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    • With fecal DNA Chen and

    2018-10-25

    With fecal DNA, Chen and colleagues reported that the overall composition of the microbiota differed between 47 CRA cases and 47 colonoscopically normal, age- and sex-matched controls (Chen et al., 2013). Nominally significant differences in relative abundance, not adjusted for multiple comparisons, were reported for six bacterial genera — two increased (Enterococcus and Streptococcus) and four decreased (Bacteroides, Clostridium, Roseburia, and Eubacterium) in CRA cases (Chen et al., 2013). Likewise, Zackular et al. identified a dozen of differentially abundant fecal taxa in CRA cases, although they did not consider multiple comparisons, overall carnitine palmitoyltransferase or composition (Zackular et al., 2014). In two very small studies, no large or statistically significant differences in the fecal microbiota of CRA cases were found (Brim et al., 2013; Mira-Pascual et al., 2014). The fecal microbiota of patients with small, benign adenoma (polyp) resembles that of normal controls (Zeller et al., 2014).
    Methods
    Results Informed consent was provided by 95 consecutive FIT+ patients. Several days prior to bowel cleansing, 68 (72%) patients returned, less than 2h after defecation, with all four vials of feces in the media-loaded vials. These 68 participants with specimens were predominantly female (59%), and they had a median age of 65 [interquartile range (IQR)=61–69] years and median body mass index (BMI) of 24 (IQR=21–27) kg/m2. Other characteristics are provided in Table 1. Cigarette smoking was reported by 21 (75%) men and 1 woman. Alcohol consumption was reported by 10 men and 2 women. Ten participants reported receiving an antibiotic within 12weeks of enrollment, 11 others received an antibiotic 12–24weeks before enrollment, and the remaining 47 had no antibiotic use within 24weeks. Variables that might confound comparison of the CRA and normal participants are presented in Supplemental Table 1. The two groups did not differ in age (P=0.86), but they were more likely to be male (P=0.04). Sex accounted completely for small differences between CRA and normal participants in BMI (P=0.12) and red meat consumption (P=0.05). CRA was associated with antibiotic exposure less than 12weeks (N=5 vs 1, P=0.04) and 12–24weeks (N=5 vs 2, P=0.07) before enrollment. One fecal DNA specimen, in a participant who refused colonoscopy, failed to amplify. In the 67 successful fecal microbiota profiles, a median of 70,583 (range=48,807–170,668) 16S rRNA sequences was clustered by 97% identity into 2922 OTUs, which were assigned to taxa from the phylum to the species level, including 18 different phyla, 38 classes, 64 orders, 115 families, 227 genera, and 303 species. Taxa in the Firmicutes and Bacteroidetes phyla were most common, followed by Proteobacteria, Actinobacteria and Fusobacteria, but individual differences were substantial (Supplemental Fig. 1).
    Discussion We found CRA in 33% of 61 Shanghai residents aged 50–74 who had occult blood in feces (FIT+) and who completed colonoscopy. The overall composition of the fecal microbiota differed significantly between CRA and normal-colonoscopy participants, with good discrimination (AUC=0.767). Unlike Zackular et al. (2014), this calculation was based on the entire microbial community rather than on a handful of taxa selected to maximize the discrimination. Of potential functional interest, we noted that CRA was associated with significantly higher abundance of fecal Proteobacteria, the phylum that includes established gut pathogens — Pseudomonas, Escherichia, Shigella, Salmonella, Serratia, Klebsiella, and Helicobacter. Our findings corroborate those from a prior study in Shanghai, in which fecal microbial communities differed between 47 CRA patients and 47 normal-colonoscopy patients (Chen et al., 2013). In that latter study, the abundance of Proteobacteria taxa was modestly higher with CRA (mean=3.7% vs 3.0%), but most of the compositional difference was attributed to other bacterial taxa (Chen et al., 2013). CRA cases also had higher abundance of Proteobacteria in feces in a small study in Spain (Mira-Pascual et al., 2014) and in biopsies of unaffected rectal mucosa (Mira-Pascual et al., 2014; Shen et al., 2010). Only one of the dozen CRA-associated taxa noted in the American study, Pseudomonas, was in the Proteobacteria phylum (Zackular et al., 2014).