Differences in the gut microbiome composition of Korean children and adult samples based on different DNA isolation kits

Abstract

Recent studies have revealed that the composition of human gut microbiota varies according to region, race, age, diet, living environment, and sampling and DNA extraction method. The purpose of this study was to broaden our understanding of the intestinal microbial composition of Koreans by conducting a 16S rRNA amplicon sequencing on 78 Korean samples composed of adults, children, normal and obese groups. We compared the microbiome composition and diversity of these groups at different levels including the phylum and genus level using two different stool DNA extraction kits of QIAamp® PowerFecal® DNA Kit (Qiagen, Hilden, Germany) and CT Max Fecal DNA Kit (Ct bio, Korea). We found that Ct bio (Ct) kit recovered higher DNA yields and OTUs than QIAamp® PowerFecal® DNA Kit (Qia). The Ct kit, which adopted more rigorous bead beating method, detected the most Gram-positive (G+) bacteria, Firmicutes, at the Phylum level, whereas the Qia kit, which used a less rigorous cell lysis method, found the most Gram-negative (G-) bacteria, Bacteroidetes. The Firmicutes-to-Bacteroidetes (F/B) ratio showed no significant difference between the obese and the normal groups of same kit; however, they were significantly different with two different kits. There was a difference in the intestinal flora between healthy Korean adults and children. The taxa that differed significantly between the adults and children were Bacteroides, Bifidobacterium, Prevotella, and Subdoligranulum. There was no significant difference in the intestinal flora between the normal weight group and the obese group in adults and children, respectively. This is probably because the difference in body mass index (BMI) between the sample groups collected in this study is statistically significant, but it is not large enough to show a clear difference in the flora. Therefore, these results should be interpreted with caution while considering the BMI values and Korean obesity criterion together.

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“…The paired-end (2 × 300 bp) sequencing was performed by the Macrogen (South Korea) using the MiSeq ™ platform (Illumina, San Diego, United States). It was completed with reference to the report of Baek et al (2022) . The details were as follows.…”

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“…The column was cleaned two times with washing buffers (solutions EA and C5, respectively). Then, a total of one hundred microliters of elution buffer (Solution C6) was applied and centrifuged at maximum speed for one minute to elute the deoxynucleic acid [ 36 ].…”

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“…In the context of the gut microbiome, this has often led researchers to define "healthy" microbiomes as those that are the most diverse (41,42). Furthermore, many previous investigations place importance on the ratio of Firmicutes to Bacteroidetes for health status since these phyla constitute large proportions of bacterial content in the gut microbiome (43); however, conflicting findings from the many cross-sectional studies with aged populations make it difficult to determine the functional significance of the Firmicutes:Bacteroidetes ratio in the context of aging (44)(45)(46)(47).…”