DOI: 10.5061/dryad.rxwdbrvjf
title: High abundance of lactobacilli in the gut microbiome of honey bees during winter

description: Honey bee gut microbiota play specific roles in promoting host growth and
 physiology by regulating the immune system, behavior, metabolism, and
 neurological processes. While the gut microbiota of honey bee queens,
 workers, and larvae has been extensively studied, less is known about the
 composition of gut microbiota in the winter worker bees. This study
 investigates the dynamics of the gut microbiota in overwintering adult
 worker bees, focusing on two commercial bee strains: Bolton™ bees and Mann
 Lake™ bees. These Apis mellifera strains were investigated under different
 storage conditions (indoor storage at 6°C and outdoor storage in natural
 conditions) during the winter months (October, November, and December).
 Utilizing 16S rRNA gene amplicon sequencing, we characterized the
 microbial composition of the whole gut. We observed the Lactobacilli
 dominated in all the overwintering honey bee guts with a significantly
 higher abundance of unclassified Lactobacillus species in November, while
 Lactobacillus apis showed significantly higher abundance in October.
 Bolton bees exhibited higher abundance levels of Bartonella,
 Bifidobacterium, and Wolbachia, while Mann Lake bees showed increased
 abundance of Commensalibacter. Our results suggest that alpha diversity is
 influenced by the month rather than by the bee strain or storage
 conditions. We also found significant differences in beta diversity by
 month. Overall, taxonomical abundance was not affected by whether the
 hives were stored outside or in constant temperature indoor storage.
 However, various bacterial species showed differences in abundance across
 different months, with slight variations observed between bee strains.
 Given the potential benefits of the honey bee gut microbiome for health
 and nutrition, our data suggests that the genus Lactobacillus may play a
 significant role in bee health during winter and overwintering storage.
description: # Data from: High abundance of lactobacilli in the gut microbiome of honey
 bees during winter
 [https://doi.org/10.5061/dryad.rxwdbrvjf](https://doi.org/10.5061/dryad.rxwdbrvjf) All .qzv file must be downloaded and uploaded to [https://view.qiime2.org/ (opens in new window)](https://view.qiime2.org/)  **alpha_rarefaction(2).qzv:** represents alpha rarefaction- sequences **16Staxabarplots_clean2.qzv:** Relative abundances of the bacteria presented in Honey bee adults **16s_MAPs_GB_H (1).txt:** represents metabarcode sequences used for sequencing **stats-dada2.qzv:** file represents filtered, denoised, merged and non chimeric reads **unweighted_unifrac_emperor.qzv:** A QIIME 2 visualization file displaying beta-diversity analysis using the unweighted UniFrac metric, which measures phylogenetic distances between microbial communities based on the presence or absence of taxa, visualized as an Emperor plot for sample clustering. **jaccard_emperor.qzv:** A QIIME 2 visualization file containing an Emperor plot that represents beta-diversity analysis using the Jaccard distance metric, which measures dissimilarity between microbial communities based on the presence or absence of taxa, and can be viewed using QIIME 2 View. **weighted_unifrac_emperor.qzv: **A QIIME 2 visualization file displaying beta-diversity analysis using the weighted UniFrac metric, which measures phylogenetic distances between microbial communities by considering both the presence and abundance of taxa, visualized as an Emperor plot for sample clustering. This file can be viewed using QIIME 2 View. **Alpha_diversiy_R_file.docx:** An R script performing Generalized Linear Mixed Models (GLMMs) to analyze alpha diversity metrics (e.g., Shannon index) in honey bee gut microbiomes across months and storage status. **alpha_amp.csv: **A CSV file containing alpha diversity metrics (e.g., Observed OTUs, Shannon, Simpson, invSimpson, Chao1, ACE) for each honey bee gut microbiome sample, including metadata such as SampleID, barcode sequence, month, bee type, hive status, and replicate information. This data is used to assess microbial diversity within individual samples. **Species_level_abundance.csv:** This file contains taxonomic abundance data for microbial species identified in the gut microbiome of honey bees (*Apis mellifera*). The data is organized by sample, bee type, month of collection, bee status (e.g., inside or outside the hive), microbial species, and their relative abundance (in percentages).