[en] We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.
Disciplines :
Entomology & pest control Microbiology
Author, co-author :
Hettiarachchi, Amanda ; Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
Cnockaert, Margo; Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
Joossens, Marie; Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
Laureys, David; Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
De Clippeleer, Jessika; Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
Vereecken, Nicolas J; Agroecology Lab, Université libre de Bruxelles, Brussels, Belgium
MICHEZ, Denis ; Université de Mons - UMONS > Faculté des Sciences > Service de Zoologie
Smagghe, Guy ; Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
de Graaf, Dirk C; Laboratory of Molecular Entomology and Bee Pathology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
Vandamme, Peter ; Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
Language :
English
Title :
Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina.
Fonds Wetenschappelijk Onderzoek F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
Funding text :
This study was funded by the FWO and F.R.S.‐FNRS joint program Excellence of Science (EOS) for the project ‘Climate change and its effects on pollination services’ (CliPS, project number 3094785).
Anderson, K.E., Russell, J.A., Moreau, C.S., Kautz, S., Sullam, K.E., Hu, Y. et al. (2012) Highly similar microbial communities are shared among related and trophically similar ant species. Molecular Ecology, 21, 2282–2296.
Ankenbrand, M.J. & Keller, A. (2016) bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome, 59, 783–791.
Audisio, M.C., Torres, M.J., Sabate, D.C., Ibarguren, C. & Apella, M.C. (2011) Properties of different lactic acid bacteria isolated from Apis mellifera L. bee-gut. Microbiological Research, 166, 1–13.
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19, 455–477.
Bell-Sakyi, L., Palomar, A.M. & Kazimirova, M. (2015) Isolation and propagation of a Spiroplasma sp from Slovakian Ixodes ricinus ticks in Ixodes spp. cell lines. Ticks and Tick-Borne Diseases, 6, 601–606.
Bonilla-Rosso, G. & Engel, P. (2018) Functional roles and metabolic niches in the honey bee gut microbiota. Current Opinion in Microbiology, 43, 69–76.
Callahan, B.J., Mcmurdie, P.J. & Holmes, S.P. (2017) Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME Journal, 11, 2639–2643.
Callegari, M., Crotti, E., Fusi, M., Marasco, R., Gonella, E., Noni, I.D. et al. (2021) Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees. Npj Biofilms and Microbiomes, 7, 42.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. et al. (2009) BLAST plus: architecture and applications. BMC Bioinformatics, 10, 421.
Cantalapiedra, C.P., Hernandez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. (2021) eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular Biology and Evolution, 38, 5825–5829.
Cini, A., Cappa, F., Petrocelli, I., Pepiciello, I., Bortolotti, L. & Cervo, R. (2018) Competition between the native and the introduced hornets Vespa crabro and Vespa velutina: a comparison of potentially relevant life-history traits. Ecological Entomology, 43, 351–362.
Cini, A., Meriggi, N., Bacci, G., Cappa, F., Vitali, F., Cavalieri, D. et al. (2020) Gut microbial composition in different castes and developmental stages of the invasive hornet Vespa velutina nigrithorax. Science of the Total Environment, 745, 140873.
Coenye, T., Falsen, E., Vancanneyt, M., Hoste, B., Govan, J.R.W., Kersters, K. et al. (1999) Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. International Journal of Systematic Bacteriology, 49, 405–413.
Crotti, E., Rizzi, A., Chouaia, B., Ricci, I., Favia, G., Alma, A. et al. (2010) Acetic acid bacteria, newly emerging symbionts of insects. Applied and Environmental Microbiology, 76, 6963–6970.
Dogsa, I., Brloznik, M., Stopar, D. & Mandic-Mulec, I. (2013) Exopolymer diversity and the role of levan in Bacillus subtilis biofilms. PLoS One, 8, e62044.
Dumolin, C., Aerts, M., Verheyde, B., Schellaert, S., Vandamme, T., van der Jeugt, F. et al. (2019) Introducing SPeDE: high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry data. mSystems, 4, e00437–e00419.
Duthoo, E., de Reu, K., Leroy, F., Weckx, S., Heyndrickx, M. & Rasschaert, G. (2022) To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period. BMC Microbiology, 22, 34.
Endo, A., Maeno, S., Tanizawa, Y., Kneifel, W., Arita, M., Dicks, L. et al. (2018) Fructophilic lactic acid bacteria, a unique group of fructose-fermenting microbes. Applied and Environmental Microbiology, 84, e01290–18.
Endo, A., Tanizawa, Y., Tanaka, N., Maeno, S., Kumar, H., Shiwa, Y. et al. (2015) Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp. BMC Genomics, 16, 1117.
Engel, P., Kwong, W.K., Mcfrederick, Q., Anderson, K.E., Barribeau, S.M., Chandler, J.A. et al. (2016) The bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions. MBio, 7, e02164–15.
Engel, P. & Moran, N.A. (2013) The gut microbiota of insects – diversity in structure and function. FEMS Microbiology Reviews, 37, 699–735.
Eren, A.M., Kiefl, E., Shaiber, A., Veseli, I., Miller, S.E., Schechter, M.S. et al. (2021) Community-led, integrated, reproducible multi-omics with anvi'o. Nature Microbiology, 6, 3–6.
Espinosa, L., Franco, S. & Chauzat, M.P. (2019) Could Vespa velutina nigrithorax be included in the World Organisation for Animal Health list of diseases, infections and infestations? Revue Scientifique Et Technique-Office International Des Epizooties, 38, 851–862.
Figueroa, L.L., Maccaro, J.J., Krichilsky, E., Yanega, D. & Mcfrederick, Q.S. (2021) Why did the bee eat the chicken? Symbiont gain, loss, and retention in the vulture bee microbiome. Mbio, 12, e02317–21.
Galperin, M.Y., Wolf, Y.I., Makarova, K.S., Alvarez, R.V., Landsman, D. & Koonin, E.V. (2021) COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Research, 49, D274–D281.
Goulson, D. (2010) Impacts of non-native bumblebees in Western Europe and North America. Applied Entomology and Zoology, 45, 7–12.
Graystock, P., Rehan, S.M. & Mcfrederick, Q.S. (2017) Hunting for healthy microbiomes: determining the core microbiomes of Ceratina, Megalopta, and Apis bees and how they associate with microbes in bee collected pollen. Conservation Genetics, 18, 701–711.
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29, 1072–1075.
Hong, S.H., Bunge, J., Leslin, C., Jeon, S. & Epstein, S.S. (2009) Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME Journal, 3, 1365–1373.
Keeling, M.J., Franklin, D.N., Datta, S., Brown, M.A. & Budge, G.E. (2017) Predicting the spread of the Asian hornet (Vespa velutina) following its incursion into Great Britain. Scientific Reports, 7, 6240.
Kim, E., Seo, J., Yang, S.H., Kim, I.-S. & Koo, Y. (2018) Intestine bacterial microbiota of Asian Hornet (Vespa velutina nigrithorax) and honey bee. Korean Journal of Environmental Agriculture, 37, 135–140.
Kim, M., Oh, H.S., Park, S.C. & Chun, J. (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 64, 346–351.
Kwong, W.K. & Moran, N.A. (2016) Gut microbial communities of social bees. Nature Reviews Microbiology, 14, 374–384.
Lagier, J.C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C. et al. (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection, 18, 1185–1193.
Laurino, D., Lioy, S., Carisio, L., Manino, A. & Porporato, M. (2020) Vespa velutina: an alien driver of honey bee colony losses. Diversity-Basel, 12, 5.
Letunic, I. & Bork, P. (2021) Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research, 49, W293–W296.
Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv, 3, 13033997.
Li, L.L., Cleenwerck, I., De Vuyst, L. & Vandamme, P. (2017) Identification of acetic acid bacteria through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and report of Gluconobacter nephelii Kommanee et al. 2011 and Gluconobacter uchimurae Tanasupawat et al. 2012 as later heterotypic synonyms of Gluconobacter japonicus Malimas et al. 2009 and Gluconobacter oxydans (Henneberg 1897) De Ley 1961 (Approved Lists 1980) emend Gossele et al. 1983, respectively. Systematic and Applied Microbiology, 40, 123–134.
Li, L.L., Praet, J., Borremans, W., Nunes, O.C., Manaia, C.M., Cleenwerck, I. et al. (2015) Bombella intestini gen. nov., sp nov., an acetic acid bacterium isolated, from bumble bee crop. International Journal of Systematic and Evolutionary Microbiology, 65, 267–273.
Lisdiyanti, P., Katsura, K., Potacharoen, W., Navarro, R.R., Yamada, Y., Uchimura, T. et al. (2003) Diversity of acetic acid bacteria in Indonesia, Thailand, and The Philippines. Microbial Culture Collection, 19, 91–99.
MacFaddin, J.F. (2000) Biochemical tests for identification of medical bacteria, 3rd edition. Baltimore, MD: Williams and Wilkins.
Maeno, S., Nishimura, H., Tanizawa, Y., Dicks, L., Arita, M. & Endo, A. (2021) Unique niche-specific adaptation of fructophilic lactic acid bacteria and proposal of three Apilactobacillus species as novel members of the group. BMC Microbiology, 21, 41.
Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E. et al. (2006) Comparative genomics of the lactic acid bacteria. Proceedings of the National Academy of Sciences of the United States of America, 103, 15611–15616.
Martinson, V.G., Danforth, B.N., Minckley, R.L., Rueppell, O., Tingek, S. & Moran, N.A. (2011) A simple and distinctive microbiota associated with honey bees and bumble bees. Molecular Ecology, 20, 619–628.
Martinson, V.G., Moy, J. & Moran, N.A. (2012) Establishment of characteristic gut bacteria during development of the honeybee worker. Applied and Environmental Microbiology, 78, 2830–2840.
McMurdie, P.J. & Holmes, S. (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One, 8, e61217.
Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P. & Goker, M. (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 14, 60.
Meier-Kolthoff, J.P. & Goker, M. (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications, 10, 2182.
Meroth, C.B., Walter, J., Hertel, C., Brandt, M.J. & Hammes, W.P. (2003) Monitoring the bacterial population dynamics in sourdough fermentation processes by using PCR denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 69, 475–482.
Monceau, K., Bonnard, O. & Thiery, D. (2014) Vespa velutina: a new invasive predator of honeybees in Europe. Journal of Pest Science, 87, 1–16.
Moran, N.A. (2015) Genomics of the honey bee microbiome. Current Opinion in Insect Science, 10, 22–28.
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C. & Kanehisa, M. (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research, 35, W182–W185.
Naser, S.M., Dawyndt, P., Hoste, B., Gevers, D., Vandemeulebroecke, K., Cleenwerck, I. et al. (2007) Identification of lactobacilli by pheS and rpoA gene sequence analyses. International Journal of Systematic and Evolutionary Microbiology, 57, 2777–2789.
O'Callaghan, J.L., Willner, D., Buttini, M., Huygens, F. & Pelzer, E.S. (2021) Limitations of 16S rRNA gene sequencing to characterize Lactobacillus species in the upper genital tract. Frontiers in Cell and Developmental Biology, 9, 641921.
Ohkuma, M. & Brune, A. (2011) Diversity, structure, and evolution of the termite gut microbial community. In: Biology of Termites: A Modern Synthesis. Dordrecht: Springer.
Olofsson, T.C. & Vasquez, A. (2008) Detection and identification of a novel lactic acid bacterial flora within the honey stomach of the honeybee Apis mellifera. Current Microbiology, 57, 356–363.
Oren, A. & Garrity, G.M. (2021) Valid publication of the names of forty-two phyla of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 71, 005056.
Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P. & Tyson, G.W. (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25, 1043–1055.
Potts, S.G., Biesmeijer, J.C., Kremen, C., Neumann, P., Schweiger, O. & Kunin, W.E. (2010) Global pollinator declines: trends, impacts and drivers. Trends in Ecology & Evolution, 25, 345–353.
Praet, J., Meeus, I., Cnockaert, M., Houf, K., Smagghe, G. & Vandamme, P. (2015) Novel lactic acid bacteria isolated from the bumble bee gut: Convivina intestini gen. nov., sp nov., Lactobacillus bombicola sp nov., and Weissella bombi sp nov. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 107, 1337–1349.
Praet, J., Parmentier, A., Schmid-Hempel, R., Meeus, I., Smagghe, G. & Vandamme, P. (2018) Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition. Environmental Microbiology, 20, 214–227.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P. et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41, D590–D596.
Requier, F., Rome, Q., Chiron, G., Decante, D., Marion, S., Menard, M. et al. (2019) Predation of the invasive Asian hornet affects foraging activity and survival probability of honey bees in Western Europe. Journal of Pest Science, 92, 567–578.
Roh, S.W., Nam, Y.D., Chang, H.W., Kim, K.H., Kim, M.S., Ryu, J.H. et al. (2008) Phylogenetic characterization of two novel commensal bacteria involved with innate immune homeostasis in Drosophila melanogaster. Applied and Environmental Microbiology, 74, 6171–6177.
Rojas-Nossa, S.V. & Calvino-Cancela, M. (2020) The invasive hornet Vespa velutina affects pollination of a wild plant through changes in abundance and behaviour of floral visitors. Biological Invasions, 22, 2609–2618.
Schmid, J., Bechtner, J., Vogel, R.F. & Jakob, F. (2019) A systematic approach to study the pH-dependent release, productivity and product specificity of dextransucrases. Microbial Cell Factories, 18, 153.
Schroeter, J. & Klaenhammer, T. (2009) Genomics of lactic acid bacteria. FEMS Microbiology Letters, 292, 1–6.
Snauwaert, I., Roels, S.P., Van Nieuwerburgh, F., Van Landschoot, A., De Vuyst, L. & Vandamme, P. (2016) Microbial diversity and metabolite composition of Belgian red-brown acidic ales. International Journal of Food Microbiology, 221, 1–11.
Steinhauer, N., Kulhanek, K., Antunez, K., Human, H., Chantawannakul, P., Chauzat, M.P. et al. (2018) Drivers of colony losses. Current Opinion in Insect Science, 26, 142–148.
Stone, B. & Morell, M.K. (2009) Chapter 9: Carbohydrates. In: WHEAT: Chemistry and Technology. Washington, DC: AACC International Press, pp. 299–362.
Suenami, S., Nobu, M.K. & Miyazaki, R. (2019) Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima. Scientific Reports, 9, 9830.
Sun, Z.H., Harris, H.M.B., Mccann, A., Guo, C.Y., Argimon, S., Zhang, W.Y. et al. (2015) Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nature Communications, 6, 8322.
Takashi, A., Yoshiya, T., Hiromitsu, M. & yasuko y, K. (1991) Comparative study of the composition of hornet larval saliva, its effect on behaviour and role of trophallaxis. Comparative Biochemistry and Physiology Part C: Comparative Pharmacology, 99, 79–84.
Takeuchi, T., Takahashi, R., Kiyoshi, T., Nakamura, M., Minoshima, Y.N. & Takahashi, J. (2017) The origin and genetic diversity of the yellow-legged hornet, Vespa velutina introduced in Japan. Insectes Sociaux, 64, 313–320.
Van Dongen, S. & Abreu-Goodger, C. (2012) Using MCL to extract clusters from networks. Methods in Molecular Biology, 804, 281–295.
Vasquez, A., Forsgren, E., Fries, I., Paxton, R.J., Flaberg, E., Szekely, L. et al. (2012) Symbionts as major modulators of insect health: lactic acid bacteria and honeybees. PLoS One, 7, e33188.
Velazquez-Hernandez, M.L., Baizabal-Aguirre, V.M., Cruz-Vazquez, F., Trejo-Contreras, M.J., Fuentes-Ramirez, L.E., Bravo-Patino, A. et al. (2011) Gluconacetobacter diazotrophicus levansucrase is involved in tolerance to NaCl, sucrose and desiccation, and in biofilm formation. Archives of Microbiology, 193, 137–149.
Vidal, C., Armisen, M., Monsalve, R., Gonzalez-Vidal, T., Lojo, S., Lopez-Freire, S. et al. (2021) Anaphylaxis to Vespa velutina nigrithorax: pattern of sensitization for an emerging problem in western countries. Journal of Investigational Allergology and Clinical Immunology, 31, 228–235.
Wels, M., Siezen, R., Van Hijum, S., Kelly, W.J. & Bachmann, H. (2019) Comparative genome analysis of Lactococcus lactis indicates niche adaptation and resolves genotype/phenotype disparity. Frontiers in Microbiology, 10, 4.
Wieme, A.D., Spitaels, F., Aerts, M., De Bruyne, K., Van Landschoot, A. & Vandamme, P. (2014) Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. International Journal of Food Microbiology, 185, 41–50.
Wisselink, H.W., Weusthuis, R.A., Eggink, G., Hugenholtz, J. & Grobben, G.J. (2002) Mannitol production by lactic acid bacteria: a review. International Dairy Journal, 12, 151–161.
Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H. et al. (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology, 67, 1613–1617.
Yoon, S.H., Ha, S.M., Lim, J., Kwon, S. & Chun, J. (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 110, 1281–1286.
Yun, J.H., Roh, S.W., Whon, T.W., Jung, M.J., Kim, M.S., Park, D.S. et al. (2014) Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host. Applied and Environmental Microbiology, 80, 5254–5264.
Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P.Z., Yang, Z.L. et al. (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Research, 46, W95–W101.
Zhang, L., Liu, F., Wang, X.L., Wang, P.H., Ma, S.L., Yang, Y. et al. (2022) Midgut bacterial communities of Vespa velutina Lepeletier (Hymenoptera: Vespidae). Frontiers in Ecology and Evolution, 10, 934054.
Zheng, J.S., Wittouck, S., Salvetti, E., Franz, C., Harris, H.M.B., Mattarelli, P. et al. (2020) A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. International Journal of Systematic and Evolutionary Microbiology, 70, 2782–2858.
