Al Kassaa I, Hober D, Hamze M, Chihib NE, Drider D (2014) Antiviral potential of lactic acid bacteria and their bacteriocins. Probiotics Antimicrob Proteins 6:177–185
CAS
PubMed
Google Scholar
Aljedani DM, Almehmadi RM (2016) Effects of some insecticides on longevity of the foragers honey bee worker of local honey bee race Apis mellifera jemenatica. Electr Phys 8:1843–1849
Google Scholar
Anderson KE, Sheehan TH, Eckholm BJ, Mott BM, Degrandi-Hoffman G (2011) An emerging paradigm of colony health: microbial balance of the honey bee and hive (Apis mellifera). Insect Soc 58:431
Google Scholar
Anderson KE, Ricigliano VA, Mott BM, Duan CC, Floyd A, SMaes P (2018) The queen’s gut refines with age: longevity phenotypes in a social insect model. Microbiome 6:108
PubMed
PubMed Central
Google Scholar
Andrea T, Daniele M, Chiara G, Alessandro Z, Lidia S, Matteo M, Linda V, Vincenzo G (2012) Assessment of the environmental exposure of honeybees to particulate matter containing neonicotinoid insecticides coming from corn coated seeds. Environ Sci Technol 46:2592
Google Scholar
Ararso Z, Ma C, Qi Y, Feng M, Han B, Hu H, Meng L, Li J (2018) Proteome comparisons between hemolymph of two honeybee strains (Apis mellifera ligustica) reveal divergent molecular basis in driving hemolymph function and high royal jelly secretion. J Proteome Res 17:402–479
CAS
PubMed
Google Scholar
Barroso As VR, Puerta F, Molero F, Vjm S (2019) Immune related genes as markers for monitoring health status of honey bee colonies. BMC Vet Res 15:72
Google Scholar
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Gordon JI (2011) Global patterns of 16s rrna diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA 108:4516–4522
CAS
PubMed
Google Scholar
Chi L, Yao M, Stegen JC, Rui J, Li J, Li X (2017) Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse. Sci Rep 7:17492
Google Scholar
Crowther LP, Wright DJ, Richardson DS, Carvell C, Bourke AFG (2019) Spatial ecology of a range-expanding bumble bee pollinator. Ecol Evol 9:986–997
PubMed
PubMed Central
Google Scholar
Dai P, Yan Z, Ma S, Yang Y, Wang Q, Hou C, Wu Y, Liu Y, Diao Q (2018) The herbicide glyphosate negatively affects midgut bacterial communities and survival of honey bee during larvae reared in vitro. J Agric Food Chem 66:7786–7793
CAS
PubMed
Google Scholar
Dolezal AG, Jimena C-T, Judd TM, Miller WA, Bonning BC, Toth AL (2019) Interacting stressors matter: diet quality and virus infection in honeybee health. Roy Soc Open Sci 6:181803
CAS
Google Scholar
Dong ZX, Li HY, Chen YF, Wang F, Deng XY, Lin LB, Zhang QL, Li JL, Guo J (2020) Colonization of the gut microbiota of honey bee (Apis mellifera) workers at different developmental stages. Microbiol Res 231:126370
CAS
PubMed
Google Scholar
Dormann CF, Oliver S, Arens P, Augenstein I, St A, Debra B, Baudry J, Billeter R, Bugter R, Bukácek R (2008) Prediction uncertainty of environmental change effects on temperate European biodiversity. Ecol Lett 11:235–244
PubMed
Google Scholar
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460
CAS
PubMed
Google Scholar
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996
CAS
PubMed
Google Scholar
Edgar RC, Haas BJ, Clemente JC, Christopher Q, Rob K (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194
CAS
PubMed
PubMed Central
Google Scholar
Ellegaard KM, Tamarit D, Javelind E, Olofsson TC, Andersson SGE, Vásquez A (2015) Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut. BMC Genom 16:284
Google Scholar
Emery O, Schmidt K, Engel P (2017) Immune system stimulation by the gut symbiont Frischella perrara in the honey bee (Apis mellifera). Mol Ecol 26:2576–2590
CAS
PubMed
Google Scholar
Engel P, Martinson VG, Moran NA (2012) Functional diversity within the simple gut microbiota of the honey bee. P Natl Acad Sci USA 109:11002–11007
CAS
Google Scholar
Engel P, Kwong W, Mcfrederick Q, Anderson K, Barribeau S, Chandler J, Scott Cornman R, Dainat J, De Miranda J, Doublet V, Emery O, Evans J, Farinelli L, Flenniken LM, Granberg F, Grasis J, Gauthier L, Hayer J, Koch H, Dainat B (2016) The bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions. MBio 7:e02164–e2215
CAS
PubMed
PubMed Central
Google Scholar
Evans JdAK, Yp C, Hetru C, Jl I, Jiang H, Kanost M, Gj T, Zou Z, Hultmark D (2006) Immune pathways and defence mechanisms in honey bees Apis mellifera. Insect Mol Biol 15:645–656
CAS
PubMed
PubMed Central
Google Scholar
Galbraith DA, Fuller ZL, Ray AM, Brockmann A, Frazier M, Gikungu MW, Jfi M, Kapheim KM, Kerby J, TKocher SD (2018) Investigating the viral ecology of global bee communities with high-throughput metagenomics. Sci Rep 8:8879
PubMed
PubMed Central
Google Scholar
Guo J, Wu J, Chen Y, Evans JD, Dai R, Luo W, Li J (2015) Characterization of gut bacteria at different developmental stages of Asian honey bees, Apis cerana. J Invertebr Pathol 127:110–114
PubMed
Google Scholar
Huang SK, Ye KT, Huang WF, Ying BH, Su X, Lin LH, Li JH, Chen YP, Li JL, Bao XL, Hu JZ (2018) Influence of feeding type and nosema ceranae infection on the gut microbiota of Apis cerana workers. mSystems 3:e00177–e218
CAS
PubMed
PubMed Central
Google Scholar
Jia HR, Dai PL, Geng LL, Jack CJ, Li YH, Wu YY, Diao QY, Ellis JD (2017) No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae). Sci Rep 7:41688
CAS
PubMed
PubMed Central
Google Scholar
Jin D, Zhang G, Su L (2015) Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA in Apis cerana cerana gut bacterial communities. Henan Sci 33:45–50
Google Scholar
Keller ABA, Mc B, Balles R, Ur A, Mj A, Sickel W (2018) Wild bees and their nests host Paenibacillus bacteria with functional potential of avail. Microbiome 6:229
PubMed
PubMed Central
Google Scholar
Kevan PG, Greco CF, Belaoussoff S (1997) Log-normality of biodiversity and abundance in diagnosis and measuring of ecosystemic health: pesticide stress on pollinators on blueberry heaths. J Appl Ecol 34:1122–1136
Google Scholar
Koch H, Schmid-Hempel P (2011) Bacterial communities in central European bumblebees: low diversity and high specificity. Microb Ecol 62:121–133
PubMed
Google Scholar
Kwong WK, Moran NA (2015) Evolution of host specialization in gut microbes: the bee gut as a model. Gut Microbes 6:214–220
PubMed
PubMed Central
Google Scholar
Kwong W, Moran N (2016) Gut microbial communities of social bees. Nat Rev Microbiol 14:374–384
CAS
PubMed
PubMed Central
Google Scholar
Lee FJ, Rusch DB, Stewart FJ, Mattila HR, Newton ILG (2015) Saccharide breakdown and fermentation by the honey bee gut microbiome. Environ Microbiol 17:796–815
CAS
PubMed
Google Scholar
Liu YLS, Zhang H, Gu Y, Li X, He M, Tan H (2017) Application of the combination index (CI)-isobologram equation to research the toxicological interactions of clothianidin, thiamethoxam, and dinotefuran in honeybee, Apis mellifera. Chemosphere 184:806–811
CAS
PubMed
Google Scholar
Luo YX, Chen LD (2018) Current situation of bee breeding in China. China Apicult 69:22–24
Google Scholar
Maes PW, Pedro APR, Oliver R, Mott BM, Anderson KE (2016) Diet related gut bacterial dysbiosis correlates with impaired development, increased mortality and nosema disease in the honey bee (Apis mellifera ). Mol Ecol 25:5439–5450
CAS
PubMed
Google Scholar
Martinson VG, Moy J, Moran NA (2012) Establishment of characteristic gut bacteria during development of the honeybee worker. Appl Environ Microb 78:2830–2840
CAS
Google Scholar
Olofsson TC, Vásquez A (2008) Detection and identification of a novel lactic acid bacterial flora within the honey stomach of the honeybee Apis mellifera. Curr Microbiol 57:356–363
CAS
PubMed
Google Scholar
Palmer YEC, Raffle TR, Mcfrederick QS (2019) pH-mediated inhibition of a bumble bee parasite by an intestinal symbiont. Parasitology 146:380–388
Google Scholar
Quast CPE, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Fo G (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–596
PubMed
PubMed Central
Google Scholar
Rachael W, Ramiro A, Vázquez DP, Gretchen LB, Aizen MA (2009) A meta-analysis of bees’ responses to anthropogenic disturbance. Ecology 90:2068–2076
Google Scholar
Raymann KSZ, Na M (2017) Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees. Plos Biol 15:e2001861
PubMed
PubMed Central
Google Scholar
Rothman JA, Carroll MJ, Meikle WG, Anderson KE, Mcfrederick QS (2018) Longitudinal effects of supplemental forage on the honey bee (Apis mellifera) microbiota and inter- and intra-colony variability. Microb Ecol 76:814–824
CAS
PubMed
Google Scholar
Schmidt EMN, Ai S-H (2019) Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus). ISME J 13:1293–1305
CAS
PubMed
PubMed Central
Google Scholar
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60
PubMed
PubMed Central
Google Scholar
Sharifpour MF, Mardani K, Ownagh A (2016) Molecular identification and phylogenetic analysis of Lactobacillus and Bifidobacterium spp. isolated from gut of honeybees (Apis mellifera) from West Azerbaijan. Ir Vet Res Forum Intern Quar J 7:287–294
Google Scholar
Tanja M, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963
Google Scholar
Tanya Y, Rey FE, Manary MJ, Indi T, Maria Gloria DB, Monica C, Magda M, Glida H, Baldassano RN, Anokhin AP (2012) Human gut microbiome viewed across age and geography. Nature 486:222–227
Google Scholar
Team R C (2016) R: A language and environment for statistical computing. 14:12–21
Thomson D (2010) Detecting the effects of introduced species: a case study of competition between Apis and Bombus. Oikos 114:407–418
Google Scholar
Tim Regan MWB, Laetsch DR, Bush SJ, Wragg D, Budge GE, Highet F, Dainat B, De Miranda JR, Watson M, Blaxter M, Freeman TC (2018) Characterisation of the British honey bee metagenome. Nat Commun 9:4995
PubMed
PubMed Central
Google Scholar
Vasemägi AVM, Kisand V (2017) Effect of environmental factors and an emerging parasitic disease on gut microbiome of wild Salmonid fish. MSphere 2:e00418–e517
PubMed
PubMed Central
Google Scholar
Zheng H, Nishida A, Kwong WK, Koch H, Engel P, Steele MI, Moran NA (2016) Metabolism of toxic sugars by strains of the Bee Gut Symbiont Gilliamella apicola. MBio 7:e01326–e1416
CAS
PubMed
PubMed Central
Google Scholar