Benchmarking microbial growth rate predictions from metagenomes

Area of Science:

• Microbial ecology
• Genomics
• Marine microbiology

Background:

• Microbial growth rates are crucial for understanding community dynamics and interactions.
• Metagenomic tools like codon usage bias (CUB) and peak-to-trough ratio (PTR) estimate microbial growth.
• Previous estimations were primarily validated using pure cultures, not complex natural populations.

Purpose of the Study:

• To evaluate the accuracy of CUB and PTR as metagenomic growth rate predictors in natural marine prokaryote populations.
• To compare these computational predictions against empirically measured growth rates.
• To assess the reliability of these methods for diverse microbial groups in situ.

Main Methods:

• Collected fresh marine prokaryotes from unamended seawater, prefiltered and diluted to approximate gross growth.
• Generated 101 metagenome-assembled genomes (MAGs) from samples collected over 44 hours.
• Measured population growth rates via cell abundance and used read recruitment to track MAGs, establishing benchmark rates.

Main Results:

• Observed growth rates ranged from 0 to 5.99 per day for various MAGs, including Actinobacteria and Verrucomicrobia.
• Peak-to-trough ratio (PTR) showed poor correlation with observed growth rates across most populations (r ≈ -0.26–0.08).
• Codon usage bias (CUB) demonstrated a moderate correlation with maximum observed growth rates (r ≈ 0.57).

Conclusions:

• Current PTR methods are generally unreliable for predicting actual marine bacterial growth rates in situ.
• CUB shows promise for approximating maximum growth rates from genomic data in marine environments.
• This study provides the first reported growth rates for several marine microbial groups, validated against genomic estimators.