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Mathieu Almeida

Mathieu Almeida

session, year:
2017 1st


Receiving laboratory:
MGP, MetaGenoPolis, Jouy-en-Josas

Country of origin:

United States of America

Country of destination:


Last available contact


Download Curriculum Vitae

Mobility project

Improving the definition, reconstruction and isolation of the most wanted bacteria from the human intestinal tract by combining large scale whole metagenomics and amplicon-based methods.

The human intestinal tract microbiota is a complex ecosystem composed mainly of bacteria that play a major role in our immune system and our nutritional intake [Doré et al., United European Gastroenterol J, 2013]. In 2012, the HMP consortium defined a list of most wanted bacteria, organisms that remain prevalent in the healthy human microbiota of American adults but with few or no isolated genomes available [Fodor et al., Plos One, 2012]. In a complementary effort, the Metahit consortium provided the first human intestinal microbiota gene catalog [Qin et al., Nature, 2010], partially reconstructed into draft genomes, including organisms potentially corresponding to the most wanted bacteria [Nielsen*, Almeida*, et al., Nature Biotechnology, 2014]. At the same time, advances in culturing methods have allowed investigators to isolate, amplify and sequence some of these most wanted organisms [Browne et al., Nature, 2016; Lagier et al., Nature Microbiology, 2016]. Despite these new methods and discoveries provided by the international scientific efforts, It is assumed that the majority of the most wanted organisms are under-represented or absent from public genome databases [Almeida et al., ISME, 2016]. This can be explained by the difficulty of culturing unknown organisms from complex microbial communities without knowing their metabolic profile, which describes the compounds required for their growth. The purpose of my project is to reconstruct the missing most wanted bacterial genomes associated with different populations, diets, health conditions and hosts. Using the reconstructed genomes, I will define their specific biomarkers to improve their detection in thousands of stool samples and define adapted media culture. To centralize the data, I propose to create the web database ARMADA (tARgeting the Most wAnteD bacteriA), which will link the genomes to their host phenotypes, their biomarkers, and their metabolic profile for adapted media culture design.

Biography & research interests

I followed Bioinformatic studies at the Université Paris-VII, where I received a Master degree in 2009. I was trained to develop software (in C, Perl, Python and R language), databases (MySQL), and model protein structural folding. Later in 2009, I had the chance to join Dr. Pierre Renault at INRA Micalis Institute (Jouy-en-Josas, France) for an internship and a PhD. My main focus was the development of a software for the visualization of bacterial genome variability (GenoVA) with the objective to apply it to food and human related bacteria. I then joined the MetaHIT consortium, coordinated by Dr. S. Dusko Ehrlich, and helped for the development of a gene binning method called Canopy, designed for large-scale metagenomics datasets. Finally, I joined Dr. Mihai Pop in 2013 at the Center For Bioinformatics and Computational Biology (College Park, USA) for a 4 year post-doctoral position, where I helped improving a reference guided metagenomic assembly method (Meta Compass). I also participated in large scale epidemiological studies with Dr. O. Colin Stine in Baltimore, USA, to infer phylogenetic relationship of pathogenic bacteria and design new primers for PCR approach.

Selected publications

Almiñana C, Corbin E, Tsikis G, et al., 2017. Oviduct extracellular vesicles protein content and their role during oviduct-embryo cross-talk. Reproduction, 154, 253-268. Doi: 10.1530/REP-17-0054.

Caballero I, Boyd J, Almiñana C, Sanchez-Lopez JA, et al., 2017. Understanding the dynamics of Toll-like Receptor 5 response to flagellin and its regulation by estradiol. Scientific Reports, 7( 3), 40981. Doi: 10.1038/srep40981.

Batista RI, Moro LN, Corbin E, Almiñana C, SouzaFabjan JM, de Figueirêdo Freitas VJ, Mermillod P, 2016. Combination of oviduct fluid and heparin to improve monospermic zygotes production during porcine in vitro fertilization. Theriogenology. 15;86(2):495-502.

Almiñana C, Corbin E, Harichaux G, et al., 2015. Interception of exosomal messages between the oviduct and the embryo: What are they tweeting about? Reproduction, Fertility and Development 28(2) 168-168.

Almiñana C., 2015. Snooping on a private conversation between the oviduct and gametes/embryos. Anim. Reprod., v.12, n.3, p.366-374.

Almiñana C. Caballero I, Heath PR, et al., 2014. The battle of the sexes starts in the oviduct: modulation of oviductal transcriptome by X and Y-bearing spermatozoa. BMC Genomics. 21;15:293.

Awards & patents

Travel grant from Stiftelsen Gunnar Sundblad (15000 SEK)

Travel grants from Knut och Alice Wallenberg Stiftelse (41100 SEK)

Young Researcher’s Challenge of the Marcus Wallenberg Foundation (www.mwp.org)

Talks in annual meetings

Targeting the most wanted human intestinal bacteria.
2018 / P6 Applied Maths / by Mathieu Almeida / Fellows Speed Presentation


Bacteria, metagenomic, genomic, biomarkers, human intestinal tract, gene clustering, bacterial culturing, metabolic profile., database, diet