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Convergent reductive evolution in bee-associated lactic acid bacteria.

Ana Pontes1,2, Marie-Claire Harrison3,4, Antonis Rokas3,4

  • 1Associate Laboratory i4HB, Institute for Health and Bioeconomy and UCIBIO, Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Applied and Environmental Microbiology
|October 23, 2024
PubMed
Summary
This summary is machine-generated.

Lactic acid bacteria (LAB) adapting to bee environments independently lost similar genes, driving convergent evolution of traits like fructophily. This genomic convergence highlights gene loss as a key driver of adaptation in bee-associated LAB.

Keywords:
bee symbiontsconvergent evolutionfructophilic lactic acid bacteria (FLAB)gene lossmachine learningreductive evolution

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Area of Science:

  • Microbiology and Evolutionary Biology
  • Genomics and Bioinformatics

Background:

  • Distantly related organisms can evolve similar traits (convergent evolution) when adapting to similar ecological niches.
  • Lactic acid bacteria (LAB) frequently inhabit floral environments, with some species showing specialized genomic and phenotypic traits linked to bee association.

Purpose of the Study:

  • To test the hypothesis that specific genomic and phenotypic traits in bee-associated LAB evolved convergently.
  • To investigate the role of gene loss in the adaptation of LAB to the floral-bee environment.

Main Methods:

  • Phylogenomic analysis of 369 LAB genomes, comparing bee-associated and non-bee-associated species.
  • Machine learning models were employed to identify genomic features distinguishing bee-associated LAB.
  • Analysis of gene content, genome size, GC content, and specific gene losses, including acetaldehyde-alcohol dehydrogenase (adhE).

Main Results:

  • Seven independent ecological shifts to the bee environment were identified in LAB.
  • Bee-associated LAB exhibited significant reductions in genome size, gene repertoire, and GC content.
  • Machine learning accurately distinguished bee-associated from non-bee-associated species (94% accuracy) based on the absence of specific genes.
  • Independent loss of key genes, including adhE, was observed across multiple bee-associated lineages, linked to the evolution of fructophily.

Conclusions:

  • Convergent evolution in bee-associated LAB is largely driven by the independent loss of the same sets of genes.
  • Gene loss significantly shapes the genomic trajectory and unique traits of LAB adapting to the bee niche.
  • Machine learning is a powerful tool for detecting adaptation fingerprints and convergent evolution.