DOI: 10.1101/494781Dec 12, 2018Paper

Comparison of microbiome and culture techniques for determination of gastrointestinal microbial communities in ceca of chickens

BioRxiv : the Preprint Server for Biology
Kimberly WilsonLisa Bielke

Abstract

The use of 16S next generation sequencing (NGS) technology to identify the relative abundance of microbial communities have become the standard when studying the intestinal microbiome. The increased use is due to the ability to identify a proportion of bacteria that cannot be observed with culture-based methods. However, culture-based techniques are acceptable to identify key bacterial groups, yet may grossly underestimate the microbial community in question. Since there is limited research comparing NGS results to colony forming units (CFU), the objective of this study was to compare total Enterobacteriaceae and lactic acid bacteria (LAB) recovery with culture techniques (CFU/g ceca) to total number of reads from operational taxonomic units (OTU) categorized as Enterobacteriaceae or LAB from Illumina MiSeq platform from matched chick cecal samples at three and 10 days of age. Both CFU recovery (1.09x109 ± 2.42x108; 1.37x108 ± 5.57x107) and reads (5460 ± 1164 ; 282 ± 163) belonging to Enterobacteriaceae decreased by 10 days of age (p < 0.001). Similarly, LAB reads decreased over time (21,128 ± 2262; 6220 ± 817, respectively p < 0.0001). However, LAB CFU recovery increased by 10 days (1.18x108 ± 1.91x107; 1.62x109 ± 5.00x108, re...Continue Reading

Related Concepts

DNA
Enterobacteriaceae
Intestines
Research
Laboratory Culture
Lactic ACID bacteria
Determination Aspects
IFI6 protein, human
Colony (Cells or Organisms)
Microbial Culture (Procedure)

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