What does the future hold for science in gut health?

Hello everyone,

Still in press, this interesting paper, published by Oladokun et al. in Poultry Science, gives us clues as to where scientific research will be heading in terms of gut health.

ABSTRACT
Poultry microbial communities are now recognized as key contributors to host nutrition, immune function, disease resilience, overall health, and performance, driving growing interest in this field of research.

CONCLUSIONS

Microbiome research in poultry is expanding rapidly, bringing with it a wealth of new opportunities and analytical tools.

To take full advantage of this growth and the possibilities offered by this field, researchers should:
- prioritize the use of appropriate tools (such as multi-omic approaches),
- select appropriate sampling sites (e.g., invasive vs. cloacal/fecal),
- standardize protocols,
- adopt uniform bioinformatics processes for the field, and
- implement standardized and cost-effective NGS workflows.

These measures will facilitate reproducibility and consistency across studies.

When applying NGS technology to poultry microbiota profiling, the field must move beyond simple microbiota censuses (“Who is there?”) toward advanced functional analyses of the microbiome (“What are they doing?”). This requires the integration of multi-omic technologies, such as amplicon sequencing, metagenomics, and metatranscriptomics, as no single approach fits all research questions.

The adoption of artificial intelligence, machine learning, and deep learning could also further accelerate progress in this field. Deep learning, in particular, offers distinct advantages for microbiome analysis by uncovering complex patterns of microbial interactions that are not easily detected with traditional statistical methods, integrating prior knowledge of feature associations, and incorporating biological information. These capabilities highlight the potential of deep learning and large-scale data integration to transform microbiome research.

Another important issue that requires attention is the revalidation of microbiota results obtained through amplicon-based sequencing or metagenomics using qPCR methods. Bioinformatic and statistical approaches may overestimate relative abundances. As in other fields, the microbiome community should prioritize the revalidation of bacterial thresholds, particularly for taxa with available primers or cultivable strains. Relative abundances should not be labeled as “high” or “low” based solely on statistical analysis; they should be revalidated and interpreted using biological and metabolic information, whenever possible.

The continued development of robust, scalable workflows and poultry-specific reference databases will be critical to translating microbiome discoveries into practical applications that improve poultry health, productivity, and sustainability.

Original article:
Samson Oladokun , Bertrand Grenier , Brian Oakley , Cristiano Bortoluzzi , Mahalingam Ramkumar , Gut check: exploring tools, techniques, and future directions in microbiome research, Poultry Science (2026), doi: https://doi.org/10.1016/j.psj.2026.106713