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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #180664
Title: ABUNDANT AND DIVERSE FUNGAL MICROBIOTA IN THE MURINE INTESTINE

Author
item SCUPHAM, ALEXANDRA
item PRESLEY, LAURA - UNIV OF CALIF, RIVERSIDE
item WEI, BO - UCLA
item BENT, ELIZABETH - UNIV OF CALIF, RIVERSIDE
item GRIFFITH, NATASHA - UCLA
item MCPHERSON, MICHAEL - UCLA
item ZHU, FEILIN - UCLA
item OLUWADARA, OLUWADAYO - UCLA
item RAO, NAGESH - UCLA
item BRAUN, JONATHAN - UCLA

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/11/2005
Publication Date: 1/20/2006
Citation: Scupham, A.J., Presley, L.L., Wei, B., Bent, E., Griffith, N., McPherson, M., Zhu, F., Oluwadara, O., Rao, N., Braun, J., Borneman, J. 2006. Abundant and diverse fungal microbiota in the murine intestine. Applied and Environmental Microbiology. 72(1):793-801.

Interpretive Summary: In this work we describe the fungal and bacterial species found in the colons and small intestines of two strains of laboratory mice; those with normal flora and those with flora associated with the development of Inflammatory Bowel Disease (IBD). IBD affects roughly 1 of every 500 people in the USA and is a condition for which most IBD sufferers will eventually need surgery to alleviate their symptoms. This work is a preliminary step for the identification of microbes associated with the disease. We analyzed 1409 fungal and 1418 bacterial gene sequences in all, and found all four major groups of fungi were represented. The majority of the bacterial sequences represented Lactobacillus, Clostridium, and Acinetobacter related species. Analysis of the mouse chow indicated that several of the bacterial and fungal species were contaminants. We used fluorescently labeled fungal DNA to determine whether the microbes could colonize intestinal epithelium, and found a diverse assortment of fungal types associated with the epithelial mucus layer. This work is the first description of the complex fungal community found in the intestines of a mammalian species, and suggests fungi may play a role in intestinal microbial function, including induction of IBD.

Technical Abstract: Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria have been broadly characterized in the intestine, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) to describe the composition of fungal and bacterial rRNA genes from intestine 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 three genera: Acinetobacter, Clostridium, and Lactobacillus. Most of the Clostridium-like rRNA gene sequences had less than 90% identity to their closest relatives. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. FISH analysis with a universal fungal small-subunit ribosomal 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-positive organisms in the cecal biofilm. These data indicate that diverse fungal taxa are present in the intestinal microbial community, both in the fecal and mucosal biofilm compartments. Their abundance suggests that they may play significant roles in enteric microbial functions.