Sample Selection Representative microbial Region Microbe density, cells/mL clades Sequencing implications Small intestine Duodenum 103 Streptococcus, Lactobacillus Low bacterial biomass decreases contents Jejunum 10-10 Escherichia, Coryne bacterium DNa yields and increases leum107-10 difficulty of non-16S sequencing approaches Large intestine 10-10 12 Bacteroidetes. Firmicutes DNA and RNA in stool samples contents and stool Actinobacteria are almost completely Proteobacteria microbial (>99%); shotgun Methanobrevibacter. Candida DNA and RNA approaches are Mucosa Small intestine: TM7 Shotgun sequencing will yield Enterobacteriaceae large numbers of host reads: Pasteurellaceae joint host and microbial data Lachnospiraceae readily obtained Eubacterium, Streptococcus Large intestine: Bacteroidetes Firmicutes, Actinobacteria Fusobacteria. AkkermansiaSample Selection