TABLE 1.
Taxonomic distribution of rRNA gene clones obtained by OFRG analysis of murine intestine with fungus-selective PCR primers
| Taxon | No. of clonesa
|
Nearest relative(s) (accession no.)b | % Identity to nearest relativesb | ||||
|---|---|---|---|---|---|---|---|
| Total | RF-C | RF-SI | SPF-C | SPF-SI | |||
| Ascomycota | 477 | 153 | 40 | 164 | 120 | ||
| Acremonium | 57 | 7 | 3 | 39 | 8 | Acremonium alternatum (AY083232) | 99 |
| Alternaria | 28 | 13 | 5 | 1 | 9 | Alternaria alternata (AF229504) | 93-97 |
| Monilinia | 151 | 70 | 1 | 28 | 52 | Monilinia laxa (Y14210) | 96-99 |
| Fusarium | 63 | 4 | 5 | 50 | 4 | Gibberella pulicaris (AF149875), Fusarium oxysporum (AF141951), Fusarium equiseti (AF141949), Fusarium culmorum (AF141948), Fusarium cerealis (AF141947), Gibberella avenacea (AF141946), | 99 |
| Cordyceps sinensis (AB067700) | |||||||
| Unidentified | 178 | 59 | 26 | 46 | 47 | ||
| Basidiomycota | 154 | 46 | 11 | 61 | 36 | ||
| Cryptococcus/Filobasidium | 51 | 1 | 4 | 40 | 6 | Filobasidium globisporum (AB075546), Filobasidium elegans (AB075545), Cryptococcus magnus (AB032643), Cryptococcus ater (AB032622), Filobasidium floriforme (D13460) | 98-99 |
| Scleroderma | 45 | 19 | 0 | 11 | 15 | Scleroderma citrina (AF026621) | 96-97 |
| Unidentified | 58 | 26 | 7 | 10 | 15 | ||
| Zygomycota and Chytridiomycota | 239 | 139 | 13 | 23 | 64 | ||
| Cluster 1 | 162 | 86 | 6 | 21 | 49 | Catenomyces sp. (AY635830), Spizellomyces punctatus (AY546684), Spizellomyces acuminatus (M59759), Neocallimastix sp. (M59761), Powellomyces sp. (AF164245), Neocallimastix frontalis (X80341), Entophlyctis helioformis (AY635826), Mortierella alpina (AJ271630), Smittium culisetae (D29950) | 94-99 |
| Mucorales | 54 | 36 | 7 | 1 | 10 | Amylomyces rouxii (AY228093), Rhizopus oryzae (AF113440), Backusella ctenidia (AF157122) | 98-99 |
| Unidentified | 23 | 17 | 0 | 1 | 5 | ||
| Mammalia | 428 | 20 | 247 | 75 | 86 | Several mammals, including Mus musculus (BK000964) and Sus scrofa (AY265350) | 98-100 |
| Unidentified | 111 | 33 | 10 | 36 | 32 | ||
a
Determined by adding the number of clones in the major taxonomic groups identified by the OFRG analysis (Fig. 1).
b
Determined by BLAST (NCBI) (3) analysis of representative clones from the major taxonomic groups identified by the OFRG analysis (Fig. 1). RF-C, colon samples from restricted-flora mice; RF-SI, small intestine samples from restricted-flora mice; SPF-C, colon samples from specific-pathogen-free mice; SPF-SI, small intestine samples from specific-pathogen-free mice.