Analysis of human and animal fecal microbiota for microbial source tracking

Abstract

Microbial compositions of human and animal feces from South Korea were analyzed and characterized. In total, 38 fecal samples (14 healthy adult humans, 6 chickens, 6 cows, 6 pigs and 6 geese) were analyzed by 454 pyrosequencing of the V2 region of the 16S rRNA gene. Four major phyla, Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes, were identified in the samples. Principal coordinate analysis suggested that microbiota from the same host species generally clustered, with the exception of those from humans, which exhibited sample-specific compositions. A network-based analysis revealed that several operational taxonomic units (OTUs), such as Lactobacillus sp., Clostridium sp. and Prevotella sp., were commonly identified in all fecal sources. Other OTUs were present only in fecal samples from a single organism. For example, Yania sp. and Bifidobacterium sp. were identified specifically in chicken and human fecal samples, respectively. These specific OTUs or their respective biological markers could be useful for identifying the sources of fecal contamination in water by microbial source tracking.

Figure 1

Clustering of fecal bacterial communities by principal coordinate analysis (PCoA) using UniFrac (• chicken, ▴ cow, ▪ goose, ⧫ pig and – human) (a) and results from network-based analysis of microbiota (b and c) (N=38). Nodes represent operational taxonomic units (OTUs), and each line indicates that an OTU was identified in the same source.