ileal inflammation. Biorxiv.

Brooks, A. W. (2019). How could ethnicity-associated microbiomes contribute to personalized therapies?. Future Medicine.

Byndloss, M. X., Litvak, Y., & Bäumler, A. J. (2019). Microbiota-nourishing Immunity and Its Relevance for Ulcerative Colitis. Inflammatory bowel diseases.

Craft, K. M., & Townsend, S. D. (2019). Mother Knows Best: Deciphering the Antibacterial Properties of Human Milk Oligosaccharides. Accounts of chemical research.

Craft, K. M., Thomas, H. C., & Townsend, S. D. (2019). Sialylated variants of lacto-N-tetraose exhibit antimicrobial activity against Group B Streptococcus. Organic & biomolecular chemistry.

Craft, K. M., Nguyen, J. M., Berg, L. J., & Townsend, S. D. (2019). Methicillin-resistant Staphylococcus aureus (MRSA): antibiotic-resistance and the biofilm phenotype. MedChemComm.

Layton, E.M., On, J., Perlmutter, J.I., Bordenstein, S.R., & Shropshire, J.D. (2019). Paternal Grandmother Age Affects the Strength of Wolbachia-Induced Cytoplasmic Incompatibility in Drosophila melanogaster. mBio.

Leigh, B.A. (2019). Cooperation among Conflict: Prophages Protect Bacteria from Phagocytosis. Cell Host and Microbe, 26,4,450-452.

Lopez, C.A., Beavers, W.N., Weiss, A.,… & Skaar, E.P. (2019). The Immune Protein Calprotectin Impacts Clostridioides difficile Metabolism through Zinc Limitation. MBio. 2019;10(6):e02289-19.

Martiny, J.B., Whiteson, K.L., Bohannan, B.J.M., … & Sachs, J.L. (2019) The emergence of Microbiome centres. Nat microbiol.

Moore, R.E, & Townsend, S.D. (2019) Temporal development of the infant gut microbiome. Royal Society.

Nicholson, M. R., Mitchell, P. D., Alexander, E., … & Gisser, J. (2019). Efficacy of Fecal Microbiota Transplantation for Clostridium difficile Infection in Children. Clinical Gastroenterology and Hepatology.

Noto, J.M., Zackular, J.P., Varga, M.G., Delgato, A., Romero-Gallo, J., Scholz, M.B., Piazuelo, M.B., Skaar, E.P., & Peek, R.M. (2019). Modification of the Gastric Mucosal Microbiota by a Strain-Specific Helicobacter pylori Oncoprotein and Carcinogenic Histologic Phenotype. mBio.

Perlmutter, J.I., Bordenstein, S.R., Unkless, R.L., LePage, D.P., Metcalf, J.A., … & Bordenstein, S.R. (2019). The phage gene wmk is a candidate for male killing by a bacterial endosymbiont. PLoS pathogens.

Rajagopala, S.V., Singh, H., Yu, Y., … & Nelson, K.E. (2019). Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy [published online ahead of print,  Microb Ecol. 10.1007/s00248-019-01448-x.

Sherwin, E., Bordenstein, S.R., Quinn, J.L., Dinan, T.G., & Cryan, J.F. (2019). Microbiota and the social brain. Science, 366, 6465.

Singh, K., Gobert, A. P., Coburn, L. A., Barry, D. P., Allaman, M. M., Luis, P. B., … & Washington, M. K. (2019). Dietary Arginine Regulates Severity of Experimental Colitis and Affects the Colonic Microbiome. Frontiers in Cellular and Infection Microbiology, 9, 66.

Tang, Z. Z., Chen, G., Hong, Q., Huang, S., Smith, H. M., Shah, R. D., … & Ferguson, J. F. (2019). Multi-omic analysis of the microbiome and metabolome in healthy subjects reveals microbiome-dependent relationships between diet and metabolites. Frontiers in Genetics10, 454.

Tuteja, S., & Ferguson, J. F. (2019). The Gut Microbiome and Response to Cardiovascular Drugs. Circulation:Genomic and Precision Medicine.

Walk, E.E., Yohe, S.L., Beckman, A., … & Berry, A.B. (2019). The Cancer Immunotherapy Biomarker Testing Landscape. Arch Pathol Lab Med. 10.5858/arpa.2018-0584-CP.

Yang, J.J., Yu, D., Yong-Bing, X. (2019). Association of Dietary Fiber and Yougurt Consumption with Lung Cancer Risk. JAMA Oncology.

Yang, L., Higginbotham, J.N., Liu, L., Zhao, G., Acra, S.A., Peek, R.M., Polk, D.B., Li, H., & Yan, F. (2019). Production of a Functional Factor, p40, by Lactobacillus rhamnosus GG Is Promoted by Intestinal Epithelial Cell-secreted Extracellular Vesicles. Infection and Immunity.

Yang, Y., Zheng, W., Cai, Q.Y., Shrubsole, M., Pei, Z., Brucker, R.M., Steinwandel, M., Bordenstein,S.R., Li, Z., Blot, W., Shu, X.O., Long, J. (2019). Cigarette smoking and oral microbiota in low-income and African-American populations. Journal of Epidemiology and Community Health.

Yang, Y., Zheng, W., Cai, Q., …& Long, J. (2019). Racial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European Ancestry. mSystems. 4(6):e00639-19.

Yoo, W., Byndloss, M.X. (2019). How to thrive in the inflamed gut. Nature microbiology.

Zackular, J. P., Kirk, L., Trindade, B. C., Skaar, E. P., & Aronoff, D. M. (2019). Misoprostol protects mice against severe Clostridium difficile infection and promotes recovery of the gut microbiota after antibiotic perturbation. Anaerobe.


Ajayi, T. A., Cantrell, S., Spann, A., & Garman, K. S. (2018). Barrett’s esophagus and esophageal cancer: Links to microbes and the microbiome. PLoS pathogens14(12), e1007384.

Brooks, A. W., Priya, S., Blekhman, R., & Bordenstein, S. R. (2018). Gut Microbiota Diversity across Ethnicities in the United States. PLoS biology16(12), e2006842.

Carroll, K. N., Adams, S. N., Gebretsadik, T., Ortiz, C. F., Adgent, M., Tylavsky, F. A., & Hartman, T. J. (2018). Association Between Maternal Prenatal Vitamin D Concentration And Child Asthma. Journal of Allergy and Clinical Immunology141(2), AB6.

Craft, K. M., Thomas, H. C., & Townsend, S. D. (2018). Sialylated variants of lacto-N-tetraose exhibit antimicrobial activity against Group B Streptococcus. Organic & biomolecular chemistry, 17(7), 1893-1900.

Goedert, J. J., Hua, X., Bielecka, A., Okayasu, I., Milne, G. L., Jones, G. S., … & Ravel, J. (2018). Postmenopausal breast cancer and oestrogen associations with the IgA-coated and IgA-noncoated faecal microbiota.  British journal of cancer118(4), 471.

Kohl, K. D., Dearing, M. D., & Bordenstein, S. R. (2018). Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract. Molecular ecology27(8), 1874-1883.

Leigh, B.A., S.R. BordensteinA.W. BrooksA. MikaelyanS.R. Bordenstein. Finer-scale phylosymbiosis: Insights from insect viromes. mSystems 3(6): e00131-18.

Maseda, D., Zackular, J. P., Trindade, B., Kirk, L., Crofford, L. J., Schloss, P. D., … & Washington, M. K. (2018). Nonsteroidal anti-inflammatory drugs alter the microbiota and exacerbate Clostridium difficile colitis while dysregulating the inflammatory response. mBio10(1), e02282-18.

Mohammadkhah, A., Simpson, E., Patterson, S., & Ferguson, J. (2018). Development of the Gut Microbiome in Children, and Lifetime Implications for Obesity and Cardiometabolic Disease. Children5(12), 160.

Romano-Keeler, J., Shilts, M. H., Tovchigrechko, A., Wang, C., Brucker, R. M., Moore, D. J., … & Tang, Y. W. (2018). Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure.  PloS one13(10), e0206366.


Humpf, H. U., Schneider, C., & Stevens, J. F. (2017). Hot Topics in 2017–Gut Microbiota, Whole Grains and Health. Molecular nutrition & food research61(1), 1770014.

Jenkins, B. J., Seyssel, K., Chiu, S., Pan, P. H., Lin, S. Y., Stanley, E., … & Vetter, W. (2017). Odd chain fatty acids; new insights of the relationship between the gut microbiota, dietary intake, biosynthesis and glucose intolerance. Scientific Reports7, 44845.

Li, K., Methe, B. A., Morris, A. M., Ghedin, E., Hochheiser, H., Collman, R. G., … & Koth, L. L. (2017). Microbiota In Alpha-1 Antitrypsin Deficiency And Sarcoidosis. In A21. IMMUNE MECHANISMS OF SARCOIDOSIS AND OTHER GRANULOMATOUS DISEASES (pp. A1069-A1069). American Thoracic Society.

Long, J., Cai, Q., Steinwandel, M., Hargreaves, M. K., Bordenstein, S. R., Blot, W. J., … & Shu, X. O. (2017). Association of oral microbiome with type 2 diabetes risk. Journal of periodontal research52(3), 636-643.

Lopez, C. A., & Skaar, E. P. (2017). Crossed Wires: Interspecies Interference Blocks Pathogen Colonization. Cell host & microbe22(6), 721-723.

Meighani, A., Hart, B. R., Bourgi, K., Miller, N., John, A., & Ramesh, M. (2017). Outcomes of fecal microbiota transplantation for clostridium difficile infection in patients with inflammatory bowel disease. Digestive diseases and sciences62(10), 2870-2875.

Noto, J. M., & Peek Jr, R. M. (2017). The gastric microbiome, its interaction with Helicobacter pylori, and its potential role in the progression to stomach cancer. PLoS pathogens13(10), e1006573.

Richards, C., Otani, S., Mikaelyan, A., & Poulsen, M. (2017). Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites. PloS one, 12(10), e0185745.

Shilts, M., Schobel, S., Tovchigrechko, A., Rosas-Salazar, C., Chappell, J. D., Larkin, E. K., … & Peebles, R. S. (2017). Respiratory Syncytial Virus (rsv) Genotypes Associated With Wheezing In Infants Have Distinct Nasopharyngeal Microbiome Community Structure During Acute Viral Infection. In B21. ALTERATIONS IN MICROBIOME AND VIROME IN LUNG DISEASE (pp. A2947-A2947). American Thoracic Society.