16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis

Abstract

Dysbiosis of human gut microbiota has been reported in association with ulcerative colitis (UC) in both children and adults using either 16S rRNA gene or shotgun sequencing data. However, these studies used either 16S rRNA or metagenomic shotgun sequencing but not both. We sequenced feces samples from 19 pediatric UC and 23 healthy children ages between 7 to 21 years using both 16S rRNA and metagenomic shotgun sequencing. The samples were analyzed using three different types of data: 16S rRNA genus level abundance, microbial species and pathway abundance profiles. We demonstrated that (a) the alpha diversity of pediatric UC cases is lower than that of healthy controls; (b) the beta diversity within children with UC is more variable than within the healthy children; (c) several microbial families including Akkermansiaceae, Clostridiaceae, Eggerthellaceae, Lachnospiraceae, and Oscillospiraceae, contain species that are depleted in pediatric UC compared to controls; (d) a few associated species unique to pediatric UC, but not adult UC, were also identified, e.g. some species in the Christensenellaceae family were found to be depleted and some species in the Enterobacteriaceae family were found to be enriched in pediatric UC; and (e) both 16S rRNA and shotgun sequencing data can predict pediatric UC status with area under the receiver operating characteristic curve (AUROC) of close to 0.90 based on cross validation. We showed that 16S rRNA data yielded similar results as shotgun data in terms of alpha diversity, beta diversity, and prediction accuracy. Our study demonstrated that pediatric UC subjects harbor a dysbiotic and less diverse gut microbial population with distinct differences from healthy children. We also showed that 16S rRNA data yielded accurate disease prediction results in comparison to shotgun data, which can be more expensive and laborious. These conclusions were confirmed in an independent data set of 7 pediatric UC cases and 8 controls.

The role of gut microbiome in inflammatory bowel disease diagnosis and prognosis

“…Notably, Veillonella parvula , E. coli , R. gnavus and Clostridium clostridioforme were significantly enriched species in CD compared with UC and healthy controls, while F. prausnitzii is the most depleted species in CD. Interestingly, Zuo et al 44 . demonstrated that although the 16s data shows similar results as shotgun sequencing data in terms of alpha diversity and beta diversity, 16S genus data (AUC = 0.869) achieved higher pediatric UC prediction performance than shotgun species data (AUC = 0.763) and pathway data (AUC = 0.764).…”

“…Interestingly, Zuo et al. 44 demonstrated that although the 16s data shows similar results as shotgun sequencing data in terms of alpha diversity and beta diversity, 16S genus data (AUC = 0.869) achieved higher pediatric UC prediction performance than shotgun species data (AUC = 0.763) and pathway data (AUC = 0.764).…”

“… 42 The prevalence and abundance of P. mirabilis were also higher in fecal and mucosal samples of patients with CD than that in controls. A recent study 43 , 44 found that Klebsiella pneumoniae (Kp) was enriched in the gut microbiota of IBD patients across geography. Isolated Kp strains induced severe intestinal inflammation and tissue damage, suggesting that the Kp strains may contribute to worsening IBD.…”

Metagenomic Analyses of Multiple Gut Datasets Revealed the Association of Phage Signatures in Colorectal Cancer

“…The human gut microbiome, the microbial communities inhabiting our gastrointestinal tract, can greatly influence human health through the immune and metabolic systems ( Holmes et al., 2012 ). Many studies have demonstrated the complicated associations between gut microbiome and human diseases such as inflammatory bowel disease (IBD) ( Norman et al., 2015 ; Zuo et al., 2022 ), metabolic diseases ( Qin et al., 2012 ) and autoimmune diseases ( Tomofuji et al., 2022 ). The human gut microbiome, which could be altered by some of the mentioned risk factors, has also been considered as one of the most important environmental factors in the development of CRC.…”

Impact on the soil microbiota of marine sediment content as an agricultural substrate: metagenomic 16S rRNA analyzes

“…With the development and availability of new technologies based on genetic sequencing, it is possible to quickly characterize, identify and quantify millions of genomic sequences. Metagenomic studies, although complex, have been used successfully in different contexts and/or applications, such as medicine, animal production, pharmacological, polluted ecosystems, soils, and water, among others, which is undoubtedly increasing the accumulated knowledge about the bacterial microbiota, its interactions with the environment and other microorganisms [2][3][4][5][6][7].…”