# Mining Microbial Dark Matter: Advanced Cultivation Techniques for Bioactive Compound Discovery

**Authors:** Minhui Ji, Bingda Ma, Jiayu Dong, Shan Liu, Ying Shi, Meiting Bu, Luoyi Wang, Ling Liu

PMC · DOI: 10.3390/ph18101583 · Pharmaceuticals · 2025-10-20

## TL;DR

This paper reviews new methods to grow hard-to-cultivate microbes and discover new drug-like compounds from them.

## Contribution

The paper presents recent cultivation and genomic techniques that enable access to previously unculturable microbes for natural product discovery.

## Key findings

- Advanced cultivation techniques have enabled the isolation of previously unculturable microbes.
- New bioactive compounds have been discovered from these microbes, showing potential for drug development.

## Abstract

The vast majority of microorganisms in the environment remain uncultured using conventional laboratory techniques, representing an immense untapped reservoir of genetic and chemical diversity. Recent innovations in cultivation strategies, combined with advances in metagenomics, single-cell genomics, and synthetic biology, have opened new avenues for accessing and harnessing bioactive natural products from these previously inaccessible microorganisms. This review highlights recent methodological and technological advancements in the cultivation and identification of novel microorganisms, and showcases the resulting discoveries of new natural products, demonstrating their potential for drug development.

## Full-text entities

- **Genes:** Bmp8b (bone morphogenetic protein 8b) [NCBI Gene 12164] {aka Op3}
- **Diseases:** cancer (MESH:D009369), injury to (MESH:D014947), infection (MESH:D007239), cytotoxic (MESH:D064420), periodontal disease (MESH:D010510), MRSA (MESH:D013203)
- **Chemicals:** nickel (MESH:D009532), methane (MESH:D008697), ester (MESH:D004952), Malacidin A (MESH:C000626256), carbon (MESH:D002244), diuron (MESH:D004237), enduracididine (MESH:C000603877), coproporphyrins (MESH:D003306), Teixobactin (MESH:C000594838), oxygen (MESH:D010100), naphthalene (MESH:C031721), teichoic acid (MESH:D013682), iron oxides (MESH:C000499), biphenyl (MESH:C010574), Misakinolide A (MESH:C104924), methicillin (MESH:D008712), Polyketides (MESH:D061065), 13C (MESH:C000615229), amide (MESH:D000577), peptides (MESH:D010455), vancomycin (MESH:D014640), lipid II (MESH:C069249), macrolide (MESH:D018942), amino acids (MESH:D000596), Lassomycin (MESH:C000595674), rifampicin (MESH:D012293), depsipeptide (MESH:D047630), RiPP (-), lipid III (MESH:C032403), methylphenylalanine (MESH:C034515), LSA (MESH:C450700), epoxide (MESH:D004852), manganese carbonate (MESH:C045327), manganese (MESH:D008345), calcium (MESH:D002118), short-chain fatty acids (MESH:D005232), lysinoalanine (MESH:D008241), beta-hydroxy aspartic acid (MESH:C011274), ATP (MESH:D000255), daptomycin (MESH:D017576), lipopeptide (MESH:D055666), pyrophosphate (MESH:C107241), agarose (MESH:D012685)
- **Species:** [Clostridium] polysaccharolyticum (species) [taxon 29364], Mus musculus (house mouse, species) [taxon 10090], Candidatus Pelagibacter communis (species) [taxon 198252], Aspergillus niger (species) [taxon 5061], Motilibacter (genus) [taxon 1434021], Lagria villosa (species) [taxon 1337086], Porifera (sponges, phylum) [taxon 6040], Purpureocillium lilacinum (species) [taxon 33203], Agathobacter rectalis (species) [taxon 39491], Hominimerdicola alba (species) [taxon 1264], Streptococcus pneumoniae (species) [taxon 1313], Streptomyces sp. TM-7 (species) [taxon 280267], Theonella swinhoei (species) [taxon 37505], Human immunodeficiency virus 1 (no rank) [taxon 11676], Staphylococcus aureus WG1 (strain) [taxon 1417991], Notamacropus eugenii (tammar wallaby, species) [taxon 9315], Gemmatimonas sp. (species) [taxon 1962908], uncultured Gammaproteobacteria bacterium (species) [taxon 86473], Enterococcus faecalis (species) [taxon 1351], Amycolatopsis sp. (species) [taxon 37632], Candidatus Endohaliclona renieramycinifaciens (species) [taxon 2565582], Stramenopiles (heterokonts, clade) [taxon 33634], Pseudomonadota (proteobacteria, phylum) [taxon 1224], Kitasatospora sp. (species) [taxon 1871188], Bulleidia extructa (species) [taxon 118748], Staphylococcus aureus (species) [taxon 1280], Rattus norvegicus (brown rat, species) [taxon 10116], Pseudoflavonifractor capillosus (species) [taxon 106588], Mycobacterium tuberculosis (species) [taxon 1773], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Nitrospina gracilis (species) [taxon 35801], Acidovorax sp. (species) [taxon 1872122], Streptomyces sp. (species) [taxon 1931], Eleftheria terrae (species) [taxon 1597781], Homo sapiens (human, species) [taxon 9606], Bifidobacterium (genus) [taxon 1678], Clostridioides difficile (species) [taxon 1496], Xylanibacter ruminicola (species) [taxon 839], Actinomycetes bacterium (species) [taxon 1883427], Polymorphobacter (genus) [taxon 1508451], Candidatus Didemnitutus mandela (species) [taxon 2055843], uncultured beta proteobacterium (species) [taxon 86027], Burkholderia gladioli (species) [taxon 28095], Prevotella dentalis (species) [taxon 52227], Enterococcus faecium (species) [taxon 1352], Beauveria bassiana (species) [taxon 176275], Metarhizium anisopliae (species) [taxon 5530], Coleoptera (beetles, order) [taxon 7041], Candidatus Entotheonella serta (species) [taxon 1652106], Bifidobacterium goeldii (species) [taxon 2306975], Leptospirillum sp. Group II (species group) [taxon 261385], Ruminococcus flavefaciens (species) [taxon 1265], Bacteroidia (class) [taxon 200643], Betaproteobacteria (b-proteobacteria, class) [taxon 28216], Bacillus anthracis (anthrax bacterium, species) [taxon 1392], Butyrivibrio hungatei (species) [taxon 185008], Bifidobacterium callimiconis (species) [taxon 2306973]
- **Mutations:** G00190R

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12566907/full.md

## References

114 references — full list in the complete paper: https://tomesphere.com/paper/PMC12566907/full.md

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Source: https://tomesphere.com/paper/PMC12566907