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The Gibbons Lab @UMassAmherst

@gibbonsgenomics.bsky.social
1.3K followers 988 following 17 posts

The Gibbons lab is in the Department of Food Science at UMass Amherst and studies fungal and bacterial genomics.

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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 03/08/2026
So excited to finally see this out!Tyler’s tour de force from his PhD. Using an evolve and resequence approach, we tracked how Listeria monocytogenes adapts to sublethal exposure to the sanitizer benzalkonium chloride. Genomics, phenotyping, and a whole lot more. journals.asm.org/doi/10.1128/...
journals.asm.org
Experimental evolution reveals genetic and transcriptomic mechanisms underlying benzalkonium chloride tolerance and fluoroquinolone cross-resistance in Listeria monocytogenes | mSystems
Listeria monocytogenes persistence in food facilities poses major public health and economic burdens. We modeled long-term exposure to sublethal benzalkonium chloride (BAC) to approximate conditions similar to those in food processing facility drains and uncovered two complementary routes to sanitizer tolerance: (i) repeated inactivation of the fepR regulator with accompanying alterations in the fepA efflux pump, driving BAC tolerance and fluoroquinolone cross-resistance, and (ii) convergence on mutations in ptsH (HPr) within the phosphotransferase system, supported by RNA-seq upregulation of phosphotransferase system (PTS) pathways and biophysical evidence of destabilized HPr variants. Efflux inhibition reduced BAC tolerance where fepR/fepA was mutated but had limited impact in a bcrABC-positive background (where bcrABC encodes a plasmid-borne BAC resistance efflux cassette), highlighting the role of genetic context. These findings connect sanitizer adaptation to antibiotic resistance and identify PTS signaling as a systems-level contributor, informing surveillance and sanitation strategies in food production.
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 29/07/2026
New work from our lab. Play around with it! It started as a need to quickly and easily visualize pairwise synteny. A few months later here we are!
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Evolutionary Studies at Vanderbilt @evolutionvu.bsky.social · 19/12/2025
The retreat opened with talks from John Gibbons, Natasha Vitek & Jen Wisecaver, exploring evolution across scales from microbial genomes & ecology to patterns in the fossil record. A strong start that set the tone for the day #Evolution #ScienceCommunication
A speaker presents research on microbial domestication, gesturing toward a projected diagram that illustrates evolutionary transitions from wild microbial communities to domesticated, stable systems shaped by ecological interactions.A speaker presents research on bridging micro- and macroevolution, standing in front of a projected slide that shows evolutionary timescales from short-term microevolution to deep-time patterns preserved in the fossil record.A speaker stands beside a projected phylogenetic tree of eukaryotic lineages, illustrating genome evolution, endosymbiosis, and relationships among major groups such as algae, plants, and protists.
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Evolutionary Studies at Vanderbilt @evolutionvu.bsky.social · 18/12/2025
Last week, faculty, trainees, alumni and friends gathered for our annual retreat. It was a day of talks, trivia and conversation spanning #evolution, medicine, ecology, and genomics. A great reminder of the interdisciplinary community that makes ESI work. More retreat highlights soon…
Group photo of faculty, trainees, alumni, and staff from the Evolutionary Studies Initiative standing together at the ESI Retreat. The group is arranged in several rows inside an industrial event space with exposed beams and wood floors, smiling toward the camera. A holiday wreath hangs on the wall behind them, and tables with notebooks and coffee cups are visible in the foreground. The photo captures a large, interdisciplinary academic community gathered for a full-day retreat.
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 11/07/2025
Our newest preprint, based on the awesome work by Colin McCarthy Masters project. We used e-tongue and dh-gc-ms to analyze flavor and sensory profiles between Aspergillus oryzae RIB40 and two Aspergillus flavus strains.
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Carl Zimmer @carlzimmer.com · 22/05/2025
The @upshot.nytimes.com has put together a vivid illustration of how the Trump administration has hollowed out American science. Gift link: nyti.ms/4kBTVql
nyti.ms
Trump Has Cut Science Funding to Its Lowest Level in Decades (Gift Article)
The lag in funding extends far beyond D.E.I. initiatives, affecting almost every area of science: chemistry, computing, engineering, materials and more.
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 19/05/2025
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 26/04/2025
Our new paper is out!
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Genome Biology and Evolution @genomebiolevol.bsky.social · 24/04/2025
Genome and phenotypic analyses support domestication of Aspergillus sojae from A. parasiticus for soy production. A. sojae shows reduced diversity, loss of aflatoxin genes, and traits suited to miso-like salt conditions. Link: doi.org/10.1093/gbe/... #soy #fungi #domestication
doi.org
Population Genomics of Aspergillus sojae is Shaped by the Food Environment
Abstract. Traditional fermented foods often contain specialized microorganisms adapted to their unique environments. For example, the filamentous mold Aspe
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 26/03/2025
A huge congrats 🍾🎉 to Kim Acevedo who successfully defended her PhD today AND had a paper based on her first chapter accepted in @genomebiolevol.bsky.social the very same day.
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 27/02/2025
After decades of dedication and zero pro contracts, I’m officially announcing my retirement from pro soccer. Tearing my ACL & MCL at 41 means giving up my dream of a late-career @usmnt.ussoccer.com debut to focus on my backup plan of running a genomics lab at @umassamherst.bsky.social ⚽️ 🦠 🧬
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Vaughn Cooper @vscooper.micropopbio.org · 10/02/2025
Detailed and concise 1-pager explaining what F&A does and how it underlies the competitive advantages of American sciences. F&A pays PEOPLE and allows universities to be the anchors of regional economies that they are! 🔗 www.cogr.edu/sites/defaul...
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Harmit Singh Malik @harmitmalik.bsky.social · 28/01/2025
If you have been affected by the fires in LA, or are concerned about your ability to keep precious Drosophila strains going during the latest funding crisis, we will host your strains as a backup. Please email me. Please amplify. If you are also able to host fly strains, add your name as well.
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 01/01/2025
Cheers to a productive new year under the rule of our fungal overlords.
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 27/11/2024
Thrilled to share that Nadia Yammoul (first year PhD student in our lab) was one of the winners of the UMass Food and Technology Innovate for Tomorrow Challenges!
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The Gibbons Lab @UMassAmherst @gibbonsgenomics.bsky.social · 11/11/2024
We’re here! Looking for more genomics, evolution, microbiology, food science and less politics and doom scrolling :)
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