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Yang C, Hu J, Su Q, Zhang Z, Du Y, Wang J, Sun H, Han B, Tang J, Guo L, Li H, Cai W, Zheng H, Zhou X, Zhang X. A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database. Insect Sci 2024. [PMID: 38594229 DOI: 10.1111/1744-7917.13365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/13/2024] [Accepted: 03/09/2024] [Indexed: 04/11/2024]
Abstract
Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.
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Affiliation(s)
- Chengfeng Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan Province, China
| | - Jiawei Hu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Zijing Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yating Du
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jieni Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Huihui Sun
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan Province, China
| | - Benfeng Han
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junbo Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lizhen Guo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan Province, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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Botero J, Peeters C, De Canck E, Laureys D, Wieme AD, Cleenwerck I, Depoorter E, Praet J, Michez D, Smagghe G, Vandamme P. A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees. Syst Appl Microbiol 2024; 47:126505. [PMID: 38564984 DOI: 10.1016/j.syapm.2024.126505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of Fructobacillus in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with Fructobacillus bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 Fructobacillus isolates from bumble bees demonstrated that they represented four species, i.e. Fructobacillus cardui, Fructobacillus fructosus, Fructobacillus tropaeoli, and the novel species Fructobacillus evanidus sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct Fructobacillus species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with F. evanidus and F. tropaeoli genomes featuring a higher number of complete metabolic pathways. While Fructobacillus genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple Fructobacillus species from several bumble bee gut samples in the present study also argued against a specific partnership between Fructobacillus species and their bumble bee hosts.
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Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ilse Cleenwerck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Jessy Praet
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000 Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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Dong JH, Xu X, Ren ZX, Zhao YH, Zhang Y, Chen L, Wu Y, Chen G, Cao R, Wu Q, Wang H. The adaptation of bumblebees to extremely high elevation associated with their gut microbiota. mSystems 2024; 9:e0121923. [PMID: 38329353 PMCID: PMC10949452 DOI: 10.1128/msystems.01219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
Bumblebees are among the most abundant and important pollinators for sub-alpine and alpine flowering plant species in the Northern Hemisphere, but little is known about their adaptations to high elevations. In this article, we focused on two bumblebee species, Bombus friseanus and Bombus prshewalskyi, and their respective gut microbiota. The two species, distributed through the Hengduan Mountains of southwestern China, show species replacement at different elevations. We performed genome sequencing based on 20 worker bee samples of each species. Applying evolutionary population genetics and metagenomic approaches, we detected genes under selection and analyzed functional pathways between bumblebees and their gut microbes. We found clear genetic differentiation between the two host species and significant differences in their microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. These extremely high-elevation bumblebees show evidence of positive selection related to diverse biological processes. Positively selected genes involved in host immune systems probably contributed to gut microbiota changes, while the butyrate generated by gut microbiota may influence both host energy metabolism and immune systems. This suggests a close association between the genomes of the host species and their microbiomes based on some degree of natural selection.IMPORTANCETwo closely related and dominant bumblebee species, distributed at different elevations through the Hengduan Mountains of southwestern China, showed a clear genomic signature of adaptation to elevation at the molecular level and significant differences in their respective microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. Bumblebees' adaptations to higher elevations are closely associated with their gut microbiota through two biological processes: energy metabolism and immune response. Information allowing us to understand the adaptive mechanisms of species to extreme conditions is implicit if we are to conserve them as their environments change.
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Affiliation(s)
- Jiu-Hong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zong-Xin Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan-Hui Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yaran Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - You Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guotao Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruiqing Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Motta EVS, Moran NA. The honeybee microbiota and its impact on health and disease. Nat Rev Microbiol 2024; 22:122-137. [PMID: 38049554 PMCID: PMC10998682 DOI: 10.1038/s41579-023-00990-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 12/06/2023]
Abstract
Honeybees (Apis mellifera) are key pollinators that support global agriculture and are long-established models for developmental and behavioural research. Recently, they have emerged as models for studying gut microbial communities. Earlier research established that hindguts of adult worker bees harbour a conserved set of host-restricted bacterial species, each showing extensive strain variation. These bacteria can be cultured axenically and introduced to gnotobiotic hosts, and some have basic genetic tools available. In this Review, we explore the most recent research showing how the microbiota establishes itself in the gut and impacts bee biology and health. Microbiota members occupy specific niches within the gut where they interact with each other and the host. They engage in cross-feeding and antagonistic interactions, which likely contribute to the stability of the community and prevent pathogen invasion. An intact gut microbiota provides protection against diverse pathogens and parasites and contributes to the processing of refractory components of the pollen coat and dietary toxins. Absence or disruption of the microbiota results in altered expression of genes that underlie immunity, metabolism, behaviour and development. In the field, such disruption by agrochemicals may negatively impact bees. These findings demonstrate a key developmental and protective role of the microbiota, with broad implications for bee health.
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Affiliation(s)
- Erick V S Motta
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas, Austin, TX, USA.
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5
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Quinn A, El Chazli Y, Escrig S, Daraspe J, Neuschwander N, McNally A, Genoud C, Meibom A, Engel P. Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi. Nat Microbiol 2024; 9:477-489. [PMID: 38225461 DOI: 10.1038/s41564-023-01572-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/30/2023] [Indexed: 01/17/2024]
Abstract
Diverse bacteria can colonize the animal gut using dietary nutrients or by engaging in microbial crossfeeding interactions. Less is known about the role of host-derived nutrients in enabling gut bacterial colonization. Here we examined metabolic interactions within the evolutionary ancient symbiosis between the honey bee (Apis mellifera) and the core gut microbiota member Snodgrassella alvi. This betaproteobacterium is incapable of metabolizing saccharides, yet colonizes the honey bee gut in the presence of a sugar-only diet. Using comparative metabolomics, 13C-tracers and nanoscale secondary ion mass spectrometry (NanoSIMS), we show in vivo that S. alvi grows on host-derived organic acids, including citrate, glycerate and 3-hydroxy-3-methylglutarate, which are actively secreted by the host into the gut lumen. S. alvi also modulates tryptophan metabolism in the gut by converting kynurenine to anthranilate. These results suggest that S. alvi is adapted to a specific metabolic niche in the honey bee gut that depends on host-derived nutritional resources.
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Affiliation(s)
- Andrew Quinn
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yassine El Chazli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Stéphane Escrig
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Neuschwander
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aoife McNally
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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Baud GLC, Prasad A, Ellegaard KM, Engel P. Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers. Genome Biol 2023; 24:283. [PMID: 38066630 PMCID: PMC10704631 DOI: 10.1186/s13059-023-03131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood. RESULTS Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states. CONCLUSIONS Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.
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Affiliation(s)
- Gilles L C Baud
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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Deng Y, Pan J, Yang X, Yang S, Chi H, Yang X, Qu X, Sun S, You L, Hou C. Dual roles of nanocrystalline cellulose extracted from jute ( Corchorus olitorius L.) leaves in resisting antibiotics and protecting probiotics. Nanoscale Adv 2023; 5:6435-6448. [PMID: 38024324 PMCID: PMC10662138 DOI: 10.1039/d3na00345k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/14/2023] [Indexed: 12/01/2023]
Abstract
Antibiotics can cure diseases caused by bacterial infections, but their widespread use can have some side effects, such as probiotic reduction. There is an urgent need for such agents that can not only alleviate the damage caused by antibiotics, but also maintain the balance of the gut microbiota. In this study, we first characterized the nanocrystalline cellulose (NCC) extracted from plant jute (Corchorus olitorius L.) leaves. Next, we evaluated the protective effect of jute NCC and cellulose on human model gut bacteria (Lacticaseibacillus rhamnosus and Escherichia coli) under antibiotic stress by measuring bacterial growth and colony forming units. We found that NCC is more effective than cellulose in adsorbing antibiotics and defending the gut bacteria E. coli. Interestingly, the low-dose jute NCC clearly maintained the balance of key gut bacteria like Snodgrassella alvi and Lactobacillus Firm-4 in bees treated with tetracycline and reduced the toxicity caused by antibiotics. It also showed a more significant protective effect on human gut bacteria, especially L. rhamnosus, than cellulose. This study first demonstrated that low-dose NCC performed satisfactorily as a specific probiotic to mitigate the adverse effects of antibiotics on gut bacteria.
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Affiliation(s)
- Yanchun Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Jiangpeng Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences Beijing 100093 P. R. China
- Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081 P. R. China
| | - Haiyang Chi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Xiushi Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Xiaoxin Qu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Shitao Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Linfeng You
- Department of Food and Biotechnology Engineering, Chongqing Technology and Business University Chongqing 400067 P. R. China
| | - Chunsheng Hou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
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Béchade B, Cabuslay CS, Hu Y, Mendonca CM, Hassanpour B, Lin JY, Su Y, Fiers VJ, Anandarajan D, Lu R, Olson CJ, Duplais C, Rosen GL, Moreau CS, Aristilde L, Wertz JT, Russell JA. Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants. ISME J 2023; 17:1751-1764. [PMID: 37558860 PMCID: PMC10504363 DOI: 10.1038/s41396-023-01490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.
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Affiliation(s)
- Benoît Béchade
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA.
| | - Christian S Cabuslay
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Yi Hu
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875, Beijing, China
| | - Caroll M Mendonca
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Bahareh Hassanpour
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Jonathan Y Lin
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Yangzhou Su
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Valerie J Fiers
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Dharman Anandarajan
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Richard Lu
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Chandler J Olson
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
- Department of Biological Sciences, University of Alabama, 1325 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Christophe Duplais
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut St., Philadelphia, PA, 19104, USA
| | - Corrie S Moreau
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - John T Wertz
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
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9
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Lariviere PJ, Ashraf AHMZ, Leonard SP, Miller LG, Moran NA, Barrick JE. Single-step genome engineering in the bee gut symbiont Snodgrassella alvi. bioRxiv 2023:2023.09.19.558440. [PMID: 37786689 PMCID: PMC10541602 DOI: 10.1101/2023.09.19.558440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Honey bees are economically relevant pollinators experiencing population declines due to a number of threats. As in humans, the health of bees is influenced by their microbiome. The bacterium Snodgrassella alvi is a key member of the bee gut microbiome and has a role in excluding pathogens. Despite this importance, there are not currently any easy-to-use methods for modifying the S. alvi chromosome to study its genetics. To solve this problem, we developed a one-step procedure that uses electroporation and homologous recombination, which we term SnODIFY (Snodgrassella-specific One-step gene Deletion or Insertion to alter FunctionalitY). We used SnODIFY to create seven single-gene knockout mutants and recovered mutants for all constructs tested. Nearly all transformants had the designed genome modifications, indicating that SnODIFY is highly accurate. Mutant phenotypes were validated through knockout of Type 4 pilus genes, which led to reduced biofilm formation. We also used SnODIFY to insert heterologous sequences into the genome by integrating fluorescent protein-coding genes. Finally, we confirmed that genome modification is dependent on S. alvi's endogenous RecA protein. Because it does not require expression of exogenous recombination machinery, SnODIFY is a straightforward, accurate, and lightweight method for genome editing in S. alvi. This workflow can be used to study the functions of S. alvi genes and to engineer this symbiont for applications including protection of honey bee health.
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Affiliation(s)
- Patrick J. Lariviere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - A. H. M. Zuberi Ashraf
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sean P. Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laurel G. Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nancy A. Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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10
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Cabirol A, Moriano-Gutierrez S, Engel P. Neuroactive metabolites modulated by the gut microbiota in honey bees. Mol Microbiol 2023. [PMID: 37718573 DOI: 10.1111/mmi.15167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Honey bees have emerged as a new model to study the gut-brain axis, as they exhibit complex social behaviors and cognitive abilities, while experiments with gnotobiotic bees have revealed that their gut microbiota alters both brain and behavioral phenotypes. Furthermore, while honey bee brain functions supporting a broad range of behaviors have been intensively studied for over 50 years, the gut microbiota of bees has been experimentally characterized only recently. Here, we combined six published datasets from metabolomic analyses to provide an overview of the neuroactive metabolites whose abundance in the gut, hemolymph and brain varies in presence of the gut microbiota. Such metabolites may either be produced by gut bacteria, released from the pollen grains during their decomposition by bacteria, or produced by other organs in response to different bacterial products. We describe the current state of knowledge regarding the impact of such metabolites on brain function and behavior and provide further hypotheses to explore in this emerging field of research.
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Affiliation(s)
- Amélie Cabirol
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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11
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Guo L, Tang J, Tang M, Luo S, Zhou X. Reactive oxygen species are regulated by immune deficiency and Toll pathways in determining the host specificity of honeybee gut bacteria. Proc Natl Acad Sci U S A 2023; 120:e2219634120. [PMID: 37556501 PMCID: PMC10438842 DOI: 10.1073/pnas.2219634120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
Host specificity is observed in gut symbionts of diverse animal lineages. But how hosts maintain symbionts while rejecting their close relatives remains elusive. We use eusocial bees and their codiversified gut bacteria to understand host regulation driving symbiotic specificity. The cross-inoculation of bumblebee Gilliamella induced higher prostaglandin in the honeybee gut, promoting a pronounced host response through immune deficiency (IMD) and Toll pathways. Gene silencing and vitamin C treatments indicate that reactive oxygen species (ROS), not antimicrobial peptides, acts as the effector in inhibiting the non-native strain. Quantitative PCR and RNAi further reveal a regulatory function of the IMD and Toll pathways, in which Relish and dorsal-1 may regulate Dual Oxidase (Duox) for ROS production. Therefore, the honeybee maintains symbiotic specificity by creating a hostile gut environment to exotic bacteria, through differential regulation of its immune system, reflecting a co-opting of existing machinery evolved to combat pathogens.
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Affiliation(s)
- Lizhen Guo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing100083, People’s Republic of China
- Sanya Institute of China Agricultural University, Sanya572000, People’s Republic of China
| | - Junbo Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing100083, People’s Republic of China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing100083, People’s Republic of China
| | - Min Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing100083, People’s Republic of China
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou215100, People’s Republic of China
| | - Shiqi Luo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing100083, People’s Republic of China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing100083, People’s Republic of China
- Sanya Institute of China Agricultural University, Sanya572000, People’s Republic of China
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12
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Lang H, Wang H, Wang H, Zhong Z, Xie X, Zhang W, Guo J, Meng L, Hu X, Zhang X, Zheng H. Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees. Nat Commun 2023; 14:2778. [PMID: 37210527 DOI: 10.1038/s41467-023-38498-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/05/2023] [Indexed: 05/22/2023] Open
Abstract
Nosema ceranae is an intracellular parasite invading the midgut of honeybees, which causes serious nosemosis implicated in honeybee colony losses worldwide. The core gut microbiota is involved in protecting against parasitism, and the genetically engineering of the native gut symbionts provides a novel and efficient way to fight pathogens. Here, using laboratory-generated bees mono-associated with gut members, we find that Snodgrassella alvi inhibit microsporidia proliferation, potentially via the stimulation of host oxidant-mediated immune response. Accordingly, N. ceranae employs the thioredoxin and glutathione systems to defend against oxidative stress and maintain a balanced redox equilibrium, which is essential for the infection process. We knock down the gene expression using nanoparticle-mediated RNA interference, which targets the γ-glutamyl-cysteine synthetase and thioredoxin reductase genes of microsporidia. It significantly reduces the spore load, confirming the importance of the antioxidant mechanism for the intracellular invasion of the N. ceranae parasite. Finally, we genetically modify the symbiotic S. alvi to deliver dsRNA corresponding to the genes involved in the redox system of the microsporidia. The engineered S. alvi induces RNA interference and represses parasite gene expression, thereby inhibits the parasitism significantly. Specifically, N. ceranae is most suppressed by the recombinant strain corresponding to the glutathione synthetase or by a mixture of bacteria expressing variable dsRNA. Our findings extend our previous understanding of the protection of gut symbionts against N. ceranae and provide a symbiont-mediated RNAi system for inhibiting microsporidia infection in honeybees.
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Affiliation(s)
- Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Hao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Haoqing Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Zhaopeng Zhong
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Xianbing Xie
- Department of Laboratory Animal Science, Nanchang University, 330006, Nanchang, China
| | - Wenhao Zhang
- Faculty of Agriculture and Food, Kunming University of Science and Technology, 650031, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650031, Kunming, China
| | - Liang Meng
- BGI-Qingdao, BGI-Shenzhen, 266555, Qingdao, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Xue Zhang
- College of Plant Protection, China Agricultural University, 100083, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China.
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13
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Botero J, Sombolestani AS, Cnockaert M, Peeters C, Borremans W, De Vuyst L, Vereecken NJ, Michez D, Smagghe G, Bonilla-Rosso G, Engel P, Vandamme P. A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont. Anim Microbiome 2023; 5:25. [PMID: 37120592 PMCID: PMC10149009 DOI: 10.1186/s42523-023-00248-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis. RESULTS The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G + C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont. CONCLUSION The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.
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Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Wim Borremans
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Nicolas J Vereecken
- Agroecology Lab, Université libre de Bruxelles, Boulevard du Triomphe CP 264/02, 1050, Brussels, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - German Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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14
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Sarton-Lohéac G, Nunes da Silva CG, Mazel F, Baud G, de Bakker V, Das S, El Chazli Y, Ellegaard K, Garcia-Garcera M, Glover N, Liberti J, Nacif Marçal L, Prasad A, Somerville V, Bonilla-Rosso G, Engel P. Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees. mBio 2023; 14:e0353822. [PMID: 36939321 PMCID: PMC10128065 DOI: 10.1128/mbio.03538-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiotas presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here, we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumblebee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host, indicating that the evolution of the social bee gut microbiota was not driven by strict codiversification but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumblebee microbiotas, we found substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. IMPORTANCE Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumblebees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees, which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major members of the gut microbiotas of six stingless bee species and sequenced their genomes. We found that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumblebees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents a basis for characterizing the symbiotic relationships between gut bacteria and stingless bees.
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Affiliation(s)
- Garance Sarton-Lohéac
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gilles Baud
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent de Bakker
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sudip Das
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yassine El Chazli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joanito Liberti
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lorena Nacif Marçal
- Department of Morphology, Instituto de Ciências Biológicas, Federal University of Amazonas, Manaus, Brazil
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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15
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Lariviere PJ, Leonard SP, Horak RD, Powell JE, Barrick JE. Honey bee functional genomics using symbiont-mediated RNAi. Nat Protoc 2023; 18:902-928. [PMID: 36460809 DOI: 10.1038/s41596-022-00778-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/22/2022] [Indexed: 12/03/2022]
Abstract
Honey bees are indispensable pollinators and model organisms for studying social behavior, development and cognition. However, their eusociality makes it difficult to use standard forward genetic approaches to study gene function. Most functional genomics studies in bees currently utilize double-stranded RNA (dsRNA) injection or feeding to induce RNAi-mediated knockdown of a gene of interest. However, dsRNA injection is laborious and harmful, and dsRNA feeding is difficult to scale cheaply. Further, both methods require repeated dsRNA administration to ensure a continued RNAi response. To fill this gap, we engineered the bee gut bacterium Snodgrassella alvi to induce a sustained host RNA interference response that reduces expression of a targeted gene. To employ this functional genomics using engineered symbionts (FUGUES) procedure, a dsRNA expression plasmid is cloned in Escherichia coli using Golden Gate assembly and then transferred to S. alvi. Adult worker bees are then colonized with engineered S. alvi. Finally, gene knockdown is verified through qRT-PCR, and bee phenotypes of interest can be further assessed. Expression of targeted genes is reduced by as much as 50-75% throughout the entire bee body by 5 d after colonization. This protocol can be accomplished in 4 weeks by bee researchers with microbiology and molecular cloning skills. FUGUES currently offers a streamlined and scalable approach for studying the biology of honey bees. Engineering other microbial symbionts to influence their hosts in ways that are similar to those described in this protocol may prove useful for studying additional insect and animal species in the future.
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Affiliation(s)
- Patrick J Lariviere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Richard D Horak
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - J Elijah Powell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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16
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Zhang Z, Guo Y, Yang F, Li J. Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella. Bioengineering (Basel) 2022; 9:544. [PMID: 36290512 PMCID: PMC9598484 DOI: 10.3390/bioengineering9100544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Gilliamella and Snodgrassella, members of core gut microbiota in corbiculate bees, have high species diversity and adaptability to a wide range of hosts. In this study, we performed species taxonomy and phylogenetic analysis for Gilliamella and Snodgrassella strains that we isolated in our laboratory, in combination with published whole-genome. Functional effects of accessory and unique genes were investigated by KEGG category and pathway annotation in pan-genome analysis. Consequently, in Gilliamella, we inferred the importance of carbohydrate metabolism, amino acid metabolism, membrane transport, energy metabolism, and metabolism of cofactors and vitamins in accessory or unique genes. The pathway mentioned above, plus infectious disease, lipid metabolism, nucleotide metabolism as well as replication and repair exert a pivotal role in accessory or unique genes of Snodgrassella. Further analysis revealed the existence of functional differentiation of accessory and unique genes among Apis-derived genomes and Bombus-derived genomes. We also identified eight and four biosynthetic gene clusters in all Gilliamella and Snodgrassella genomes, respectively. Our study provides a good insight to better understand how host heterogeneity influences the bacterial speciation and affects the versatility of the genome of the gut bacteria.
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