Pattern extraction of structural responses of gut microbiota to rotavirus infection via multivariate statistical analysis of clone library data

Abstract

This study developed a new statistical strategy for analyzing clone library data to observe whether there is a defined pattern in structural responses of gut microbiota to environmental perturbations. A large clone library of genus Bacteroides was constructed with fecal samples for each subject in rotavirus-infected (Group R) and healthy children (Group H). In all, 665 clones of the 12 Group H subjects and 284 clones of the nine Group R subjects were sequenced and classified into 34 operational taxonomic units (OTUs) with a similarity cutoff at 98%. Partial least squares-discriminant analysis was used to observe the change of the Bacteroides spp. composition caused by rotavirus infection and to identify the most relevant species contributing to this shift. It was revealed that H subjects and R subjects were well separated. Bacteroides vulgatus, Bacteroides stercoris and Bacteroides fragilis were identified as the most important discriminating OTUs between two groups. The increased abundance of B. fragilis and the decreased populations of B. vulgatus and B. stercoris in infected guts observed in this study were in agreement with previous culture-based studies. The strategy developed in this work can be used to reveal patterns in structural responses of gut microbiota to environmental perturbations from large-scale 16S rRNA gene-based sequencing data.

Human milk oligosaccharides shorten rotavirus-induced diarrhea and modulate piglet mucosal immunity and colonic microbiota

“…The increase in pH and decrease in DM in the lumen were likely the result of an acid-base and electrolyte disturbance and increased intestinal secretion in response to RV infection (Gennari and Weise, 2008). The infection also reduced gut microbial diversity and increased Bacteroides relative abundance, which is consistent with the greater abundance of Bacteroides fragilis reported in RV-infected children compared with healthy controls (Zhang et al, 2009). B. fragilis is a commensal gut bacteria but is also recognized as an opportunistic pathogen commonly associated with diarrheal disease and clinical infections (Kato et al, 1999).…”

Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice

“…C Zhang et al Zhang et al, 2009). The application of PLS-DA to bar-coded pyrosequencing data was robust and also sensitive enough to identify specific members of gut microbiota with health-relevant responses to diet, genotype or health phenotypes, including both minor species (at 1-5%) and major species (410% of total gut populations).…”

Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH

“…Archaeal and bacterial amo A clusters were classified according to Nicol et al (2008) and Zhang et al (2009), respectively. See Figure 1 for soil names.…”

“…In contrast, Jia and Conrad (2009) found that, after ammonium addition, the changes in nitrification activity were paralleled by changes in the abundances of AOB but not of AOA. Thus, the likely involvement of the AOA in the process (Caffrey et al, 2007; Zhang et al, 2009; Wessén et al, 2011; Yao et al, 2011) suggested that AOA, in conjunction with AOB, should be used as proxies to monitor nitrification. Accordingly, both AOA and AOB have been recently suggested as good indicators of soil quality (Wessén and Hallin, 2011).…”