Dysbiosis of fecal microbiota in Crohnʼs disease patients as revealed by a custom phylogenetic microarray

Abstract

The microarray detected differences in abundance of bacterial populations within the phylum Firmicutes that had been reported previously for the same samples based on phylogenetic analysis of metagenomic clone libraries. In addition, the microarray showed that Enterococcus sp. was in higher abundance in the CD patients. This microarray should be another useful tool to examine the diversity and abundance of human intestinal microbiota.

Moving beyond microbiome-wide associations to causal microbe identification

“…This outcome provides insight into the clinical observations that the abundance of Lachnospiraceae is inversely correlated to risk of IBD and suggests a causal relationship. Moreover, our findings offer critical preclinical support for use of C. immunis as a probiotic in patients with IBD and lower abundances of Lachnospiraceae 5,13–15 .…”

“…This family of Gram-positive, anaerobic, non-spore-forming bacteria was associated with survival from DSS-induced colitis; its abundance was negligible in MMb mice, intermediate in SPF and co-housed mice, and high in HMb mice (Fig 2F). Interestingly, the Lachnospiraceae have been identified in multiple human studies as inversely correlated with IBD 5,13–15 , although the significance of this association remains unclear.…”

Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon

“…Generation and fluorescent labelling of cRNA The methods described by Kang et al (2010) were used with several modifications. First, greater amounts of total DNA (100-500 ng) extracted from the biopsy samples were used for the PCR amplification of the Archaea and Bacteria rrs genes, using the primers described in Table 1.…”

“…The relevant probe and other methodological details have previously been described by Kang et al (2010) and are accessible at the GEO database (http://ncbi.nlm.nih.gov/GEO, under GPL9543 and GSE18933). In brief, the microarrays include 593 probes specific for human intestinal bacteria and archaea derived from the published literature, another 163 newly designed probes using the GoArray algorithm (Rimour et al, 2005), as well as 10 probes (6 positive and 4 negative mismatch controls) targeting the human mitochondrial rrs gene.…”

“…However, they were unable to conclusively reveal evidence of biogeographical trends along the colonic mucosa, and suggested that higher resolution studies using microarray and/or next-generation sequencing technologies, as well as alternative methods of data analysis, were needed. Both phylogenetic microarrays (Paliy et al, 2009;Rajilic-Stojanovic et al, 2009;Kang et al, 2010) and high-throughput sequencing methods are now used more frequently to examine gut microbiome diversity, but the development of robust quantitative methods to reveal the biogeographical features of the gut microbiota is considered a 'great challenge' and 'the diversity and biogeography of the gut microbiota needs to be defined at varying scales of resolution' (Peterson et al, 2008). Although some clustering and ordination methods of numerical ecology are commonly used to compare microbial community profiles through open source software (for example, QIIME (Caporaso et al, 2010)), and increasingly used in gut microbiomics research (Fuentes et al, 2008;Biagi et al, 2010;Janczyk et al, 2010), we contend that, in addition to those methods, there are additional useful numerical ecology methods that can be used.…”