Reena Debray
@DebrayReena
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microbiome ecology & evolution incoming group leader @MPI_EVA_Leipzig 🇩🇪 PhD ‘23 @berkeleyIB 🐻
Joined August 2018
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Pinned Tweet
The Social Microbiome Group is coming to
@MPI_EVA_Leipzig
and we are recruiting at multiple levels! You will work closely with me and Dr. Jenny Tung
@jtung5
. Apply by Sep 1 with a cover letter and CV. Please share 🔁
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Thank you
@maxplanckpress
for this opportunity to start my first research group!! I am recruiting at the MSc, PhD, and student assistant levels. More info on how to join us coming very soon ☺️🦠
Great news!! 🥳😊 Reena Debray
@DebrayReena
(seen here w/ the Otto Hahn medal awardees) was chosen for a Minerva Fast Track position. Her new research group will start
@MPI_EVA_Leipzig
soon & will study the gut microbiomes of non-human primates. 🐒
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Our paper on priority effects and within-host microbial evolution is out today in
@NatureEcoEvo
!! 🥳🥳🥳
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Our new
@AnnualReviews
paper, "Ecology and Evolution of the Social Microbiome" is now available in advance of the Nov 2024 issue!
Animal microbiomes often reflect the social organization of their hosts. We dive into some important unanswered questions about this pattern:
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Our paper on belowground effects on the phyllosphere microbiome is now out in
@NewPhyt
! We found that water limitation & disrupting mycorrhizal colonization had extremely similar effects on aboveground communities – down to individual indicator species.
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Passed my quals & advanced to PhD candidacy
@berkeleyIB
today!! Cheers to never looking at this binder again 😅
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Our article on priority effects was featured as the cover of this month’s issue of
@NatureRevMicro
!
@RA_Herbert
@alexander_jaffe
@acritschristoph
@bkoskella
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I graduated two days ago, and I am already finding myself making the slides for a talk on the way to said talk. I guess academic instincts kick in fast
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New preprint! 🍄🌱🦠
If you like plant microbiomes, soil ecology, aboveground-belowground interactions, or agroecosystems, keep reading!
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Excited to share two pubs from my PhD this week, one on historical contingency in ecology and the other on historical contingency in evolution, and some thoughts on what these two subfields can learn from each other. 🧵(1/10)
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More good news this week: our publication on effective doctoral student mentorship is now available! We asked students in the biological sciences at
@UCBerkeley
to anonymously answer questions about their advisor, lab, and program. A few key takeaways (read the paper for more!):
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Very excited to share our new paper, “Priority effects in microbiome assembly”, in
@NatureRevMicro
! Huge thanks to coauthors
@RA_Herbert
@acritschristoph
@alexander_jaffe
@bkoskella
as well as the editorial team for the beautiful redrawings! Check out Robin’s thread for more ⬇️
Want to know what bacterial dispersal across fungal hyphae, plant competition for light, & short-chain fatty acid production in the gut have in common? Check out our review on priority effects (PEs) in
#microbiome
assembly!
@NatureRevMicro
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If you’re at
#ASMicrobe2019
and curious about how bacteriophages shape the microbiome and influence plant-pathogen interactions, come see my poster at EEB-495 all day Saturday!
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Excited to share our new preprint about reversibility and entrenchment in bacterial evolution!
Host-pathogen coevolution is constantly changing & often selects for costly pathogen resistance. I wanted to know how these costs would manifest over time...
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Thanks for having me
#BAEEID2019
! Always a pleasure to show people how cool phages are ✨
Having a great day at the Bay Area EEID meeting, and particularly proud of my labmate
@DebrayReena
who gave a great talk!!!
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Coping with cabin fever, and marking time during this strange moment in history, by adding a new patch to my quilt each day. Today is day 36 for Berkeley.
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Excited/nervous to start mentoring two awesome undergrad researchers this summer. It’s a bit surreal as I was on the other side of that relationship just a year ago... Trying hard to channel all the amazing mentors & role models I’ve had!!
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Had a great time writing for the
@BerkeleySciRev
-- check out the article below & beautiful visualization by
@jtorvs
!
When it comes to electronics, good things come in small packages: The Salahuddin lab
@Berkeley_EECS
is scaling materials down to the
#nanometer
. Learn more in
@DebrayReena
's
#Issue40
#labscope
, designs by Julia
@jtorvs
.
#ferroelectricity
#nanotech
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So excited to see our work on reshaping the C. elegans microbiome out today, led by
@GeorgiosMarino3
and Inga Hamerich. It was great to be part of this collaboration that truly bridged theory and the lab!
🎉 Thrilled to share our latest work on reshaping microbial communities! A fantastic collaboration with
@SchulenburgLab
, led by
@GeorgiosMarino3
and Inga Hamerich.
@CRC1182
@kieluni
@pmi
@medinflame
Dive into our findings here:
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After some early setbacks (two broken wrists in the first week of the program) we weren’t sure what would happen w/ this project. But Griffin wanted to continue so we made it work. Very proud of my mentee, can’t wait to see where that spirit & resilience takes her ✨
A great write-up about one of our summer student researchers!
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Missing my summer at
@MLBS_UVA
a little extra today. Check out our paper, and congratulations to
@Mitchem_Liza
for leading this work!
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This has been my favorite article to write so far – this unique lab started from scratch at the beginning of the COVID-19 pandemic and changed many scientists' lives and research trajectories along the way. The beautiful illustrations were drawn by
@_nanonat
!
Flush with opportunity: Using
#wastewater
monitoring to track
#COVID19
in the Bay Area.
@DebrayReena
takes us through the team's two-year journey in this
#Issue41
#FromtheField
Designs: Natalie
@_nanonat
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Or to see outstanding work by
@_cathyhernandez
on bacteria-phage coevolution in plant hosts, check out her poster talk during S199 and her poster EEB-521!!
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@BramVDBe
We showed genetic background effects on likelihood of evolutionary reversal in bacteria!
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Receiving a microbiome inoculation from nutrient-limited conditions in the field wasn’t any better for nutrient-limited plants (in terms of disease resistance) than a microbiome from nutrient-rich conditions. But any microbiome inoculation at all was better than none! 🦠✨
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3) Cultivating unknown species from wild animal gut microbiomes (MSc research assistant, option to progress to MSc thesis):
4) Student assistant position in bacterial culture lab (BSc or MSc student, **deadline July 15)
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Full paper here!
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We manipulated soil irrigation, phosphorus fertilization, and access to arbuscular mycorrhizae in a large-scale field experiment, then sequenced bacterial and fungal communities in the tomato plant phyllosphere.
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Here is the original thread:
Since posting the preprint, we also sequenced the genomes at the reviewers' suggestion. As expected from the phenotypic data – we found strong signatures of parallel evolution in genes implicated in plant colonization.
Excited to share two pubs from my PhD this week, one on historical contingency in ecology and the other on historical contingency in evolution, and some thoughts on what these two subfields can learn from each other. 🧵(1/10)
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Both water stress and disrupting AMF associations decreased aboveground microbial diversity & reshaped communities. Rare bacterial species were more vulnerable than common ones, while dominant species were affected most in the fungal microbiome.
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1) Microbiome evolution within hosts (PhD thesis):
2) Social effects on animal microbiomes (PhD thesis):
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In terms of interactions, we thought AMF would minimize the effects of water stress. But the effects were actually strongest in mycorrhizal plants! Perhaps the AMF-regulated drought response benefits plants but not their microbiota (e.g. via rapid stomatal closure).
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Separately, water stress and disrupting AMF resulted in parallel shifts in phyllosphere communities – down to individual indicator species! This suggests that soil conditions were affecting phyllosphere microbes via systemic changes in plants (as opposed to direct dispersal).
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Thanks to all coauthors (including Emily Dewald-Wang and Nina De Luna, not on twitter) and also to
@RA_Herbert
@acritschristoph
@alexander_jaffe
for helping me get interested in priority effects in the first place. My PhD would have looked very different without you!
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Our experimental evolution study in tomato seedlings showed that early-colonizing bacteria can rapidly adapt to alter priority effects. Read the preprint for more! (4/10)
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Are these microbiome shifts adaptive for plants? We know that plants use root exudates to enrich for beneficial rhizosphere microbes under stressful conditions, but what about the phyllosphere? We transplanted microbes from the field experiment onto plants in the growth chamber.
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Congratulations
@kamalanichock
!! Welcome to the best lab 🌱
The 2019 Ford Fellowship list is now out, and I am very excited to announce our newest lab member,
@kamalanichock
is among the predoc recipients! A huge congratulations to you Kama on this well-deserved recognition.
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Second is our paper on evolutionary reversal of phage resistance, now out in MBE. 🥳 There are many possible mutations that allow bacteria to block phage infection, permitting some randomness in which one arises & sweeps first in a given population. (5/10)
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With
@yvonnesocolar
@_cathyhernandez
@soilsandbees
@bkoskella
@bowleslab
, and our amazing undergraduate researchers Griffin, Alex, and Rose!
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Very proud of this whole team, but I have some special shoutouts – to
@yvonnesocolar
for her knowledge of agricultural systems & leadership in the field that made this all possible, and undergrad
@GriffinKaulbach
for her unmatched initiative, resilience, & enthusiasm for science!
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Please share with any undergraduate or high school students you know who are interested in learning about genomics!
It is happening! We launched and we will be teaching two workshops this summer on Genomes and Plant Health, our goal is to expose research undergraduates and high school students to genomics, bioinformatics and how to use them to improve plant health.
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Congratulations, Pierre!!
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These two studies, which don't seem very similar at first glance, both show us when to expect history to affect eco/evo outcomes, and when those outcomes translate to consequences at the level of ecosystem function or longer-term evolution. (10/10)🧵
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Link to paper:
PS: The Social Microbiome Group at
@MPI_EVA_Leipzig
is currently recruiting MSc and PhD students! If these questions interest you, get in touch or browse our open positions here:
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Thank you to co-authors
@ennis_katherine
and Emily Dewald-Wang, the
@berkeleyIB
dept for providing seed funding, and all survey participants. Even a small study like this one has taught me a lot about my mentoring priorities as I step into my first group leader role this year.
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@microbeemoji
I heard that you’ve been working super hard at mcb104, your co-GSIs are proud of you!
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The
@maxplanckpress
is a really unique & incredible place to work – I feel lucky to be surrounded by so much cutting-edge science here. Please reach out with any questions about the institute or life in Leipzig!
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We selected & sequenced 22 phage-resistant isolates of Pseudomonas syringae. Nearly every isolate had a different resistance mutation, though all located within the same few LPS biosynthesis genes. Resistant bacteria grew more slowly than their phage-sensitive counterparts:
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This might be because certain types of mutations are intrinsically less reversible than others. For example, some of the isolates had originally acquired phage resistance thru large deletions (up to 252 bp) – and we never saw them re-evolve sensitivity.
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Basic research is so important!
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First, our preprint on priority effects in the plant microbiome (w/
@PlanetAzor
@xnszhang
@bkoskella
). Priority effects occur when community assembly depends on arrival timing. We have decades of ecological theory & data on this phenomenon... (2/10)
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Really excited to share this new preprint! In it, we ask what strain-resolved metagenomics can tell us about microbiome transmission, especially in natural host populations. 🧵
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We experimentally evolved each isolate in the absence of phages for 36 days. Phage sensitivity re-appeared in several populations and completely restored fitness in those pops. Sensitivity re-evolved thru a mixture of reversion mutations and de novo mutations.
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@evisher
@sethfinnegan1
So it does seem like convergence increases with scale -- but would be so interested to see a case where the opposite is true like you suggest!
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Even at a progressive institution with well-funded DEI initiatives like Berkeley, there are still major disparities b/w experiences of students from different demographic backgrounds. For students with multiple marginalized identities, the effects were compounded (!!)
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Students who had frequent, standing meetings with their advisors had a clearer sense of what was expected of them and a stronger belief that they belonged in science and their research mattered, and were more likely to be on track to graduate on time.
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Informal mentoring networks like peers, other faculty outside of the primary advisor, research museums, and interdisciplinary graduate groups somewhat helped to close outcome gaps between students with good & poor experiences with their primary advisor.
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Among students from minority backgrounds, those who worked with an advisor from a similar bg. to their own also felt more confident that they belonged in science & their research mattered, were more on track to graduate, & were more likely to have completed a first-author paper.
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Gould imagined rewinding & replaying the history of life to see how it would change each time – and lamented the experiment wasn’t possible. But with experimental evolution it is! By replaying evolution we showed that res mutations were predisposed to reversion or compensation.
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We showed that this single random event has lasting consequences for phenotypic and genomic evolution, including reversibility. Certain resistance mutations were eventually reversed in the absence of phages, while others repeatedly persisted despite their fitness costs. (6/10)
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@evisher
@sethfinnegan1
When we "replay the tape" with bacteria evolving phage resistance we see: same phenotype (at least as we observe/measure it), the same few resistance genes again and again, and a LOT of variation in the exact resistance mutations within those genes.
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Some thoughts on historical contingency: it may seem less satisfying to study than "deterministic" factors that more clearly lend themselves to general predictions. But we actually can (& should!) synthesize across systems to predict when, how, and why history matters. (7/10)
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@evisher
@sethfinnegan1
John Beatty said it better than I can so I'll just link this figure of his:
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@luis_valentin26
If you want something a bit more serious but still character-focused, Pierre and I just read A Man Called Ove and we both loved it
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@evisher
@sethfinnegan1
For sure! I think those are cases where different populations might respond differently to the same selection pressure b/c of their evolutionary histories. Also possible is identical starting populations ending up on diff trajectories b/c of the order of random mutations, etc
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@DianeKarloff
Medical staff are the most essential & overburdened workers right now, but not sure how we could increase supply besides the few local movements recruiting other scientists for diagnostics
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Why is this important? Two species that use similar resources may affect their environment differently (i.e. “requirement” vs. “impact” niches). Two mutations with similar fitness in one setting may constrain future evolution in different ways. We found examples of both. (9/10)
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@sethfinnegan1
@evisher
Just starting to write it up... I think it will be a while 🙃 I can let you know when it's out in case it's still helpful!
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(6/9) But when we tried the same approach in a less controlled setting – a long-term field study of wild primates – strain sharing was strongly driven by dietary and environmental similarities, even for individuals that never interacted or were never even alive at the same time.
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@luis_valentin26
If you’re in the mood for something light, Liane Moriarty is one of my favorite authors. Her characters are so well-developed & lovable that I find myself rooting for all of them even though they’re all at odds with each other!
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But… the majority of populations remained phage-resistant, yet improved their fitness at a similar rate. This suggests compensatory mutations, but why did some populations do this while others reversed the trait? Was it a matter of chance?
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@butch_brodie
@bkoskella
@sse_evolution
@MLBS_UVA
Thanks
@butch_brodie
!! The training I got in experimental design & writing at MLBS has helped so much with proposals like this 😊
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@DianeKarloff
Not online or highly trained, but my hometown (and hopefully others) is hiring people who are out of work to help stock grocery shelves & deliver meals.
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But most work has been done in plant or animal communities, where evolution is assumed to happen too slowly to influence eco processes. Unclear how to translate this knowledge to microbial communities, where evolution can happen FAST. (3/10)
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@luis_valentin26
If you want a page turner check out Dan Brown or Michael Crichton. Dan Brown’s characters are ehhhh but the plots are fun. Crichton’s are extremely well researched AND one of them is about bacteria! It’s called Prey
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@fz5656
I think a lot of people pursuing their dream careers (science, medicine, teaching, entertainment) end up unhappy with many aspects of them— imo those industries can get away with asking an unhealthy amount of devotion/sacrifice in the name of “passion”
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@acritschristoph
3. Yes! 3/22 populations re-evolved sensitivity in my initial experiment. Then I repeated the evolution with 10 reps of each genotype and saw 17 of those 30 revert. We concluded certain res mutations are predisposed for loss vs. compensatory evolution
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@acritschristoph
Thanks Alex!
1. Only LPS, & that’s been the case other times people in our lab have evolved phage resistance in this system as well.
2. A synonymous mutation would be equally detectable wouldn’t it? My guess is large deletion / inversion not picked up by short-read sequencing…
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In our study, the ancestral genotype could acquire resistance thru 17+ different mutations – likely a matter of chance which one arises in a given population. Our work shows that such chance events have lasting impacts even after the original selection pressure has subsided.
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In our microbiome study, arrival history mattered most between closely related bacteria w/ similar niches. In our phage resistance study, history mattered because many possible resistance mutations had similar fitness at the time of selection. (8/10)
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@TLowePower
We do this because it’s often not feasible to sample communities on the same day we need to use them for inocula. I would only trust CFUs/mL after thawing— they drop a lot in the freezer, even with the glycerol.
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It’s also likely that phage resistance mechanisms affect fitness in different ways, with different compensatory mutations that restore their costs. Sure enough – we found that populations with the same res mutation acquired more similar mutations over time.
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