Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects

• Published in: Journal of applied microbiology 2011-08, Vol.111 (2), p.467-473
• Main Authors: O'Sullivan, Ó, Coakley, M, Lakshminarayanan, B, Claesson, M.J, Stanton, C, O'Toole, P.W, Ross, R.P
• Format: Article
• Language: English
• Subjects: Adult; Aged; Bacteria; bacterial culture; bifidobacteria; Bifidobacterium; Bifidobacterium - genetics; Bifidobacterium - isolation & purification; Biological and medical sciences; Colony Count, Microbial; Computational Biology; correlation; Culture Media; DNA, Bacterial - genetics; elderly; elderly Irish; Enterobacteriaceae; Enterobacteriaceae - genetics; Enterobacteriaceae - isolation & purification; feces; Feces - microbiology; Fundamental and applied biological sciences. Psychology; genes; Genes, rRNA; high-throughput nucleotide sequencing; Humans; intestinal microorganisms; Intestines - microbiology; lactobacilli; Lactobacillus; Lactobacillus - genetics; Lactobacillus - isolation & purification; Microbiology; people; plate count; ribosomal RNA; selective media; Sequence Analysis, DNA; sequencing
• ISSN: 1364-5072; 1365-2672
• DOI: 10.1111/j.1365-2672.2011.05067.x

Aims: The aim of this investigation was to establish the degree of correlation between measurements from culture-dependent microbiological techniques and from next generation sequencing technologies. Methods and Results: Data generated by both techniques were collected from faecal samples from 185 elderly Irish people involved in the ongoing ELDERMET study (http://eldermet.ucc.ie). The results for three groups of intestinal bacteria were compared. Bifidobacterium sp., Lactobacillus sp. and Enterobacteriaceae were enumerated on selective media through culture-dependent techniques, whereas proportions of these bacteria were determined through sequencing technology against the background of other bacteria. The Spearman's rank correlation coefficient determined a good correlation between results from culture-dependent microbiology and culture-independent techniques for all three bacterial groups assessed (correlation coefficients for Bifidobacterium sp., Lactobacillus sp. and Enterobacteriaceae were 0·380, 0·366 and 0·437, respectively). Conclusion: Correlation between the two methods implies that a single method is capable of profiling intestinal Bifidobacterium, Lactobacillus and Enterobacteriaceae populations. However, both methods have advantages that justify their use in tandem. Significance and Impact of the Study: This is the first extensive study to compare bacterial counts from culture-dependent microbiological techniques and from next generation sequencing technologies.