May 2022

A post-doc extension awarded by the INRAe department ECODIV will allow us to continue working on our results until the end of 2022. The COVID outbreak caused many delays to the project so we are very grateful indeed to INRAe for granting this extension, ensuring that the project aims can be realised.

February 2022

The virome libraries for the 2021 data were sequenced at MGX Montpellier and the three metabarcoding libraries were sequenced at ARCAD and GenSeq, also Montpellier. Now were are busy cleaning the datasets and are excited to see the first combined results of the study, following our 18 colonies over two years.

October 2021

The volunteers were once again completely brilliant. Despite many challenges, not least the pandemic, the sampling at all sites throughout the summer went very well. Now we are busy in the lab to extract the DNA and RNA for this year.

July 2021

The samples collected in 2020 (June-September) have all been extracted (RNA/DNA) and sequenced. Both the metagenomic approach to retrieve viruses and the metabarcoding (for bats, insects, fungi and plants) have worked very well. Most of the viruses are insect viruses but there were also plant and bat viruses too. Using the metabarcoding approach, we detected not simply the prey eaten by the bats, but insect pests, the plants eaten by insects and many fungi too.

May 2021

Although we started a little late in the first year due to the pandemic, the volunteers are all on track to start the 5 months of sampling for 2021. We were very happy to present (virtually) the results of the protocol testing we did at the European Bat Research Symposium, Turku Finland. The Finnish team did a really excellent job in keeping the meeting vibrant and exciting with many social events even though we couldn’t meet in person. Kiitos!

January 2021


Using a small subset of samples, we conducted test runs for the metagenomic (virome) analysis in order to chose an optimised protocol. Likewise, we tested many different primer pairs for fungi and plants in particular, to chose the best performing to add to the metabarcoding protocol already optimised by Galan et al. 2018.

October 2020

We were delighted to be able to present a poster explaining our approach for “Next-generation biodiversity monitoring” at the Biodiversity Genomics Meeting 2020 (online) organised by the Welcome Sanger Institute.

August 2020

Bumpy start

After some delays due to the COVID-19 outbreak our project finally began officially in June. Just like for many people we have had to adjust to these new circumstances and try to work as best as we can within the restrictions.


France has already experienced the hottest start of the year on record, with higher temperatures particularly in the south, and the driest July since 1959, particularly in the north-east. Globally, the hottest temperature ever (54.4 °C) was recorded in the USA, and in my own country (Ireland), there was no real summer this year, with cool wet weather and little sunshine.

We will be using detailed weather data from 18 weather stations close to our sampling sites throughout the project to try to understand the impact of climate on ecosystems.

Field work

Thanks to the regional coordinators (E. Petit in Brittany, L. Arthur in Centre, S. Dool & S. Puechmaille in Occitanie/PACA) and the very motivated volunteers, the sampling has gone well so far (June, July, August), with just one sampling session left for this year (September).


After lots of reading and discussions with experts, we are ready to start testing several new protocols to get the best and most efficient results for both the metabarcoding and metagenomic analyses.

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