Assessment of fecal DNA extraction protocols for metagenomic studies
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Assessment of fecal DNA extraction protocols for metagenomic studies. / Yang, Fangming; Sun, Jihua; Luo, Huainian; Ren, Huahui; Zhou, Hongcheng; Lin, Yuxiang; Han, Mo; Chen, Bing; Liao, Hailong; Brix, Susanne; Li, Junhua; Yang, Huanming; Kristiansen, Karsten; Zhong, Huanzi.
In: GigaScience, Vol. 9, No. 7, giaa071, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Assessment of fecal DNA extraction protocols for metagenomic studies
AU - Yang, Fangming
AU - Sun, Jihua
AU - Luo, Huainian
AU - Ren, Huahui
AU - Zhou, Hongcheng
AU - Lin, Yuxiang
AU - Han, Mo
AU - Chen, Bing
AU - Liao, Hailong
AU - Brix, Susanne
AU - Li, Junhua
AU - Yang, Huanming
AU - Kristiansen, Karsten
AU - Zhong, Huanzi
PY - 2020
Y1 - 2020
N2 - BACKGROUND: Shotgun metagenomic sequencing has improved our understanding of the human gut microbiota. Various DNA extraction methods have been compared to find protocols that robustly and most accurately reflect the original microbial community structures. However, these recommendations can be further refined by considering the time and cost demands in dealing with samples from very large human cohorts. Additionally, fungal DNA extraction performance has so far been little investigated. RESULTS: We compared 6 DNA extraction protocols, MagPure Fast Stool DNA KF Kit B, Macherey Nagel™ NucleoSpin™®Soil kit, Zymo Research Quick-DNA™ Fecal/Soil Microbe kit, MOBIO DNeasy PowerSoil kit, the manual non-commercial protocol MetaHIT, and the recently published protocol Q using 1 microbial mock community (MMC) (containing 8 bacterial and 2 fungal strains) and fecal samples. All samples were manually extracted and subjected to shotgun metagenomics sequencing. Extracting DNA revealed high reproducibility within all 6 protocols, but microbial extraction efficiencies varied. The MMC results demonstrated that bead size was a determining factor for fungal and bacterial DNA yields. In human fecal samples, the MagPure bacterial extraction performed as well as the standardized protocol Q but was faster and more cost-effective. Extraction using the PowerSoil protocol resulted in a significantly higher ratio of gram-negative to gram-positive bacteria than other protocols, which might contribute to reported gut microbial differences between healthy adults. CONCLUSIONS: We emphasize the importance of bead size selection for bacterial and fungal DNA extraction. More importantly, the performance of the novel protocol MP matched that of the recommended standardized protocol Q but consumed less time, was more cost-effective, and is recommended for further large-scale human gut metagenomic studies.
AB - BACKGROUND: Shotgun metagenomic sequencing has improved our understanding of the human gut microbiota. Various DNA extraction methods have been compared to find protocols that robustly and most accurately reflect the original microbial community structures. However, these recommendations can be further refined by considering the time and cost demands in dealing with samples from very large human cohorts. Additionally, fungal DNA extraction performance has so far been little investigated. RESULTS: We compared 6 DNA extraction protocols, MagPure Fast Stool DNA KF Kit B, Macherey Nagel™ NucleoSpin™®Soil kit, Zymo Research Quick-DNA™ Fecal/Soil Microbe kit, MOBIO DNeasy PowerSoil kit, the manual non-commercial protocol MetaHIT, and the recently published protocol Q using 1 microbial mock community (MMC) (containing 8 bacterial and 2 fungal strains) and fecal samples. All samples were manually extracted and subjected to shotgun metagenomics sequencing. Extracting DNA revealed high reproducibility within all 6 protocols, but microbial extraction efficiencies varied. The MMC results demonstrated that bead size was a determining factor for fungal and bacterial DNA yields. In human fecal samples, the MagPure bacterial extraction performed as well as the standardized protocol Q but was faster and more cost-effective. Extraction using the PowerSoil protocol resulted in a significantly higher ratio of gram-negative to gram-positive bacteria than other protocols, which might contribute to reported gut microbial differences between healthy adults. CONCLUSIONS: We emphasize the importance of bead size selection for bacterial and fungal DNA extraction. More importantly, the performance of the novel protocol MP matched that of the recommended standardized protocol Q but consumed less time, was more cost-effective, and is recommended for further large-scale human gut metagenomic studies.
KW - DNA extraction
KW - gut microbiota
KW - human fecal sample
KW - shotgun metagenomic sequencing
U2 - 10.1093/gigascience/giaa071
DO - 10.1093/gigascience/giaa071
M3 - Journal article
C2 - 32657325
AN - SCOPUS:85087904244
VL - 9
JO - GigaScience
JF - GigaScience
SN - 2047-217X
IS - 7
M1 - giaa071
ER -
ID: 245221745