DOI: 10.5061/dryad.cnp5hqcdv
title: Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut

description: The maintenance of bacterial diversity at both species- and strain-levels
 is crucial for the sustainability of honey bee gut microbiota and host
 health. Periodic or random fluctuation in diet typically alters the
 metabolic niches available to gut microbes, thereby continuously reshaping
 bacterial diversity and interspecific interactions. It remains unclear how
 closely related bacteria adapt to these fluctuations and maintain
 coexistence within the bee gut. Here, we demonstrate that the five
 predominant Gilliamella species associated with Apis cerana, a widely
 distributed Asiatic honey bee, have diverged in carbohydrate metabolism to
 adapt to distinct nutrient niches driven by dietary fluctuation.
 Specifically, the glycan-specialists gain improved growth on a pollen-rich
 diet, but are overall inferior in competition to non-glycan-specialist on
 either a simple sugar or sugar-pollen diet, when co-inoculated in the bee
 host and transmitted across generations. Strikingly, despite of their
 disadvantage in a high-sugar condition, the glycan-specialists are found
 prevalent in natural A. cerana guts. We further reveal that these bacteria
 have adopted a life history strategy characterized by high biomass yield
 on a low-concentration sugar diet, allowing them to thrive under poor
 nutritional conditions, such as when the bee hosts undergo periodical
 starvation. Transcriptome analyses indicate that the divergence in life
 history strategies is attributed to gene expression programming rather
 than genetic variation. This study highlights the importance of
 integrative metabolic strategies in carbohydrate utilization, which
 facilitate the coexistence of closely related Gilliamella species in a
 changing bee gut environment.
description: # Life history strategies complement niche partitioning to support the
 coexistence of closely related *Gilliamella* species in the bee gut
 [https://doi.org/10.5061/dryad.cnp5hqcdv](https://doi.org/10.5061/dryad.cnp5hqcdv) ## Description of the data and file structure This repository is associated with Yang C, Han B, Tang J, Hu J, Qiu L, Cai W, Zhou X, Zhang X, Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut, The ISME Journal, 2025; wraf016, [https://doi.org/10.1093/ismejo/wraf016](https://doi.org/10.1093/ismejo/wraf016) This repository contains the raw data necessary to produce all associated figures behind the publication. ### Files and variables #### File: FigureData.xlsx **Description:** This files contains all raw data for the figures in the main text and supplementary materials. Each sheet in the file is named after the figure of which it contains the raw data.  ##### Variables * Fig1A: Matrix of identities of 16S rRNA enes between pairs of strains of Gilliamella associated to Apis cerana. Column "Strain" gives the Gilliamella strain name. * Fig1CD: Matrix of the pairwise average nucleotide identity (ANI) of Gilliamella strains. Column "Strain" gives the Gilliamella strain name. * Fig1EF: Matrix of the Jaccard similarity coefficient based on the pairwise gene content. Column "Strain" gives the Gilliamella strain name. * Fig1G: Percentage of A. cerana individuals across China and Japan harboring multiple Gilliamella species Column "No. of Gilliamella species" gives the number of Gilliamella strains in the gut of individual bee Column "No. of individual" gives the the corresponding number of honey bees. Column "Proportion (%)" gives the the proportion of bees containing the corresponding number of Gilliamella strains in total bees Column "Country" gives the country where the honey bees were collected. The component of Gilliamella species in each A. cerana gut microbiome see sheet "FigS1". * Fig2Aleft: Prevalence of genes essential to sugar utilization among strains of each Gilliamella species, if one of the genes in a pathway is missing, that is, the prevalence is 0, the species will be considered unable to metabolize the sugar. Check data S2 for the occurrence of full carbohydrate utilization gene profiles. Column "Sugar" gives the sugar name. Column "CAZy/gene" gives the genes essential to sugar utilization. Column "GA1_B2776" to "GA5_B3788" give the prevalence of genes among strains of each Gilliamella species. * Fig2Aright: The carrying capacity of the type strains of each Gilliamella species cultured in a carbohydrate-free heart infusion agar (cfHIA) medium containing 10 mM of the defined sugar as carbon source. Column "Sugar" gives the sugar name. Column "GA1_B2776" to "GA5_B3788" give the bacterial biomass measured by optical density at 600 nm (OD600) and averaged from 3 biological replicates. * Fig2C: The carrying capacity of the type Gilliamella strains cultured in cfHIA medium with a gradient concentration of homogalacturonan (HG). Column "Sugar" gives the sugar name. Column "Con. of sugar" gives the sugar concentration. Column "GA1_B2776" to "GA5_B3788" give the bacterial biomass measured by optical density at 600 nm (OD600) and averaged from 3 biological replicates. * Fig3B: The relative abundance (%) of each type strain under the sucrose only diet. Column "SampleID" gives the honey bee sample ID. Column "Time (d)" gives the days post colonization. Column "GA1_B2776" to "GA5_B3788" give the relative abundance (%) of each type strain. * Fig3C: The relative abundance (%) of each type strain under the sucrose and pollen diet. Column "SampleID" gives the honey bee sample ID. Column "Time (d)" gives the days post colonization. Column "GA1_B2776" to "GA5_B3788" give the relative abundance (%) of each type strain. The relative abundance (%) of each type strain showed in Fig3BC is calculated by the function of READS(species)/READS(G)*100, where READS(species) represents the number of reads mapped to the focal species and READS(G) represents the number of reads mapped to all Gilliamella.  * Fig3D: The absolute abundance of each Gilliamella strain between two different dietary regimes on Day 10. Column "SampleID" gives the honey bee sample ID. Column "Diet" gives the dietary regimes. Column "GA1_B2776" to "GA5_B3788" give the absolute abundance of each type strain. The absolute abundance of each Gilliamella type strains showed in Fig3D is calculated by multiplying the relative abundance of each species by the total number of Gilliamella cells detected by qPCR. * Fig3E: Cell density measured by fluorescence intensity of GA1_B2776::gfp and GA5_B3788::rfp under a sucrose or GalA medium Column "Sugar" gives the sugar medium. Column "Method" gives the methods of culture. Column "Strain" gives the experimental strain. Column "Time (h)" gives bacterial culture time in hour. Column "Fluorescence intensity" gives the fluorescence intensity of fluorescent proteins expressed by each strain. * Fig3G: The absolute abundances of strain GA1_B2776 and GA5_B3788 under either dietary regimes. Column "Diet" gives the dietary regimes. Column "Cell count" gives the absolute abundances of strain GA1_B2776 and GA5_B3788 under either dietary conditions. Column "Relative abundance (%)" gives the relative abundances (%) of strain GA1_B2776 and GA5_B3788 under either dietary conditions. * Fig3H: The absolute abundances of the wild-type and GalA-mutant strain of GA1_B2776 under either dietary conditions. Column "Diet" gives the dietary regimes. Column "Cell count" gives the absolute abundances of the wild-type and GalA-mutant strain of GA1_B2776 under either dietary conditions. Column "Relative abundance (%)" gives the relative abundances (%) of the wild-type and GalA-mutant strain of GA1_B2776 under either dietary conditions. The cell count per gut is determined using the qPCR method and the strain-specific gene primers (listed in table S1). The relative abundance (%) of each type strain showed in Fig3GH is calculated by dividing the cell count of each strain by the total cell count of both strains per gut. * Fig4A: The relative growth of GA1_B2776 and GA5_B3788 in co-culture compared to their mono-culture. Column "GA1_B2776" gives the relative growth of GA1_B2776 in co-culture compared to its mono-culture. Column "GA5_B3788" gives the relative growth of GA5_B3788 in co-culture compared to its mono-culture. The relative growth is calculated by the function of AUC (co-culture) / AUC (mono-culture), AUC is the area under the growth curve. * Fig4B: Interactions between GA1_B2776 and GA5_B3788 in cfHIA medium with 10 mM sucrose. Column "Interaction strength" gives the interactions between GA1_B2776 and GA5_B3788 in cfHIA medium with 10 mM sucrose. Column "Pvalue" gives significance. Interaction strength is calculated by the function of log10 (AUC [co-culture] / AUC [mono-culture]), and the AUC value see sheet "AUC". A Student’s t-test was used to calculate the significance of the interaction. * Fig4D: The absolute abundances of GA_1B2776 and GA5_B3788 in mono- or co-colonized bees. Column "Method" gives the methods of inoculation. Column "Strain" gives the experimental strain. Column "Cell count" gives the absolute abundances of strain GA1_B2776 and GA5_B3788 under either inoculation conditions. * Fig4F: The absolute and relative abundances of GA1_B2776 and GA5_B3788 over three passages. Column "Passage" gives the number of generation. Column "Cell count" gives the absolute abundances of strain GA1_B2776 and GA5_B3788 in each passage. Column "Relative abundance (%)" gives the relative abundances of strain GA1_B2776 and GA5_B3788 in each passage. * Fig4G: The relative growth of GA1_B2776 and GA5_B3788 in co-culture compared to their mono-culture in cfHIA medium supplemented with 10 mM of a defined simple sugar. Column "Sugar" gives the sugar medium. Column "GA1_B2776" gives the relative growth of GA1_B2776 in co-culture compared to its mono-culture. Column "GA5_B3788" gives the relative growth of GA5_B3788 in co-culture compared to its mono-culture. * Fig4H: Interactions between GA1_B2776 and GA5_B3788 in cfHIA medium with 10 mM of a defined simple sugar. Column "Sugar" gives the sugar medium. Column "Interaction strength" gives the interactions between GA1_B2776 and GA5_B3788 in cfHIA medium with 10 mM sucrose. Column "Pvalue" gives significance. The Interaction strength and Pvalue were calculated as Fig4AB. * Fig5BC: The absolute (B) and relative (C) abundances (%) of GA1_B2776 and GA5_B3788 cultured in a sucrose solution of a high (50% w/v) or low (10% w/v) concentration measured on day 5. Column "Con. of suc (%, w/v)" gives the concentration of sucrose. Column "Cell count" gives the absolute abundances of strain GA1_B2776 and GA5_B3788 under different sucrose concentrations. Column "Relative abundance (%)" gives the relative abundances of strain GA1_B2776 and GA5_B3788 under different sucrose concentrations. * Fig5D: The growth traits of the Gilliamella type strains, including carrying capacity and maximum growth rates, across all common sugar substrates. Column "Feature" gives the growth traits. Column "Sugar" gives the sugar medium. Column "GA1_B2776" to "GA5_B3788" give the value of each feature for each type strain. The growth yields and maximum growth rates were determined from the growth curves of monoculture in cfHIA media containing defined sugars see sheet FigS2.  * Fig5E: Relative abundance of Gilliamella species in wild bees collected in summer or winter. Column "Season" gives the season in which the honey bees were collected. Column "SampleID" gives the honey bee sample ID. Column "GA1_B2776" to "GA5_B3788" give the relative abundance (%) of each type strain in honey bee gut. The relative abundances of each Gilliamella species in the gut were quantified using amplicon sequencing of the frr gene. * Fig5F: Differentially expressed genes between strain GA1_B2776 and GA5_B3788. Column "GeneID" gives the geneID presented by GA5_B3788. Column "gene_name" gives the gene name. Column "log2FoldChange" gives the log2(FoldChange) of the differentially expressed genes. Column "pvalue" gives the P value. Column "padj" gives the adjusted p-values using the Benjamini and Hochberg’s approach. Column "GA1_B2776" gives the normalized read count of GA1_B2776. Column "GA5_B3788" gives the normalized read count of GA5_B3788. * Fig5G: KEGG pathways significantly enriched from differentially expressed genes of GA1_B2776 and GA5_B3788. Column "ID" gives the KEGG pathway ID. Column "Description" gives the description of KEGG pathway. Column "Gene ratio" gives the number of differential genes enriched in this pathway/all the differential genes that can be enriched in KEGG. Column "BgRatio" gives the total number of genes in the pathway/the total number of genes in the species with KEGG information Column "pvalue" gives gives the P value. Column "padj" gives the adjusted p-values using the Benjamini and Hochberg’s approach. Column "qvalue" gives the multitested p value Column "geneID" gives the ID presented by GA5_B3788 of the gene enriched in the pathway. Column "Count" gives the count of genes in a pathway. Column "Enrichment" gives the pathway enriched in strain GA1_B2776 or GA5_B3788. The orthologous gene ID of the two strains is indicated by that in GA5_B3788. Information of the orthologous genes see sheet "Orthologous genes". * FigS1: Component of Gilliamella species in Apis cerana gut microbiome. Column "SampleID" gives ID of the honey bee sample. Column "Country" gives the country where the honey bees were collected. Column "GA1" to "GA5" give the relative abundance (%) of each Gilliamella species in honey bee gut. The relative abundances of each Gilliamella species in the gut microbiome were quantified using MIDAS from metagenomic sequencing data. * FigS2: Growth curves of the type strains of each Gilliamella species. Column "Sugar" gives the sugar medium. Column "Time (h)" gives bacterial culture time in hour. Column "GA1_B2776" to "GA5_B3788" give the bacterial biomass measured by optical density at 600 nm (OD600) of three technical replicates per conditionfor for each type strain. * FigS3C: The carrying capacity of the type Gilliamella strains cultured in cfHIA medium with a gradient concentration of galacturonic acids (GalA). Column "Sugar" gives the sugar name. Column "Con. of sugar" gives the sugar concentration. Column "GA1_B2776" to "GA5_B3788" give the bacterial biomass measured by OD600 and averaged from 3 biological replicates. * FigS4: Absolute abundance of Gilliamella type strains inoculated in microbiome-depleted (MD) bee guts under either a sucrose-only or a sucrose and pollen diet. Column "Diet" gives the dietary regimes. Column "Strain" gives the Gilliamella type strain. Column "Cell count" gives the absolute abundances of type strains under either inoculation conditions. * FigS5A: Cell density of wild-type strain GA1_B2776 grown in spent media of GA1_B2776 and GA5_B3788 mono- or co-cultures. Column "Sugar" gives the sugar medium. Column "Medium" gives the spent medium. Column "Time (h)" gives bacterial culture time in hour. Column "GA1_B2776" gives the bacterial biomass measured by optical density at 600 nm (OD600) of three technical replicates per conditionfor for strain GA1_B2776. * FigS6A: The relative expression (FPKM) of genes related to flagella assembly between strain GA1_B2776 and GA5_B3788. Column "GeneID" gives the geneID presented by GA5_B3788. Column "gene_name" gives the gene name. Column "GA1_B2776" gives the relative expression of flagella assembly genes in GA1_B2776. Column "GA5_B3788" gives the relative expression of flagella assembly genes in GA5_B3788. * FigS6C: Motility diameter comparison between GA1_B2776 and GA5_B3788 Column "GA1_B2776" gives motility diameter of GA1_B2776 on HIA agar plates with 0.4% w/v agar. Column "GA5_B3788" gives motility diameter of GA5_B3788 on HIA agar plates with 0.4% w/v agar. * AUC: The area under growth curves (AUC) calculated from growth curve. Column "Sugar" gives the sugar medium. Column "Mono-culture" gives the AUC value of strain GA1_B2776 and GA5_B3788 in mono-culture. Column "Co-culture" gives the AUC value of strain GA1_B2776 and GA5_B3788 in co-culture. * Barcode: The barcode sequences used for demultiplex reads from a pooled sequencing sample, the sequencing data have been submitted to NCBI under BioProject PRJNA1134693. Column "SampleID" gives the ID of each sample. Column "Barcode" gives the sequences of the 6-bp barcode. Column "Sequencing sample" gives the sequencing sample ID which typically a mixed sample. Column "BioProject" gives the BioProject No. of the sequencing data submitted to NCBI. * Orthologous genes: The orthologs found by OrthoFinder.  Column "OG_id" gives the ID of orthologs. Column "GA1_B2776_id" gives the gene ID of GA1_B2776. Column "GA5_B3788_id" gives the gene ID of GA5_B3788. #### File: Dataset\_S1.xlsx **Description:** This file contains the whole genome informations on Gilliamella related to the genera Apis and Bombus, as well as other bacterial species as outgroups in the phylogenetic tree. ##### Variables Column "Genus" gives genus name of bacteria. Column "Species" gives species name of bacteria. Column "Strain" gives strain name of bacteria. Column "Host" gives species name of the bacterial host. Column "Size/Mbp" gives bacterial genome size in Mbp. Column "Contig" gives number of contigs. Column "Accession" gives NCBI accession number. #### File: Dataset\_S2.xlsx **Description:** This file contains the carbohydrate utilization gene profiles of Gilliamella related to A. cerana. The genome were annotated using CAZyme, MetaCyc and KEGG database, and the carbohydrate utilization pathways of Gilliamella were ultimately constructed based on these three gene sets. ##### Variables Column "Pathway" gives the carbohydrate utilization pathways Column "EC" gives the EC number. Column "B2737" to "B3835" gives the number of metabolic enzyme genes. #### File: Dataset\_S3.xlsx **Description:** This file contains the sample information of adult worker bees collected in one apiary in Qinghai. ##### Variables Column "SampleID" gives the honey bee sample ID. Column "Species" gives species name of the collected honey bee. Column "Colletion time" gives sample collection date. Column "Country" gives the country where the honey bees were collected. Column "Province" gives the province where the honey bees were collected. Column "City" gives the city where the honey bees were collected. Column "County" gives the county where the honey bees were collected. Column "Latitude" gives the latitude of the collection site. Column "Longitude" gives the longitude of the collection site. Column "Altitude/m" gives the altitude of the collection site in m. Column "Season" gives the season in which the honey bees were collected. #### File: Dataset\_S4.xlsx **Description:** This file contains the differentially expressed genes bewteen strain GA1_B2776 and GA5_B3788 which were analyzed using the R package ‘DESeq2’ (v.1.20.0). ##### Variables Column "Gene_id" gives the gene ID presented by GA5_B3788. Column "gene" gives the gene name. Column "description" gives the description of gene. Column "log2FoldChange" gives the log2(FoldChange) of the differentially expressed genes. Column "pvalue" gives the P value. Column "padj" gives the adjusted p-values using the Benjamini and Hochberg’s approach. #### File: Alignment\_and\_Trees.zip **Description:** This file contains six files, including a non-redundant sequence alignment file named core_gene_alignment.aln.reduced, and five files containing raw data of phylogenetic tree, named RAxML_bestTree.core_gene_alignment_outgroup_209.tree, RAxML_bipartitions.core_gene_alignment_outgroup_209.tree, RAxML_bipartitionsBranchLabels.core_gene_alignment_outgroup_209.tree, RAxML_bootstrap.core_gene_alignment_outgroup_209.tree, RAxML_info.core_gene_alignment_outgroup_209.tree. The file core_gene_alignment.aln.reduced were used to construct a maximum-likelihood phylogeny using RAxML (version 8.2.12; option ‘-m GTRGAT’). Fig1C showed the result file of RAxML_bipartitions.core_gene_alignment_outgroup_209.tree, which was visualized using iTOL (version 6.8.1). ## Code/software * The orthologs were found by OrthoFinder v2.5.5.  * The scripts for sequencing analysis are available on Github ([https://github.com/cfyang911007](https://github.com/cfyang911007)). ## Access information Other publicly accessible locations of the data: * The sequencing data have been submitted to NCBI ([https://www.ncbi.nlm.nih.gov](https://www.ncbi.nlm.nih.gov)),under BioProject PRJNA1134693, including RNA-seq and marker gene amplicon sequences used in this study. Data was derived from the following sources: * Bacterial genomes used for the phylogeny and carbohydrate metabolism analysis were download from NCBI the accession numbers see Dataset_S1.xlsx.