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The Nutrition and Gut Microbiome Lab Contributing to research and academic progression in -omics


Nutrition and Gut microbiome

Lavefve L, Howard LR, and Carbonero F* (2018). Berry polyphenols metabolism and impact on human gut microbiota and health.  Food and Function; In Press

AlJahdali N, Gadonna-Widehem P, Anton PM, and Carbonero F* (2019). Gut microbiota modulation by dietary barley malts melanoidins. Nutrients; In Press

Lavefve L, Marasini D and Carbonero F* (2019). Microbial ecology of plant-based fermented foods and current knowledge on their impact on human health. Advances in Food Science and Nutrition, 87, 147-186

Ashley D, Marasini D, Brownmiller C, Lee JA, Franck Carbonero and Lee SO (2019). Impact of grain sorghum polyphenols on microbiota of normal weight and overweight/obese subjects during in vitro fecal fermentation. Nutrients, 11(2), 217

Mayta-Apaza AC, Pottgen E, De Bodt J, Papp N, Abranko L, Van de Wiele T, Lee SO and Carbonero F* (2018).Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo. Journal of Nutritional Biochemistry, 59, 160-172 DOI: 10.1016/j.jnutbio.2018.04.001

Tsai T, Sales MA, Kim H, Erf GF, Vo NFranck Carbonero, Van Der Merwe M, Kegley EA, Buddington RK, Wang X, Maxwell CV and Zhao J (2018). Isolated rearing at lactation increases gut microbial diversity and improves post-weaning performance in pigs. Frontiers in Microbiology, 9: 2889

ALJahdali N, Gadonna-Widehem P, Delayre-Orthez C, Marier D, Garnier B, Carbonero F*, Anton PM (2017). Repeated Oral Exposure to N ε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice. Digestive Diseases and Science.; 62 (12), 3370-3384

ALJahdali NCarbonero F* (2017). Impact of Maillard Reaction products on Nutrition and Health: Current knowledge and need to understand their fate in the human digestive system. Critical Reviews in Food Science and Nutrition; 2017 Sep 13:0. doi: 10.1080/10408398.2017.1378865.

Mayta-Apaza ACMarasini DCarbonero F* (2017). Tart Cherries and health: Current knowledge and need for a better understanding of the fate of phytochemicals in the human gastrointestinal tract. Critical Reviews in Food Science and Nutrition; Sep 28:0. doi: 10.1080/10408398.2017.1384918.

Sheflin AM, Melby CM, Carbonero F and Weir TL (2017). Linking Dietary Patterns with Gut Microbial Composition and Function. Gut Microbes; 8(2):113-129

O’Keefe SJD, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, Posma JM, Kinross J, Wahl E, Rude E, Vipperla K, Naidoo VD, Mtshali L, Tims S, Puylaert PGB, DeLany J, Krasinskas A, Benefiel AC, Kaseb HO, Newton K, de Vos WM, Gaskins HR, Zoetendal EG, Nicholson JK (2015). Fat, Fiber and Cancer Risk in African Americans and Rural Africans. Nature Communications; 6:6342

Shen W, Wolf PG, Carbonero F, Zhong W, Reid T, Gaskins HR, McIntosh MK (2014). Intestinal and systemic inflammatory responses are positively associated with sulfidogenic bacteria abundance in high-fat-fed male C57BL/6J mice. Journal of Nutrition; 144(8):1181-7


Gut microbiome research

Gomez A, Sharma A, Mallott E, Petrzelkova K, Robinson CJ, Yeoman CJ, Carbonero F, Pafco B, Rothman J, Ulanov A, Vlckova K, Amato KR, Schnorr S, Dominy N, Modry D, Todd A, Torralba M, Nelson KE, Burns M, Blekhman R, Remis M, Stumpf RM, Wilson BA, Gaskins HR, Garber P, White BA, Leigh SR (2019). Plasticity in the human gut microbiome defies evolutionary constraints. mSphere 4 (4), e00271-19

Carbonero F*Mayta-Apaza AC, Bolea M, Yu JZ, Lindebald M, Lyubimov A, Neri F, Szilagyi E and Bartholomew A (2018). Specific members of the gut microbiota are reliable biomarkers of irradiation intensity and lethality in large animal models of human health. Radiation Research Journal, 191 (1), 107-121

Carbonero F*Mayta-Apaza AC, Yu JZ, Lindebald M, Lyubimov A, Neri F, Szilagyi E and Bartholomew A (2018). A Comparative Analysis of Gut Microbiota disturbances in the Gottingen Minipig and Rhesus Macaque Models of Acute Radiation Syndrome following bioequivalent radiation exposures. Radiation and Environmental Biophysics, 57 (4), 419-426

Vo N, Tsai TC, Maxwell C, Carbonero F* (2017). Early exposure to agricultural soil accelerates the maturation of the early-life pig gut microbiota. Anaerobe; 45:31-39

Turroni S, Rampelli S, Biagi E, Consolandi C, Severgnini M, Peano C, Quercia S, Soverini M, Carbonero F, Bianconi G, Rettberg P, Canganella F, Brigidi P, Candela M (2017). Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500. Microbiome; 5(1):39

Carbonero F* (2017). Human epigenetics and microbiome: the potential for a revolution in both research areas by integrative studies. Future Science OA; 3(3).

Cureau N, AlJahdali N, Vo NCarbonero F* (2016).Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives. Epigenomics; 8(9): 1259-73

Gomez A, Ptrzelkova K, Yeoman C, Burns MB, Amato KR, Vlckova K, Modry D, Todd A, Robbinson CA, Remis M, Torralba M, Nelson KE, Carbonero F, Gaskins HR, Wilson B, Stumpf R, White B, Leigh S and Blekhman R (2016). Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Reports; 4(9):2142-53

Gomez A, Petrzelkova K, Yeoman CJ, Vlckova K, Mrázek J, Koppova I, Carbonero F, Ulanov A, Modry D, Todd A, Torralba M, Nelson KE, Gaskins HR, Wilson B, Stumpf RM, White BA, Leigh SR (2015). Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology. Molecular Ecology; 10:2551-65

Candela M, Turroni S, Biagi E, Carbonero F, Rampelli S, Fiorentini, and Brigidi P (2014). Inflammation and colorectal cancer, when microbiota-host mutualism breaks. World Journal of Gastroenterology; 20(4):908-22

Ou J, Carbonero F+, Zoetendal E, Umeakunne K, DeLany J, Wang M, Newton K, Gaskins HR, and O’Keefe SJD (2013). Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. American Journal of Clinical Nutrition; 98(1): 111-120

Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA and Leigh SR (2013). Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME Journal; 7 (7), 1344-1353

Nava G. M., Carbonero F+, Croix JA, Greenberg E and Gaskins HR (2012). Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon. The ISME Journal. 6(1):57-70

Carbonero F, Benefiel AC and Gaskins HR (2012). Contributions of the hydrogen economy to colonic homeostasis. Nature Reviews Gastroenterology and Hepatology. 9:504-518

Nava GM, Carbonero F+, Ou J, Benefiel AC, O’Keefe SJD and Gaskins HR (2012). Hydrogenotrophic microbiota distinguish native Africans from African and European Americans. Environmental Microbiology Reports. 4(3):307–315

Carbonero F, Benefiel AC, Alizadeh A and Gaskins HR (2012). Microbial sulfur metabolisms in the human colon and their link with health and disease. Frontiers in gastrointestinal sciences. 3:448

Carbonero F, Nava GM, Benefiel AC, Greenberg E and Gaskins HR (2011). Microbial DNA extraction from intestinal biopsies is improved by avoiding mechanical cell disruption. Journal of Microbiological Methods. 87:125-127

Croix JA, Carbonero F, Nava GM, Russel M, Benefiel AC, Greenberg E and Gaskins HR (2011). On the relationship between sialomucin and sulfomucin expression and hydrogenotrophic microbes in the human colonic mucosa. PLOS One. I6:e24447


Microbial ecology

Walker LM, Cedeño-Sanchez M, Herre EA, Carbonero F, Turner BL, Wright SJ, and Stephenson SL (2018). The response of litter-associated myxomycete communities to 14 years of N, P and K addition in a lowland tropical rain forest. Journal of Eukaryotic Biology, Online First,

Walden C, Carbonero F*, Zhang W (2017). Assessing impacts of DNA extraction methods on next generation sequencing of water and wastewater samples. Journal of Microbiological Methods; 141:10-16

Rodhouse L, Carbonero F* (2017). Overview of craft brewing specificities and potentially associated microbiota. Critical Reviews in Food Science and Nutrition; 2017 Sep 14:1-12. doi: 10.1080/10408398.2017.1378616.

Johnson WH, Douglas MR, Lewis JA, Stuecker TN, Carbonero FG, Austin BJ, Evans-White MA, Entrekin SA, Douglas ME (2017). Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas. BMC Microbiology; 17(1):29

Baker CA, Rubinelli PM, Park SH, Carbonero F, Ricke SC (2016). Shiga toxin-producing Escherichia coli in food: Incidence, ecology, and detection strategies. Food Control; 59:407-419

Walden, C, Carbonero, F, and Zhang, W (2015). Preliminary Assessment of Bacterial Community Change Impacted by Chlorine Dioxide in a Water Treatment Plant. Journal of Environmental Engineering; 42(2)

Carbonero F, Oakley BB and Purdy KJ (2013). Metabolic flexibility as a major predictor of spatial distribution in microbial communities. PLoS One; 9(1):e85105

Hayot Carbonero C, Carbonero F, Smith LMJ and Brown TA (2013). Cytological characterisation of the underutilized forage crop Onobrychis viciifolia Scop. and other members of the Onobrychis genus. Genetic Resources and Crop Evolution; 60 (7), 1987-1996

Carbonero F, Oakley BB, Hawkins RJ and Purdy KJ (2012). Genotypic distribution of Methanosaeta, a specialist model microorganism, along an estuary: Does metabolic restriction limit niche differentiation potential? Microbial Ecology. 63(4): 856-864

Oakley BB, Carbonero F, Dowd SE, Hawkins RJ and Purdy KJ (2012). Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter. The ISME Journal. 6:905–914

Hayot Carbonero C, Carbonero F, Smith LMJ and Brown TA (2012). Phylogenetic characterisation of Onobrychis species with special focus on the forage crop Onobrychis viciifolia. Genetic Resources and Crop Evolution; 59 (8), 1777-1788

Carbonero F, Oakley BB and Purdy KJ. (2010) Improving the isolation of anaerobes on solid media: The example of the fastidious Methanosaeta. Journal of Microbiological Methods; 80(2):203-205

Oakley BB, Carbonero F, van der Gast CJ, Hawkins RJ and Purdy KJ (2010). Evolutionary divergence and biogeography of sympatric niche-differentiated bacterial populations. The ISME Journal; 4(4):488–497