Comparison of the fecal microbiota of two monogastric herbivorous and five omnivorous mammals

Anim Sci J. Jan-Dec 2020;91(1):e13366. doi: 10.1111/asj.13366.


Fecal microbiota in seven different monogastric animal species, elephant, horse, human, marmoset, mouse, pig and, rat were compared using the same analytical protocol of 16S rRNA metagenome. Fecal microbiota in herbivores showed higher alpha diversity than omnivores except for pigs. Additionally, principal coordinate analysis based on weighted UniFrac distance demonstrated that herbivores and pigs clustered together, whereas other animal species were separately aggregated. In view of butyrate- and lactate-producing bacteria, predominant genera were different depending on animal species. For example, the abundance of Faecalibacterium, a known butyrate producer, was 8.02% ± 3.22% in human while it was less than 1% in other animal species. Additionally, Bifidobacterium was a predominant lactate producer in human and marmoset, while it was rarely detected in other omnivores. The abundance of lactate-producing bacteria in herbivores was notably lower than omnivores. On the other hand, herbivores as well as pig possess Fibrobacter, a cellulolytic bacterium. This study demonstrated that fecal microbiota in herbivorous animals is similar, sharing some common features such as higher alpha diversity and higher abundance of cellulolytic bacterium. On the other hand, omnivorous animals seem to possess unique fecal microbiota. It is of interest that pigs, although omnivore, have fecal microbiota showing some common features with herbivores.

Keywords: fecal microbiota; feeding habitat; herbivore; monogastric animal; omnivore.

Publication types

  • Comparative Study

MeSH terms

  • Animals
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Feces / microbiology*
  • Female
  • Gastrointestinal Microbiome*
  • Humans
  • Male
  • Mammals / microbiology*
  • Metagenome
  • RNA, Ribosomal, 16S


  • RNA, Ribosomal, 16S