Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

Baud, Gilles; Ellegaard, Kirsten; Engel, Philipp

doi:10.1101/2022.12.29.522137

Cited by 2 publications

(3 citation statements)

References 87 publications

(195 reference statements)

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“…The proportion of polymorphic sites was similar over the samples with around 0.11 % (SD=0.72 %), and 0.02 % (SD=0.03 %) for S. thermophilus and L. delbrueckii, respectively (SFig. 1), which is comparatively low with respect to bacteria found in non-food fermentation systems like in the gut of animals (3 % and 2-10 % polymorphic sites within species in the gut microbiota of human (42) and honey bees (43), respectively).…”

Section: Resultsmentioning

confidence: 85%

Genomic and phenotypic imprints of microbial domestication on cheese starter cultures

Somerville,

Thierer,

Schmidt

et al. 2024

Preprint

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Domestication – the artificial selection of wild species to obtain variants with traits of human interest– was integral to the rise of civilization. During the neolithic, the oversupply of food enabled by the domestication of crop plants and farm animals was associated with the invention of food preservation strategies through microbial fermentation. However, it remains unclear whether fermented food microbes show similar signs of domestication by humans like plants or animals. Only a few eukaroytic have been studied so far in this respect (e.g., yeasts used in mantou or wine), whereas little is known for bacteria. Here, we tested if cheese starter cultures harbour typical hallmarks of domestication by characterising over 100 community samples and over 100 individual strains isolated from historical and modern traditional Swiss cheese starter cultures. We find that cheese starter cultures have low genetic diversity both at the species and strain-level and are taxonomically and phenotypically stable. Our analyses further suggest that the evolutionary origin of the bacteria in cheese starter cultures coincided with the start of cheesemaking as reported from archeological records. Finally, we find evidence for ongoing genome decay and pseudogenization via transposon insertion related to a reduction of their niche breadth. These characteristics suggest that cheese starter cultures were domesticated by humans before knowing about microbes, potentially starting as early as the neolithics. Future work documenting the prevalence of these hallmarks across diverse fermented food systems and geographic regions will be key to unveiling the joint history of humanity with fermented food microbes.

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Section: Resultsmentioning

confidence: 85%

Genomic and phenotypic imprints of microbial domestication on cheese starter cultures

Somerville,

Thierer,

Schmidt

et al. 2024

Preprint

Self Cite

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“…A comprehensive list of all packages used and their version is available in the GitHub repository (https:// github. com/ Aiswa rya-prasad/ Publi cation_ Baud_ metaG_ NvsF_ 2023) [76].…”

Section: Statistics and Data Visualizationmentioning

confidence: 99%

“…The scripts required to run the analyses and produce the figures are available on GitHub: https:// github. com/ Aiswa rya-prasad/ Publi cation_ Baud_ metaG_ NvsF_ 2023 [76] and Zenodo: https:// zenodo. org/ recor ds/ 10183 178 [79].…”

Section: Supplementary Informationmentioning

confidence: 99%

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

Baud,

Prasad,

Ellegaard

et al. 2023

Genome Biol

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Background Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood. Results Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell–cell interactions specifically associated with the two behavioral states. Conclusions Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.

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Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

Cited by 2 publications

References 87 publications

Genomic and phenotypic imprints of microbial domestication on cheese starter cultures

Genomic and phenotypic imprints of microbial domestication on cheese starter cultures

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

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