Microbiome Research and the Growing Need for Automated Solutions

Anaerobes often require: (1) ultra-low redox potential, (2) precise gas mixes and antioxidants, (3) slow growth timelines, and (4) cofactor or partner-organism dependencies. Practically, that translates to large plate counts, long incubations, and delicate handling inside glove boxes—conditions that make manual colony picking slow, biased towards common strains, and risky for viability.

Automation directly addresses the pain points that keep valuable anaerobes out of strain libraries:

1. Throughput and yield - Automated pickers routinely process thousands of colonies per hour, converting  operations from weeks to days while maintaining traceable barcodes and images.
2. Reduced selection bias and better phenotype capture - Imaging-guided selection (size, circularity, texture, color) and multi-plate tiling help recover morphotypes that can be overlooked—critical for slow-growing, small, or translucent anaerobes. Custom camera-assisted systems have already underpinned high-throughput strain isolation campaigns.
3. Viability preservation - Robots shorten plate-to-well transfer times and standardize contact pressure, which improves recovery of oxygen-sensitive colonies compared with manual loops/needles.
4. True anaerobic compatibility - Newer pickers are specifically designed to operate inside hypoxic/anaerobic chambers or integrate directly with them—avoiding plate shuttling through pass-boxes and the associated oxygen spikes. Examples include systems demonstrated within anaerobic biobanks and models marketed for seamless chamber operation.
5. Closed-loop data & QC - Automated imaging + LIMS hooks create a per-colony audit trail (growth time, plate coordinates, morphology snapshot, destination well), which supports downstream genomics, metabolomics, and gnotobiotic validation.

Next-generation automation solutions