A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas
The comparison of metagenomes is crucial for studying the relationship between microbial communities and environmental factors. One recently published alignment-free whole metagenome comparison method based on k-mer frequencies, Libra, showed higher resolutions than the present fastest method, Mash,...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2020.01061/full |
| _version_ | 1828417223242285056 |
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| author | Jiuhong Dong Shuai Liu Shuai Liu Yaran Zhang Yaran Zhang Yi Dai Qi Wu |
| author_facet | Jiuhong Dong Shuai Liu Shuai Liu Yaran Zhang Yaran Zhang Yi Dai Qi Wu |
| author_sort | Jiuhong Dong |
| collection | DOAJ |
| description | The comparison of metagenomes is crucial for studying the relationship between microbial communities and environmental factors. One recently published alignment-free whole metagenome comparison method based on k-mer frequencies, Libra, showed higher resolutions than the present fastest method, Mash, on whole metagenomic sequencing reads, but it did not perform as well on the assembled contigs. Here, we developed a new alignment-free tool, KmerFreqCalc, for the comparison of the whole metagenomic data, which first calculated the frequencies of both forward and reverse complementary sequences of k-mers like Mash and then computed the cosine distance between the samples based on k-mer frequency vectors like Libra. We applied KmerFreqCalc on the assembled contigs of the gut microbiomes of wild giant pandas and compared the results to Libra and Mash. The results indicated that KmerFreqCalc was able to detect the subtle difference between giant panda samples caused by seasonal diet change, showing better clustering than Libra and Mash. Therefore, KmerFreqCalc has high resolution and accuracy for assembled contigs, being very suitable for comparison of samples with low dissimilarity. |
| first_indexed | 2024-12-10T14:17:42Z |
| format | Article |
| id | doaj.art-4c995fea8745414c9b3f0d16aa6b64f3 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-10T14:17:42Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-4c995fea8745414c9b3f0d16aa6b64f32022-12-22T01:45:18ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-06-011110.3389/fmicb.2020.01061529768A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant PandasJiuhong Dong0Shuai Liu1Shuai Liu2Yaran Zhang3Yaran Zhang4Yi Dai5Qi Wu6State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, ChinaInstitute of Physical Science and Information Technology, Anhui University, Hefei, ChinaKey Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, ChinaState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, ChinaState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, ChinaThe comparison of metagenomes is crucial for studying the relationship between microbial communities and environmental factors. One recently published alignment-free whole metagenome comparison method based on k-mer frequencies, Libra, showed higher resolutions than the present fastest method, Mash, on whole metagenomic sequencing reads, but it did not perform as well on the assembled contigs. Here, we developed a new alignment-free tool, KmerFreqCalc, for the comparison of the whole metagenomic data, which first calculated the frequencies of both forward and reverse complementary sequences of k-mers like Mash and then computed the cosine distance between the samples based on k-mer frequency vectors like Libra. We applied KmerFreqCalc on the assembled contigs of the gut microbiomes of wild giant pandas and compared the results to Libra and Mash. The results indicated that KmerFreqCalc was able to detect the subtle difference between giant panda samples caused by seasonal diet change, showing better clustering than Libra and Mash. Therefore, KmerFreqCalc has high resolution and accuracy for assembled contigs, being very suitable for comparison of samples with low dissimilarity.https://www.frontiersin.org/article/10.3389/fmicb.2020.01061/fullwhole metagenome comparisonk-mer frequenciesreverse complementary sequencecosine distancewild giant pandasgut microbiomes |
| spellingShingle | Jiuhong Dong Shuai Liu Shuai Liu Yaran Zhang Yaran Zhang Yi Dai Qi Wu A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas Frontiers in Microbiology whole metagenome comparison k-mer frequencies reverse complementary sequence cosine distance wild giant pandas gut microbiomes |
| title | A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas |
| title_full | A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas |
| title_fullStr | A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas |
| title_full_unstemmed | A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas |
| title_short | A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas |
| title_sort | new alignment free whole metagenome comparison tool and its application on gut microbiomes of wild giant pandas |
| topic | whole metagenome comparison k-mer frequencies reverse complementary sequence cosine distance wild giant pandas gut microbiomes |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2020.01061/full |
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