Indra Roux
@indraroux.bsky.social
Postdoc at U of Cambridge MRC Tox🇬🇧 PhD UWA🇦🇺Biotech UNQ🇦🇷 🧬🛠️ Functional genomics and engineering biology for microbiome applications. 🔎Microbiome toxicology. She/her Latinx https://scholar.google.com/citations?user=RNoSH60AAAAJ&hl=en
Pinned
Indra Roux
@indraroux.bsky.social
· Jun 26
"What does Engineering Biology mean to you?"
We invited members of the #EngBio community to share their definition of this evolving field. This is what Dr Indra Roux (@indraroux.bsky.social), Postdoctoral Researcher at the MRC Toxicology Unit (@mrc-tu.bsky.social), had to say.
#FacesOfEngBio
We invited members of the #EngBio community to share their definition of this evolving field. This is what Dr Indra Roux (@indraroux.bsky.social), Postdoctoral Researcher at the MRC Toxicology Unit (@mrc-tu.bsky.social), had to say.
#FacesOfEngBio
My definition of #EngineeringBiology has expanded: from synthetic biology in model chassis to designing diverse synthetic microbial communities. Many complex and resilient functions emerge at the microbiome level, so synthetic ecology is a promising approach for robust biotech. #FacesOfEngBio 🧬⚒️🧫
Reposted by Indra Roux
A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor
doi.org/10.1016/j.ce...
doi.org/10.1016/j.ce...
February 1, 2026 at 2:29 PM
A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor
doi.org/10.1016/j.ce...
doi.org/10.1016/j.ce...
Reposted by Indra Roux
Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage www.nature.com/articles/s41...
Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage - Nature Biotechnology
Biologics are delivered to the gut using phage that infects resident commensal bacteria.
www.nature.com
January 30, 2026 at 3:22 PM
Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage www.nature.com/articles/s41...
Reposted by Indra Roux
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by Indra Roux
Excited to announce a new Science article, co-authored by Dr. Rohr! In this work, Rohr and collaborators show that chronic, low-dose exposure to chlorpyrifos, a widely used insecticide, speeds up aging in a common lake fish by shortening its telomeres, thus leading to premature death. Check it out!
Chronic low-dose exposure to chlorpyrifos reduces life span in a wild fish by accelerating aging
Low concentrations of chemicals are widespread in the environment, but exploration of the effects of their chronic exposures on animal life span in the wild is limited. Field investigations showed tha...
www.science.org
January 15, 2026 at 8:06 PM
Excited to announce a new Science article, co-authored by Dr. Rohr! In this work, Rohr and collaborators show that chronic, low-dose exposure to chlorpyrifos, a widely used insecticide, speeds up aging in a common lake fish by shortening its telomeres, thus leading to premature death. Check it out!
Reposted by Indra Roux
First evidence that healthy donor fecal microbiota transplant, added to immunotherapy, can enhance efficacy vs cancer
3 clinical trial reports (renal, small cell lung, melanoma)
nature.com/articles/s41...
nature.com/articles/s41...
nature.com/articles/s41...
Holy 💩!
3 clinical trial reports (renal, small cell lung, melanoma)
nature.com/articles/s41...
nature.com/articles/s41...
nature.com/articles/s41...
Holy 💩!
Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial - Nature Medicine
In a phase 2 trial evaluating healthy donor fecal microbial transplantation plus either anti-PD-1 in patients with non-small cell lung cancer or anti-PD-1 and anti-CTLA-4 in patients with melanoma, en...
nature.com
January 28, 2026 at 3:31 PM
First evidence that healthy donor fecal microbiota transplant, added to immunotherapy, can enhance efficacy vs cancer
3 clinical trial reports (renal, small cell lung, melanoma)
nature.com/articles/s41...
nature.com/articles/s41...
nature.com/articles/s41...
Holy 💩!
3 clinical trial reports (renal, small cell lung, melanoma)
nature.com/articles/s41...
nature.com/articles/s41...
nature.com/articles/s41...
Holy 💩!
Reposted by Indra Roux
We seek candidates for this vacancy who can bridge technological innovation with biological insight, whether through novel in vitro systems, advanced molecular techniques, computational methods, or integrated multi-omics approaches.
💷 Competitive
🗓️ Apply by 15 February 2026
➡️ buff.ly/W3Sphca
💷 Competitive
🗓️ Apply by 15 February 2026
➡️ buff.ly/W3Sphca
January 28, 2026 at 8:45 AM
We seek candidates for this vacancy who can bridge technological innovation with biological insight, whether through novel in vitro systems, advanced molecular techniques, computational methods, or integrated multi-omics approaches.
💷 Competitive
🗓️ Apply by 15 February 2026
➡️ buff.ly/W3Sphca
💷 Competitive
🗓️ Apply by 15 February 2026
➡️ buff.ly/W3Sphca
Reposted by Indra Roux
Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...
Novel artificial selection method improves function of simulated microbial communities
Author summary Artificial selection has been extremely powerful in improving properties of complex biological or biochemical entities. The most familiar examples come from the breeding of animals and ...
journals.plos.org
January 27, 2026 at 1:41 PM
Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...
Reposted by Indra Roux
Also a big thanks to @cresslab.bsky.social and @therubinlab.bsky.social who came up with the idea to start this meeting and were instrumental in making it happen! And congratulations to @therubinlab.bsky.social and @paulwilmes.bsky.social for their elections as vice-chairs for the next one!
January 19, 2026 at 1:58 PM
Also a big thanks to @cresslab.bsky.social and @therubinlab.bsky.social who came up with the idea to start this meeting and were instrumental in making it happen! And congratulations to @therubinlab.bsky.social and @paulwilmes.bsky.social for their elections as vice-chairs for the next one!
Reposted by Indra Roux
It was a true privilege to co-chair the inaugural GRC meeting on Microbiome Editing together with @jenniferdoudna.bsky.social . The positive energy and quality of the Science presented were truly inspiring. I look forward to the next one chaired by KC Huang and @omalleylab.bsky.social !!!
January 19, 2026 at 1:53 PM
It was a true privilege to co-chair the inaugural GRC meeting on Microbiome Editing together with @jenniferdoudna.bsky.social . The positive energy and quality of the Science presented were truly inspiring. I look forward to the next one chaired by KC Huang and @omalleylab.bsky.social !!!
Reposted by Indra Roux
20 | Peer Bork and the scientific candy shop
Apple: podcasts.apple.com/us/podcast/n...
Spotify: open.spotify.com/episode/17ux...
Apple: podcasts.apple.com/us/podcast/n...
Spotify: open.spotify.com/episode/17ux...
20 | Peer Bork and the scientific candy shop
Podcast Episode · Night Science · 09/02/2022 · 29m
podcasts.apple.com
January 18, 2026 at 12:52 AM
20 | Peer Bork and the scientific candy shop
Apple: podcasts.apple.com/us/podcast/n...
Spotify: open.spotify.com/episode/17ux...
Apple: podcasts.apple.com/us/podcast/n...
Spotify: open.spotify.com/episode/17ux...
Reposted by Indra Roux
Very sad to hear about the passing of Peer Bork, one of true giants of computational biology
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 7:44 PM
Very sad to hear about the passing of Peer Bork, one of true giants of computational biology
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
Reposted by Indra Roux
A fungal commensal secretes a protein that stimulates cellular regeneration in injured gut tissue in mice, with probiotic potential for treating gut-related conditions. #NBThighlight www.nature.com/articles/s41...
Fungal commensal promotes intestinal repair via its secreted peptide in mice - Nature Microbiology
A short peptide derived from a commensal-fungal-secreted protein promotes repair in models of colon epithelial damage when delivered directly or via probiotic microbes.
www.nature.com
January 16, 2026 at 11:22 AM
A fungal commensal secretes a protein that stimulates cellular regeneration in injured gut tissue in mice, with probiotic potential for treating gut-related conditions. #NBThighlight www.nature.com/articles/s41...
Reposted by Indra Roux
Cool work! Mining 7 ancient (1-2ky) human coprolite metagenomes for ORFs with AMP potential: 160 peptide candidates > 40 synthesised > 36 active at <100 µM in vitro with ~2/3 being Segatella copri–derived
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Identification of antimicrobial peptides from ancient gut microbiomes - Nature Communications
Here, the authors develop AMPLiT a tool for screening antimicrobial peptides in metagenomic datasets, and apply it to human coprolite metagenomes, finding that Segatella copri, an ancient prevalent hu...
www.nature.com
January 15, 2026 at 2:08 PM
Cool work! Mining 7 ancient (1-2ky) human coprolite metagenomes for ORFs with AMP potential: 160 peptide candidates > 40 synthesised > 36 active at <100 µM in vitro with ~2/3 being Segatella copri–derived
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Indra Roux
This is shaping up to be one of the top conferences on microbiome editing!!
We're excited to help launch the inaugural Gordon research conference on #microbiome editing, coming up in January in Pomona, CA! Learn more and register here: https://ow.ly/a6Am50X9XkE
January 13, 2026 at 11:45 PM
This is shaping up to be one of the top conferences on microbiome editing!!
Reposted by Indra Roux
Such a privilege to share the Phage Foundry (phagefoundry.org) team’s work at the inaugural GRC meeting on Microbiome Editing 🎉🎊.
January 13, 2026 at 11:56 PM
Such a privilege to share the Phage Foundry (phagefoundry.org) team’s work at the inaugural GRC meeting on Microbiome Editing 🎉🎊.
Reposted by Indra Roux
If you're doing innovative research about #microbiota and received an MD &/or PhD in last 10 yrs don’t forget to apply for the NOSTER & @science.org Microbiome Prize! Grand Prize: $25K & your essay published in Science Magazine
Deadline: Feb 14th
Enter: buff.ly/5GKZgUN
Deadline: Feb 14th
Enter: buff.ly/5GKZgUN
January 12, 2026 at 1:30 PM
If you're doing innovative research about #microbiota and received an MD &/or PhD in last 10 yrs don’t forget to apply for the NOSTER & @science.org Microbiome Prize! Grand Prize: $25K & your essay published in Science Magazine
Deadline: Feb 14th
Enter: buff.ly/5GKZgUN
Deadline: Feb 14th
Enter: buff.ly/5GKZgUN
Reposted by Indra Roux
Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change
doi.org/10.64898/202...
doi.org/10.64898/202...
January 8, 2026 at 7:36 AM
Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change
doi.org/10.64898/202...
doi.org/10.64898/202...
Reposted by Indra Roux
Interesting review on sub-MIC antibiotic exposures from food/environment on the gut microbiome/resistome with suggested mechanisms impacting it. Interesting comments on methods/approaches + current regulatory framework too.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
January 11, 2026 at 4:42 PM
Interesting review on sub-MIC antibiotic exposures from food/environment on the gut microbiome/resistome with suggested mechanisms impacting it. Interesting comments on methods/approaches + current regulatory framework too.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Indra Roux
I get ~100 emails a day, but such an email is rare:
"Dr. Moon,
On behalf of Chairs Jennifer Doudna and David Bikard..."
So excited to see the Nobel laureate again, chair a session & give a talk at #microbiome editing GRC! See you all!
@dbikard.bsky.social
www.grc.org/microbiome-e...
"Dr. Moon,
On behalf of Chairs Jennifer Doudna and David Bikard..."
So excited to see the Nobel laureate again, chair a session & give a talk at #microbiome editing GRC! See you all!
@dbikard.bsky.social
www.grc.org/microbiome-e...
January 9, 2026 at 8:28 PM
I get ~100 emails a day, but such an email is rare:
"Dr. Moon,
On behalf of Chairs Jennifer Doudna and David Bikard..."
So excited to see the Nobel laureate again, chair a session & give a talk at #microbiome editing GRC! See you all!
@dbikard.bsky.social
www.grc.org/microbiome-e...
"Dr. Moon,
On behalf of Chairs Jennifer Doudna and David Bikard..."
So excited to see the Nobel laureate again, chair a session & give a talk at #microbiome editing GRC! See you all!
@dbikard.bsky.social
www.grc.org/microbiome-e...
Reposted by Indra Roux
Approaches for accelerating microbial gene function discovery using artificial intelligence www.nature.com/articles/s41... #jcampubs
Approaches for accelerating microbial gene function discovery using artificial intelligence - Nature Microbiology
In this Review, the authors discuss how artificial intelligence can aid microbial gene function discovery.
www.nature.com
January 7, 2026 at 5:34 PM
Approaches for accelerating microbial gene function discovery using artificial intelligence www.nature.com/articles/s41... #jcampubs
Reposted by Indra Roux
New preprint from the lab is out! 🥳
We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions.
www.biorxiv.org/content/10.6...
👇
We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions.
www.biorxiv.org/content/10.6...
👇
Systematic profiling of growth interactions in human gut microbiome species
Microbial interactions shape the composition and stability of the human gut microbiome. Yet, the molecular mechanisms underlying these relationships remain poorly understood. Here, we systematically p...
www.biorxiv.org
December 22, 2025 at 11:21 AM
New preprint from the lab is out! 🥳
We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions.
www.biorxiv.org/content/10.6...
👇
We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions.
www.biorxiv.org/content/10.6...
👇
Reposted by Indra Roux
🎉 New year, NEW PREPRINT!
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1
January 6, 2026 at 4:09 PM
🎉 New year, NEW PREPRINT!
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Bacteria exhibit astonishing genetic diversity, but where do new genes come from?
My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
Reposted by Indra Roux
Reposted by Indra Roux
UCLA's Garud Lab seeks a postdoctoral researcher in population genetics, focusing on evolutionary dynamics and the human gut microbiome. Candidates should have a relevant Ph.D. and strong programming skills. More info: https://garud.eeb.ucla.edu. #postdoc
Garud Lab
Garud Lab
garud.eeb.ucla.edu
January 6, 2026 at 2:49 AM
UCLA's Garud Lab seeks a postdoctoral researcher in population genetics, focusing on evolutionary dynamics and the human gut microbiome. Candidates should have a relevant Ph.D. and strong programming skills. More info: https://garud.eeb.ucla.edu. #postdoc
Reposted by Indra Roux
New study reveals a high-resolution genetic map of how E. coli adapts to the gut, showing diet- and inflammation-dependent metabolism, niche shifts, and unexpected roles for mobile genetic elements.
✍️ @amandinemaire.bsky.social & coll.
📖 shorturl.at/DYSTv
#Microbiome #Pathogenesis #Microsky
✍️ @amandinemaire.bsky.social & coll.
📖 shorturl.at/DYSTv
#Microbiome #Pathogenesis #Microsky
January 6, 2026 at 4:55 AM
New study reveals a high-resolution genetic map of how E. coli adapts to the gut, showing diet- and inflammation-dependent metabolism, niche shifts, and unexpected roles for mobile genetic elements.
✍️ @amandinemaire.bsky.social & coll.
📖 shorturl.at/DYSTv
#Microbiome #Pathogenesis #Microsky
✍️ @amandinemaire.bsky.social & coll.
📖 shorturl.at/DYSTv
#Microbiome #Pathogenesis #Microsky