The microbial community structure of the cotton rat nose

Abstract

The cotton rat nose is commonly used as a model for Staphylococcus aureus colonization, as it is both physiologically and anatomically comparable to the human nares and can be easily colonized by this organism. However, while the colonization of the human anterior nares has been extensively studied, the microbial community structure of cotton rat noses has not been reported so far. We describe here the microbial community structure of the cotton rat (Sigmodon hispidus) nose through next-generation sequencing of 16S rRNA gene amplicons covering the V1-V2 region and the analysis of nearly full length 16S rRNA genes of the major phylotypes. Roughly half of the microbial community was composed of two undescribed species of the genus Campylobacter, with phylotypes belonging to the genera Catonella, Acholeplasma, Streptobacillus and Capnocytophaga constituting the predominant community members. Thus, the nasal community of the cotton rat is uniquely composed of several novel bacterial species and may not reflect the complex interactions that occur in human anterior nares. Mammalian airway microbiota may, however, be a rich source of hitherto unknown microbes.

Ursodeoxycholic Acid and Its Taurine- or Glycine-Conjugated Species Reduce Colitogenic Dysbiosis and Equally Suppress Experimental Colitis in Mice

“…The V1 to V2 region of the 16S rRNA gene was amplified as previously described (69). Briefly, in a first 20-cycle PCR, the 16S rRNA gene target was enriched using the well-documented 27F and 338R primers (70,71), as previously specified (72). This reaction mixture was used as the template in a second 15-cycle PCR with primers comprising sequences complementary to the Illumina-specific adaptors to the 5= ends (69).…”

Streptobacillus ratti sp. nov., isolated from a black rat (Rattus rattus)

“…Furthermore, various phylotypes of Streptobacillus consistent with 16S rRNA gene-based operational taxonomic units have been described from Philippine mustard, fish and microbiomes of squirrels, cotton rats, dogs, ducks, dolphins, sea lions and humans (Bik et al, 2010;Chaves-Moreno et al, 2015;Dewhirst et al, 2012;Hullar et al, 2015;Larcia et al, 2011;Maher et al, 1995;Palmer et al, 1994;Strong et al, 2013;Xenoulis et al, 2008) (Fig. S1, available in the online Supplementary Material).…”

Approved and novel strategies in diagnostics of rat bite fever and otherStreptobacillusinfections in humans and animals

“…51 Some other isolates formerly assigned to S. moniliformis exist, from which S. notomytis from a spinifex hopping mouse (Notomys alexis) and from black rats (Rattus rattus) and S. ratti from an asymptomatically colonized black rat were recently described. 52,53 Contrarily to Nolan et al, 54 various potentially novel Streptobacillus species and phylotypes consistent with operational taxonomic units have been identified in the last few years from Atlantic salmon 55 and microbiomes of digestive tracts in dolphins and sea lions, [56][57][58] upper respiratory tracts in cotton rats, 37 digestive tracts in dogs, 39,59,60 intestinal tract of a ducks, 61 genital tracts in livestock, 32 and skin and gut microbiomes in humans (Fig. 1).…”

“…4,13,[16][17][18][19][20][21][22] Recently, various publications suggest that Streptobacillus species might be far more common and distributed in the environment or as commensal microbiota than previously thought. 32,37,[59][60][61][62][63] It could recently be shown that the natural reservoir for the very rare cases of human S. hongkongensis infection known to date is indeed the human oropharynx à and presumably not an unidentified animal or environmental reservoir. 49 Despite a certain amount of annually published case reports, most of which have solely used 16S rRNA sequencing alone for definite diagnosis, there has not been much progress in the diagnosis of acute clinical cases of RBF in the last decades.…”

“…Anecdotally, streptobacilli have been described from exotic host species like gerbils and squirrels that were occasionally named "Streptothrix paraxeri cepapi" after Smith's bush squirrel (Paraxerus cepapi), [33][34][35] partially with involvement of human infection resembling RBF, 33,36 but these isolates have also not been stored. Based on metagenomics data from cotton rats 37 it may be possible that streptobacilli in other rodent species might in fact represent separate species (Fig. 1).…”