The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal...

Area of Science:

• Environmental Science
• Microbiology
• Genomics

Background:

• High-throughput sequencing transformed environmental microbiome research, offering insights into nucleic acid targets.
• Microbial community structure data are vital for environmental analytical microbiology and pollutant assessment.
• Relative abundance data from sequencing limit cross-sample and cross-study comparisons.

Purpose of the Study:

• To systematically review absolute quantification (AQ) methods for environmental microbiomes.
• To identify and advocate for appropriate AQ approaches for complex environmental samples.
• To establish reporting standards for reproducible microbiome research.

Main Methods:

• Systematic review of existing absolute quantification (AQ) techniques.
• Critical comparison of the strengths and limitations of various AQ methods.
• Identification of cellular internal standard-based high-throughput sequencing as a preferred method.

Main Results:

• Various AQ methods were summarized, detailing their applications for microbial cell and genetic element abundance.
• Cellular internal standard-based high-throughput sequencing is recommended for complex environmental matrices.
• Essential reporting elements and a checklist for technical considerations were outlined.

Conclusions:

• Propose absolute microbiome quantification using cellular internal standards for environmental analytical microbiology.
• Anticipate significant benefits for future environmental microbiome studies.
• Emphasize the importance of standardized reporting for reproducibility.