Table 2 Summary of DNA isolation methods: yield, fragment quality, and suitability for various sample types

From: Cross-comparison of gut metagenomic profiling strategies

Kit

Advantages

Disadvantages

Qiagen

• Suitable for certain applications

• Lowest DNA yield among the kits

• Higher levels of host DNA contamination

• Less accurate in representing microbial diversity

Invitrogen

• Good overall quality

• Higher variability in yield and fragment length compared to Z and MN kits

• High amount of DNA from stool samples

• Less optimal performance with GMS samples

• Consistent results in various libraries and sequencing methods

• Less effective in certain sample types (e.g., MCS and GMS) compared to Zymo and MN

• Closest match to theoretical composition in MCS samples

Macherey-Nagel

• High overall DNA yield

• Shorter average DNA fragment length

• Better performance in GMS samples

• Good alignment with theoretical microbial composition in MCS samples

• Comparable yield to Z kit when adjusted for initial volume

Zymo Research

• High DNA yield in canine fecal and MCS samples, highest in GMS sample

• Less accurate representation in MCS

• Provides high-quality DNA

• Longest average DNA fragment length

• Superior performance in MCS samples

• Closest match to theoretical composition in GMS samples

• Consistent results and performance for LRS and WGS libraries

• Stable performance with low relative dispersion

  1. This table details the advantages and disadvantages of various DNA isolation kits, including Zymo Research, Qiagen, Macherey-Nagel, and Invitrogen. Key factors include DNA yield, fragment length, contamination levels, and overall performance across different sample types.
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