Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ 1990, Basic local alignment search tool. Journal of Molecular Biology, 215: 403-410.
Ansaloni, LS, Kristl, J, Domingues, CEC & Gregorc, A 2025, An overview of the nutritional requirements of honey bees (Apis mellifera Linnaeus, 1758). Insects, 16(1): 97, DOI: 10.3390/insects16010097.
Bankevich, A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin, AV, Sirotkin, AV, Vyahhi, N, Tesler, G & Alekseyev, MA 2012, Pevzner PASPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19: 455-477.
Blin, K, Shaw, S, Augustijn, HE, Reitz, ZL, Biermann, F, Alanjary, M, Fetter, A, Terlouw, BR, Metcalf, WW, Helfrich, EJN, van Wezel, GP, Medema, MH, Weber, T 2023, antiSMASH 7.0: New and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Research, 51(W1): W46-W50, DOI: 10.1093/nar/gkad344.
Bolger, AM, Lohse, M & Usadel, B 2014, Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15): 2114-2120, DOI: 10.1093/bioinformatics/btu170.
Gaggìa, F, Jakobsen, RR, Alberoni, D, Baffoni, L, Cutajar, S, Mifsud, D, Nielsen, DS, Di Gioia, D 2023, Environment or genetic isolation? An atypical intestinal microbiota in the Maltese honey bee Apis mellifera spp. ruttneri. Frontiers in Microbiology, 14: 1127717, DOI: 10.3389/fmicb.2023.1127717
Gupta, R & Gaur, S 2025, Effect of diet and lifestyle on microbiome composition. International Review of Cell and Molecular Biology, 395: 157-174, DOI: 10.1016/bs.ircmb.2024.12.008.
Jabal-Uriel, C, Alba, C, Higes, M
et al. 2022, Effect of
Nosema ceranae infection and season on the gut bacteriome composition of the European honeybee (
Apis mellifera).
Scientific Reports, 12: 9326,
https://doi.org/ 10.1038/s41598-022-13337-4.
Kanehisa, M & Sato, Y 2020, KEGG Mapper for inferring cellular functions from protein sequences. Protein Science, 29(1): 28-35, DOI: 10.1002/pro.3711.
Kearse, M, Moir, R, Wilson, A, Stones-Havas, S, Cheung, M, Sturrock, S, Buxton, S, Cooper, A, Markowitz, S, Duran, C, Thierer, T, Ashton, B, Meintjes, P, Drummond, A 2012, Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28(12): 1647-1649, DOI: 10.1093/bioinformatics/bts199.
Liberti J, Kay T, Quinn A, Kesner L, Frank ET, Cabirol A, Richardson TO, Engel P, Keller L. The gut microbiota affects the social network of honeybees. Nat Ecol Evol. 2022 Oct;6(10):1471-1479. DOI: 10.1038/s41559-022-01840-w.
Liu, Y, Chen, J, Lang, H, Zheng, H 2022, Bartonella choladocola sp. nov. and Bartonella apihabitans sp. nov., two novel species isolated from honey bee gut. Systematic and Applied Microbiology, 45(6): 126372, DOI: 10.1016/j.syapm.2022.126372.
Liu, J-p, Zhou, Q, Zhang, C, Wu, Y, Ma, X-j, Qi, R 2025, Pan-genome classification of the virulence spectrum of Bartonella and the variation of heme-binding protein virulence factor in isolates from the Tibetan Plateau. Microbiology Spectrum, 13(12): e0046525, DOI: 10.1128/spectr.
Luo, YY, Yu, D, Zhang, HZ, Liu, ZX, Hong, RD, Hong, M, Ai, ZQ, Zhu, JJ, Yin, JX 2023, Molecular detection of Bartonella species in wild small mammals in western Yunnan Province, China. Frontiers in Veterinary Science, 10: 1301316, DOI: 10.3389/fvets.2023.1301316.
Moran, NA, McCutcheon, JP & Nakabachi, A 2008, Genomics and evolution of heritable bacterial symbionts. Annual Review of Genetics, 42: 165-90, DOI: 10.1146/annurev.genet.41.110306.
Moran, NA 2002, Microbial minimalism: genome reduction in bacterial pathogens. Cell, 108(5): 583-586, DOI: 10.1016/s0092-8674(02)00665-7.
Motta, EVS, Mak, M, De Jong, TK, Powell, JE, O'Donnell, A, Suhr, KJ, Riddington, IM, Moran, NA 2020, Oral or topical exposure to glyphosate in herbicide formulation impacts the gut microbiota and survival rates of honey bees. Applied and Environmental Microbiology, 86(18): e01150-20, DOI: 10.1128/AEM.01150-20.
Nakayama, T, Harada, R, Yabuki, A, Nomura, M, Shiba, K, Inaba, K, Inagaki, Y 2025, Marked genome reduction driven by a parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate. Microbes and Environments, 40(2): ME25005, DOI: 10.1264/jsme2.ME25005.
Prasad, A, Pallujam, AD, Siddaganga, R
et al. 2025, Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.
Nature Communications, 16: 9069,
https://doi.org/10.1038/s41467-025-64115-5.
Ruiz-Perez, CA, Conrad, RE & Konstantinidis, KT 2021, MicrobeAnnotator: A user-friendly, comprehensive functional annotation pipeline for microbial genomes.
BMC Bioinformatics, 22: 11,
https://doi.org/10.1186/ s12859-020-03940-5.
Schadron, T, van den Beld, M, Mughini-Gras, L, Franz, E 2024, Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis. Frontiers in Microbiology, 15: 1460335, DOI: 10.3389/fmicb.2024.1460335.
Sachs, JL, Essenberg, CJ & Turcotte, MM 2011, New paradigms for the evolution of beneficial infections. Trends in Ecology & Evolution, 26(4): 202-209, DOI: 10.1016/j.tree.2011.01.010.
Segers, FH, Kešnerová, L, Kosoy, M, Engel, P 2017, Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen. ISME Journal, 11(5): 1232-1244, DOI: 10.1038/ismej.2016.201.
Sonenshine, DE & Stewart, PE 2021 Nov 25, Microbiomes of blood-feeding arthropods: Genes coding for essential nutrients and relation to vector fitness and pathogenic infections. A review. Microorganisms, 9(12): 2433, DOI: 10.3390/microorganisms9122433.
Tatusova, T, DiCuccio, M, Badretdin, A, Chetvernin, V, Nawrocki, EP, Zaslavsky, L, Lomsadze, A, Pruitt, KD, Borodovsky, M & Ostell, J 2016, NCBI prokaryotic genome annotation pipeline. Nucleic Acids Research, 44(14): 6614-6624, DOI: 10.1093/nar/gkw569.
Weiland-Bräuer, N 2021, Friends or Foes-Microbial Interactions in Nature. Biology (Basel). 10(6): 496, DOI: 10.3390/biology10060496.
Wolf, YI & Koonin, EV 2013, Genome reduction as the dominant mode of evolution. Bioessays. 35(9): 829-837, DOI: 10.1002/bies.201300037.
Xu, M, Guo, L, Gu, S, Wang, O, Zhang, R, Peters, BA, Fan, G, Liu, X, Xu, X, Deng, L & Zhang, Y 2020, TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads. Gigascience, 9(9): giaa094, DOI: 10.1093/gigascience/giaa094.
Zientz, E, Silva, FJ & Gross, R 2001, Genome interdependence in insect-bacterium symbioses. Genome Biology, 2(12): Reviews1032, DOI: 10.1186/gb-2001-2-12-reviews1032.