# Dynamic Analysis of Stool Microbiota of Simmental Calves and Effects of Diarrhea on Their Gut Microbiota

## TL;DR

This study tracks gut microbiota changes in Simmental calves before weaning and compares healthy and diarrheic calves to identify potential probiotic targets.

## Contribution

The study reveals age-related shifts in gut microbiota and identifies specific beneficial bacteria associated with healthy calves, offering insights for probiotic development.

## Key findings

- Healthy calves had higher levels of Lactobacillus johnsonii, Faecalibacterium prausnitzii, and Limosilactobacillus compared to diarrheic calves.
- Microbial structure in calves changed significantly with age, clustering differently at various time points.
- Key functions of the gut microbiota included metabolic pathways and antibiotic biosynthesis.

## Abstract

Simmental cattle is a renowned breed that is extensively raised because of its high beef and milk fat content. The early establishment of the gut microbiota is closely related to the gut health of calves. However, the structure and function of the gut microbiota in Simmental calves before weaning remain unclear. The development of gut microbiota in neonatal calves is a multifaceted process affected by numerous factors. Gastrointestinal microbiota profoundly affect animal health, productivity, and disease susceptibility, necessitating further study of specific microbial functions during early development. Diarrhea stands out as the most prevalent ailment among lactating calves. Changes in the structure and functionality of the gut microbiota can precipitate gut disorders, ultimately leading to diarrhea. Therefore, thorough investigations of the early colonization patterns of Simmental calves, along with an understanding of the gut microbiota in healthy calves versus those afflicted by diarrhea, have significant implications for diarrhea prevention and development of probiotic interventions.

The objective of this study was to explore the dynamic changes in the gut microbiota of Simmental calves before weaning and to compare the microbial composition and functionality between healthy calves and those with diarrhea. Fourteen neonatal Simmental calves were divided into a healthy group (n = 8) and a diarrhea group (n = 6). Rectal stool samples were collected from each calf on days 1, 3, 5, 7, 9, 12, 15, 18, 22, 26, 30, 35, and 40. High-throughput sequencing of the 16S rRNA gene V1–V9 region was conducted to examine changes in the gut microbiota over time in both groups and to assess the influence of diarrhea on microbiota structure and function. Escherichia coli, Bacteroides fragilis, and B. vulgatus were the top three bacterial species in preweaning Simmental calves. Meanwhile, the major functions of the fecal microbiota included “metabolic pathways”, “biosynthesis of secondary metabolites”, “biosynthesis of antibiotics”, “microbial metabolism in diverse environments”, and “biosynthesis of amino acids”. For calves in the healthy group, PCoA revealed that the bacterial profiles on days 1, 3, 5, 7, and 9 differed from those on days 15, 18, 22, 26, 30, 35, and 40. The profiles on day 12 clustered with both groups, indicating that microbial structure changes increased with age. When comparing the relative abundance of bacteria between healthy and diarrheic calves, the beneficial Lactobacillus johnsonii, Faecalibacterium prausnitzii, and Limosilactobacillus were significantly more abundant in the healthy group than those in the diarrhea group (p < 0.05). This study provides fundamental insights into the gut microbiota composition of Simmental calves before weaning, potentially facilitating early interventions for calf diarrhea and probiotic development.