Thomas GuiraudBordeaux Sciences Agro · Feed and Food
I explore the genome of microbial strains of agronomical interest and develop characterization and monitoring tools.
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
Molecular biologist graduated of the University of Bordeaux (France), I worked until 2011 in plant sciences at the INRAE on research topics covering from plant virology to the development of flower and fruit. From 2012 to 2021, I worked at Bordeaux Sciences Agro on various microbiology topics (from control of flavobacteriosis in trout farms to soil sciences). Recently, still in BdxSA, I moved on a biosolutions topics (genome mining, bioprospecting, molecular microbiology, etc.).
September 2021 - present
- Characterization of microbial strains and exploration of avenues for agronomic and biotechnological valorization. Development of molecular tools for microbial colonisation's monitoring. Bioprospecting for new strains of interest.
October 2017 - March 2021
- Mapping and characterization (pedology, microbial ecology) of the wetlands of the urban community of Bordeaux (France). Occasional participant in the second campaign of the French Soil Quality Monitoring Network (RMQS2).
May 2012 - September 2017
- PostDoc Position
- Development of qPCR detection test for F. psychrophilum and several probiotic bacteria. Development of an efficient and low cost protocol for genomic DNA extraction from fish intestinal samples. Optimization of fish eggs disinfection protocols.
Tocochromanols constitute the different forms of vitamin E (VTE), essential for the human diet and display a high membrane protectant activity. By combining interval mapping and genome‐wide association studies (GWAS) we unveiled the genetic determinants of tocochromanol accumulation in tomato fruits. To enhance the nutritional value of this highly...
The effective conditions of glutaraldehyde, chloramine-T, bronopol, Incimaxx Aquatic ® and hydrogen peroxide as some biocides commonly used by the aquaculture industry were investigated against F. psychrophilum in sanitization of rainbow trout eyed eggs. Bacteriostatic tests as well as bactericidal tests using ethidium monoazide bromide PCR assays...
The capacity of Lettuce mosaic virus to overcome the lettuce resistance conferred by the mo1(1) and mo1(2) alleles of the gene for eukaryotic translation initiation factor 4E (eIF4E) was analysed using reverse genetics. Mutations in the virus genome-linked protein (VPg) allowed mo1(1) only to be overcome, but mutations in the C-terminal portion of...
With the aim to characterize plant and viral factors involved in the molecular interactions between plants and potyviruses, a Lettuce mosaic virus (LMV)-Arabidopsis thaliana pathosystem was developed. Screening of Arabidopsis accessions with LMV isolates indicated the existence of a large variability in the outcome of the interaction, allowing the...
Lettuce mosaic virus (LMV)-Most isolates can infect and are seed-borne in cultivars containing the mo1 gene. A reverse transcription and polymerase chain reaction (RT-PCR)-based test was developed for the specific detection of LMV-Most isolates. Based on the complete genome sequences of three LMV isolates belonging respectively to the Most type, th...
/////Preamble: This poster is a slightly improved version of the poster presented at the "Phages in Bordeaux" conference in Bordeaux (France) on 24 and 25 September 2018. This poster has been presented in French but we also offer an English version. ///// Intensive farming practices expose the French trout farming sector to various health challenge...
/////Preamble: This poster has been presented in French but we also offer an English version.///// Flavobacterium psychrophilum is a bacterium that infects farmed salmonids causing the bacterial cold water disease (BCWD), affecting adult fish on the American continent, or rainbow trout fry syndrome (RTFS) causing significant economic losses in Eur...
Intensive farming practices expose the French trout farming sector to various health challenges, among which the most problematic so far is the emergence of Flavobacterium psychrophilum, the causative agent of Rainbow Trout Fry Syndrome (RTFS). In parallel with the prophylactic measures undertaken to limit the spread of the pathogen, the intensive...
Sensory perception of fruit quality by consumers depends on various attributes such as visual aspect, flavour, and texture. For instance, fruit size and content in sugars and organic acids strongly depend on the early stages of fruit development, during which cell number and size are established and the carbon reserves accumulated. In tomato, as in...
The functional characterisation of the vitamin E pathway has been carried in tomato using two key enzymes of the tocochromanols biosynthetic pathway: the p-HydroxyPhenylPyruvate Dioxygenase (HPPD) and the prephenate dehydrogenase (PDH). Tocopherols and tocotrienols, commonly named vitamin E, are known as essential antioxidant components of both hum...
(Publication in french) By a reverse genetics approach, we identified the viral factors restoring the compatibility of Lettuce mosaic virus (LMV) with resistant lettuce varieties encoding a defective form of the translation initiation factor elF4E. We built a series of LMV chimeras exchanging genomic portions of two isolates differing in their abil...
In parallel with a project I am currently working on ("BiodiverCité", the inventory and characterization of the wetlands of the urban area of Bordeaux in France), partners will have to opportunity to collect samples of water over a few dozen streams carefully selected. While they are interested in the hydrological and chemical characteristics of these rivers and their associated fauna, I had the idea to take advantage of this sampling campaign to focus on the microflora and, later, possibily establish a link between the different data produced.
I am interested in two types of microflora : on the one hand, bacteria, archaea and other unicellular organisms (but mainly bacteria I must admit) and, on the other hand, the viral microflora.
Concerning the bacterial flora, I will unfortunately exclude any pasteurian approach, because of lack of time and lack of means.
I started with the idea of centrifuging the collected water samples and carrying out a DNA extraction which would join a DNA library to be analyzed once the financial means have been collected.
For the viral flora, I thought to carry out a precipitation of 1M NaCl, PEG6000 10% on the supernatant to concentrate the viruses in a volume easily handled and storable to have a phagolibrary in which to possibly find phages directed against bacterial species of interest (eg F. psychrophilum or other pathogenic species in aquaculture) and secondly, carry out a phage nucleic acid extraction to constitute a phagoDNAlibrary exploitable in the longer term.
My questions are:
1) What volume of sample should be collected to have enough bacterial DNA to make metabarcoding ? For the soil, the specialists of Genosol (INRA, France) urge me to extract from at least 500 mg of soil for bacterial and 1 g for fungal. But for water ?
2) Is the NaCl / PEG6000 precipitation suitable for a long-term phago-library ? I fear that this step is too brutal for some phages and that even if I concentrate theoretically in number of viral particles, I lose in infectivity (due to damage to viral fibrils). If this technique is suitable, is the use of PEG8000 better recommended to ensure a wider enrichment spectrum (for podoviridae for example, more difficult to precipitate if I understand my literature) ?
3) I know there are publications on viromics but I have not looked into detail: what minimum sample volume (before precipitation) is desirable to have enough DNA for metagenomics (or just qPCR detection of well known virus) ? 200 ml ? 1L ? 10L ??? (2 ml :) ?)
Thank you for your attention.
While I was reading this article ("Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples", Robin et al., 2013) concerning the influence of temperature and storage time of soil samples on metagenomic results, I wondered why microbial ecologists do not use fixative solutions commonly used in other areas of molecular biology.
Among the possible fixatives, the first that comes to my mind is the RNA later (and alternative products) which is used, for example, to store animal or plant samples before nucleic acid extraction when we don't have liquid nitrogen. I am also thinking about fixatives that are more or less classically used in histology and that have the particularity to preserve nucleic acids (cf. "Effect of fixatives and tissue processing on the content and integrity of nucleic acids", Srinivasan et al., 2003).
Do these products destroy cell membranes (like ethanol ?) ? Are there steps in soil microbiology (sieving ?) that make these products ultimately very impractical?
The different components of the forest systems, in particular the plants of the different vegetal strata and the soil, can fix significant amounts of carbon through different processes. However, after a forest fire, the ecosystem releases the carbon previously fixed from the atmosphere. Given the proliferation of forest fires in the SUDOE area, REMAS was born from the need to quantify the carbon emission risk, through a remote sensing model that links the carbon contained in the aerial and radicular biomass and in the soil. REMAS offers solutions based on scientific analysis to identify critical areas with a higher risk of emissions based on the amount of carbon accumulated in the forest ecosystem, in order to focus the prevention, management, extinction and restoration efforts. REMAS will transfer its knowledge to other competent authorities in risk prevention and management and to forest owners through technical training. REMAS will capitalize its results in medium-long-term strategies of the EU and each country of the consortium in terms of adaptation to climate change, forests and carbon management, integrated into regional strategies to improve governance in the planning and management of the renewable natural resources. https://www.sudoeremas.com Interreg-SUDOE SOE3/P4/E0954
Intensive farming practices expose the French trout farming sector to various health challenges, among which the most problematic so far is the emergence of Flavobacterium psychrophilum, the causative agent of Rainbow Trout Fry Syndrome (RTFS). In parallel with the prophylactic measures undertaken to limit the spread of the pathogen, the intensive use of antibiotic curative treatments leads to the emergence of antibiotic-resistant strains that become of concern for both the fish industry and human health. Phagotherapy is a promising alternative approach to antibiotic therapy. In this context, we initiated a campaign to collect fish samples (water, infected fish organs) to isolate lytic viral particles for F. psychrophilum.