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Michalik A, C. Franco D, Szklarzewicz T, Stroiński A, Łukasik P. Facultatively intrabacterial localization of a planthopper endosymbiont as an adaptation to its vertical transmission. mSystems 2024; 9:e0063424. [PMID: 38934538 PMCID: PMC11264691 DOI: 10.1128/msystems.00634-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Transovarial transmission is the most reliable way of passing on essential nutrient-providing endosymbionts from mothers to offspring. However, not all endosymbiotic microbes follow the complex path through the female host tissues to oocytes on their own. Here, we demonstrate an unusual transmission strategy adopted by one of the endosymbionts of the planthopper Trypetimorpha occidentalis (Hemiptera: Tropiduchidae) from Bulgaria. In this species, an Acetobacteraceae endosymbiont is transmitted transovarially within deep invaginations of cellular membranes of an ancient endosymbiont Sulcia-strikingly resembling recently described plant virus transmission. However, in males, Acetobacteraceae colonizes the same bacteriocytes as Sulcia but remains unenveloped. Then, the unusual endobacterial localization of Acetobacteraceae observed in females appears to be a unique adaptation to maternal transmission. Further, the symbiont's genomic features, including encoding essential amino acid biosynthetic pathways and its similarity to a recently described psyllid symbiont, suggest a unique combination of the ability to horizontally transmit among species and confer nutritional benefits. The close association with Acetobacteraceae symbiont correlates with the so-far-unreported level of genomic erosion of ancient nutritional symbionts of this planthopper. In Sulcia, this is reflected in substantial changes in genomic organization, reported for the first time in the symbiont renowned for its genomic stability. In Vidania, substantial gene loss resulted in one of the smallest genomes known, at 108.6 kb. Thus, the symbionts of T. occidentalis display a combination of unusual adaptations and genomic features that expand our understanding of how insect-microbe symbioses may transmit and evolve.IMPORTANCEReliable transmission across host generations is a major challenge for bacteria that associate with insects, and independently established symbionts have addressed this challenge in different ways. The facultatively endobacterial localization of Acetobacteraceae symbiont, enveloped by cells of ancient nutritional endosymbiont Sulcia in females but not males of the planthopper Trypetimorpha occidentalis, appears to be a unique adaptation to maternal transmission. Acetobacteraceae's genomic features indicate its unusual evolutionary history, and the genomic erosion experienced by ancient nutritional symbionts demonstrates the apparent consequences of such close association. Combined, this multi-partite symbiosis expands our understanding of the diversity of strategies that insect symbioses form and some of their evolutionary consequences.
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Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Diego C. Franco
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Adam Stroiński
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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Maccaro JJ, Figueroa LL, McFrederick QS. From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees. Mol Ecol 2024; 33:e17421. [PMID: 38828760 DOI: 10.1111/mec.17421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.
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Affiliation(s)
- Jessica J Maccaro
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Laura L Figueroa
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California Riverside, Riverside, California, USA
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3
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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 SCIENCE 2024. [PMID: 38594229 DOI: 10.1111/1744-7917.13365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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4
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Kim M, Kim WJ, Park SJ. Analyzing Gut Microbial Community in Varroa destructor-Infested Western Honeybee ( Apis mellifera). J Microbiol Biotechnol 2023; 33:1495-1505. [PMID: 37482801 DOI: 10.4014/jmb.2306.06040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
The western honeybee Apis mellifera L., a vital crop pollinator and producer of honey and royal jelly, faces numerous threats including diseases, chemicals, and mite infestations, causing widespread concern. While extensive research has explored the link between gut microbiota and their hosts. However, the impact of Varroa destructor infestation remains understudied. In this study, we employed massive parallel amplicon sequencing assays to examine the diversity and structure of gut microbial communities in adult bee groups, comparing healthy (NG) and Varroa-infested (VG) samples. Additionally, we analyzed Varroa-infested hives to assess the whole body of larvae. Our results indicated a notable prevalence of the genus Bombella in larvae and the genera Gillamella, unidentified Lactobacillaceae, and Snodgrassella in adult bees. However, no statistically significant difference was observed between NG and VG. Furthermore, our PICRUSt analysis demonstrated distinct KEGG classification patterns between larval and adult bee groups, with larvae displaying a higher abundance of genes involved in cofactor and vitamin production. Notably, despite the complex nature of the honeybee bacterial community, methanogens were found to be present in low abundance in the honeybee microbiota.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, Jeju 63243, Republic of Korea
| | - Woo Jae Kim
- Center for Life Science (HCLS), Harbin Institute of Technology, No.92 West Dazhi Street, Nangang District, Harbin City, Hei Longjiang Province, P.R. China
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju 63243, Republic of Korea
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5
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Román-Camacho JJ, García-García I, Santos-Dueñas IM, García-Martínez T, Mauricio JC. Latest Trends in Industrial Vinegar Production and the Role of Acetic Acid Bacteria: Classification, Metabolism, and Applications-A Comprehensive Review. Foods 2023; 12:3705. [PMID: 37835358 PMCID: PMC10572879 DOI: 10.3390/foods12193705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Vinegar is one of the most appreciated fermented foods in European and Asian countries. In industry, its elaboration depends on numerous factors, including the nature of starter culture and raw material, as well as the production system and operational conditions. Furthermore, vinegar is obtained by the action of acetic acid bacteria (AAB) on an alcoholic medium in which ethanol is transformed into acetic acid. Besides the highlighted oxidative metabolism of AAB, their versatility and metabolic adaptability make them a taxonomic group with several biotechnological uses. Due to new and rapid advances in this field, this review attempts to approach the current state of knowledge by firstly discussing fundamental aspects related to industrial vinegar production and then exploring aspects related to AAB: classification, metabolism, and applications. Emphasis has been placed on an exhaustive taxonomic review considering the progressive increase in the number of new AAB species and genera, especially those with recognized biotechnological potential.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
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Hettiarachchi A, Cnockaert M, Joossens M, Laureys D, De Clippeleer J, Vereecken NJ, Michez D, Smagghe G, de Graaf DC, Vandamme P. Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina. INSECT MOLECULAR BIOLOGY 2023; 32:510-527. [PMID: 37204105 DOI: 10.1111/imb.12847] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023]
Abstract
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.
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Affiliation(s)
- Amanda Hettiarachchi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Marie Joossens
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jessika De Clippeleer
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
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Härer L, Stýblová S, Ehrmann MA. Bombella pluederhausensis sp. nov., Bombella pollinis sp. nov., Bombella saccharophila sp. nov. and Bombella dulcis sp. nov., four Bombella species isolated from the environment of the western honey bee Apis mellifera. Int J Syst Evol Microbiol 2023; 73. [PMID: 37339070 DOI: 10.1099/ijsem.0.005927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
Four strains of members of the genus Bombella were isolated from samples associated with the western honey bee Apis mellifera, which could not be assigned to a species with a validly published name. Strains TMW 2.2543T, TMW 2.2556T, TMW 2.2558T and TMW 2.2559T exhibit in silico DNA-DNA hybridisation (isDDH) and orthologous average nucleotide identity (orthoANI) values below species delineation thresholds compared with all described species of the genus Bombella and with each other. TMW 2.2556T and TMW 2.2558T form their own clade within the genus. The major respiratory quinone of all strains was Q-10. The composition of cellular fatty acids was diverse between strains. All strains stained Gram-negative, were rod-shaped, strictly aerobic, pellicle-forming, catalase-positive, oxidase-negative, mesophilic and grew over a wide pH range; they were halosensitive but glucose-tolerant. Unlike the other studied strains, TMW 2.2558T was non-motile. Phylogenetic, chemotaxonomic and physiological analyses revealed a clear distinction between all the strains and species with validly published names. All the data support the proposition of four novel species within the genus Bombella, namely Bombella pluederhausensis sp. nov., Bombella pollinis sp. nov., Bombella saccharophila sp. nov. and Bombella dulcis sp. nov., with the respective type strains Bombella pluederhausensis sp. nov. TMW 2.2543T (= DSM 114872T, = LMG 32791T), Bombella pollinis sp. nov. TMW 2.2556T (= DSM 114874T, = LMG 32792T), Bombella saccharophila sp. nov. TMW 2.2558T (= DSM 114875T, = LMG 32793T) and Bombella dulcis sp. nov. TMW 2.2559T (= DSM 114877T, = LMG 32794T). Moreover, three genomes available in the NCBI database that have not yet been described as species with validly published names could be assigned to the proposed species. Bombella sp. ESL0378 and Bombella sp. ESL0385 to Bombella pollinis sp. nov. and Bombella sp. AS1 to Bombella saccharophila sp. nov.
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Affiliation(s)
- Luca Härer
- Chair of Microbiology, Technical University of Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Sabrina Stýblová
- Chair of Microbiology, Technical University of Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Matthias A Ehrmann
- Chair of Microbiology, Technical University of Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
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8
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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: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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9
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Guzman J, Won M, Poehlein A, Sombolestani AS, Mayorga-Ch D, Laureys D, Clippeleer JD, Kämpfer P, Daniel R, Vilcinskas A, Vandamme P, Kwon SW. Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749681 DOI: 10.1099/ijsem.0.005699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Acetic acid bacteria (family Acetobacteraceae) are found in the gut of most insects. Two clades are currently recognized: Commensalibacter-Entomobacter and Bombella-Oecophyllibacter. The latter group is only found in hymenopteran insects and the described species have been isolated from bees and ants. In this study, two new strains DDB2-T1T (=KACC 21507T=LMG 31759T) and DM15PD (=CCM 9165=DSM 112731=KACC 22353=LMG 32454) were isolated from wasps collected in the Republic of Korea and Germany, respectively. Molecular and phenotypic analysis revealed that the strains are closely related, with 16S rRNA gene sequences showing 100 % identity and genomic average nucleotide identity (ANI) values ≥99 %. The closest related species based on type strain 16S rRNA gene sequences are Swingsia samuiensis, Acetobacter peroxydans, Bombella favorum and Bombella intestini (94.8-94.7% identity), whereas the closest related species based on type strain genome analysis are Saccharibacter floricola and Bombella intestini (ANI values of 68.8 and 68.2 %, respectively). The reconstruction of a phylogenomic tree based on 107 core proteins revealed that the branch leading to DDB2-T1T and DM15PD is localized between Oecophyllibacter and Saccharibacter-Bombella. Further genomic distance metrics such as ANI, percentage of conserved proteins and alignment fraction values were consistent with these strains belonging to a new genus. The key phenotypic characteristics were one MALDI-TOF-MS peak (m/z=4601.9±2.0) and the ability to produce acid from d-arabinose. Based on this polyphasic approach, including phylogenetics, phylogenomics, genome distance calculations, ecology and phenotypic characteristics, we propose to name the novel strains Aristophania vespae gen. nov., sp. nov., with the type strain DDB2-T1T (=KACC 21507T=LMG 31759T).
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Daniela Mayorga-Ch
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - David Laureys
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jessika De Clippeleer
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
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10
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Wang H, Lei L, Chen W, Chi X, Han K, Wang Y, Ma L, Liu Z, Xu B. The Comparison of Antioxidant Performance, Immune Performance, IIS Activity and Gut Microbiota Composition between Queen and Worker Bees Revealed the Mechanism of Different Lifespan of Female Casts in the Honeybee. INSECTS 2022; 13:772. [PMID: 36135473 PMCID: PMC9506344 DOI: 10.3390/insects13090772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/20/2022] [Accepted: 08/20/2022] [Indexed: 06/16/2023]
Abstract
Queen bees and worker bees both develop from fertilized eggs, whereas queens live longer than workers. The mechanism of this phenomenon is worth exploring. Antioxidant capacity, immune and IIS are the conserved mechanisms of aging. The importance of gut bacteria for health prompted us to connect with bee aging. Therefore, the differences of antioxidant, immune, IIS and gut microflora between queen and worker bees were compared to find potential mechanisms of queens' longevity. The results showed queens had stronger antioxidant capacity and lower immune pathway and IIS activity than workers. The higher expression level of catalase and SOD1/2 in queens resulted in the stronger ROS scavenging ability, which leads to the lower ROS level and the reduced accumulation of oxidative damage products in queens. The lower IMD expression and higher antimicrobial peptides (AMPs) expressions in queens suggested that queens maintain lower immune pathway activity and stronger immune capacity than workers. Gut bacteria composition analysis indicated that queens had supernal Acetobacteraceae (notably Commensalibacter and Bombella), Lactobacillus and Bifidobacterium over workers. In conclusion, antioxidant, immune, IIS, and gut symbiotic bacteria all contribute to the longevity of queens. This study provides more insights into revealing the mechanisms of queens' longevity.
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11
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Yun BR, Truong AT, Choi YS, Lee MY, Kim BY, Seo M, Yoon SS, Yoo MS, Van Quyen D, Cho YS. Comparison of the gut microbiome of sacbrood virus-resistant and -susceptible Apis cerana from South Korea. Sci Rep 2022; 12:10010. [PMID: 35705585 PMCID: PMC9200864 DOI: 10.1038/s41598-022-13535-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
Honey bees are important pollinators for the conservation of the ecosystem and agricultural products and provide a variety of products important for human use, such as honey, pollen, and royal jelly. Sacbrood disease (SD) is a devastating viral disease in Apis cerana; an effective preventive measure for SD is urgently needed. In this study, the relationship between the gut microbiome of honey bees and SD was investigated by pyrosequencing. Results revealed that sacbrood virus (SBV)-resistant A. cerana strains harbour a unique acetic acid bacterium, Bombella intestini, and the lactic acid bacteria (LAB) Lactobacillus (unclassified)_uc, Bifidobacterium longum, B. catenulatum, Lactococcus lactis, and Leuconostoc mesenteroides in larvae and Hafnia alvei, B. indicum, and the LAB L. mellifer and Lactobacillus HM215046_s in adult bees. Changes in the gut microbiome due to SBV infection resulted in loss of bacteria that could affect host nutrients and inhibit honey bee pathogens, such as Gilliamella JFON_s, Gilliamella_uc, Pseudomonas putida, and L. kunkeei in A. cerana larvae and Frischella_uc, Pantoea agglomerans, Snodgrassella_uc, and B. asteroides in adult bees. These findings provide important information for the selection of probiotics for A. cerana larvae and adults to prevent pathogenic infections and keep honey bees healthy.
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Affiliation(s)
- Bo-Ram Yun
- Parasitic and Insect Disease Laboratory, Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.,Division of Vectors and Parasitic Diseases, Korea Disease Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Heungdeok-gu, Cheongju, Chungbuk, 28159, Republic of Korea.,Department of Veterinary Medicine, College of Veterinary Medicine, Kyungpook National University, Buk-gu, Daegu, 41566, Republic of Korea
| | - A-Tai Truong
- Parasitic and Insect Disease Laboratory, Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.,Faculty of Biotechnology, Thai Nguyen University of Sciences, Thai Nguyen, 250000, Vietnam
| | - Yong Soo Choi
- Department of Agricultural Biology, National Institute of Agricultural Science, Wanju, 55365, Republic of Korea
| | - Man Young Lee
- Department of Agricultural Biology, National Institute of Agricultural Science, Wanju, 55365, Republic of Korea
| | | | - Minjung Seo
- ChunLab Inc., Seoul, 06194, Republic of Korea
| | - Soon-Seek Yoon
- Parasitic and Insect Disease Laboratory, Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Mi-Sun Yoo
- Parasitic and Insect Disease Laboratory, Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Dong Van Quyen
- University of Science and Technology of Ha Noi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
| | - Yun Sang Cho
- Parasitic and Insect Disease Laboratory, Bacterial Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
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12
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Chua KO, Liew YJM, See-Too WS, Tan JY, Yong HS, Yin WF, Chan KG. Formicincola oecophyllae gen. nov. sp. nov., a novel member of the family Acetobacteraceae isolated from the weaver ant Oecophylla smaragdina. Antonie van Leeuwenhoek 2022; 115:995-1007. [DOI: 10.1007/s10482-022-01750-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
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13
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Comparative Genomics of Acetic Acid Bacteria within the Genus Bombella in Light of Beehive Habitat Adaptation. Microorganisms 2022; 10:microorganisms10051058. [PMID: 35630502 PMCID: PMC9147383 DOI: 10.3390/microorganisms10051058] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/10/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
It is known that the bacterial microbiota in beehives is essential for keeping bees healthy. Acetic acid bacteria of the genus Bombella colonize several niches in beehives and are associated with larvae protection against microbial pathogens. We have analyzed the genomes of 22 Bombella strains of different species isolated in eight different countries for taxonomic affiliation, central metabolism, prophages, bacteriocins and tetracycline resistance to further elucidate the symbiotic lifestyle and to identify typical traits of acetic acid bacteria. The genomes can be assigned to four different species. Three genomes show ANIb values and DDH values below species demarcation values to any validly described species, which identifies them as two potentially new species. All Bombella spp. lack genes in the Embden–Meyerhof–Parnas pathway and the tricarboxylic acid cycle, indicating a focus of intracellular carbohydrate metabolism on the pentose phosphate pathway or the Entner–Doudoroff pathway for which all genes were identified within the genomes. Five membrane-bound dehydrogenases were identified that catalyze oxidative fermentation reactions in the periplasm, yielding oxidative energy. Several complete prophages, but no bacteriocins, were identified. Resistance to tetracycline, used to prevent bacterial infections in beehives, was only found in Bombella apis MRM1T. Bombella strains exhibit increased osmotolerance in high glucose concentrations compared to Gluconobacter oxydans, indicating adaption to high sugar environments such as beehives.
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14
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Abstract
Diet and gut microbiomes are intricately linked on both short and long timescales. Changes in diet can alter the microbiome, while microbes in turn allow hosts to access novel diets. Bees are wasps that switched to a vegetarian lifestyle, and the vast majority of bees feed on pollen and nectar. Some stingless bee species, however, also collect carrion, and a few have fully reverted to a necrophagous lifestyle, relying on carrion for protein and forgoing flower visitation altogether. These “vulture” bees belong to the corbiculate apid clade, which is known for its ancient association with a small group of core microbiome phylotypes. Here, we investigate the vulture bee microbiome, along with closely related facultatively necrophagous and obligately pollinivorous species, to understand how these diets interact with microbiome structure. Via deep sequencing of the 16S rRNA gene and subsequent community analyses, we find that vulture bees have lost some core microbes, retained others, and entered into novel associations with acidophilic microbes found in the environment and on carrion. The abundance of acidophilic bacteria suggests that an acidic gut is important for vulture bee nutrition and health, as has been found in other carrion-feeding animals. Facultatively necrophagous bees have more variable microbiomes than strictly pollinivorous bees, suggesting that bee diet may interact with microbiomes on both short and long timescales. Further study of vulture bees promises to provide rich insights into the role of the microbiome in extreme diet switches.
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15
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Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie van Leeuwenhoek 2021; 115:41-58. [PMID: 34761294 PMCID: PMC8776678 DOI: 10.1007/s10482-021-01676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022]
Abstract
Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.
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16
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Abstract
Bumblebees (Bombus) are charismatic and important pollinators. They are one of the best studied insect groups, especially in terms of ecology, behavior, and social structure. As many species are declining, there is a clear need to understand more about them. Microbial symbionts, which can influence many dimensions of animal life, likely have an outsized role in bumblebee biology. Recent research has shown that a conserved set of beneficial gut bacterial symbionts is ubiquitous across bumblebees. These bacteria are related to gut symbionts of honeybees, but have not been studied as intensively. Here we synthesize studies of bumblebee gut microbiota, highlight major knowledge gaps, and suggest future directions. Several patterns emerge, such as symbiont-host specificity maintained by sociality, frequent symbiont loss from individual bees, symbiont-conferred protection from trypanosomatid parasites, and divergence between bumblebee and honeybee microbiota in several key traits. For many facets of bumblebee-microbe interactions, however, underlying mechanisms and ecological functions remain unclear. Such information is important if we are to understand how bumblebees shape, and are shaped by, their gut microbiota. Bumblebees may provide a useful system for microbiome scientists, providing insights into general principles of host-microbe interactions. We also note how microbiota could influence bumblebee traits and responses to stressors. Finally, we propose that tinkering with the microbiota could be one way to aid bumblebee resilience in the face of global change.
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Affiliation(s)
- Tobin J. Hammer
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703
- Corresponding author:
| | - Eli Le
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703
| | - Alexia N. Martin
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703
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17
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Smith EA, Anderson KE, Corby-Harris V, McFrederick QS, Parish AJ, Rice DW, Newton ILG. Reclassification of seven honey bee symbiont strains as Bombella apis. Int J Syst Evol Microbiol 2021; 71. [PMID: 34546865 DOI: 10.1099/ijsem.0.004950] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture's most important pollinator. One factor that may influence colony health is the microbial community. Although honey bee worker guts have a characteristic community of bee-specific microbes, the honey bee queen digestive tracts are colonized predominantly by a single acetic acid bacterium tentatively named 'Parasaccharibacter apium'. This bacterium is related to flower-associated microbes such as Saccharibacter floricola, and initial phylogenetic analyses placed it as sister to these environmental bacteria. We used a combination of phylogenetic and sequence identity methods to better resolve evolutionary relationships among 'P. apium', strains in the genus Saccharibacter, and strains in the closely related genus Bombella. Interestingly, measures of genome-wide average nucleotide identity and aligned fraction, coupled with phylogenetic placement, indicate that many strains labelled as 'P. apium' and Saccharibacter species are all the same species as Bombella apis. We propose reclassifying these strains as Bombella apis and outline the data supporting that classification below.
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Affiliation(s)
- Eric A Smith
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Present address: Diversigen, INC, New Brighton, MN, USA
| | - Kirk E Anderson
- Carl Hayden Bee Research Center, USDA-ARS, Tucson, Arizona, USA
| | | | - Quinn S McFrederick
- Department of Entomology, University of California, Riverside, California, USA
| | - Audrey J Parish
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Danny W Rice
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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18
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Hilgarth M, Redwitz J, Ehrmann MA, Vogel RF, Jakob F. Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera. Int J Syst Evol Microbiol 2021; 71. [PMID: 33439113 DOI: 10.1099/ijsem.0.004633] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella. Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella, for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).
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Affiliation(s)
- Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Johannes Redwitz
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Frank Jakob
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
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19
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Sombolestani AS, Cleenwerck I, Cnockaert M, Borremans W, Wieme AD, De Vuyst L, Vandamme P. Characterization of novel Gluconobacter species from fruits and fermented food products : Gluconobacter cadivus sp. nov. , Gluconobacter vitians sp. nov. and Gluconobacter potus sp. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 33709905 DOI: 10.1099/ijsem.0.004751] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains LMG 1744T, LMG 1745, LMG 31484T, LMG 1764T and R-71646 were isolated from rotting fruits and fermented food products. A phylogenomic analysis based on 107 single-copy core genes revealed that they grouped in a Gluconobacter lineage comprising Gluconobacter oxydans, Gluconobacter roseus, Gluconobacter sphaericus, Gluconobacter kanchanaburiensis, Gluconobacter albidus, Gluconobacter cerevisiae, Gluconobacter kondonii and Gluconobacter aidae. OrthoANIu and digital DNA hybridization analyses demonstrated that these five strains represented three novel Gluconobacter species, which could be differentiated from the type strains of closely related Gluconobacter species by multiple phenotypic characteristics. We therefore propose to classify strains LMG 1744T and LMG 1745 in the novel species Gluconobacter cadivus sp. nov., with LMG 1744T (=CECT 30141T) as the type strain; to classify strain LMG 31484T as the novel species Gluconobacter vitians sp. nov., with LMG 31484T (=CECT 30132T) as the type strain; and to classify strains LMG 1764T and R-71646 in the novel species Gluconobacter potus sp. nov., with LMG 1764T (=CECT 30140T) as the type strain.
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Affiliation(s)
- Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-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, B-1050 Brussels, Belgium
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, 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, B-1050 Brussels, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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20
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Elzeini HM, Ali ARAA, Nasr NF, Hassan M, Hassan AAM, Elenany YE. Probiotic capability of novel lactic acid bacteria isolated from worker honey bees gut microbiota. FEMS Microbiol Lett 2021; 368:6168380. [PMID: 33705519 DOI: 10.1093/femsle/fnab030] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
The study aimed to evaluate the probiotic and safety properties of lactic acid bacterial (LAB) strains isolated from the gut microbiota of honey bee Apis mellifera L., since this source remains a promising reservoir of microbial diversity. A total of five bacterial isolates were molecularly identified using 16S rRNA gene sequencing as Enterococcus faecalis-HBE1, Lactobacillus brevis-HBE2, Enterococcus faecalis-HBE3, Enterococcus faecalis-HBE4 and Lactobacillus casei-HBE5. Gut tolerance conditions (low pH and bile salt) were evaluated. Exopolysaccharides (EPS) production, hemolytic, antioxidant activity, resistance toward antibiotics and technological characteristics (starter activity, pH and proteolysis) were examined. The five isolates showed a high survival rate (>95%), under gastrointestinal tract conditions indicating excellent potential for application as probiotics. The isolates showed no hemolytic activities and good acidification rates in the range of pH 4.6-4.98 after incubation at 37°C for 24h. The isolates exhibited promising proteolytic activity as well as DPPH radical scavenging activity in the range of 16.52-59.39%. All the tested isolates had the capability to produce exopolysaccharides except Lactobacillus casei-HBE5. These results put forward that lactic acid bacterial strain isolated from honey bee workers can be considered as promising candidates for future applications as starter cultures and could constitute new potential probiotics for the production of functional dietary products promoting health benefits.
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Affiliation(s)
- Hoda Mahmoud Elzeini
- Department of Dairy Science, Faculty of Agriculture, Cairo University, Giza, Egypt
| | | | - Nasr Fawzy Nasr
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mariam Hassan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Yasser Essam Elenany
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza, Egypt
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21
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Guzman J, Sombolestani AS, Poehlein A, Daniel R, Cleenwerck I, Vandamme P, Vilcinskas A. Entomobacter blattae gen. nov., sp. nov., a new member of the Acetobacteraceae isolated from the gut of the cockroach Gromphadorhina portentosa. Int J Syst Evol Microbiol 2021; 71. [PMID: 33528344 DOI: 10.1099/ijsem.0.004666] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium designated G55GPT and pertaining to the family Acetobacteraceae was isolated from the gut of the Madagascar hissing cockroach Gromphadorhina portentosa. The Gram-negative cells were rod-shaped and non-motile. The complete 16S rRNA sequence of the strain G55GPT showed the highest pairwise similarity to Gluconacetobacter johannae CFN-Cf-55T (95.35 %), suggesting it represents a potential new genus of the family Acetobacteraceae. Phylogenetic analysis based on 16S rRNA gene and 106 orthologous housekeeping protein sequences revealed that G55GPT forms a monophyletic clade with the genus Commensalibacter, which thus far has also been isolated exclusively from insects. The G55GPT genome size was 2.70 Mbp, and the G+C content was 45.4 mol%, which is lower than most acetic acid bacteria (51-68 mol%) but comparable to Swingsia samuiensis AH83T (45.1 mol%) and higher than Commensalibacter intestini A911T (36.8 mol%). Overall genome relatedness indices based on gene and protein sequences strongly supported the assignment of G55GPT to a new genus within the family Acetobacteraceae. The percentage of conserved proteins, which is a useful metric for genus differentiation, was below 54 % when comparing G55GPT to type strains of acetic acid bacteria, thus strongly supporting our hypothesis that G55GPT is a member of a yet-undescribed genus. The fatty acid composition of G55GPT differed from that of closely related acetic acid bacteria, particularly given the presence of C19 : 1 ω9c/ω11c and the absence of C14 : 0 and C14 : 0 2-OH fatty acids. Strain G55GPT also differed in terms of metabolic features such as its ability to produce acid from d-mannitol, and its inability to produce acetic acid from ethanol or to oxidize glycerol to dihydroxyacetone. Based on the results of combined genomic, phenotypic and phylogenetic characterizations, isolate G55GPT (=LMG 31394T=DSM 111244T) is considered to represent a new species in a new genus, for which we propose the name Entomobacter blattae gen. nov., sp. nov.
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.,Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany.,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
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22
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Sombolestani AS, Cleenwerck I, Cnockaert M, Borremans W, Wieme AD, Moutia Y, Spaepen S, De Vuyst L, Vandamme P. Gluconacetobacter dulcium sp. nov., a novel Gluconacetobacter species from sugar-rich environments. Int J Syst Evol Microbiol 2020; 71. [PMID: 33351739 DOI: 10.1099/ijsem.0.004569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phylogenomic analysis based on 107 single-copy core genes revealed that three strains from sugar-rich environments, i.e. LMG 1728T, LMG 1731 and LMG 22058, represented a single, novel Gluconacetobacter lineage with Gluconacetobacter liquefaciens as nearest validly named neighbour. OrthoANIu and digital DNA-DNA hybridization analyses among these strains and Gluconacetobacter type strains confirmed that the three strains represented a novel Gluconacetobacter species. Biochemical characteristics and MALDI-TOF mass spectra allowed differentiation of this novel species from the type strains of G. liquefaciens and other closely related Gluconacetobacter species. We therefore propose to classify strains LMG 1728T, LMG 1731 and LMG 22058 in the novel species Gluconacetobacter dulcium sp. nov., with LMG 1728T (=CECT 30142T) as the type strain.
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Affiliation(s)
- Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-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, B-1050 Brussels, Belgium
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Yvan Moutia
- Plant Pathology Department, Mauritius Sugarcane Industry Research Institute, Mauritius Cane Industry Authority, 1, Moka Road, Réduit, Mauritius.,Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 - Box 2460, B-3001 Heverlee, Belgium
| | - Stijn Spaepen
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 - Box 2460, B-3001 Heverlee, 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, B-1050 Brussels, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina. J Microbiol 2020; 58:988-997. [DOI: 10.1007/s12275-020-0325-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/19/2020] [Accepted: 09/10/2020] [Indexed: 01/06/2023]
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24
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Sombolestani AS, Cleenwerck I, Cnockaert M, Borremans W, Wieme AD, De Vuyst L, Vandamme P. Novel acetic acid bacteria from cider fermentations: Acetobacter conturbans sp. nov. and Acetobacter fallax sp. nov. Int J Syst Evol Microbiol 2020; 70:6163-6171. [PMID: 33052084 DOI: 10.1099/ijsem.0.004511] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains LMG 1627T, LMG 1636T and LMG 1637 were all isolated from cider fermentations in the 1940s and 1950s. A recent study based on MALDI-TOF MS and dnaK gene sequence analyses suggested they represented novel Acetobacter species. In the present study, we determined the whole-genome sequences of these strains and analysed their phenotypic and chemotaxonomic characteristics. A phylogenomic analysis based on 107 single-copy core genes revealed that they represented a single Acetobacter lineage with Acetobacter aceti, Acetobacter sicerae, Acetobacter musti and Acetobacter oeni, Acetobacter estunensis and with Acetobacter nitrogenifigens as an outgroup to this cluster. OrthoANIu value and dDDH analyses among these and other Acetobacter type strains confirmed that these three strains represented two novel Acetobacter species, which could be differentiated from other closely related type strains of Acetobacter by different phenotypic tests, such as ketogenesis from glycerol. We therefore propose to classify strain LMG 1627T in the novel species Acetobacter conturbans sp. nov., with LMG 1627T (=NCIMB 8945T) as the type strain, and to classify strains LMG 1636T and LMG 1637 in the novel species Acetobacter fallax sp. nov., with LMG 1636T (=NCIMB 8956T) as the type strain.
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Affiliation(s)
- Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-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, B-1050 Brussels, Belgium
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, 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, B-1050 Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Smith EA, Newton ILG. Genomic Signatures of Honey Bee Association in an Acetic Acid Symbiont. Genome Biol Evol 2020; 12:1882-1894. [PMID: 32870981 PMCID: PMC7664317 DOI: 10.1093/gbe/evaa183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture's most important pollinator. Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. One factor that may influence colony health is the microbial community. Indeed, the honey bee worker digestive tract harbors a characteristic community of bee-specific microbes, and the composition of this community is known to impact honey bee health. However, the honey bee is a superorganism, a colony of eusocial insects with overlapping generations where nestmates cooperate, building a hive, gathering and storing food, and raising brood. In contrast to what is known regarding the honey bee worker gut microbiome, less is known of the microbes associated with developing brood, with food stores, and with the rest of the built hive environment. More recently, the microbe Bombella apis was identified as associated with nectar, with developing larvae, and with honey bee queens. This bacterium is related to flower-associated microbes such as Saccharibacter floricola and other species in the genus Saccharibacter, and initial phylogenetic analyses placed it as sister to these environmental bacteria. Here, we used comparative genomics of multiple honey bee-associated strains and the nectar-associated Saccharibacter to identify genomic changes that may be associated with the ecological transition to honey bee association. We identified several genomic differences in the honey bee-associated strains, including a complete CRISPR/Cas system. Many of the changes we note here are predicted to confer upon Bombella the ability to survive in royal jelly and defend themselves against mobile elements, including phages. Our results are a first step toward identifying potential function of this microbe in the honey bee superorganism.
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Affiliation(s)
- Eric A Smith
- Department of Biology, Indiana University, Bloomington
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26
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Marič L, Cleenwerck I, Accetto T, Vandamme P, Trček J. Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar. Microorganisms 2020; 8:E1178. [PMID: 32756518 PMCID: PMC7465234 DOI: 10.3390/microorganisms8081178] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 01/18/2023] Open
Abstract
Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S-23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S-23S rRNA gene ITS of AV382 was to Komagataeibacter kakiaceti LMG 26206T (91.6%), of AV436 to Komagataeibacter xylinus LMG 1515T (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to K. kakiaceti (ANIb 88.2%) and AV436 to K. xylinus (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus Komagataeibacter. The strain AV382 can be differentiated from its closest relatives K. kakiaceti and Komagataeibacter saccharivorans by its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C19:0 cyclo ω8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relatives K. xylinus, Komagataeibacter sucrofermentans, and Komagataeibacter nataicola by its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C18:1ω7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382T and AV436T represent novel species of the genus Komagataeibacter, for which the names Komagataeibactermelaceti sp. nov. and Komagataeibacter melomenusus are proposed, respectively. The type strain of Komagataeibacter melaceti is AV382T (= ZIM B1054T = LMG 31303T = CCM 8958T) and of Komagataeibacter melomenusus AV436T (= ZIM B1056T = LMG 31304T = CCM 8959T).
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Affiliation(s)
- Leon Marič
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, SI-2000 Maribor, Slovenia;
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, B-9000 Ghent, Belgium; (I.C.); (P.V.)
| | - Tomaž Accetto
- Animal Science Department, Biotechnical Faculty, University of Ljubljana, SI-1230 Domžale, Slovenia;
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, B-9000 Ghent, Belgium; (I.C.); (P.V.)
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, SI-2000 Maribor, Slovenia;
- Faculty of Chemistry and Chemical Engineering, University of Maribor, SI-2000 Maribor, Slovenia
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Insect pollination: an ecological process involved in the assembly of the seed microbiota. Sci Rep 2020; 10:3575. [PMID: 32107443 PMCID: PMC7046713 DOI: 10.1038/s41598-020-60591-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 02/13/2020] [Indexed: 11/08/2022] Open
Abstract
The assembly of the seed microbiota involves some early microbial seed colonizers that are transmitted from the maternal plant through the vascular system, while other microbes enter through the stigma. Thus, the seed microbiota consists of microbes not only recruited from the plant vascular tissues, but also from the flower. Flowers are known to be a hub for microbial transmission between plants and insects. This floral-insect exchange opens the possibility for insect-transmitted bacteria to colonize the ovule and, subsequently, the seed to pass then into the next plant generation. In this study, we evaluated the contribution of insect pollination to the seed microbiota through high-throughput sequencing. Oilseed rape (OSR) flowers were exposed to visits and pollination by honey bees (Apis mellifera), red mason bees (Osmia bicornis), hand pollinated or left for autonomous self-pollination (ASP). Sequence analyses revealed that honey bee visitation reduced bacterial richness and diversity in seeds, but increased the variability of seed microbial structure, and introduced bee-associated taxa. In contrast, mason bee pollination had minor effects on the seed microbiota. Our study provides the first evidence that insect pollination is an ecological process involved in the transmission of bacteria from flowers to seeds.
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28
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Jakob F, Quintero Y, Musacchio A, Estrada‐de los Santos P, Hernández L, Vogel RF. Acetic acid bacteria encode two levansucrase types of different ecological relationship. Environ Microbiol 2019; 21:4151-4165. [DOI: 10.1111/1462-2920.14768] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Frank Jakob
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München Gregor‐Mendel‐Straße 4, 85354 Freising Germany
| | - Yamira Quintero
- Grupo Tecnología de Enzimas, Centro de Ingeniería Genética y Biotecnología (CIGB) Ave 31 entre 158 y 190, Apartado Postal 6162, Habana 10600 Cuba
| | - Alexis Musacchio
- Departamento de Biología de Sistemas Centro de Ingeniería Genética y Biotecnología (CIGB) Ave 31 entre 158 y 190, Apartado Postal 6162, Habana 10600 Cuba
| | - Paulina Estrada‐de los Santos
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. de Carpio y Plan de Ayala s/n Col. Santo Tomás C.P., 11340 Cd. de México Mexico
| | - Lázaro Hernández
- Grupo Tecnología de Enzimas, Centro de Ingeniería Genética y Biotecnología (CIGB) Ave 31 entre 158 y 190, Apartado Postal 6162, Habana 10600 Cuba
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München Gregor‐Mendel‐Straße 4, 85354 Freising Germany
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29
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Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01497-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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30
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Praet J, Parmentier A, Schmid-Hempel R, Meeus I, Smagghe G, Vandamme P. Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition. Environ Microbiol 2017; 20:214-227. [PMID: 29076622 DOI: 10.1111/1462-2920.13973] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 10/16/2017] [Accepted: 10/21/2017] [Indexed: 12/13/2022]
Abstract
A total of 1940 isolates from gut samples of 60 bumblebees representing Bombus pascuorum, Bombus terrestris, Bombus lucorum and Bombus lapidarius was collected and identified through state-of the-art taxonomic methods. The bacterial species diversity in these Bombus species exceeded that suggested by phylotype analysis through 16S rRNA amplicon sequencing, and revealed that B. pascuorum and B. terrestris had a unique microbiota composition, each. Representatives of most phylotypes reported earlier and detected in the present study were effectively isolated, and included several novel bacterial taxa and species reported for the first time in the bumblebee gut. Isolates were screened in pectin degradation assays and growth inhibition assays against the honeybee pathogens Paenibacillus larvae, Melissococcus plutonius and Ascosphaera apis and the bumblebee parasite Crithidia bombi. While inhibitory activity against each of these pathogens was observed, only one single culture was able to degrade pectin and polygalacturonic acid in vitro. The availability of accurately identified microbial isolates will facilitate future evaluation of the functional potential of the bumblebee gut microbiota.
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Affiliation(s)
- Jessy Praet
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, Ghent B-9000, Belgium
| | - Anneleen Parmentier
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | | | - Ivan Meeus
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, Ghent B-9000, Belgium
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Draft Genome Sequences of Saccharibacter sp. Strains 3.A.1 and M18 Isolated from Honey and a Honey Bee ( Apis mellifera) Stomach. GENOME ANNOUNCEMENTS 2017; 5:5/30/e00744-17. [PMID: 28751408 PMCID: PMC5532846 DOI: 10.1128/genomea.00744-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The annotated draft genome sequences of two recent Saccharibacter sp. strains isolated from honey and a honey bee stomach in 2014 are reported here. Currently, two Saccharibacter whole-genome sequences are available in databases; thus, the sequences of our new isolates will contribute to a better understanding of Saccharibacter genomes.
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32
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Yun JH, Lee JY, Hyun DW, Jung MJ, Bae JW. Bombella apis sp. nov., an acetic acid bacterium isolated from the midgut of a honey bee. Int J Syst Evol Microbiol 2017; 67:2184-2188. [PMID: 28671528 DOI: 10.1099/ijsem.0.001921] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As part of a study to investigate the microbial diversity in the intestine of Apis mellifera, we isolated strain MRM1T from the midgut. MRM1T was a Gram-stain-negative, strictly aerobic, non-motile, non-spore forming and rod-shaped bacteria. Creamy beige-coloured colonies were circular with entire margins in Lactobacilli MRS agar. The strain grew at 25-37 °C (optimum, 30-37 °C) and at a pH range of 4.0 to 9.0 (optimum pH, 7.0-8.5). The strain tolerated 0-1 % (w/v) NaCl (optimal growth occurred in the absence of NaCl). On the basis of the results of a phylogenetic analysis based on the 16S rRNA gene sequences, we determined that MRM1T represents a member of the genus Bombella with the highest sequence similarity to Bombella intestini LMG 28161T (98.8 %). The major quinone was Q10, and dominant fatty acids (>10 %) were C19 : 0cyclo ω8c (33.6 %), C16 : 0 (22.2 %), C18 : 1ω7c (15.9 %) and C14 : 0 (12.5 %). The polar lipid profile of MRM1T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified phospholipid and four unidentified lipids. The DNA G+C content of MRM1T was 59.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, MRM1T represents a novel species of the genus Bombella, for which the name Bombella apis sp. nov. is proposed with the type strain MRM1T (=KCTC 52452T=JCM 31623T).
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Affiliation(s)
- Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius. PLoS One 2016; 11:e0165611. [PMID: 27851750 PMCID: PMC5112900 DOI: 10.1371/journal.pone.0165611] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/15/2016] [Indexed: 11/19/2022] Open
Abstract
The whole-genome sequence of Bombella intestini LMG 28161T, an endosymbiotic acetic acid bacterium (AAB) occurring in bumble bees, was determined to investigate the molecular mechanisms underlying its metabolic capabilities. The draft genome sequence of B. intestini LMG 28161T was 2.02 Mb. Metabolic carbohydrate pathways were in agreement with the metabolite analyses of fermentation experiments and revealed its oxidative capacity towards sucrose, D-glucose, D-fructose and D-mannitol, but not ethanol and glycerol. The results of the fermentation experiments also demonstrated that the lack of effective aeration in small-scale carbohydrate consumption experiments may be responsible for the lack of reproducibility of such results in taxonomic studies of AAB. Finally, compared to the genome sequences of its nearest phylogenetic neighbor and of three other insect associated AAB strains, the B. intestini LMG 28161T genome lost 69 orthologs and included 89 unique genes. Although many of the latter were hypothetical they also included several type IV secretion system proteins, amino acid transporter/permeases and membrane proteins which might play a role in the interaction with the bumble bee host.
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Abstract
The gut microbiota can have profound effects on hosts, but the study of these relationships in humans is challenging. The specialized gut microbial community of honey bees is similar to the mammalian microbiota, as both are mostly composed of host-adapted, facultatively anaerobic and microaerophilic bacteria. However, the microbial community of the bee gut is far simpler than the mammalian microbiota, being dominated by only nine bacterial species clusters that are specific to bees and that are transmitted through social interactions between individuals. Recent developments, which include the discovery of extensive strain-level variation, evidence of protective and nutritional functions, and reports of eco-physiological or disease-associated perturbations to the microbial community, have drawn attention to the role of the microbiota in bee health and its potential as a model for studying the ecology and evolution of gut symbionts.
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Affiliation(s)
- Waldan K Kwong
- Department of Integrative Biology, University of Texas, Austin, Texas 78712, USA
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas, Austin, Texas 78712, USA
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35
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Wang B, Shao Y, Chen T, Chen W, Chen F. Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics. Sci Rep 2015; 5:18330. [PMID: 26691589 PMCID: PMC4686929 DOI: 10.1038/srep18330] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/16/2015] [Indexed: 12/11/2022] Open
Abstract
Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.
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Affiliation(s)
- Bin Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Tao Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Wanping Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Fusheng Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China.,Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068, Hubei Province, P. R. China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
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36
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Pelistega suis sp. nov., isolated from domestic and wild animals. Int J Syst Evol Microbiol 2015; 65:4909-4914. [DOI: 10.1099/ijsem.0.000673] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biochemical and molecular genetic studies were performed on three novel Gram-stain-negative, catalase- and oxidase-positive, bacilli-shaped organisms isolated from the tonsils of two pigs and one wild boar. The micro-organism was identified as a species of the genus Pelistega based on its cellular morphological and biochemical tests. The closest phylogenetic relative of the novel bacilli was Pelistega indica HM-7T (98.2 % 16S rRNA gene sequence similarity to the type strain). groEL and gyrB sequence analysis showed interspecies divergence from the closest 16S rRNA gene phylogenetic relative, P. indica of 87.0.% and 69 %, respectively. The polyamine pattern contains predominantly putrescine and 2-hydroxyputrescine. The major quinone is ubiquinone Q-8 and in the polar lipid profile, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid are predominant. The novel bacterial isolate can be distinguished from P. indica by several biochemical characteristics, such as the production of l-pyrrolydonil arylamidase but not gamma-glutamyl-transferase, and the utilization of different carbon sources. Based on both phenotypic and phylogenetic findings, the novel bacterium is classified as representing a novel species of the genus Pelistega, for which the name Pelistega suis sp. nov. is proposed. The type strain is 3340-03T ( = CECT 8400T = CCUG 64465T).
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