Associations between microbial composition and post-weaning diarrhea

The intestinal microbiome has co-evolved to play important roles in the biology of humans and animals. In pigs, undigested carbohydrates, like resistant starch, reach the colon where they are fermented by the microbiota to produce short-chain fatty acids. When protein reaches the distal colon, the slow transit time and limited host absorption facilitate microbial proteolysis and accumulation of metabolic end products; some of which may be detrimental to the host. Many microbial species contribute to proteolytic fermentation, including pathogenic species associated with pig enteric diseases such as (toxin producing) Escherichia coli and Salmonella Typhimurium. It is suggested that the weaning process is accompanied by stress, malnutrition, changes in microbiota, and overall wellbeing. One of the hypotheses in our project is that undigested protein transits to the large intestine, where it can be utilized by the residing microbiota as energy substrate. However, fermentation of protein commonly produces byproducts that are toxic to the host epithelium at elevated concentrations, e.g. ammonia, hydrogen sulfide, branched-chain fatty acids, or polyamines.
We observed increased protein fermentation metabolites, e.g. ammonia, in piglets with diarrhea. This result was seen irrespective of farm, indicating a common intestinal response during diarrhea. To further characterize differences between animals, we isolated DNA from stool samples, PCR-amplified and sequenced prokaryotic 16S ribosomal RNA genes for microbiota compositional analysis. Compositional analysis based on amplified sequence variants (ASVs) revealed that diversity (Shannon) and richness of the microbiota was significantly reduced in diarrheagenic animals. Microbial diversity and richness have been associated with intestinal health, but recent observations indicate this might be confounded by changes in feacal transit time or stool consistency. Therefore, it is important to be critical on associating these parameters with health and disease.
To gain more insight into the microbiological changes and quantify actual differences between these two groups, we first reduced the large datasets to find common discriminant features. This indicated significantly increased relative abundance of proteobacterial species, commonly associated with protein fermentation as described above. However, relative differences based on compositional (16S rRNA gene) data is sometimes difficult to interpret or translate to actual bacterial load. In piglets, increased abundance of toxin producing bacteria are commonly associated with PWD, so we investigated whether the predictions we see in E. coli pathogenesis are associated with a specific toxin. In piglets having diarrhea, we observed a significant increase in the heat-stable protein A (STa) encoding gene per ng DNA, indicating that enterotoxigenic E. coli (ETEC) might play an important role in the observed diarrhea phenotype.