Sean GibbonsTo continue our recent preprint whirlwind 🌪️, we just posted a revision of @jpjl57's manuscript on in vivo bacterial population growth phase estimation from metagenomic time series.
Here's what's new 🧵
@isbsci
As a refresher, we describe how stool samples from adult humans represent a steady-state endpoint of internal dynamics.
A consequence of this interpretation is that abundance fluctuations from day to day are not representative of growth or death rates.
However, we can calculate peak-to-trough ratios (PTRs) in order to get instantaneous estimates of growth/replication rates for abundant taxa from metagenomic samples, thanks to prior work by @tkorem et al. https://pubmed.ncbi.nlm.nih.gov/26229116/
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples - PubMed
Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a …
We wanted to know whether or not we could extract information about in situ dynamics or the phase of growth for organisms exiting the gut in stool, leveraging measures of growth rate and abundance.
We looked at 4 BIO-ML stool donors with long, dense metagenomic time series, where we could calculate PTR & abundance trajectories for multiple taxa. Average PTRs & abundances of organisms were positively associated within people (but noisy), suggesting quasi-exponential growth.
We added new data from 84 stool donors. Most bacterial taxa show a wide range of PTRs, suggesting that these values are comparable across these groups. The average positive associations between PTRs and abundances across people were significant, even when controlling for taxonomy