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Microbiome research is a thriving field focused on characterizing the composition and functionality of microbial populations or microbiomes from a wide array of ecological niches. Microbiomes occupy living organisms, soil, the atmosphere, and bodies of water and exist in moderate and extreme climates. Understanding the intractable microbial universes in various environments is challenging and potentially rewarding to humankind. Historically, elucidating pathogenic microbes and their impact on host species has dominated microbiome-based studies. Moreover, a tiny percentage of microbes can be cultured using classical culturing methods. With advancements in high throughput experimentation and computational tools derived from microbial ecology, there is a driving force to gain insight into the entire microbial consortium from various environmental and biological locations. Metagenomics, the study of all the microbial genomes in a sample using sequencing techniques (e.g., 16s rRNA amplicon sequencing and shotgun sequencing), has so far dominated the types of investigations conducted in the field of microbiome research. More recently, however, researchers are becoming increasingly interested in better understanding the complex microbe-associated molecular network and specific protein and metabolite functions associated with microbial genetic potential. Metaproteomic, meta transcriptomics, and metabolomics are three potent methods to accumulate information about microbial proteins, messenger RNA, and metabolites in a microbial community. These methods are currently being applied in laboratory settings to address our general lack of understanding of microbe-microbe interactions and microbe-environment interactions.
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Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions
Abstract The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non‐bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.
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- Award ID(s):
- 2144304
- PAR ID:
- 10503187
- Publisher / Repository:
- Molecular Ecology
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 33
- Issue:
- 2
- ISSN:
- 0962-1083
- Page Range / eLocation ID:
- e17223
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1111/mec.17223
