Massive lateral gene transfer under strain coexistence in the gut

Frazão, N.; Seixas, E.; Barreto, H.C.; Mischler, M.; Güleresi, D.; Gordo, I.

doi:10.1101/2023.09.25.559333

Cited by 4 publications

(1 citation statement)

References 32 publications

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“…In this high-diversity limit, even basic questions about the effects of community structure remain unresolved: how does the benefit of a mutation depend on the diversity of the community and the metabolic overlap between its members? Do mutations primarily compete with their parent strain, or do they continue to stably diversify, as suggested by recent evidence from the gut microbiome ( 5 , 6 , 25 ) and some in vitro communities ( 26 , 27 )?…”

mentioning

confidence: 99%

Predicting the First Steps of Evolution in Randomly Assembled Communities

McEnany,

Good

2023

Preprint

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Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

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mentioning

confidence: 99%

Predicting the First Steps of Evolution in Randomly Assembled Communities

McEnany,

Good

2023

Preprint

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Predicting the first steps of evolution in randomly assembled communities

McEnany,

Good

2024

Nat Commun

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Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

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Community context influences the conjugation efficiency of Escherichia coli

Bustamante,

Koopman,

Martens

et al. 2024

FEMS Microbes

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In urinary tract infections, different bacteria can live in a polymicrobial community consisting of different species. It is unknown how community members affect the conjugation efficiency of uropathogenic Escherichia coli. We investigated the influence of individual species often co-isolated from urinary infections (UTIs) on the conjugation efficiency of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing the pOXA-48 plasmid and six uropathogenic E. coli isolates, in the presence and absence of five different species commonly co-isolated in polymicrobial UTIs to elucidate their effect on the conjugation efficiency of E. coli. We found that the basal conjugation rates of pOXA-48, in the absence of other species, are dependent on the bacterial host genetic background. Additionally, we found that bacterial interactions have an overall positive effect on the conjugation rate of pOXA-48. Particularly, Gram-positive enterococcal species were found to enhance the conjugation rates towards uropathogenic E. coli isolates. We hypothesize that the nature of the co-culture and physical interactions are important for these increased conjugation rates in an artificial urine medium environment.

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Massive lateral gene transfer under strain coexistence in the gut

Cited by 4 publications

References 32 publications

Predicting the First Steps of Evolution in Randomly Assembled Communities

Predicting the First Steps of Evolution in Randomly Assembled Communities

Predicting the first steps of evolution in randomly assembled communities

Community context influences the conjugation efficiency of Escherichia coli

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