Niche partitioning facilitates coexistence of closely related honey bee gut bacteria

Elife. 2021 Jul 19:10:e68583. doi: 10.7554/eLife.68583.


Ecological processes underlying bacterial coexistence in the gut are not well understood. Here, we disentangled the effect of the host and the diet on the coexistence of four closely related Lactobacillus species colonizing the honey bee gut. We serially passaged the four species through gnotobiotic bees and in liquid cultures in the presence of either pollen (bee diet) or simple sugars. Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. However, coexistence was only possible in the presence of pollen, and not in simple sugars, independent of the environment. Using metatranscriptomics and metabolomics, we found that the four species utilize different pollen-derived carbohydrate substrates indicating resource partitioning as the basis of coexistence. Our results show that despite longstanding host association, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments.

Keywords: bacterial coexistence; ecology; gut microbiota; honey bee; infectious disease; lactobacillus firm5; microbiology; niche partitioning.

Plain language summary

Microbes colonize nearly every environment on Earth, from the ocean and soil to the inner and outer surfaces of animals, such as the gut or skin. They form communities that are usually made up of a diverse range of bacteria, often containing closely related species – a key factor for a successful community. But closely related bacteria can battle for the same resources, so it is unclear how they manage to live alongside each other without competing against one another. While diet is thought to play a key role in enabling closely related bacterial species to co-exist in the gut of an animal, experimental evidence is lacking, due to the difficulty in replicating these systems in the laboratory. One strategy for investigating microbial communities is using honeybees. A major dietary source for honeybees is pollen, which can also be applied in the laboratory to grow diverse types of bacteria found in the honeybee gut. In addition, scientists can generate bees that lack microbial communities in the gut, allowing them to add specific types of bacteria to study their impact. Brochet et al. used this approach with Western honeybees to assess whether diet enables closely related bacteria to live alongside one another in the gut. First, they colonized bees that lacked gut microbes with four closely related bacteria of the genus Lactobacillus, alone or together, and fed the bees either sugar water or sugar water and pollen. After five days, the gut bacteria were analysed. This revealed that bees fed on sugar water only had one dominant Lactobacillus species present in their gut, while bees fed with additional pollen harboured all four Lactobacillus species. Further analysis of these four bacterial species revealed that each of them activates distinct genes when grown on pollen, allowing the different species to consume specific nutrients from broken down pollen. These findings show that closely related bacteria can coexist in the gut by sharing the different nutrients provided in the diet of the host. Consequently, differences in dietary intake in honeybees and other animals may affect the diversity of gut bacteria, and potentially the health of an animal.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacteria
  • Bees / microbiology*
  • Communicable Diseases
  • Diet
  • Ecology
  • Flavonoids
  • Gastrointestinal Microbiome / physiology*
  • Lactobacillus / metabolism
  • Metabolomics
  • Plant Extracts
  • Pollen / chemistry
  • Sugars / metabolism
  • Symbiosis
  • Transcriptome


  • Flavonoids
  • Plant Extracts
  • Sugars

Associated data

  • GEO/GSE166724

Grants and funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.