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Ashley Shade, Ph.D.

@ashley17061.bsky.social
1K followers 294 following 26 posts

Director of Research, CNRS | Microbial Ecologist | incoming EIC for American Society for Microbiology journal #mSystems | ERC #MicroRescue

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Ashley Shade, Ph.D. @ashley17061.bsky.social · 04/08/2026
It's been a delight to work with @microbe700.bsky.social over the last year to create the 3rd edition of Processes in Microbial Ecology. If you teach undergrads or need a holistic reference for your lab library (that includes both aquatic and terrestrial systems!) - look no further than PME 3
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 17/07/2026
Our new paper is out in #mSystems! Quantify total and active bacterial cells from environmental samples with MATRIX! @asm.org @cnrs.fr @universitelyon.bsky.social journals.asm.org/doi/10.1128/...
journals.asm.org
MATRIX: rapid quantification of total and active microbial cells with single-cell phenotypes for environmental microbiomes | mSystems
Microbiome studies commonly rely on relative abundance data, which cannot distinguish whether compositional shifts reflect true population growth, declines in total community size, or both. Without ex...
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 29/06/2026
I am so EXCITED to engage in this GRC in a two weeks! Hope to see many of you there to discuss unifying ecology across scales!
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 25/06/2026
fascinating read, especially for young ecologists and microbial ecologists, funding agencies, and university administrators - how to maintain competitiveness and valued, specific expertise in a research ecosystem that is rapidly AI-driven onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com
AI, Comparative Advantage, and the Next Decade of Ecological Research
Click on the article title to read more.
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Reposted by Ashley Shade, Ph.D.
Ira Blader @bladerlab.bsky.social · 09/06/2026
Breaking: A new Special Collection in @asm.org #mSphere and #mSystems – “Lab Launches - New Leaders, New Discoveries”. We started it bc that first paper is important – it communicates the group’s identity as well as the discoveries that propel a scientific career. journals.asm.org/doi/10.1128/...
journals.asm.org
Lab Launches—New Leaders, New Discoveries | mSphere
In the United States and some other countries, many small businesses mark their beginnings by posting their first earned dollar (or whatever relevant currency) from their very first transaction on a p...
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 10/04/2026
Re-bonjour Bluesky community! I promise I will check in more often. I had a teeny bit of a social media fast, given Everything. Quoi de neuf? My team has a preprint for quantification of microbiome sizes (# individuals) And, it has a cool acronym: MATRIX www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Ashley Shade, Ph.D.
Sean Gibbons 🦠💩 @gibbological.bsky.social · 02/07/2025
Excited to be back at #mSystems (@asm.org), now as a Senior Editor, working to support our new Editor-in-Chef @ashley17061.bsky.social 🤩 Support society journals! If you have work at the boundary between microbiology & systems biology, send us your manuscript! journals.asm.org/journal/msys...
journals.asm.org
mSystems Board of Editors
Members of the mSystems Editorial Board
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 02/07/2025
Yesterday, I started my term as Editor in Chief of @asm.org journal #mSystems Looking forward to working with this amazing community to advance publication of our highest quality and most rigorous science! journals.asm.org/doi/10.1128/...
journals.asm.org
Humanity’s urgent challenges need solutions from systems microbiology | mSystems
It is with great excitement and sincere dedication that I assume the role of editor in chief of mSystems. Building on the momentum and reputation that mSystems has achieved in its first decade, we wil...
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 30/06/2025
Check out this new piece about critical precautions and controls needed to conduct microbiome analyses on low biomass samples (like seed endophytes!) Thanks to @noahfierer.bsky.social & @greening.bsky.social for leading the charge! www.nature.com/articles/s41...
nature.com
Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology
In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 21/05/2025
Tomorrow #TeamRhizo and project #MicroRescue are attending the Indo-French workshop on the "Plant microbiome as a driver for the next green agricultural revolution" - so looking forward to meeting new colleagues from India, sharing research, and thinking about harnessing microbes for plant health
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 19/05/2025
#TeamRhizo & @erc.europa.eu #ERC project #MicroRescue were in the field collecting soil for our big upcoming host-mediated-microbiome-engineering experiment! Can't wait to find out which microbes respond to the plant's stress signals! @ecomicrolyon.bsky.social @cnrsecologie.bsky.social
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 28/03/2025
thanks to @ou.edu Biological Sciences and especially Kara De León for hosting me for a seminar today - It was great to meet with students and share some new #MicroRescue @erc.europa.eu data!
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 13/03/2025
The recording of Part 2 of the ASM #mSystems Critical Concepts in Dormancy Webinar is now available An inspiring panel of researchers share their thoughts about how to measure and discriminate different levels of microbial activity Enjoy! www.youtube.com/watch?v=RZub...
youtube.com
Critical Concepts in Dormancy Part II: Discriminating States of Microbial Activity
YouTube video by American Society for Microbiology
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Reposted by Ashley Shade, Ph.D.
Ákos T Kovács @evolvedbiofilm.bsky.social · 25/02/2025
Embracing the systems complexity of microbial ecology and evolution: call for papers #mSystems Editorial by a group of editors, senior editors & editor-in-chief @leonorabit.bsky.social @gilbertjacka.bsky.social @ashley17061.bsky.social @markjmandel.bsky.social journals.asm.org/doi/10.1128/...
journals.asm.org
Embracing the systems complexity of microbial ecology and evolution: call for papers | mSystems
Microbial ecology and evolution are broad disciplines that seek to understand the underlying processes that drive the diversification, distributions, and dynamics of microbial cells, populations, comm...
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 14/02/2025
Congrats to @sambarnett15.bsky.social on our team's paper accepted at the special issue of Soil Biology & Biochemistry We use a 7 year spatio-temporal study of heat disturbance in soil to investigate the coupling of viral community dynamics with bacterial. www.sciencedirect.com/science/arti...
sciencedirect.com
Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils
Viruses are important components of the soil microbiome, influencing microbial population dynamics and the functions of their hosts. However, the rela…
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 05/02/2025
Join us for the upcoming American Society for Microbiology #mSystems webinar on microbial dormancy and activity! Free registration here: asm.org/Webinars/mSy...
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 09/01/2025
9 minutes ago Free registration is open for our next Critical Concepts in Dormancy webinar 20 Feb, hosted by American Society for Microbiology journal mSystems! asm.org/Webinars/mSy... Discuss how to evaluate microbial activity, including in challenging environments! A stellar speaker line up 🤩
asm.org
mSystems Thinking Series
mSystems, an open-access ASM journal publishing diverse systems microbiology research, hosts a webinar series that features editors discussing a variety of topics in an interactive forum.
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 17/12/2024
Check out this article about defining microbial activity and dormancy, and why it's important for thinking about climate change There will be an in-depth symposium moderated by me at the ASM #Microbe2025 in LA! and, good news you can still submit your abstract! asm.org/Articles/202...
asm.org
Why Dormant Microbes Matter in a Changing Climate | ASM.org
Most microbes on Earth are dormant, yet they play key roles in the evolution and function of microbial populations. How can we harness microbial dormancy to promote human and environmental health?
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 06/12/2024
Congrats to my EcoMicroLyon colleagues on their new publication about pollution gradients, microbial communities, and mosquito larvae! Nice assessment of host-environment-microbiome systems in urban environments academic.oup.com/femsec/artic...
academic.oup.com
Pollution gradients shape microbial communities associated with Ae. albopictus larval habitats in urban community gardens
Microbial composition of larval habitats covaried differentially along the pollution gradients according to the presence/absence of larvae. Noncolonized wa
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 04/12/2024
Look at the new cover of mSystems! Beautiful seeds and their microbiomes In this study we found stable transmission of particular bacterial taxa across plant generations via the seed, despite parent plant exposure to stress @microbialmarie.bsky.social journals.asm.org/toc/msystems...
journals.asm.org
mSystems Table of Contents Volume 9, Issue 11
mSystems: Table of Contents Volume 9, Issue 11
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 26/11/2024
Submit your abstract for the American Society for Microbiology #Microbe2025 annual meeting in Los Angeles! I'm organizing a symposium on Microbial Dormancy! Hope to receive your abstract and discuss with you there. Early abstracts close Dec 3, don't delay! abstractsonline.com/pp8/#!/20974...
abstractsonline.com
Program Planner
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 22/11/2024
Did you catch our Thinking Series Webinar on Microbial Dormancy? If not, no fret: it's available on youtube! www.youtube.com/watch?v=Ytz1...
youtube.com
Critical Concepts in Dormancy Part I: Dormancy in Human Health and the Environment
YouTube video by American Society for Microbiology
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Ashley Shade, Ph.D. @ashley17061.bsky.social · 21/11/2024
I am proud to have represented our research #MicroRescue and THE MICROBES at the recent colloquium by the Fondation Pierre Verots My talk (in English!) is an accessible overview as to why microbes are important for climate change
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