This study explores the microbiome of the ant Formica exsecta, and compares this to the microbiome found in the nest material. We found fundamental differences in both the bacterial and the fungal communities between ants and their nest material, but no significant differences in the bacterial and fungal communities among colonies. Species diversity, species richness, and evenness were all significantly lower for bacteria in ants than in nest material, whereas for fungi only species richness was lower in ants, than in nest material. No such differences were found among ants from diffrent colonies.

We sampled F. exsecta workers from six colonies in the Tvärminne archipelago SW Finland, each on 2-4 occasions in different years between June 2011 and August 2015, in total 18 samples consisting of ~15 ants each. Within the same time frame, we also collected nest material from five of these colonies, with one colony represented by two samples taken in different years. Extracted DNA was submitted to Illumina MiSeq sequencing. Preparation of libraries, sequencing and bioinformatics pipeline were done according to (Lindström et al., 2018, PeerJ 6: e5289.). The reads were filtered and OTUs clustered (at 97% identity) using UPARSE v.8.1 (Edgar, 2013, Bioinformatics 34: 2371–2375; Edgar and Flyvbjerg, 2015, Bioinformatics 31: 3476–3482). The SILVAv132 (Quast et al., 2013, Nucleic Acids Res 41: 590–6), and the UNITE v7.2 (Kõljalg et al., 2013, Mol Ecol 22: 5271–5277) databases were used as reference for the alignment of the bacterial and fungal sequences, respectively. For taxonomic classification, we used the RDP16s training set 16 v2.12  (bacteria) (Wang et al., 2007, Appl Environ Microbiol 73: 5261–7), and RDP ITS Warcup training set v4 (fungi) (Deshpande et al., 2016, Mycologia 108: 1–5). 

Four files, two each for bacteria and fungi, one of which contains data for ant samples alone, and one data from ants and their corresponding nest material

All files provide rarefied reads for prokaryotes or fungi, respectively, identified in the Ant&Nest and Ant Data. The taxonomic (nomenclature) and systematic position of the bacterial samples were determined based on LPSN (List of Prokaryotic names with Standing in Nomenclature) https://lpsn.dsmz.de/, and those of the fungal samples were based on MycoBank (https://www.mycobank.org/ (both accessed 19.12 2021).  The taxonomical and systematic assignment should be considered tentative, as these are in many cases likely to change when new data become available, and phylogenetic relationships are resolved or updated.      

Candidate bacterial phyla, which have not been validly published according to the list are indicated with apostrophes (""). Taxa indicated in boldface in the Ant&Nest data were absent in the Ant data, and vice versa.

In the Ant&Nest data low counts of eukaryotes (Streptophyta, Cercozoa, Chlorophyta, Ochrophyta), and Cyanobacteria were found in addition to bacteria. In the Ant data eukaryotic plant material (Streptophyta) was found in modest counts in a few samples, and green algae (Bacillariophyta) in very low counts. These are not included in the files.