The identification of fungi collected from the ceca of commercial poultry

Abstract

Under normal conditions, fungi are ignored unless a disease/syndrome clinical signs are reported. The scientific communities are largely unaware of the roles fungi play in normal production parameters. Numerous preharvest interventions have demonstrated that beneficial bacteria can play a role in improving productions parameters; however, most researchers have ignored the impact that fungi may have on production. The goal of the present study was to record fungi recovered from commercial broiler and layer houses during production. Over 3,000 cecal samples were isolated using conventional culture methodology and over 890 samples were further characterized using an automated repetitive sequence-based PCR (rep-PCR) methodology. Eighty-eight different fungal and yeast species were identified, including Aspergillus spp., Penicillium spp., and Sporidiobolus spp, and 18 unknown genera were separated using rep-PCR. The results from the present study will provide a normal fungi background genera under commercial conditions and will be a stepping stone for investigating the impact of fungi on the gastrointestinal tract and on the health of poultry.

Effects of dietary supplementation with lysozyme on the structure and function of the cecal microbiota in broiler chickens

“…However, their role in cecal microbiology is not clear. As with the data of Byrd et al [31], it seems probable that most are unlikely to grow under the anaerobic conditions in the cecum and arrived there after ingestion as dormant spores, which are able to withstand the hostile anaerobic and low pH conditions encountered within the cecum. Consequently, these data raise several interesting questions, including whether any of the fungi found there are strict anaerobes and whether they exist within the cecum as actively growing hyphae.…”

“…What role these fungi might play there is poorly understood, as similar published data are scarce. Byrd et al [31] using culture-dependent methods, managed to identify a large number of fungi in the cecum of broilers using rep-PCR. However, their culture method was not carried out under the anaerobic conditions found in the cecum, and most identified fungi appeared to be common highly sporulating airborne fungi, whereas some could not be identified.…”

Chicken Intestinal Mycobiome: Initial Characterization and Its Response to Bacitracin Methylene Disalicylate

“…Besides Candida, Trichosporon, Geotrichum, Rhodotorula, and Saccharomyces have been reported in chickens as well (21)(22)(23). However, one other culture-dependent study reported the identification of 88 fungal species from over 3,000 cecal samples of broiler and layer chickens, with Aspergillus, Penicillium, Verticillium, and Sporidiobolus being the top four genera (25), whereas a cultureindependent 454 pyrosequencing method only revealed two fungal species, Cladosporium sp. and Cladosporium sphaerospermum, in the cecum of broilers fed unmedicated diets (20), presumably due to a lack of sequencing depth.…”

“…In limited poultry mycobiome studies, all but one were culture based, and most were restricted only to the cecum (20)(21)(22)(23)(24)(25). Candida or Aspergillus was revealed to be predominant in the chicken cecum in culture-dependent studies.…”

Effects of Hardwood Biochar on Methane Production, Fermentation Characteristics, and the Rumen Microbiota Using Rumen Simulation

“…Biochar supplementation at 800 mg/d also significantly increased the abundance of two OTUs classified as Vishniacozyma victoriae (5.4 × 10 7 -fold increase, phylum Ascomycota) and Sporobolomyces ruberrimus (5.4 × 10 7 -fold increase). V. victoriae (also known as Cryptococcus victoriae ) and S. ruberrimus are both species of yeast; V. victoriae has been identified in cow’s milk (Delavenne et al, 2011) and meat processing plants (Nielsen et al, 2008) and S. ruberrimus in chicken ceca (Byrd et al, 2017).…”