# Utilizing an In Vitro Fermentation Model to Assess Probiotics on Eimeria-Disturbed Cecal Microbiome and Metabolome

## TL;DR

This study shows how two probiotics affect a chicken gut microbiome disrupted by Eimeria, with Lactobacillus rhamnosus being more effective at restoring balance and metabolism.

## Contribution

The study introduces an in vitro model to assess host-independent effects of probiotics on Eimeria-perturbed chicken gut microbiota and metabolome.

## Key findings

- Eimeria infection increased harmful bacteria and disrupted metabolism in chicken cecal microbiota.
- Lactobacillus rhamnosus restored microbial balance and corrected 107 metabolites related to cell membranes.
- Bacillus subtilis partially restored balance but corrected fewer metabolites, mainly related to secondary metabolism.

## Abstract

This study used an in vitro model to test how two probiotics affect a chicken gut microbiome interrupted by Eimeria. We found that the coccidial infection increased harmful bacteria in the cecal microbiota and disrupted bacterial metabolism. Adding Lactobacillus rhamnosus directly helped restore bacterial balance and corrected disrupted metabolites linked to cell membranes. Bacillus subtilis also improved bacterial balance but was less effective at fixing the metabolic problems. The results suggest that LR can directly repair partial microbial damage, while BS’s full benefits may depend on the host’s response.

Rectifying the microbiome perturbed by Eimeria invasion might alleviate the adverse effects of coccidia on broiler growth. This study employed an in vitro fermentation model to investigate the direct, host-independent effects of two probiotics—Lactobacillus rhamnosus (LR) and Bacillus subtilis (BS)—on the cecal microbiome and metabolome perturbed by Eimeria tenella. Four in vitro fermentation treatments consisted of a healthy control (cecal slurry samples from health broilers), an Eimeria-disturbed control (slurry samples from infected broilers), an LR treatment (Eimeria-infected slurry + 3 × 105 of LR cfu/mL), and a BS treatment (Eimeria-disturbed group + 3 × 105 of BS cfu/mL). 16S rRNA sequencing and metabolomic analysis revealed that Eimeria infection resulted in an increase in microbial alpha diversity, promoted opportunistic pathogens, including Helicobacter and Bacteroides, and suppressed commensals like Lactobacillus, concurrently altering 530 intracellular metabolites. Probiotic supplementation partially restored microbial composition. Notably, LR inoculation rectified 107 metabolites across pathways including galactose metabolism and phosphotransferase systems, primarily affecting membrane phospholipid balance. In contrast, BS addition restored only 64 metabolites, largely related to secondary metabolism. The current in vitro study indicates that LR can directly modulate key metabolic disturbances in a dysbiotic microbiota, while the BS may be more dependent on host-mediated interactions.