Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing

Abstract

The feline gastrointestinal microbiota have direct influence on feline health and also human health as a reservoir for potential zoonotic pathogens and antibiotic resistant bacterial strains. In order to describe the feline gastrointestinal microbial diversity, fecal samples from cats have been characterized using both culture-dependent and culture-independent methods. However, data correlating total microbial composition and their functions are lacking. Present descriptive study evaluated both phylogenetic and metabolic diversity of the feline intestinal microbiota using GS Junior titanium shotgun pyrosequencing. A total of 152,494 pyrosequencing reads (5405 assembled contigs) were generated and classified into both phylogenetic and metabolic profiles of the feline intestinal microbiota. The Bacteroides/Chlorobi group was the most predominant bacterial phylum comprising ~68% of total classified diversity, followed by Firmicutes (~13%) and Proteobacteria (~6%) respectively. Archaea, fungi and viruses made up the minor communities in the overall microbial diversity. Interestingly, this study also identified a range of potential enteric zoonotic pathogens (0.02-1.25%) and genes involved in antimicrobial resistance (0.02-0.7%) in feline fecal materials. Based on clustering among nine gastrointestinal metagenomes from five different monogastric hosts (dog, human, mice, cat and chicken), the cat metagenome clustered closely together with chicken in both phylogenetic and metabolic level (>80%). Future studies are required to provide deeper understandings on both intrinsic and extrinsic effects such as impact of age, genetics and dietary interventions on the composition of the feline gastrointestinal microbiome.

Gastrointestinal microorganisms in cats and dogs: a brief review

“…For example, a recent metagenomic study showed that bacteria may represent as much as 98% of all fecal microbiota in dogs, with Archaea, Eukaryotes, and viruses representing only about 2% (Swanson et al 2011). Similarly, a recent study also used a metagenomic approach and showed that Eukaryotes, Archaea, and viruses were minor constituents (< 3%) of the fecal microbiota in cats, while bacteria represented the great majority (97.8%) (Tun et al 2012).…”

“…However, the exact proportions of each bacterial group vary widely throughout the literature. For example, one study showed that healthy cats and dogs may harbor > 90% of Firmicutes in faeces (Handl et al 2011), while others have shown that these animal species may only harbor ~ 13% (cats) and ~ 35% (dogs) of this phylum also in faeces (Swanson et al 2011, Tun et al 2012. The reasons for these discrepancies (see below) are unknown but may include differences in DNA extraction protocols (Zoetendal et al 2001), intra-stool variability of intestinal microorganisms (Garcia-Mazcorro et al 2009), inter-individual differences (Handl et al 2011), the target region of the 16S rRNA gene (Baker et al 2003), as well as inherent differences among the techniques utilized to characterize the microbiota (Zoetendal et al 2004, Kunin et al 2010.…”

“…Clostridium was the most abundant genus in both cats and dogs ( > 20% on average in both studies) but it does not appear in this figure due to uncertain taxonomic classification. At the phylum level, we also included the approximate estimates (*) published by Swanson et al (2011) and Tun et al (2012) using a metagenomics approach (please see main text for more details).…”

“…A recent study sequenced the gene encoding the universal 60 kDa chaperonin and showed that the faecal microbiota of cats was dominated by Actinobacteria (~ 53%) and Firmicutes (~ 40%) (Desai et al 2009). Recent studies using 454-pyrosequencing suggest that > 90% of all sequences obtained from feces of healthy cats belong to the Phylum Firmicutes (Garcia-Mazcorro et al 2011, Handl et al 2011, especially members of the family Clostridiaceae, while a metagenomic study suggests that Bacteroidetes/Chlorobi is the most abundant bacterial group (~ 68%), followed by Firmicutes (~ 13%) and Proteobacteria (~ 6%) also in faeces of cats (Tun et al 2012). However, it is important to point out that the study by Tun et al also reports that Bacteroidetes only represented ~ 9% of the obtained sequence reads, while the phyla Chlorobi and Chloroflexi represented less than 1% of the reads.…”

The Microbiome

“…102,121 Similarly, DNA shotgun sequencing of feline fecal samples revealed 97% of sequences as of bacterial origin, 1% from eukaryota, 0.1% from archaea, and 0.1% from DNA viruses. 122 Pyrosequencing of the fungal 18 S rRNA gene reported Aspergillus and Saccharomyces as the most abundant fungal genera in pooled fecal samples of cats. 44 In another study, 76% of dogs were positive for fungal DNA on duodenal biopsies.…”