We predicted the metabolites that could be cross-fed & validated by LC-MS. Metabolite signatures were consistent with secretion, not cell lysis + release.
This means that the prototroph was able to break down the nutrient, then secrete breakdown components to the auxotroph, enabling growth.
This means that the prototroph was able to break down the nutrient, then secrete breakdown components to the auxotroph, enabling growth.
December 13, 2025 at 9:46 AM
We predicted the metabolites that could be cross-fed & validated by LC-MS. Metabolite signatures were consistent with secretion, not cell lysis + release.
This means that the prototroph was able to break down the nutrient, then secrete breakdown components to the auxotroph, enabling growth.
This means that the prototroph was able to break down the nutrient, then secrete breakdown components to the auxotroph, enabling growth.
In every case, we found that the prototroph supported the growth of the auxotrophic strain in every nutrient-lineage-pair combination. This went both ways: When the role of auxotroph and prototroph were reversed by using a different nutrient, the prototroph always supported auxotroph growth.
December 13, 2025 at 9:46 AM
In every case, we found that the prototroph supported the growth of the auxotrophic strain in every nutrient-lineage-pair combination. This went both ways: When the role of auxotroph and prototroph were reversed by using a different nutrient, the prototroph always supported auxotroph growth.
Onto my favourite part of this project: cross-feeding between lineages. We co-cultured a nutrient auxotroph with a prototroph, physically seperated in Transwells (4x substrates, 5x lineages, n=3 distinct isolates per lineage).
December 13, 2025 at 9:46 AM
Onto my favourite part of this project: cross-feeding between lineages. We co-cultured a nutrient auxotroph with a prototroph, physically seperated in Transwells (4x substrates, 5x lineages, n=3 distinct isolates per lineage).
August 5, 2025 at 1:41 AM
🚨New Pub🚨Protection Elicited by Glutamine Auxotroph of #Yersinia pestis w/ Dr F. Sebbane
@pasteurlille.bsky.social @chulille.bsky.social @univlille.bsky.social @cnrs-hautsdefrance.bsky.social @inserm.fr
@pasteurlille.bsky.social @chulille.bsky.social @univlille.bsky.social @cnrs-hautsdefrance.bsky.social @inserm.fr
www.mdpi.com
April 2, 2025 at 12:19 PM
🚨New Pub🚨Protection Elicited by Glutamine Auxotroph of #Yersinia pestis w/ Dr F. Sebbane
@pasteurlille.bsky.social @chulille.bsky.social @univlille.bsky.social @cnrs-hautsdefrance.bsky.social @inserm.fr
@pasteurlille.bsky.social @chulille.bsky.social @univlille.bsky.social @cnrs-hautsdefrance.bsky.social @inserm.fr
Final notes: Whereas the genomes of leafy liverworts harbor putative lipid transporters, which are essential for the transfer of fatty acids to auxotroph fungi involved in the arbuscular mycorrhizae, we did not detect the orthologs to be transcriptionally responsive under ericoid mycorrhizae.
April 2, 2025 at 11:59 AM
Final notes: Whereas the genomes of leafy liverworts harbor putative lipid transporters, which are essential for the transfer of fatty acids to auxotroph fungi involved in the arbuscular mycorrhizae, we did not detect the orthologs to be transcriptionally responsive under ericoid mycorrhizae.
Let's be frank: correctly identifying deletionsto design tight and reliable auxotrophs is extremely challenging😫. Often, implementing a single auxotroph strain takes several months and trial-and-error iterations... 🤯2/
March 4, 2025 at 8:38 PM
Let's be frank: correctly identifying deletionsto design tight and reliable auxotrophs is extremely challenging😫. Often, implementing a single auxotroph strain takes several months and trial-and-error iterations... 🤯2/
We just #published an end-to-end work for the computer-aided design💻, construction🛠️, validation✅, characterization🔬 & application💪 of #auxotroph metabolic sensors, the work-horses of in vivo growth-coupled selection screening systems-using glycolate as test case. 🧵👇1/
www.nature.com/articles/s41...
www.nature.com/articles/s41...
March 4, 2025 at 8:38 PM
We just #published an end-to-end work for the computer-aided design💻, construction🛠️, validation✅, characterization🔬 & application💪 of #auxotroph metabolic sensors, the work-horses of in vivo growth-coupled selection screening systems-using glycolate as test case. 🧵👇1/
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Let's be frank: correctly identifying deletionsto design tight and reliable auxotrophs is extremely challenging😫. Often, implementing a single auxotroph strain takes several months and trial-and-error iterations... 🤯2/
March 4, 2025 at 8:29 PM
Let's be frank: correctly identifying deletionsto design tight and reliable auxotrophs is extremely challenging😫. Often, implementing a single auxotroph strain takes several months and trial-and-error iterations... 🤯2/
I don't follow. Imagine an auxotroph for a rare amino acid -tryptophan is about 1% of biomass. Assuming equal yields on tryp for donor and recip I only need about 1% of the donor population to die to permit growth of the recipient. You incubated for 5 days, so plenty of time for 1% to die.
February 10, 2025 at 11:12 AM
I don't follow. Imagine an auxotroph for a rare amino acid -tryptophan is about 1% of biomass. Assuming equal yields on tryp for donor and recip I only need about 1% of the donor population to die to permit growth of the recipient. You incubated for 5 days, so plenty of time for 1% to die.
Cool dataset. In the co-culture experiment, what direct evidence do you have that the donor strains are leaking the metabolite to the auxotroph? From the way the experiment was done (donor in agar), it looks like a passive mechanism such as cell lysis could explain the results as well.
February 10, 2025 at 9:42 AM
Cool dataset. In the co-culture experiment, what direct evidence do you have that the donor strains are leaking the metabolite to the auxotroph? From the way the experiment was done (donor in agar), it looks like a passive mechanism such as cell lysis could explain the results as well.
The results show that indeed auxotrophic isolates were able to grow in coculture:
31% grew in auxotroph-auxotroph combinations and
84% grew in auxotroph-prototroph combinations
31% grew in auxotroph-auxotroph combinations and
84% grew in auxotroph-prototroph combinations
January 30, 2025 at 7:51 AM
The results show that indeed auxotrophic isolates were able to grow in coculture:
31% grew in auxotroph-auxotroph combinations and
84% grew in auxotroph-prototroph combinations
31% grew in auxotroph-auxotroph combinations and
84% grew in auxotroph-prototroph combinations
Class II systems use NECs to make molecules that are then used by cells.
A great example is Ru-catalysed deprotection of alloc-PABA (Lee 2013)
Providing alloc-PABA and a Ru catalyst to E. coli auxotrophic for PABA allows the cells to survive, making cellular metabolism dependent on an NEC.
A great example is Ru-catalysed deprotection of alloc-PABA (Lee 2013)
Providing alloc-PABA and a Ru catalyst to E. coli auxotrophic for PABA allows the cells to survive, making cellular metabolism dependent on an NEC.
November 27, 2024 at 1:15 PM
Class II systems use NECs to make molecules that are then used by cells.
A great example is Ru-catalysed deprotection of alloc-PABA (Lee 2013)
Providing alloc-PABA and a Ru catalyst to E. coli auxotrophic for PABA allows the cells to survive, making cellular metabolism dependent on an NEC.
A great example is Ru-catalysed deprotection of alloc-PABA (Lee 2013)
Providing alloc-PABA and a Ru catalyst to E. coli auxotrophic for PABA allows the cells to survive, making cellular metabolism dependent on an NEC.
Future computationally designed biosensors-on-demand, optimised in barcoded HT screens may allow making TFs responsive to any enzyme product a realistic option, which would overcome the current limitation of enzymatic activity in vivo selections to detox / auxotroph-complementing enzymes. 2/2
November 21, 2024 at 9:15 AM
Future computationally designed biosensors-on-demand, optimised in barcoded HT screens may allow making TFs responsive to any enzyme product a realistic option, which would overcome the current limitation of enzymatic activity in vivo selections to detox / auxotroph-complementing enzymes. 2/2
(2/6) We follow a urinary tract isolate over its history and show two same-strain sub-populations with one lacking the L-histidine biosynthetic operon, (L-histidine auxotroph). This mixed frozen stock remained undetected over 10 years and across several subsequent studies
November 21, 2024 at 6:26 AM
(2/6) We follow a urinary tract isolate over its history and show two same-strain sub-populations with one lacking the L-histidine biosynthetic operon, (L-histidine auxotroph). This mixed frozen stock remained undetected over 10 years and across several subsequent studies
Ever worried about anemia? Heme transport is super imp.
Moving heme into, out & within cells with heme transporters Hrg-1 & Mrp-5. Gene discovery and pathway analysis in heme auxotroph C. elegans & cell biology in vertebrates.
Interactive seminar by Iqbal Hamza UofMaryland at DBS-TIFR
Moving heme into, out & within cells with heme transporters Hrg-1 & Mrp-5. Gene discovery and pathway analysis in heme auxotroph C. elegans & cell biology in vertebrates.
Interactive seminar by Iqbal Hamza UofMaryland at DBS-TIFR
November 15, 2024 at 7:22 AM
Ever worried about anemia? Heme transport is super imp.
Moving heme into, out & within cells with heme transporters Hrg-1 & Mrp-5. Gene discovery and pathway analysis in heme auxotroph C. elegans & cell biology in vertebrates.
Interactive seminar by Iqbal Hamza UofMaryland at DBS-TIFR
Moving heme into, out & within cells with heme transporters Hrg-1 & Mrp-5. Gene discovery and pathway analysis in heme auxotroph C. elegans & cell biology in vertebrates.
Interactive seminar by Iqbal Hamza UofMaryland at DBS-TIFR
Higher-Order Interactions in Auxotroph Communities Enhance Their Resilience to Resource Fluctuations https://www.biorxiv.org/content/10.1101/2024.05.22.595348v1
Higher-Order Interactions in Auxotroph Communities Enhance Their Resilience to Resource Fluctuations https://www.biorxiv.org/content/10.1101/2024.05.22.595348v1
Auxotrophs are prevalent in microbial communities, enhancing their diversity and stability-a counter
www.biorxiv.org
May 27, 2024 at 5:33 AM
Higher-Order Interactions in Auxotroph Communities Enhance Their Resilience to Resource Fluctuations https://www.biorxiv.org/content/10.1101/2024.05.22.595348v1
And a new preprint (2/2): researchsquare.com/article/rs-3...
Our papers on the evolution of drug use are here: anthro.vancouver.wsu.edu/people/hagen...
Our papers on the evolution of drug use are here: anthro.vancouver.wsu.edu/people/hagen...
January 28, 2024 at 8:17 PM
And a new preprint (2/2): researchsquare.com/article/rs-3...
Our papers on the evolution of drug use are here: anthro.vancouver.wsu.edu/people/hagen...
Our papers on the evolution of drug use are here: anthro.vancouver.wsu.edu/people/hagen...
Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium https://www.biorxiv.org/content/10.1101/2024.01.08.574620v1
Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium https://www.biorxiv.org/content/10.1101/2024.01.08.574620v1
Methionine biosynthesis relies on the sequential catalysis of multiple enzymes. Escherichia coli, th
www.biorxiv.org
January 9, 2024 at 12:46 AM
Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium https://www.biorxiv.org/content/10.1101/2024.01.08.574620v1
Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium https://www.biorxiv.org/content/10.1101/2024.01.08.574620v1
Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium https://www.biorxiv.org/content/10.1101/2024.01.08.574620v1
Methionine biosynthesis relies on the sequential catalysis of multiple enzymes. Escherichia coli, th
www.biorxiv.org
January 9, 2024 at 12:46 AM
Engineering of methionine-auxotroph Escherichia coli via parallel evolution of two enzymes from Corynebacterium glutamicum's direct-sulfurylation pathway enables its recovery in minimal medium https://www.biorxiv.org/content/10.1101/2024.01.08.574620v1
bottleneck → adenine accumulates → adenine diffuses from cell → auxotroph uses adenine → auxotroph reciprocates → coexistence
15/49 R. pal isolates do this or something like it.
Proud of grad student 1st author Ella Chuang.
Thanks also to our great collaborators.
www.biorxiv.org/content/10.1...
15/49 R. pal isolates do this or something like it.
Proud of grad student 1st author Ella Chuang.
Thanks also to our great collaborators.
www.biorxiv.org/content/10.1...
October 18, 2023 at 3:09 PM
bottleneck → adenine accumulates → adenine diffuses from cell → auxotroph uses adenine → auxotroph reciprocates → coexistence
15/49 R. pal isolates do this or something like it.
Proud of grad student 1st author Ella Chuang.
Thanks also to our great collaborators.
www.biorxiv.org/content/10.1...
15/49 R. pal isolates do this or something like it.
Proud of grad student 1st author Ella Chuang.
Thanks also to our great collaborators.
www.biorxiv.org/content/10.1...
Visualization of the role of host heme on the virulence of the heme auxotroph Streptococcus agalactiae http://disq.us/t/2i8jjl4
Visualization of the role of host heme on the virulence o...
Heme is essential for several cellular key functions but ...
disq.us
December 8, 2024 at 5:07 AM
Visualization of the role of host heme on the virulence of the heme auxotroph Streptococcus agalactiae http://disq.us/t/2i8jjl4