Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 8

gen. nov., sp. nov., a novel actinobacterial genus isolated from beehive through cross-feeding interactions Open Access

Abstract

Most micro-organisms remain unculturable under standard laboratory conditions, limiting our understanding of microbial diversity and ecological interactions. One major cause of this uncultivability is the loss of access to essential cross-fed metabolites when bacteria are removed from their natural communities. During a bioprospecting campaign targeting actinomycetes of an beehive, we identified five isolates (DT32, DT45, DT55, DT59 and DT194) that required co-cultivation for growth recovery, suggesting a dependence on microbial interactions in their native habitat. Whole-genome sequencing and phylogenetic analysis positioned these isolates within a distinct lineage of , separate from the five officially recognized clades of the genus. A combination of microscopic, chemotaxonomic and physiological characterizations further supported their uniqueness. Notably, they exhibited high auxotrophy, being unable to use all carbon sources tested, likely due to genome reduction (4.6 Mbp) compared to other . Pangenomic comparisons with their closest relatives revealed gene losses in key metabolic pathways, including the glyoxylate bypass and the Entner–Doudoroff pathway, which may explain their metabolic reliance. These findings reveal a highly specialized, ecologically adapted lineage with deep evolutionary divergence and further support microbial interdependence isolation strategies to explore the microbial dark matter. We propose as a novel genus and species within the phylum, with isolate DT45 as the representative type species and type strain, which has been deposited in public collections under the accession numbers DSM 117791 and LMG 33580.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): auxotrophy , bioprospecting , insect-associated bacteria , microbial cross-feeding , microbial dark matter and uncultured bacteria
Funding
This study was supported by the:
  • Université de Liège (Award Mind Project, grant R.CFRA-3306)
    • Principal Award Recipient: SébastienRigali
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006868
2025-08-11
2025-12-13

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/8/ijsem006868.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006868&mimeType=html&fmt=ahah

References

  1. Zha Y, Chong H, Yang P, Ning K. Microbial dark matter: from discovery to applications. Genom Proteom Bioinform 2022; 20:867–881 [View Article] [PubMed]
     [Google Scholar]
  2. Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14: [View Article]
     [Google Scholar]
  3. Adam D, Maciejewska M, Naômé A, Martinet L, Coppieters W et al. Isolation, characterization, and antibacterial activity of hard-to-culture actinobacteria from cave moonmilk deposits. Antibiotics 2018; 7:28 [View Article] [PubMed]
     [Google Scholar]
  4. Maciejewska M, Adam D, Martinet L, Naômé A, Całusińska M et al. A phenotypic and genotypic analysis of the antimicrobial potential of cultivable Streptomyces isolated from cave moonmilk deposits. Front Microbiol 2016; 7:1455 [View Article] [PubMed]
     [Google Scholar]
  5. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Evol Microbiol 1966; 16:313–340 [View Article]
     [Google Scholar]
  6. Stulanovic N, Kerdel Y, Belde L, Rezende L, Deflandre B et al. Nitrogen fertilizers activate siderophore production by the common scab causative agent Streptomyces scabiei. Metallomics 2024; 16:mfae048 [View Article] [PubMed]
     [Google Scholar]
  7. Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA. Practical Streptomyces Genetics: A Laboratory Manual Norwich: John Innes Foundation; 2000
     [Google Scholar]
  8. Maciejewska M, Pessi IS, Arguelles-Arias A, Noirfalise P, Luis G et al. Streptomyces lunaelactis sp. nov., a novel ferroverdin A-producing Streptomyces species isolated from a moonmilk speleothem. Antonie van Leeuwenhoek 2015; 107:519–531 [View Article] [PubMed]
     [Google Scholar]
  9. Zech H, Thole S, Schreiber K, Kalhöfer D, Voget S et al. Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Prpteomics 2009; 9:3677–3697 [View Article] [PubMed]
     [Google Scholar]
  10. Schumann P. 5 - Peptidoglycan structure. In Rainey F, Oren A. eds Methods in Microbiology Academic Press; pp 101–129
     [Google Scholar]
  11. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids
     [Google Scholar]
  12. Vieira S, Huber KJ, Neumann-Schaal M, Geppert A, Luckner M et al. Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  13. Vilchèze C, Jacobs WR. Isolation and analysis of Mycobacterium tuberculosis mycolic acids. Curr Protoc Microbiol 2007; Chapter 10:Unit 10A.3 [View Article] [PubMed]
     [Google Scholar]
  14. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  15. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology John Wiley & Sons, Ltd; pp 330–393 [View Article]
     [Google Scholar]
  16. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  17. Madeira F, Madhusoodanan N, Lee J, Eusebi A, Niewielska A et al. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Res 2024; 52:W521–W525 [View Article] [PubMed]
     [Google Scholar]
  18. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  19. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
     [Google Scholar]
  20. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  21. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  22. Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 2024; 52:W78–W82 [View Article] [PubMed]
     [Google Scholar]
  23. Cornet L, Durieu B, Baert F, D’hooge E, Colignon D et al. The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics. GigaScience 2022; 12:giad022 [View Article]
     [Google Scholar]
  24. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  25. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  26. Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genom Biol 2021; 22:178 [View Article] [PubMed]
     [Google Scholar]
  27. Cornet L, Baurain D. Contamination detection in genomic data: more is not enough. Genom Biol 2022; 23:60 [View Article] [PubMed]
     [Google Scholar]
  28. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genom Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  29. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
     [Google Scholar]
  30. Criscuolo A, Gribaldo S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 2010; 10:210 [View Article]
     [Google Scholar]
  31. Roure B, Rodriguez-Ezpeleta N, Philippe H. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol 2007; 7 Suppl 1:S2 [View Article] [PubMed]
     [Google Scholar]
  32. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  33. Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD et al. Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria. ISME Commun 2021; 1:16 [View Article] [PubMed]
     [Google Scholar]
  34. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 2015; 3:e1319 [View Article] [PubMed]
     [Google Scholar]
  35. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  36. Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG et al. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res 2023; 51:D603–D610 [View Article] [PubMed]
     [Google Scholar]
  37. Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH et al. A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 2020; 16:60–68 [View Article] [PubMed]
     [Google Scholar]
  38. Kohl M, Wiese S, Warscheid B. Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 2011; 696:291–303 [View Article] [PubMed]
     [Google Scholar]
  39. Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018; 8:525 [View Article] [PubMed]
     [Google Scholar]
  40. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  41. Magarvey NA, Keller JM, Bernan V, Dworkin M, Sherman DH. Isolation and characterization of novel marine-derived actinomycete taxa rich in bioactive metabolites. Appl Environ Microbiol 2004; 70:7520–7529 [View Article] [PubMed]
     [Google Scholar]
  42. Hardisson C, Suarez JE. Fine structure of spore formation and germination in Micromonospora chalcea. Microbiology 1979; 110:233–237 [View Article]
     [Google Scholar]
  43. Cronan JE, Laporte D. Tricarboxylic acid cycle and glyoxylate bypass. EcoSal Plus 2005; 1:10 [View Article] [PubMed]
     [Google Scholar]
  44. Spaans SK, Weusthuis RA, van der Oost J, Kengen SWM. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6: [View Article]
     [Google Scholar]
  45. Chavarría M, Nikel PI, Pérez-Pantoja D, de Lorenzo V. The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol 2013; 15:1772–1785 [View Article] [PubMed]
     [Google Scholar]
  46. Reher M, Fuhrer T, Bott M, Schönheit P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J Bacteriol 2010; 192:964–974 [View Article] [PubMed]
     [Google Scholar]
  47. Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N et al. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456 [View Article] [PubMed]
     [Google Scholar]
  48. Mayer F, Müller V. ATP synthases from archaea: structure and function. In Roberts GCK. eds Encyclopedia of Biophysics Berlin, Heidelberg: Springer; pp 122–129
     [Google Scholar]
  49. Carro L, Golinska P, Nouioui I, Bull AT, Igual JM et al. Micromonospora acroterricola sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil. Int J Syst Evol Microbiol 2019; 69:3426–3436 [View Article] [PubMed]
     [Google Scholar]
  50. C Garcia L, Martínez-Molina E, Trujillo ME. Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum. Int J Syst Evol Microbiol 2010; 60:331–337 [View Article] [PubMed]
     [Google Scholar]
  51. Xiang W, Yu C, Liu C, Zhao J, Yang L et al. Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger). Int J Syst Evol Microbiol 2014; 64:495–500 [View Article] [PubMed]
     [Google Scholar]
  52. Tamura T, Hatano K, Suzuki K-I. A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov. Int J Syst Evol Microbiol 2006; 56:1959–1964 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006868
Loading
Melissospora conviva gen. nov., sp. nov., a novel actinobacterial genus isolated from beehive through cross-feeding interactions
Int J Syst Evol Microbiol 75, 006868 (2025); https://doi.org/10.1099/ijsem.0.006868
/content/journal/ijsem/10.1099/ijsem.0.006868
/content/journal/ijsem/10.1099/ijsem.0.006868
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error