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Tang J, Zuo W, Guo L, Han Z, Yang C, Han B, Dai L, Zhang X, Zhou X. Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria. Nat Commun 2024; 15:6937. [PMID: 39138170 PMCID: PMC11322527 DOI: 10.1038/s41467-024-51365-y] [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: 11/30/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it is unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two honeybee gut bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro and in vivo, Bifidobacterium provides complementary demethylation service to promote Gilliamella growth on methylated homogalacturonan, an enriched polysaccharide of pectin. In exchange, Gilliamella shares digestive products with Bifidobacterium, through which a positive interaction is established. This positive interaction vanishes when Bifidobacterium is not required on a non-methylated diet. Results from biochemical and gene expression analyses combined with model simulation further suggest that the ratio change of the two major homogalacturonan breakdown products, galacturonic acid (GalA) and di-GalA, determines the bacterial interaction. This study unravels how glycan metabolism may shape the interactions between honeybee gut bacteria.
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Affiliation(s)
- Junbo Tang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lizhen Guo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Zhihao Han
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Chengfeng Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Benfeng Han
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Department of Microbiology and Immunology, College of Biological Science, China Agricultural University, Beijing, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, 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, China.
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Todorov SD, Alves MV, Bueno GCA, Alves VF, Ivanova IV. Bee-Associated Beneficial Microbes-Importance for Bees and for Humans. INSECTS 2024; 15:430. [PMID: 38921144 PMCID: PMC11204305 DOI: 10.3390/insects15060430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024]
Abstract
Bees are one of the best-known and, at the same time, perhaps the most enigmatic insects on our planet, known for their organization and social structure, being essential for the pollination of agricultural crops and several other plants, playing an essential role in food production and the balance of ecosystems, being associated with the production of high-value-added inputs, and a unique universe in relation to bees' microbiota. In this review, we summarize information regarding on different varieties of bees, with emphasis on their specificity related to microbial variations. Noteworthy are fructophilic bacteria, a lesser-known bacterial group, which use fructose fermentation as their main source of energy, with some strains being closely related to bees' health status. The beneficial properties of fructophilic bacteria may be extendable to humans and other animals as probiotics. In addition, their biotechnological potential may ease the development of new-generation antimicrobials with applications in biopreservation. The concept of "One Health" brings together fundamental and applied research with the aim of clarifying that the connections between the different components of ecosystems must be considered part of a mega-structure, with bees being an iconic example in that the healthy functionality of their microbiota is directly and indirectly related to agricultural production, bee health, quality of bee products, and the functional prosperity for humans and other animals. In fact, good health of bees is clearly related to the stable functionality of ecosystems and indirectly relates to humans' wellbeing, a concept of the "One Health".
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Affiliation(s)
- Svetoslav Dimitrov Todorov
- ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
- CISAS-Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, 4900-347 Viana do Castelo, Portugal
| | - Marcos Vinício Alves
- ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | | | - Virgínia Farias Alves
- Faculdade de Farmácia, Universidade Federal de Goiás (UFG), Goiânia 74605-170, GO, Brazil (V.F.A.)
| | - Iskra Vitanova Ivanova
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University St. Kliment Ohridski, 8, Bul. Dragan Tzankov, 1164 Sofia, Bulgaria;
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Amin A, Mekadim C, Modrackova N, Bolechova P, Mrazek J, Neuzil-Bunesova V. Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions. Anim Microbiome 2024; 6:21. [PMID: 38698458 PMCID: PMC11064412 DOI: 10.1186/s42523-024-00311-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.
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Affiliation(s)
- Ahmad Amin
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Petra Bolechova
- Department of Ethology and Companion Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Jakub Mrazek
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic.
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Yew WC, Young GR, Nelson A, Cheung W, Stewart CJ, Bridge SH, Granger C, Berrington JE, Embleton ND, Smith DL. The core phageome and its interrelationship with preterm human milk lipids. Cell Rep 2023; 42:113373. [PMID: 37967008 DOI: 10.1016/j.celrep.2023.113373] [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: 03/24/2023] [Revised: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023] Open
Abstract
Phages and lipids in human milk (HM) may benefit preterm infant health by preventing gastrointestinal pathobiont overgrowth and microbiome modulation. Lipid association may promote vertical transmission of phages to the infant. Despite this, interrelationships between lipids and phages are poorly characterized in preterm HM. Shotgun metagenomics and untargeted lipidomics of phage and lipid profiles from 99 preterm HM samples reveals that phages are abundant and prevalent from the first week and throughout the first 100 days of lactation. Phage-host richness of preterm HM increases longitudinally. Core phage communities characterized by Staphylococcus- and Propionibacterium-infecting phages are significantly correlated with long-chain fatty acid abundances over lactational age. We report here a phage-lipid interaction in preterm HM, highlighting the potential importance of phage carriage in preterm HM. These results reveal possible strategies for phage carriage in HM and their importance in early-life microbiota development.
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Affiliation(s)
- Wen C Yew
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Gregory R Young
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - William Cheung
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Simon H Bridge
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Claire Granger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Neonatal Medicine, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Janet E Berrington
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Neonatal Medicine, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Nicholas D Embleton
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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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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Micro"bee"ota: Honey Bee Normal Microbiota as a Part of Superorganism. Microorganisms 2022; 10:microorganisms10122359. [PMID: 36557612 PMCID: PMC9785237 DOI: 10.3390/microorganisms10122359] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Honey bees are model organisms for microbiota research. Gut microbiomes are very interesting for surveys due to their simple structure and relationship with hive production. Long-term studies reveal the gut microbiota patterns of various hive members, as well as the functions, sources, and interactions of the majority of its bacteria. But the fungal non-pathogenic part of gut microbiota is almost unexplored, likewise some other related microbiota. Honey bees, as superorganisms, interact with their own microorganisms, the microbial communities of food stores, hive surfaces, and other environments. Understanding microbiota diversity, its transition ways, and hive niche colonization control are necessary for understanding any separate microbiota niche because of their interplay. The long coevolution of bees with the microorganisms populating these niches makes these systems co-dependent, integrated, and stable. Interaction with the environment, hive, and other bees determines caste lifestyle as well as individual microbiota. In this article, we bring together studies on the microbiota of the western honey bee. We show a possible relationship between caste determination and microbiota composition. And what is primary: caste differentiation or microbiota composition?
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