Jenna M. Lang edited Results.md  about 10 years ago

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##Plate Counts  The aerobic, anaerobic, yeast and mold plate counts are shown in Table 4. The meals ranged in the total numbers of microorganisms from 2.2 X 104 CFU to 1.2 X 109 CFU with the aerobic and anaerobic plate counts being among the highest and the yeast and mold plate counts being among the lowest across all meals. The USDA dietary pattern had the highest total microorganisms for the day at 1.3 X 109 CFU mostly due to the higher amounts of anaerobic bacteria in the morning snack (5.4 X 107 CFU) and higher amounts of aerobic and anaerobic bacteria in the afternoon snack (5.5 X 108 and 6 X 108 CFU respectively). Not surprisingly, both of these meals contained fermented products, in the first case yogurt, and in the second case cottage cheese. The AA and VEG dietary patterns had 3 orders of magnitude less total microorganisms than the USDA dietary patterns, with total microorganisms of 1.4 X 106 CFU and 6 X 106 CFU respectively. Neither the AA nor the VEG dietary pattern meals contained fermented foods that were not heat treated as part of meal preparation. The AA lunch and dinner contained cheese that was either cooked on a grill or baked in the oven and the VEG lunch contained tofu, which was cooked in the vegetable broth. The USDA lunch also had the highest amounts of yeast and mold (1 X 106^ and 2.6 X 106 CFU respectively) of all the meals, and this meal also had relatively high amounts of aerobic bacteria (3.3 X 107 CFU). In the VEG dietary pattern, the morning snack had the highest amounts of aerobic and anaerobic bacteria (2 X 106 and 1.7 X 106 CFU respectively).   ##Sequence Processing and Summary Statistics  The number of high-quality sequences per meal ranged from 168,669-318,956. After OTU assignment, mitochondrial and chloroplast sequences were filtered out, and sequences that were observed only once (globally) were removed. After filtration, the range of sequences per sample decreased to 974-279,136. All subsequent diversity analyses were performed on samples that were rarefied to 974 sequences per sample.  ##Taxonomic Composition and Diversity of the Different Dietary Patterns  ##Factors Driving the Differences in Microbial Community Composition and Diversity of Individual Meals