ArticlemSphere2020
Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome.
Article in mSphere, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Stability in flexibility: Shifting alliances stabilize the symbioses of marine animals over 150 million years.Science advances · 2026Article
- Bacteriophage Density Influences the Rate of Resistance Evolution.Bulletin of mathematical biology · 2026Article
- MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.Bioinformatics (Oxford, England) · 2026Article
- The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.Nature communications · 2026Article
- Article
- Bacteriophage density influences the rate of resistance evolution.bioRxiv : the preprint server for biology · 2025Article
- Effects of priority on strain-level composition of the honey bee gut community.Applied and environmental microbiology · 2025Article
- Antibiotic treatment of honey bee colonies alters early gut microbiome assembly and induces persistent dysbiosis in newly emerged workers.Scientific reports · 2025Article
- Diet affects reproductive development and microbiota composition in honey bees.Animal microbiome · 2024Article
- Type VI secretion systems promote intraspecific competition and host interactions in a bee gut symbiont.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The honeybee microbiota and its impact on health and disease.Nature reviews. Microbiology · 2024Review
- Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.Microbial ecology · 2024Article
- Shotgun metagenomics reveals the gut microbial diversity and functions inFrontiers in microbiology · 2024Article
- Social transmission of bacterial symbionts homogenizes the microbiome within and across generations of group-living spiders.ISME communications · 2023Article
- A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont.Animal microbiome · 2023Article
- Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium.Microbiome · 2022Article
- Article
- The Role of Feeding Characteristics in Shaping Gut Microbiota Composition and Function of Ensifera (Orthoptera).Insects · 2022Article
- Amplicon Sequencing of Single-Copy Protein-Coding Genes Reveals Accurate Diversity for Sequence-Discrete Microbiome Populations.Microbiology spectrum · 2022Article
- Article
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Authors and funding
3 authors.
Funding
Abstract
Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.