title: Abundant and diverse fungal microbiota in the murine intestine.
abstract: Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4',6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.
authors.affiliation: National Animal Disease Center, Ames, Iowa 50010, USA.
authors.forename: Alexandra J
authors.initials: AJ
authors.lastname: Scupham
authors.forename: Laura L
authors.initials: LL
authors.lastname: Presley
authors.forename: Bo
authors.initials: B
authors.lastname: Wei
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Bent
authors.forename: Natasha
authors.initials: N
authors.lastname: Griffith
authors.forename: Michael
authors.initials: M
authors.lastname: McPherson
authors.forename: Feilin
authors.initials: F
authors.lastname: Zhu
authors.forename: Oluwadayo
authors.initials: O
authors.lastname: Oluwadara
authors.forename: Nagesh
authors.initials: N
authors.lastname: Rao
authors.forename: Jonathan
authors.initials: J
authors.lastname: Braun
authors.forename: James
authors.initials: J
authors.lastname: Borneman
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D004271:DNA, Fungal / Q000032:analysis / Q000302:isolation & purification; D005260:Female; D005658:Fungi / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D020459:Genes, rRNA; D017404:In Situ Hybridization, Fluorescence; D007420:Intestine, Large / Q000382:microbiology*; D007421:Intestine, Small / Q000382:microbiology*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes; D016133:Polymerase Chain Reaction; D012335:RNA, Ribosomal / Q000235:genetics; D017422:Sequence Analysis, DNA; D013047:Specific Pathogen-Free Organisms
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D015345:Oligonucleotide Probes; D012335:RNA, Ribosomal