Publications

[23] Rossmann M, Thomas AM, Guima SS, […] , Setubal JC. (2021). Microbiomes of Field-Grown Maize and Soybean in Southeastern and Central Brazil Inferred by High-Throughput 16S and Internal Transcribed Spacer Amplicon Sequencing. Microbiol Resour Announc. 10:e00528-21. 

[22] Danko D, Bezdan D, Afshin EE, […] , Mason CE. (2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell.184, 3376–3393. 

[21] Thomas AM, Asnicar F, Kroemer G, Segata N. (2021). Genes Encoding Microbial Acyl Coenzyme A Binding Protein /Diazepam-Binding Inhibitor Orthologs Are Rare in the Human Gut Microbiome and Show No Links to Obesity. Applied and Environmental Microbiology. 87:12 e00471-21.

[20] Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S, Zitvogel L. (2021). Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment. Cell Death Differ.

[19] Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N.  (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife.10:e65088. 

[18] Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, Leeming E, Gibson R, Le Roy C, Al Khatib H, Francis L, Mazidi M, Mompeo O, Valles-Colomer M, Tett A, Beghini F, Dubois L, Bazzani D, Thomas AM, Mirzayi C, Khleborodova A, Oh S, Hine R, Bonnett C, Capdevila J, Danzanvilliers S, Giordano F, Geistlinger L, Waldron L, Davies R, Hadjigeorgiou G, Wolf J, Ordovás JM, Gardner C, Franks PW, Chan AT, Huttenhower C, Spector TD, Segata N. (2021). Microbiome connections with host metabolism and habitual diet from 1098 deeply phenotyped individuals. Nature Medicine. 27;321–332

[17] Felestrino ÉB, Sanchez AB, Caneschi WL, Lemes CG, Assis RD, Cordeiro IF, Fonseca NP, Villa MM, Vieira IT, Kamino LH, do Carmo FF, da Silva AM, Thomas AM, Patané JSL, Ferreira FC, de Freitas LG, Varani AM, Ferro JA, Silva RS, Almeida NF, Garcia CCM, Setubal JC, Moreira LM. (2020). Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant. PloS one. Nov 5;15(11):e0241546.

[16] Ianiro G, Rossi E, Thomas AM, Schinzari G, Masucci L, Quaranta G, Settanni CR, Lopetuso LR, Armanini F, Blanco-Miguez A, Asnicar F, Consolandi C, Iacovelli R, Sanguinetti M, Tortora G, Gasbarrini A, Segata N, Cammarota G. (2020). Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma. Nature Communications 11, 4333.

[15] Sato FT, Yap YA, Crisma AR, Portovedo M, Murata GM, Hirabara SM, Ribeiro WR, Ferreira CM, Cruz MM, Pereira JNB, Payolla TB, Guima SES, Thomas AM, Setubal JC, Alonso-Vale MIC, Santos MF, Curi R, Marino R, Vinolo MAR. (2020). Tributyrin Attenuates Metabolic and Inflammatory Changes Associated with Obesity through a GPR109A-Dependent Mechanism. Cells 9(9), 2007. 

[14] Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. (2020). Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications 11, 2500.

[13] Al Assal K, Prifti E, Belda E, Sala P, Clément K, Dao MC, Doré J, Levenez F, Taddei CR, Fonseca DC, Rocha IM, Balmant BD, Thomas AM, Santo MA, Dias-Neto E, Setubal JC, Zucker JD, Belarmino G, Torrinhas RS, Waitzberg D. (2020). Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission. Nutrients 12(2), 278.

[12] Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Luc AR, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A, Cordero F. (2019). Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples. Msystems 4(5) e00289-19.

[11] Fukumori C, Casaro MB, Thomas AM, Mendes E, Ribeiro WR, Crisma AR, Murata GM, Bizzarro B, Dias-Neto E, Setubal JC, Oliveira MA, Tavares-de-Lima W, Curi R, Bordin S, Sartorelli P, Ferreira CM. (2019). Maternal supplementation with a synbiotic has distinct outcomes on offspring gut microbiota formation in A/J and C57BL/6 mice, differentially affecting airway inflammatory cell infiltration and mucus production. Journal of Functional Foods. 61(103496).

[10] Thomas AM & Segata N. (2019). Multiple levels of the unknown in microbiome research. BMC Biology. 17(48).

[9] Fachi JL, Felipe JS, Pral LP, da Silva BK, Corrêa RO, de Andrade MCP, da Fonseca DM, Basso PJ, Câmara NOS, de Sales E Souza ÉL, Dos Santos Martins F, Guima SES, Thomas AM, Setubal JC, Magalhães YT, Forti FL, Candreva T, Rodrigues HG, de Jesus MB, Consonni SR, Farias ADS, Varga-Weisz P, Vinolo MAR. (2019). Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism. Cell Reports. 27(3):750-761.

[8] Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. (2019). Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. 25;667–678. 

[7] Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai RP, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G. (2019). Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine. 25;679-689. 

[6] Mendes E, Acetturi BG, Thomas AM, Martins FS, Crisma AR, Murata G, Braga TT, Camâra NOS, Franco ALS, Setubal JC, Ribeiro WR, Valduga CJ, Curi R, Dias-Neto E, Tavares-de-Lima W, Ferreira CM. (2017). Prophylactic Supplementation of Bifidobacterium longum 51A Protects Mice from Ovariectomy-Induced Exacerbated Allergic Airway Inflammation and Airway Hyperresponsiveness. Front. Microbiol. 8:1732.

[5] GE4GAC group. (2017). Genomics and epidemiology for gastric adenocarcinomasApplied Cancer Research 37:7.

[4] Antunes LP, Martins LF, Pereira RV, Thomas AM, Barbosa D, Lemos LN, Silva GMM, Moura LMS, Epamino GWC, Digiampietri LA, Lombardi KC, Ramos PL, Quaggio RB, Oliveira JCF, Pascon RC, Cruz JB, Silva AM, Setubal JC. (2016). Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomicsScientific Reports 6:38915.

[3] Thomas AM,  Jesus EC, Lopes A, Aguiar S Jr., Begnami MD, Rocha RM, Carpinetti PA, Camargo AA, Hoffmann C,  Freitas HC,  Silva IT, Nunes DN,  Setubal JC, Dias-Neto E. (2016). Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling. Front. Cell. Infect. Microbiol. 6:179.

[2] Kinker GS, Thomas AM, Carvalho VJ, Lima FP, Fujita A. (2016). Deletion and low expression of NFKBIA are associated with poor prognosis in lower-grade glioma patients. Scientific Reports 6:24160.

[1] Thomas AM, Gleber-Netto F, Fernandes GR, Amorim M, Barbosa LF, Francisco ALN, Guerra de Andrade A, Setubal JC, Kowalski LP, Nunes DN, Dias-Neto E. (2014). Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilmsBMC Microbiology 14:250.

Book chapters:

[1] Thomas AM, Lima FP, Moura LMS, Silva AM, Dias-Neto E, Setubal JC. (2016). Comparative MetagenomicsMethods Mol Biol 1704:243-260. 

Prizes:

2020 – Best Oral Presentation, 5th Annual Meeting of Alleanza Contro il Cancro, Rome, Italy. 

2019 – Best PhD thesis, Prêmio CAPES de teses (área de Biológicas I), Brazil.

2019 – Best research in oncology, X Prêmio Octávio Frias de Oliveira, São Paulo, Brazil.  

2017 – Best experimental work poster, 19th Research Forum on Clinical and Experimental Nutrition, Brazil. 

2012 – Best Graduate Oral Presentation – Microorganism Genetics, Brazilian Genetics Society.

Lectures:

2020 The oncomicrobiome viewed through the lenses of metagenomics (in portuguese).

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