Barcoding populations of<i>Pseudomonas fluorescens</i>SBW25

Theodosiou, Loukas; Farr, Andrew D; Rainey, Paul B.

doi:10.1101/2022.09.30.510243

Cited by 2 publications

(2 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The high-resolution colonization dynamics could also be extended by barcoding pathogenic species, such as P. aeruginosa and S. enterica, which are more aggressive colonizers than E. coli K12. Recently, the successful barcoding of Pseudomonas fluorescens SBW25, 84 demonstrates the potential applicability of our approach for generating a library of more than 10 5 barcodes. Additionally, our use of the Tn7 integration site, conserved among Gram-negative bacteria, suggests that our method could be easily extended to other bacteria in this group.…”

Section: Discussionmentioning

confidence: 92%

Quantifying the intra- and inter-species community interaction in a microbiome by dynamic covariance mapping

Serohijos,

Gencel,

Hui

et al. 2024

Preprint

View full text Add to dashboard Cite

A microbiome’s composition, stability, and response to perturbations is dictated by the community interaction matrix 1-10 that is commonly assayed by pair-wise species competition. In their natural environment however, microbes concurrently experience multiple species, face conditions that may be difficult to mimic in vitro, and have members that are impractical to isolate. Additionally, due to overlapping of evolutionary and ecological timescales, the community interaction matrix is also influenced by intra-species diversity, but how and to what extent remains poorly understood 11-14. Here, we develop a general approach called Dynamic Covariance Mapping (DCM) to estimate the interaction matrix of multispecies microbiome community in its natural environment from abundance time-series data. Together with intra-species high-resolution lineage tracking via chromosomal barcoding, we quantify the inter- and intra-species community interaction matrix during E. coli colonization of mice gut microbiome with increasing complexity: germ-free, antibiotic-perturbed, and innate microbiota. With DCM, we differentiate three temporal phases of invasion in the susceptible communities: 1) initial loss of community stability as E. coli enters; 2) recolonization of some gut bacteria; and 3) recovery of stability with E. coli clones coexisting with resident bacteria in a quasi-steady state. These phases are influenced by specific interactions between E. coli sub-lineages with other species in the community. These results highlight the transient nature and time-dependence of community interaction networks in microbiomes driven by the persistent coupling of ecological and evolutionary dynamics. Our theoretical and experimental approach can be applied to characterize coupled ecological-evolutionary dynamics of bacterial communities in vitro and in situ.

show abstract

Section: Discussionmentioning

confidence: 92%

Quantifying the intra- and inter-species community interaction in a microbiome by dynamic covariance mapping

Serohijos,

Gencel,

Hui

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…This check was made by sequencing across the Tn7 insertion site in 96 independent clones. The resultant data showed that all 96 contained unique barcodes [see (Theodosiou et al 2023)].…”

Section: Design and Construction Of Barcoded Integrative Plasmidsmentioning

confidence: 99%

Barcoding Populations of Pseudomonas fluorescens SBW25

2023

Self Cite

View full text Add to dashboard Cite

In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.

show abstract

Barcoding populations ofPseudomonas fluorescensSBW25

Cited by 2 publications

References 40 publications

Quantifying the intra- and inter-species community interaction in a microbiome by dynamic covariance mapping

Quantifying the intra- and inter-species community interaction in a microbiome by dynamic covariance mapping

Barcoding Populations of Pseudomonas fluorescens SBW25

Contact Info

Product

Resources

About