Sophie Jean Walton
@sophiejwalton.bsky.social
Stanford Biophysics PhD Student with Dmitri Petrov and Ben Good. evolution, ecology, genomics, microbiomes, biophysics :) she/her
https://sophiejwalton.github.io
https://sophiejwalton.github.io
We also examined whether strain-level competition outcomes were correlated across species. Interestingly, we found little evidence for strain-level cohesion during coalescence, despite prior co-selection during community assembly and within each host. (16/n)
November 11, 2025 at 5:15 PM
We also examined whether strain-level competition outcomes were correlated across species. Interestingly, we found little evidence for strain-level cohesion during coalescence, despite prior co-selection during community assembly and within each host. (16/n)
Our observations of strain-level coexistence were surprising because community mixtures did not have elevated diversity compared to autologous controls! (14/n)
November 11, 2025 at 5:15 PM
Our observations of strain-level coexistence were surprising because community mixtures did not have elevated diversity compared to autologous controls! (14/n)
However, selection shifted at later generations in many competitions! Moreover, these shifts also tended to be biased towards maintaining coexistence. (12/n)
November 11, 2025 at 5:15 PM
However, selection shifted at later generations in many competitions! Moreover, these shifts also tended to be biased towards maintaining coexistence. (12/n)
We then estimated the time-varying relative fitnesses of conspecific strains. We found that selection during earlier generations was quite strong and predicted that one strain would dominate in most competitions. (11/n)
November 11, 2025 at 5:15 PM
We then estimated the time-varying relative fitnesses of conspecific strains. We found that selection during earlier generations was quite strong and predicted that one strain would dominate in most competitions. (11/n)
We found that the dynamics of competing strains were characterized by large and deterministic shifts. These shifts exceeded what could be generated by measurement noise or drift, demonstrating that these dynamics were driven by strong selection. (10/n)
November 11, 2025 at 5:15 PM
We found that the dynamics of competing strains were characterized by large and deterministic shifts. These shifts exceeded what could be generated by measurement noise or drift, demonstrating that these dynamics were driven by strong selection. (10/n)
We then monitored the dynamics of competing conspecific strains from each host through the course of the coalescence through shotgun metagenomics. This approach allowed us to follow pairwise strain competitions across many species in parallel! (9/n)
November 11, 2025 at 5:15 PM
We then monitored the dynamics of competing conspecific strains from each host through the course of the coalescence through shotgun metagenomics. This approach allowed us to follow pairwise strain competitions across many species in parallel! (9/n)
We collected fecal samples from donors in the Bay Area and assembled in vitro gut communities from these samples in anaerobic conditions. Communities from different hosts shared some species, but harbored diverged strains of those species. (8/n)
November 11, 2025 at 5:15 PM
We collected fecal samples from donors in the Bay Area and assembled in vitro gut communities from these samples in anaerobic conditions. Communities from different hosts shared some species, but harbored diverged strains of those species. (8/n)
Microbial community coalescence experiments have been used to gain a lot of intuition on species-level selection. We were also inspired by strain level data that had been obtained from FMTs in therapeutic contexts (fig from DOI: 10.1126/science.aad8852). (7/n)
November 11, 2025 at 5:15 PM
Microbial community coalescence experiments have been used to gain a lot of intuition on species-level selection. We were also inspired by strain level data that had been obtained from FMTs in therapeutic contexts (fig from DOI: 10.1126/science.aad8852). (7/n)
It’s hard to distinguish between these models in natural microbiomes, so turned to lab systems to get some intuition. Specifically, we performed whole community competitions, or community coalescence, with in vitro gut communities derived from different human donors. (6/n)
November 11, 2025 at 5:15 PM
It’s hard to distinguish between these models in natural microbiomes, so turned to lab systems to get some intuition. Specifically, we performed whole community competitions, or community coalescence, with in vitro gut communities derived from different human donors. (6/n)
Others have proposed that conspecific strains may compete as ‘ecological species’ and coexist via niche partitioning because we see lots of examples of multiple conspecific strains persisting in the same microbiome. (5/n)
November 11, 2025 at 5:15 PM
Others have proposed that conspecific strains may compete as ‘ecological species’ and coexist via niche partitioning because we see lots of examples of multiple conspecific strains persisting in the same microbiome. (5/n)
Complex microbial communities, like the human gut microbiome, can harbor extensive strain-level diversity, with strains of the same species from different hosts differing by ~10k mutations. However, the fitness consequences of this diversity in community contexts are not well understood. (2/n)
November 11, 2025 at 5:15 PM
Complex microbial communities, like the human gut microbiome, can harbor extensive strain-level diversity, with strains of the same species from different hosts differing by ~10k mutations. However, the fitness consequences of this diversity in community contexts are not well understood. (2/n)
We also examined whether strain-level competition outcomes were correlated across species. Interestingly, we found little evidence for strain-level cohesion during coalescence, despite prior co-selection during community assembly and within each host. (16/n)
November 11, 2025 at 5:02 PM
We also examined whether strain-level competition outcomes were correlated across species. Interestingly, we found little evidence for strain-level cohesion during coalescence, despite prior co-selection during community assembly and within each host. (16/n)
Our observations of strain-level coexistence were surprising because community mixtures did not have elevated diversity compared to autologous controls! (14/n)
November 11, 2025 at 5:02 PM
Our observations of strain-level coexistence were surprising because community mixtures did not have elevated diversity compared to autologous controls! (14/n)
However, selection shifted at later generations in many competitions! Moreover, these shifts also tended to be biased towards maintaining coexistence. (12/n)
November 11, 2025 at 5:02 PM
However, selection shifted at later generations in many competitions! Moreover, these shifts also tended to be biased towards maintaining coexistence. (12/n)
We then estimated the time-varying relative fitnesses of conspecific strains. We found that selection during earlier generations was quite strong and predicted that one strain would dominate in most competitions. (11/n)
November 11, 2025 at 5:02 PM
We then estimated the time-varying relative fitnesses of conspecific strains. We found that selection during earlier generations was quite strong and predicted that one strain would dominate in most competitions. (11/n)
We found that the dynamics of competing strains were characterized by large and deterministic shifts. These shifts exceeded what could be generated by measurement noise or drift, demonstrating that these dynamics were driven by strong selection. (10/n)
November 11, 2025 at 5:02 PM
We found that the dynamics of competing strains were characterized by large and deterministic shifts. These shifts exceeded what could be generated by measurement noise or drift, demonstrating that these dynamics were driven by strong selection. (10/n)
We then monitored the dynamics of competing conspecific strains from each host through the course of the coalescence through shotgun metagenomics. This approach allowed us to follow pairwise strain competitions across many species in parallel! (9/n)
November 11, 2025 at 5:02 PM
We then monitored the dynamics of competing conspecific strains from each host through the course of the coalescence through shotgun metagenomics. This approach allowed us to follow pairwise strain competitions across many species in parallel! (9/n)
We collected fecal samples from donors in the Bay Area and assembled in vitro gut communities from these samples in anaerobic conditions. Communities from different hosts shared some species, but harbored diverged strains of those species. (8/n)
November 11, 2025 at 5:02 PM
We collected fecal samples from donors in the Bay Area and assembled in vitro gut communities from these samples in anaerobic conditions. Communities from different hosts shared some species, but harbored diverged strains of those species. (8/n)
Microbial community coalescence experiments have been used to gain a lot of intuition on species-level selection. We were also inspired by strain level data that had been obtained from FMTs in therapeutic contexts (fig from DOI: 10.1126/science.aad8852). (7/n)
November 11, 2025 at 5:02 PM
Microbial community coalescence experiments have been used to gain a lot of intuition on species-level selection. We were also inspired by strain level data that had been obtained from FMTs in therapeutic contexts (fig from DOI: 10.1126/science.aad8852). (7/n)
It’s hard to distinguish between these models in natural microbiomes, so turned to lab systems to get some intuition. Specifically, we performed whole community competitions, or community coalescence, with in vitro gut communities derived from different human donors. (6/n)
November 11, 2025 at 5:02 PM
It’s hard to distinguish between these models in natural microbiomes, so turned to lab systems to get some intuition. Specifically, we performed whole community competitions, or community coalescence, with in vitro gut communities derived from different human donors. (6/n)
Others have proposed that conspecific strains may compete as ‘ecological species’ and coexist via niche partitioning because we see lots of examples of multiple conspecific strains persisting in the same microbiome. (5/n)
November 11, 2025 at 5:02 PM
Others have proposed that conspecific strains may compete as ‘ecological species’ and coexist via niche partitioning because we see lots of examples of multiple conspecific strains persisting in the same microbiome. (5/n)
Complex microbial communities, like the human gut microbiome, can harbor extensive strain-level diversity, with strains of the same species from different hosts differing by ~10k mutations. However, the fitness consequences of this diversity in community contexts are not well understood. (2/n)
November 11, 2025 at 5:02 PM
Complex microbial communities, like the human gut microbiome, can harbor extensive strain-level diversity, with strains of the same species from different hosts differing by ~10k mutations. However, the fitness consequences of this diversity in community contexts are not well understood. (2/n)
a couple of days late, but wanted to thank the organizers of #Evol2025 for an amazing conference! My favorite talk by far was @jbyoder.org 's IDEAL talk, which quite literally brought me to tears. Luckily its on youtube! www.youtube.com/live/vfDKMEy...
June 27, 2025 at 7:55 PM
a couple of days late, but wanted to thank the organizers of #Evol2025 for an amazing conference! My favorite talk by far was @jbyoder.org 's IDEAL talk, which quite literally brought me to tears. Luckily its on youtube! www.youtube.com/live/vfDKMEy...
Super excited for #Evol2025! I will be sharing some cool work on selection in the gut microbial communities at 9:30 am on Monday in the Evolutionary Ecology I session (Parthenon 2)!! Looking forward to chatting with folks as well!
June 20, 2025 at 4:35 PM
Super excited for #Evol2025! I will be sharing some cool work on selection in the gut microbial communities at 9:30 am on Monday in the Evolutionary Ecology I session (Parthenon 2)!! Looking forward to chatting with folks as well!
