Biology subjects

Newbury, A.

Publications and source records attributed to Newbury, A..

4 recordsLinked to original sources

bioRxiv2025

Diversity Between but Not Within Microbial Communities Increases With the Diversity of Supplied Nutrients

Greater resource diversity within a habitat is typically expected to support greater biodiversity in the resident ecological community (-diversity). It may also make community composition less deterministic since a wider range of species have a chance establishing themselves and affecting subsequent community assembly processes. However, the relationship between microbial diversity and the diversity of resources exogenously supplied is complicated by cross-feeding between microbes, since much of the resource diversity encountered will be generated by the community. Here, we assembled microbial communities in simple growth media (where cross-feeding will be important) with 1 to 3 carbon sources and asked how increasing nutrient diversity affects diversity within and between communities. While there was (i) no clear difference in -diversity, increasing the number of carbon sources led to communities that varied (ii) more within and (iii) less between the different abiotic conditions. (i) is at odds with classical ecological theory, but fits predictions from a consumer-resource model that accounts for cross-feeding. (ii) shows an increase in the stochasticity of community assembly. (iii) demonstrates strong abiotic selection in the single carbon source communities. We then went on to show that this is leads to phylogenetic clustering (co-occurrence of more closely related strains).

microbiology↗

bioRxiv2025

Competition between plasmids conferring the same antimicrobial resistance leads to plasmid-host network specialisation

Plasmids have a key role in disseminating antimicrobial resistance (AMR). Previous work has shown that in the presence of antibiotics, plasmids conferring AMR will spread to a larger number and a more phylogenetically diverse group of host organisms. However, this pattern may be complicated when multiple plasmids confer the same resistance. Here, we analyse host-plasmid networks in experimental communities of three bacterial species cultured for six weeks with three incompatible plasmids (plasmids that cannot stably coexist within a single cell) conferring tetracycline resistance. The communities are cultured either without tetracycline, or with a low or high dose of the antibiotic. We find that while antibiotic selection leads to higher plasmid prevalence, it does not change the structure of host-plasmid networks. Under all conditions, the networks become highly specialised, as specific host-plasmid pairings emerge. This result is supported by a previously published mathematical model parameterised to match our experimental set-up. Our study reiterates the importance of fitness effects of plasmids in determining the structure of bacteria-plasmid networks. The spread of a given AMR plasmid is reduced when fitness differences are reduced due to other plasmids carrying AMR genes, leading to more specialised bacteria-plasmid networks.

microbiology↗

bioRxiv2024

Bayesian Estimation of Cooccurrence Affinity with Dyadic Regression

O_LIEstimating underlying co-occurrence relationships between pairs of species has long been a challenging task in ecology as the extent to which species co-occur is partially dependent on their prevalence. While recent work has taken large steps towards solving this problem, the next question is how to assess the factors that influence co-occurrence. C_LIO_LIHere, I show that a recently proposed co-occurrence metric can be improved upon by assigning Bayesian priors to the latent co-occurrence relationships being estimated. In the context of analysing the factors that affect co-occurrence relationships, I demonstrate the need for a generalised linear model (GLM) that takes raw data (co-occurrences and species prevalence) not derived quantities (co-occurrence metrics) as its data. Next, I show the form that such a GLM should take in order to perform Bayesian inference while accounting for non-independence of dyadic matrix data (e.g. distance and co-occurrence matrices). C_LIO_LII then present 3 example analyses to highlight the types of scientific questions these methods can help answer, using existing data sets - measuring the effects of trait dissimilarity among dung beetle species and relatedness between ant species on co-occurrence, and constructing co-occurrence networks of bacteria found in cystic fibrosis patient sputum samples. C_LIO_LIFinally, I present the software package CooccurrenceRegression.jl, which provides a straightforward interface for researchers to put these methods into practice. C_LI

ecology↗

bioRxiv2024

Conjugation related costs have reduced impact on in silico plasmid persistence

Due to the important role they play in the antimicrobial resistance (AMR) crisis and in microbial evolution in general, a great deal of empirical and theoretical work is currently underway, trying to understand plasmid ecology. One of the key questions is how these often costly genetic elements persist in host populations. Here I show that when modelling plasmid population dynamics, it is not sufficient to treat them as always costly (or beneficial). I argue that conjugation related costs may be more important to plasmids in nature than they are in benign laboratory settings. Furthermore, I show that these conjugation related costs can be very severe and still not lead to extinction of a plasmid from a host population.

microbiology↗