Déborah Tellatin, Luc Cornet, Valdes Snauwaert​, Philippe Compère, Marc Ongena​, Loïc Quinton, Nudzejma Stulanovic, Silvia Ribeiro Monteiro, Augustin Rigolet, Pierre Burguet, Petra Van Damme, Lorena Carro and Sébastien Rigali
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 Apis mellifera beehive, we identified five isolates (DT32, DT45T, 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 Micromonosporaceae, separate from the five officially recognized clades of the Micromonospora 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 Micromonosporaceae. Pangenomic comparisons with their closest Micromonospora 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 Melissospora conviva as a novel genus and species within the Actinomycetota phylum, with isolate DT45T as the representative type species and type strain, which has been deposited in public collections under the accession numbers DSM 117791 and LMG 33580.
https://doi.org/10.1099/ijsem.0.006868

*Marta Maciejewska, Magdalena Całusińska, Luc Cornet,Delphine Adam, Igor S. Pessi 1, Sandrine Malchair, Philippe Delfosse,Denis Baurain, Hazel A. Barton,Monique Carnol, and Sébastien Rigali
Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave “Grotte des Collemboles” via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population. Next to actinobacterial operational taxonomic units (OTUs) attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of the absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of the OTUs unlinked to the culturable Streptomyces strains that were previously isolated from the same deposits. Furthermore, 43% of the OTUs were shared between the three studied collection points, while 34% were exclusive to one deposit, indicating that distinct speleothems host their own population, despite their nearby localization. This important spatial diversity suggests that prospecting within different moonmilk deposits should result in the isolation of unique and novel Actinobacteria. These speleothems also host a wide range of non-streptomycetes antibiotic-producing genera, and should therefore be subjected to methodologies for isolating rare Actinobacteria.
https://doi.org/10.3390/antibiotics7020027