# Gut check: Exploring tools, techniques, and future directions in microbiome research

**Authors:** Samson Oladokun, Bertrand Grenier, Brian Oakley, Cristiano Bortoluzzi, Mahalingam Ramkumar

PMC · DOI: 10.1016/j.psj.2026.106713 · 2026-02-27

## TL;DR

This paper summarizes a symposium on tools and techniques for studying poultry microbiomes and their impact on bird health and productivity.

## Contribution

The paper highlights recent advancements and challenges in microbiome research and emphasizes opportunities for practical applications in poultry production.

## Key findings

- Next-generation sequencing and machine learning are advancing microbiome profiling.
- Standardization and reproducibility remain major challenges in the field.
- Microbiome insights can lead to disease control and sustainable poultry practices.

## Abstract

Poultry microbial communities are now recognized as key contributors to host nutrition, immune function, disease resilience, and overall health and performance, driving growing interest in this research field. This symposium brought together leading experts to discuss the latest advancements in analytical tools and technologies for investigating the poultry microbiome. Presentations highlighted current progress in microbiome profiling techniques, next-generation sequencing technologies, advanced data analysis methods such as machine learning, and the integration of cutting-edge approaches in microbiome research. A roundtable discussion further engaged participants in identifying key challenges in the field, including method standardization, reproducibility, and data interpretation, while emphasizing emerging opportunities to translate microbiome insights into practical strategies for disease control, antibiotic alternatives, and sustainable poultry production. The knowledge shared in this symposium is highly relevant to poultry researchers and the industry, as they work to enhance bird health, welfare, and productivity.

## Full-text entities

- **Diseases:** infectious bronchitis (MESH:D001991), MDR (MESH:D018088), AMR (MESH:D060467), dysbiosis (MESH:D064806), necrotic enteritis (MESH:D004751), coccidiosis (MESH:D003048), weight gain (MESH:D015430)
- **Chemicals:** SCFA (MESH:D005232), glycan (MESH:D011134), prebiotics (MESH:D056692), hydrogen (MESH:D006859), PB (-)
- **Species:** Salmonella (genus) [taxon 590], Gallus gallus (bantam, species) [taxon 9031], Homo sapiens (human, species) [taxon 9606], Listeria (genus) [taxon 1637], Lactobacillus (genus) [taxon 1578], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Mycoplasmatota (phylum) [taxon 544448], gut metagenome (species) [taxon 749906], Bacillus (genus) [taxon 55087], Campylobacter (genus) [taxon 194], Actinomycetota (actinobacteria, phylum) [taxon 201174], Bacteroidia (class) [taxon 200643], Clostridium (genus) [taxon 1485], Bacillota (clostridial firmicutes, phylum) [taxon 1239], Geobacter (genus) [taxon 28231], Acinetobacter (genus) [taxon 469], Methanobrevibacter (genus) [taxon 2172]

## Figures

2 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13010936/full.md

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Source: https://tomesphere.com/paper/PMC13010936