Metagenome Assembled Genomes (MAGs) from faecal microbiomes of great tits and blue tits

Overview: The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited data on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). High and Medium quality Metagenome Assembled Genomes (MAGs) were assembled from these metagenomes and are made available as a catalogue in this archive. Methods: Metagenomic reads were trimmed, and quality controlled using FastP configured to a minimum phred score of 20 and minimum length of 50 bp. In order to avoid contamination of the bins by eukaryotic sequences, Tiara v1.0.3 was used to classify contigs longer than 3.000 kb into their high-level kingdoms, allowing to exclude sequences of a eukaryotic or of an organelle origin, and only retaining all unclassified contigs and prokaryotic contigs for the binning step. Contigs were binned using MaxBin2 v2.2.7 , SemiBin2 v2.1.0 and Metabat2 v 2.15 independently. The bins were refined using DasTool v 1.1.7 using a min score threshold of 0.3. The quality of the refined bins was obtained using CheckM2 v 1.0.2, and any bin with a contamination above 10% were excluded. The final MAGs were classified as Low-quality (<50% completeness, <10% contamination), medium-quality (>50% completeness, <10% contamination) and high-quality (>90% completeness, <5% contamination), as recommended by the MIMAG specification . Finally, the MAGs were dereplicated using an dRep v 3.4.3 with an ANI of 95% and classified using gtdb-tk v2.4.0 using the gtdb database release220. Files: The MAGs_sequences_v1.0.0 contains the fasta sequence for the individual MAGs assembled in this project The MAGs_catalogue_v1.0.0.xlsx contains a description of the quality, taxonomic annotation and characteristics of each MAGs in the datasetOverview: 脊椎动物肠道微生物组在宿主健康与疾病进程中发挥关键调控作用。然而当前野生鸟类微生物组的相关数据较为匮乏，且绝大多数仅局限于条形码序列。为此，本研究针对两种在生态学研究中广泛用作模式生物的野生鸟类——大山雀（Parus major）与欧亚蓝山雀（Cyanistes caeruleus）的粪便微生物组开展鸟枪宏基因组测序分析。从上述宏基因组数据中组装得到高质量及中等质量的宏基因组组装基因组（Metagenome Assembled Genomes, MAGs），并将其作为数据集目录收录于本归档文件中。 Methods: 宏基因组读长经FastP进行质控与修剪，参数设置为最低Phred值20、最低序列长度50 bp。为避免真核序列污染分箱结果，本研究使用Tiara v1.0.3对长度大于3.000 kb的重叠群（contig）进行高级界水平分类，以排除真核来源及细胞器来源序列，仅保留未分类序列与原核序列用于后续分箱步骤。 分别使用MaxBin2 v2.2.7、SemiBin2 v2.1.0及Metabat2 v2.15独立进行重叠群分箱，随后通过DasTool v1.1.7对分箱结果进行优化，设置最低得分阈值为0.3。使用CheckM2 v1.0.2评估优化后分箱的质量，剔除污染率高于10%的分箱。 按照宏基因组组装基因组最低信息标准（Minimum Information about a Metagenome-Assembled Genome, MIMAG）的推荐规范，将最终得到的MAGs划分为三类：低质量（完整性<50%、污染率<10%）、中等质量（完整性>50%、污染率<10%）及高质量（完整性>90%、污染率<5%）。最后，使用dRep v3.4.3以95%平均核苷酸一致性（Average Nucleotide Identity, ANI）阈值对MAGs进行去冗余，并通过GTDB-Tk v2.4.0结合GTDB数据库Release220完成分类注释。 Files: MAGs_sequences_v1.0.0 包含本研究组装得到的单条MAGs的FASTA序列文件。 MAGs_catalogue_v1.0.0.xlsx 包含数据集中每一条MAGs的质量信息、分类学注释及特征详情。