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Use of high throughput amplicon sequencing and ethidium monoazide dye to track microbiota changes in an equol-producing menopausal woman receiving a long-term isoflavones treatment.

Guadamuro L, Azcárate-Peril MA, Tojo R, Mayo B, Delgado S.

AIMS Microbiol. 2019 Mar 22;5(1):102-116. doi: 10.3934/microbiol.2019.1.102. eCollection 2019.


The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome.

Divaris K, Shungin D, Rodríguez-Cortés A, Basta PV, Roach J, Cho H, Wu D, Ferreira Zandoná AG, Ginnis J, Ramamoorthy S, Kinchen JM, Kwintkiewicz J, Butz N, Ribeiro AA, Azcarate-Peril MA.

Methods Mol Biol. 2019;1922:525-548. doi: 10.1007/978-1-4939-9012-2_40.


Gut microbiome and brain functional connectivity in infants-a preliminary study focusing on the amygdala.

Gao W, Salzwedel AP, Carlson AL, Xia K, Azcarate-Peril MA, Styner MA, Thompson AL, Geng X, Goldman BD, Gilmore JH, Knickmeyer RC.

Psychopharmacology (Berl). 2019 May;236(5):1641-1651. doi: 10.1007/s00213-018-5161-8. Epub 2019 Jan 2.


A randomized clinical trial examining the impact of LGG probiotic supplementation on psychological status in middle-aged and older adults.

Sanborn V, Azcarate-Peril MA, Updegraff J, Manderino LM, Gunstad J.

Contemp Clin Trials Commun. 2018 Nov 14;12:192-197. doi: 10.1016/j.conctc.2018.11.006. eCollection 2018 Dec.


Prebiotics for Lactose Intolerance: Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus.

Arnold JW, Simpson JB, Roach J, Bruno-Barcena JM, Azcarate-Peril MA.

Nutrients. 2018 Oct 16;10(10). pii: E1517. doi: 10.3390/nu10101517.


Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations.

Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM, Kuhn L.

Nat Commun. 2018 Oct 9;9(1):4169. doi: 10.1038/s41467-018-06473-x.


Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl.

Pérez-Díaz IM, Hayes JS, Medina E, Webber AM, Butz N, Dickey AN, Lu Z, Azcarate-Peril MA.

Food Microbiol. 2019 Feb;77:10-20. doi: 10.1016/ Epub 2018 Aug 7.


A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology.

Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST.

Cell Mol Gastroenterol Hepatol. 2018 May 22;6(3):301-319. doi: 10.1016/j.jcmgh.2018.05.004. eCollection 2018.


Exposures Related to House Dust Microbiota in a U.S. Farming Population.

Lee MK, Carnes MU, Butz N, Azcarate-Peril MA, Richards M, Umbach DM, Thorne PS, Beane Freeman LE, Peddada SD, London SJ.

Environ Health Perspect. 2018 Jun 1;126(6):067001. doi: 10.1289/EHP3145. eCollection 2018 Jun.


Osteoarthritis induced by destabilization of the medial meniscus is reduced in germ-free mice.

Ulici V, Kelley KL, Azcarate-Peril MA, Cleveland RJ, Sartor RB, Schwartz TA, Loeser RF.

Osteoarthritis Cartilage. 2018 Aug;26(8):1098-1109. doi: 10.1016/j.joca.2018.05.016. Epub 2018 May 30.


Gut microbiome of Moroccan colorectal cancer patients.

Allali I, Boukhatem N, Bouguenouch L, Hardi H, Boudouaya HA, Cadenas MB, Ouldim K, Amzazi S, Azcarate-Peril MA, Ghazal H.

Med Microbiol Immunol. 2018 Aug;207(3-4):211-225. doi: 10.1007/s00430-018-0542-5. Epub 2018 Apr 23.


Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential.

Arnold JW, Simpson JB, Roach J, Kwintkiewicz J, Azcarate-Peril MA.

Front Microbiol. 2018 Feb 20;9:242. doi: 10.3389/fmicb.2018.00242. eCollection 2018.


Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples.

Jones RB, Zhu X, Moan E, Murff HJ, Ness RM, Seidner DL, Sun S, Yu C, Dai Q, Fodor AA, Azcarate-Peril MA, Shrubsole MJ.

Sci Rep. 2018 Mar 7;8(1):4139. doi: 10.1038/s41598-018-22408-4.


An Attenuated Salmonella enterica Serovar Typhimurium Strain and Galacto-Oligosaccharides Accelerate Clearance of Salmonella Infections in Poultry through Modifications to the Gut Microbiome.

Azcarate-Peril MA, Butz N, Cadenas MB, Koci M, Ballou A, Mendoza M, Ali R, Hassan H.

Appl Environ Microbiol. 2018 Feb 14;84(5). pii: e02526-17. doi: 10.1128/AEM.02526-17. Print 2018 Mar 1.


A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults.

Anderson JR, Carroll I, Azcarate-Peril MA, Rochette AD, Heinberg LJ, Peat C, Steffen K, Manderino LM, Mitchell J, Gunstad J.

Sleep Med. 2017 Oct;38:104-107. doi: 10.1016/j.sleep.2017.07.018. Epub 2017 Aug 2.


A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.

Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA.

BMC Microbiol. 2017 Sep 13;17(1):194. doi: 10.1186/s12866-017-1101-8.


Infant Gut Microbiome Associated With Cognitive Development.

Carlson AL, Xia K, Azcarate-Peril MA, Goldman BD, Ahn M, Styner MA, Thompson AL, Geng X, Gilmore JH, Knickmeyer RC.

Biol Psychiatry. 2018 Jan 15;83(2):148-159. doi: 10.1016/j.biopsych.2017.06.021. Epub 2017 Jun 27.


Maternal Gut Microbiome Biodiversity in Pregnancy.

Smid MC, Ricks NM, Panzer A, Mccoy AN, Azcarate-Peril MA, Keku TO, Boggess KA.

Am J Perinatol. 2018 Jan;35(1):24-30. doi: 10.1055/s-0037-1604412. Epub 2017 Jul 27.


The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries.

Ribeiro AA, Azcarate-Peril MA, Cadenas MB, Butz N, Paster BJ, Chen T, Bair E, Arnold RR.

PLoS One. 2017 Jul 5;12(7):e0180621. doi: 10.1371/journal.pone.0180621. eCollection 2017.


Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk.

Seidel DV, Azcárate-Peril MA, Chapkin RS, Turner ND.

Semin Cancer Biol. 2017 Oct;46:191-204. doi: 10.1016/j.semcancer.2017.06.009. Epub 2017 Jul 1. Review.


Preliminary Evidence for an Association Between the Composition of the Gut Microbiome and Cognitive Function in Neurologically Healthy Older Adults.

Manderino L, Carroll I, Azcarate-Peril MA, Rochette A, Heinberg L, Peat C, Steffen K, Mitchell J, Gunstad J.

J Int Neuropsychol Soc. 2017 Sep;23(8):700-705. doi: 10.1017/S1355617717000492. Epub 2017 Jun 23.


Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation During Aging in Mice by Altering the Intestinal Microbiota.

Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT, Kang A, Chen W, Azcarate-Peril MA, Gulati AS, Fargo DC, Guarente L, Li X.

Gastroenterology. 2017 Sep;153(3):772-786. doi: 10.1053/j.gastro.2017.05.022. Epub 2017 May 26.


Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants.

Arnold JW, Monteagudo-Mera A, Altermann E, Cadenas MB, Thompson AL, Azcarate-Peril MA.

Genome Announc. 2017 Apr 6;5(14). pii: e00107-17. doi: 10.1128/genomeA.00107-17.


Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals.

Azcarate-Peril MA, Ritter AJ, Savaiano D, Monteagudo-Mera A, Anderson C, Magness ST, Klaenhammer TR.

Proc Natl Acad Sci U S A. 2017 Jan 17;114(3):E367-E375. doi: 10.1073/pnas.1606722113. Epub 2017 Jan 3.


Reassessment of the succession of lactic acid bacteria in commercial cucumber fermentations and physiological and genomic features associated with their dominance.

Pérez-Díaz IM, Hayes J, Medina E, Anekella K, Daughtry K, Dieck S, Levi M, Price R, Butz N, Lu Z, Azcarate-Peril MA.

Food Microbiol. 2017 May;63:217-227. doi: 10.1016/ Epub 2016 Dec 1.


The Salivary Microbiome and Oral Cancer Risk: a Pilot Study in Fanconi Anemia.

Furquim CP, Soares GM, Ribeiro LL, Azcarate-Peril MA, Butz N, Roach J, Moss K, Bonfim C, Torres-Pereira CC, Teles FR.

J Dent Res. 2017 Mar;96(3):292-299. doi: 10.1177/0022034516678169. Epub 2016 Nov 13.


Modeling human enteric dysbiosis and rotavirus immunity in gnotobiotic pigs.

Twitchell EL, Tin C, Wen K, Zhang H, Becker-Dreps S, Azcarate-Peril MA, Vilchez S, Li G, Ramesh A, Weiss M, Lei S, Bui T, Yang X, Schultz-Cherry S, Yuan L.

Gut Pathog. 2016 Nov 8;8:51. eCollection 2016.


Emerging Technologies for Gut Microbiome Research.

Arnold JW, Roach J, Azcarate-Peril MA.

Trends Microbiol. 2016 Nov;24(11):887-901. doi: 10.1016/j.tim.2016.06.008. Epub 2016 Jul 15. Review.


Oral colostrum priming shortens hospitalization without changing the immunomicrobial milieu.

Romano-Keeler J, Azcarate-Peril MA, Weitkamp JH, Slaughter JC, McDonald WH, Meng S, Latuga MS, Wynn JL.

J Perinatol. 2017 Jan;37(1):36-41. doi: 10.1038/jp.2016.161. Epub 2016 Sep 29.


High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome.

Monteagudo-Mera A, Arthur JC, Jobin C, Keku T, Bruno-Barcena JM, Azcarate-Peril MA.

Benef Microbes. 2016;7(2):247-64. doi: 10.3920/BM2015.0114. Epub 2016 Feb 3.


Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods.

Medina E, Pérez-Díaz IM, Breidt F, Hayes J, Franco W, Butz N, Azcarate-Peril MA.

J Food Sci. 2016 Jan;81(1):M121-9. doi: 10.1111/1750-3841.13158. Epub 2015 Nov 25.


Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children.

Bahr SM, Tyler BC, Wooldridge N, Butcher BD, Burns TL, Teesch LM, Oltman CL, Azcarate-Peril MA, Kirby JR, Calarge CA.

Transl Psychiatry. 2015 Oct 6;5:e652. doi: 10.1038/tp.2015.135.


Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery.

Becker-Dreps S, Allali I, Monteagudo A, Vilchez S, Hudgens MG, Rogawski ET, Carroll IM, Zambrana LE, Espinoza F, Azcarate-Peril MA.

Am J Trop Med Hyg. 2015 Dec;93(6):1187-93. doi: 10.4269/ajtmh.15-0322. Epub 2015 Sep 8.


Space Environmental Factor Impacts upon Murine Colon Microbiota and Mucosal Homeostasis.

Ritchie LE, Taddeo SS, Weeks BR, Lima F, Bloomfield SA, Azcarate-Peril MA, Zwart SR, Smith SM, Turner ND.

PLoS One. 2015 Jun 17;10(6):e0125792. doi: 10.1371/journal.pone.0125792. eCollection 2015.


Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing.

Tzanetakis GN, Azcarate-Peril MA, Zachaki S, Panopoulos P, Kontakiotis EG, Madianos PN, Divaris K.

J Endod. 2015 Aug;41(8):1226-33. doi: 10.1016/j.joen.2015.03.010. Epub 2015 Apr 21.


Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain.

Allali I, Delgado S, Marron PI, Astudillo A, Yeh JJ, Ghazal H, Amzazi S, Keku T, Azcarate-Peril MA.

Gut Microbes. 2015;6(3):161-72. doi: 10.1080/19490976.2015.1039223.


Characterization of the microbial diversity in yacon spontaneous fermentation at 20 °C.

Reina LD, Pérez-Díaz IM, Breidt F, Azcarate-Peril MA, Medina E, Butz N.

Int J Food Microbiol. 2015 Jun 16;203:35-40. doi: 10.1016/j.ijfoodmicro.2015.03.007. Epub 2015 Mar 7.


Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis.

Ritchie LE, Sturino JM, Carroll RJ, Rooney LW, Azcarate-Peril MA, Turner ND.

FEMS Microbiol Ecol. 2015 Mar;91(3). pii: fiv008. doi: 10.1093/femsec/fiv008. Epub 2015 Jan 14.


Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome.

Thompson AL, Monteagudo-Mera A, Cadenas MB, Lampl ML, Azcarate-Peril MA.

Front Cell Infect Microbiol. 2015 Feb 5;5:3. doi: 10.3389/fcimb.2015.00003. eCollection 2015.


Galacto-oligosaccharides and Colorectal Cancer: Feeding our Intestinal Probiome.

Bruno-Barcena JM, Azcarate-Peril MA.

J Funct Foods. 2015 Jan;12:92-108.


Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052.

Sandoval-Espinola WJ, Makwana ST, Chinn MS, Thon MR, Azcárate-Peril MA, Bruno-Bárcena JM.

Microbiology. 2013 Dec;159(Pt 12):2558-70. doi: 10.1099/mic.0.069534-0. Epub 2013 Sep 25.


Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon.

Devine AA, Gonzalez A, Speck KE, Knight R, Helmrath M, Lund PK, Azcarate-Peril MA.

PLoS One. 2013 Aug 27;8(8):e73140. doi: 10.1371/journal.pone.0073140. eCollection 2013.


Diet complexity and estrogen receptor β status affect the composition of the murine intestinal microbiota.

Menon R, Watson SE, Thomas LN, Allred CD, Dabney A, Azcarate-Peril MA, Sturino JM.

Appl Environ Microbiol. 2013 Sep;79(18):5763-73. doi: 10.1128/AEM.01182-13. Epub 2013 Jul 19.


Heterologous expression of a bioactive β-hexosyltransferase, an enzyme producer of prebiotics, from Sporobolomyces singularis.

Dagher SF, Azcarate-Peril MA, Bruno-Bárcena JM.

Appl Environ Microbiol. 2013 Feb;79(4):1241-9. doi: 10.1128/AEM.03491-12. Epub 2012 Dec 14.


Acute necrotizing enterocolitis of preterm piglets is characterized by dysbiosis of ileal mucosa-associated bacteria.

Azcarate-Peril MA, Foster DM, Cadenas MB, Stone MR, Jacobi SK, Stauffer SH, Pease A, Gookin JL.

Gut Microbes. 2011 Jul-Aug;2(4):234-43. doi: 10.4161/gmic.2.4.16332. Epub 2011 Jul 1.


The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?

Azcárate-Peril MA, Sikes M, Bruno-Bárcena JM.

Am J Physiol Gastrointest Liver Physiol. 2011 Sep;301(3):G401-24. doi: 10.1152/ajpgi.00110.2011. Epub 2011 Jun 23. Review.


Construction of vectors for inducible and constitutive gene expression in Lactobacillus.

Duong T, Miller MJ, Barrangou R, Azcarate-Peril MA, Klaenhammer TR.

Microb Biotechnol. 2011 May;4(3):357-67. doi: 10.1111/j.1751-7915.2010.00200.x. Epub 2010 Sep 1.


Role of antioxidant enzymes in bacterial resistance to organic acids.

Bruno-Bárcena JM, Azcárate-Peril MA, Hassan HM.

Appl Environ Microbiol. 2010 May;76(9):2747-53. doi: 10.1128/AEM.02718-09. Epub 2010 Mar 19.


Development and application of a upp-based counterselective gene replacement system for the study of the S-layer protein SlpX of Lactobacillus acidophilus NCFM.

Goh YJ, Azcárate-Peril MA, O'Flaherty S, Durmaz E, Valence F, Jardin J, Lortal S, Klaenhammer TR.

Appl Environ Microbiol. 2009 May;75(10):3093-105. doi: 10.1128/AEM.02502-08. Epub 2009 Mar 20.


Role of autoinducer-2 on the adhesion ability of Lactobacillus acidophilus.

Buck BL, Azcarate-Peril MA, Klaenhammer TR.

J Appl Microbiol. 2009 Jul;107(1):269-79. doi: 10.1111/j.1365-2672.2009.04204.x. Epub 2009 Mar 16.

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