###### Abstract  
Honey bees face new challenges, ranging from climate crisis to emerging pathogens such as _Vairimorpha (Nosema) ceranae_ that synergistically cause a syndrome designated as colony collapse disorder (CCD). This study employed a metataxonomic approach in order to investigate if _V. ceranae_ affects gut microbiota (bacteria and fungi) of adult _A. mellifera_ honey bees as well as microbiota of bee bread (BB) stored in colonies demonstrating severe _V. ceranae_ infection (spore counts >2,500,000 per bee) as compared with colonies exhibiting very low spore counts (<40,000 per bee). Alpha-diversity analysis revealed an overall decrease in microbial diversity reflected by number of observed unique operating taxonomic units (OTUs) regarding both bacteria and fungi in honey bee and BB samples. Further analysis demonstrated that _Podosphaera_ spp. were absent in BB samples collected from colonies with high spore counts, while relative abundance of _Blumeria_ spp. was significantly decreased. Interestingly, relative abundance of _Rosenbergiella_ spp. was increased in BB samples collected from colonies with high spore counts. The reason for these findings remains elusive. Although further research is warranted, overall reduced microbial diversity and relative abundance of certain microbial groups may serve as biomarkers of colony collapse. Apis mellifera; honey bee; _Vairimorpha (Nosema) ceranae_; Nosemosis; bee bread; microbiota; biomarker +
Footnote †: journal: Accepted: 9 November 2022  
collection, precocious foraging and, most importantly, increased bee mortality [7]. Often, in combination with other stressors, Nosemosis ends in significant colony weakening or to sudden colony collapse. The gut microbiome plays a pivotal role in health and disease of the honey bee, contributing to various functions such as metabolism, immune response, protection against pathogens, growth and development [8]. The hindgut of an _A. mellifera_ adult worker contains a few specialized core bacterial clusters (phylotypes) that are commonly present in other eusocial corobiculate species of bees (other _Apis_ species, stingless bees, bumblebees) [9]. These phylotypes are _Snodgrassella alvi_, _Gilliamella apicola_, the _Bifidobacterium_ cluster group and _Lactobacillus_ Firm-4 and Firm-5. Several other phylotypes have been frequently associated with _A. mellifera_ and the hive environment, though they are not necessarily ubiquitous among all workers in a given colony. This auxiliary bacterium includes _Bartonella apis_, _Frischella perrara_, Alpha 2.2 (known as _Parasacharibacter apium_) and _Commensalibacter_ sp. (also referred to as Alpha 2.1) [9]. Of note is that the structure of the honey bee gut microbiome is variable depending on age and development [10]. Therefore, abundance of several microbial groups is significantly variable in newly emerged bees and nurse bees as compared with adult workers, which are usually the main focus of microbiota surveys [10]. The mycobiome of _A. mellifera_ is less consistent and more diverse across members of the same colony [11]. Recent studies using culture-independent methods revealed that predominant phyla were _Ascomycata_ and _Basidiomycata_[12, 13]. [PERSON] et al. identified _Tremellomycetes_, _Dothideomycetes_ and _Saccharomyces_ as the most abundant classes [12]. Furthermore, these researchers identified sequences associated with the genera _Metschnikowia_, _Alternaria_ and _Clatosporium_ as well as some unspecified members of _Mycosphaerellaceae_ and _Cryptococcus_[12]. Hive-stored bee pollen, also known as bee bread (BB), is collected by forager bees, processed and stored in hive combs, where it undergoes lactic acid fermentation [14]. Chemical and microbial composition of BB depends on several factors, such as botanical origin, climate, season and soil type, as well as the honey bee microbial inoculum. BB is the main source of protein, fatty acids and nutrients for the colony and can also act as a probiotic [15].