Metagenomics: A viable tool for reconstructing herbivore diet.
Metagenomics: A viable tool for reconstructing herbivore diet.
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DOI：
10.1111/1755-0998.13425
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发表时间：
2021-10
影响因子：
7.7
通讯作者：
Bohmann K
中科院分区：
文献类型：
--
作者：
Chua PYS;Crampton-Platt A;Lammers Y;Alsos IG;Boessenkool S;Bohmann K
宏基因组学可以生成食草动物饮食的数据，而不需要元条形码中所必需的引物选择和PCR富集步骤。饮食分析的宏基因组方法仍然相对未开发，需要生物信息学步骤的验证。目前，没有宏基因组食草动物饮食研究利用叶绿体和核标记作为参考序列用于植物鉴定，这将增加可以在分类学上提供信息的读数的数量。在这里，我们探讨了如何在硅片模拟的宏基因组数据集类似于从粪便样本中获得的序列可以用来验证分类分配。使用一个已知的序列列表来创建模拟数据集，我们推导出可靠的识别参数序列的分类分配。我们应用这些参数来表征位于挪威的西方capercaillies（Tetrao urogallus）的饮食，并将结果与从相同样品产生的metabarcoding trnL P6环数据进行比较。这两种方法在鉴定的植物分类群的数量上表现相似（宏基因组学42个分类群，metabarcoding 43个分类群），在物种分辨率上没有显著差异（宏基因组学24%，metabarcoding 23%）。我们进一步观察到，虽然宏基因组学受到粪便样本年龄的强烈影响，新鲜样本优于旧样本，但元条形码不受样本年龄的影响。另一方面，宏基因组学使我们能够同时获得西部刺山柑的线粒体基因组，从而提供额外的生态信息。我们的研究证明了利用宏基因组学进行饮食重建的潜力，但也强调了与未来利用该技术的元条形码相比的关键考虑因素。
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
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影响因子：
3.7
作者：
Hibert F;Taberlet P;Chave J;Scotti-Saintagne C;Sabatier D;Richard-Hansen C
通讯作者：
Richard-Hansen C
影响因子：
3.7
作者：
Hawlitschek O;Fernández-González A;Balmori-de la Puente A;Castresana J
通讯作者：
Castresana J
从高度降解的样品中回收的DNA损伤的量化 - 对粪便中DNA的案例研究。
影响因子：
2.8
作者：
Deagle BE;Eveson JP;Jarman SN
通讯作者：
Jarman SN
DOI：
10.1093/bioinformatics/bty630
发表时间：
2019-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gourlé H;Karlsson-Lindsjö O;Hayer J;Bongcam-Rudloff E
通讯作者：
Bongcam-Rudloff E
影响因子：
1.9
作者：
Alsos, IG;Elvebakk, A;Gabrielsen, GW
通讯作者：
Gabrielsen, GW