Abundant and diverse fungal microbiota in the murine intestine.
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.
Scupham
Alexandra J
AJ
National Animal Disease Center, Ames, Iowa 50010, USA.
Presley
Laura L
LL
Wei
Bo
B
Bent
Elizabeth
E
Griffith
Natasha
N
McPherson
Michael
M
Zhu
Feilin
F
Oluwadara
Oluwadayo
O
Rao
Nagesh
N
Braun
Jonathan
J
Borneman
James
J
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
D004269:DNA, Bacterial; D004271:DNA, Fungal; D015345:Oligonucleotide Probes; D012335:RNA, Ribosomal