DOI: 10.5061/dryad.n5tb2rbz1
title: Supplementary tables for Honey Bee symbiont buffers larvae against nutritional stress and supplements lysine

description: Honey bees have suffered dramatic losses in recent years, largely due to
 multiple stressors underpinned by poor nutrition. Nutritional stress
 especially harms larvae, who mature into workers unable to meet the needs
 of their colony. In this study, we characterize the metabolic capabilities
 of a honey bee larvae-associated bacterium, Bombella apis (formerly
 Parasaccharibacter apium), and its effects on the nutritional resilience
 of larvae. We found that B. apis is the only bacterium associated with
 larvae that can withstand the antimicrobial larval diet. Further, we found
 that B. apis can synthesize all essential amino acids and significantly
 alters the amino acid content of synthetic larval diet, largely by
 supplying the essential amino acid lysine. Analyses of gene gain/loss
 across the phylogeny suggest that four amino acid transporters were gained
 in recent B. apis ancestors. In addition, the transporter LysE is
 conserved across all sequenced strains of B. apis. Finally, we tested the
 impact of B. apis on developing honey bee larvae subjected to nutritional
 stress and found that larvae supplemented with B. apis are bolstered
 against mass reduction despite limited nutrition. Together, these data
 suggest a novel role of B. apis as a nutritional mutualist of honey bee
 larvae.
description: To define orthologs, protein sequences were extracted from NCBI
 annotated sequence files for the listed accesions (Supplementary Table 3).
 Reciprocal best BLAST hits were calculated, and genes clustered into
 ortholog groups using complete linkage. Conserved core orthologs were used
 to generate the species tree for these genera and this was used, in
 conjunction with GLOOME to infer branch-specific gene gain/loss events
 (Supplementary Table 2). To define presence/absence of amino acid
 biosynthesis genes (Supplementary Table 1), ortholog representatives were
 run against GapMind to find amino acid biosynthetic genes in the
 proteomes. Additionally, annotation based on NCBI’s PGAP was used, in
 conjunction with DOE’s IMG/M, to confirm the putative function of
 orthologous groups of genes.
description: Supplementary Table 1 – All sequenced <em>B.
 apis</em> strains retain the ability to synthesize all amino acids.
 Table generated from conserved core orthologs across the included strains
 showing presence/absence of amnio acid biosynthesis genes. ‘oid’ refers to
 the ortholog ID in our analysis of orthologous genes, ‘Name’ refers to the
 amino acid biosynthesis gene annotation, ‘Pathways/steps/scores’ refers to
 the biosynthetic pathway in which each gene is found, the enzymatic step
 in the pathway, and the GapMind score. GapMind score is either 2 (high
 confidence), 1 (medium confidence), or 0 (low confidence). In the columns
 below each sequenced strain, ‘1’ means that a given gene was identified in
 the corresponding genome and ‘0’ means that it was not
 identified. Supplementary Table 2- All <em>B.
 apis</em> genomes contain multiple cationic amino acid transporter
 orthologs. Gene gain/loss analysis showing all the gains and losses across
 the phylogeny of all sequenced <em>B. apis</em> strains and
 related microbes in Figure 3. ‘oid’ refers to the ortholog ID in our
 analysis of orthologous genes, ‘Name’ refers to proteins identified across
 all genomes analyzed. In the columns below each sequenced strain, ‘g’
 means that a given gene was gained by that strain and ‘l’ means that it
 was lost. Supplementary Table 3 – Accession numbers for
 all sequenced strains used in this work.