Keystone species are organisms that, despite their relatively low abundance, have a disproportionately large impact on the structure and function of their ecosystems. In microbial communities, identifying these keystone species is crucial for understanding ecological dynamics and maintaining ecosystem stability. Advancements in metagenomics have significantly enhanced our ability to detect and study these pivotal microorganisms.


Keystone Research in Metagenomics

Metagenomics, the comprehensive analysis of genetic material from environmental samples, has become an indispensable tool in microbial ecology. It allows researchers to bypass traditional culturing methods, providing insights into the composition and functional potential of entire microbial communities. This approach has been instrumental in identifying keystone species within these communities.
A notable study introduced a top-down approach to identify keystone taxa in the microbiome. By analyzing microbial interaction networks, the researchers pinpointed species that play essential roles in ecosystem stability, despite their low abundance. This method offers a framework for recognizing keystone species across various environments.

Recent Major Findings

Human Gut Microbiome:
Research utilizing metagenomic sequencing has uncovered that individual variations in the human gut microbiome may be attributed to specific keystone species. For instance, distinct keystone species like Bacteroides fragilis and Bacteroides stercosis have been identified in different individuals, suggesting that these microbes significantly influence the unique composition of each person's gut microbiota.
Interkingdom Associations:
A study employing shotgun metagenomics revealed interkingdom associations between bacteria and fungi in Crohn's disease patients. Notably, the fungus Debaryomyces hansenii was identified as a keystone species, implicating its potential role in the disease's pathology.
Early Successional Microbial Communities:
Recent research has demonstrated that central taxa act as keystone microbes during early succession in ecosystems. These central microbes substantially enhance biodiversity and ecosystem functions, underscoring their critical roles in ecological succession.
Anthosphere Microbiomes:
A study focusing on the anthosphere—the above-ground parts of plants—identified microbial generalists as keystone species. These generalists construct core network structures, contributing to the stability and resilience of plant-associated microbial communities.
Ecological Network Construction:
Through genome-resolved metagenomics, researchers have constructed ecological networks revealing keystone taxa such as Rhizobiaceae, Xanthobacteraceae, and Burkholderiaceae. These findings provide insights into the complex interactions within microbial communities and their implications for ecosystem functioning.

Conclusion

Metagenomic approaches have revolutionized our understanding of microbial keystone species, highlighting their critical roles in maintaining ecosystem balance and health. Ongoing research continues to uncover the complexities of microbial interactions, paving the way for targeted interventions in health, agriculture, and environmental management.

URL for references used

• Banerjee, S., Schlaeppi, K., & van der Heijden, M. G. A. (2018). Keystone taxa as drivers of microbiome structure and functioning. Nature Reviews Microbiology, 16(9), 567-576. https://doi.org/10.1038/s41579-018-0024-1
• Berry, D., & Widder, S. (2014). Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Frontiers in Microbiology, 5, 219. https://doi.org/10.3389/fmicb.2014.00219
• Herren, C. M., & McMahon, K. D. (2018). Keystone taxa predict compositional change in microbial communities. Environmental Microbiology, 20(6), 2207-2217. https://doi.org/10.1111/1462-2920.14268
• Liu, Y.-Y., Chen, X., & Slotine, J.-J. (2023). Identifying keystone species in microbial communities using deep learning. Nature Communications, 14, 3945. https://doi.org/10.1038/s41467-023-39459-5
• Shi, Y., Li, Y., Xiang, X., Sun, R., Yang, T., He, D., ... & Chu, H. (2022). Central taxa are keystone microbes during early succession in glacier forelands. Environmental Microbiology, 24(1), 343-356. https://doi.org/10.1111/1462-2920.15797