Pérez-Valera Eduardo, Elhottová Dana
INRAE, University Bourgogne, Institut Agro Dijon, Department of Agroecology, 17 rue de Sully, Dijon, 21000, France.
Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, České Budějovice, 370 05, Czech Republic.
Data Brief. 2025 Jun 3;61:111748. doi: 10.1016/j.dib.2025.111748. eCollection 2025 Aug.
This data report presents 111 metagenome-assembled genomes (MAGs) reconstructed from manure, soil and manured soil samples from microcosms after enriching for non-fermenting Gram-negative bacteria (NFGNB). Two independent microcosm experiments were conducted to investigate the spread of NFGNB from the fresh manure of dairy cows under antibiotic prophylaxis to the pasture soil of two organic farms. After sampling the microcosms on days 2, 14 and 28, the manure and soil samples were plated in duplicate on CHROMagar Acinetobacter medium for NFGNB enrichment and incubated at 28°C for 24 h. DNA was extracted from the cultures and sequenced using the Illumina NovaSeq 6000 platform with 150-bp paired-end reads. Reads were assembled with metaSPAdes both individually and by co-assembly. MAGs were reconstructed using MetaBAT, MaxBin, SemiBin2, COMEbin, and AVAMB, and then de-replicated at >95 % ANI (pairwise comparisons) using dRep. A total of 111 MAGs of at least medium quality (MIMAG standard) were obtained. These included 10 high-quality MAGs (>90 % completeness, <5 % contamination, rRNA genes and tRNA for at least 18 amino acids), 47 putative high-quality MAGs (>90 % completeness, <5 % contamination) and 54 medium-quality MAGs (>50 % completeness, <10 % contamination). The FASTA files of the MAGs as well as their taxonomic identifications, completeness and contamination, origin, genomic statistics and rRNA sequences are publicly available in a Zenodo dataset and the genomes in the NCBI database. The majority of MAGs (99) were assigned to Pseudomonadota, mainly (28 MAGs), (20 MAGs) and (18 MAGs), while the remaining 12 MAGs belonged to Bacteroidota. Most MAGs (44) were of manure origin, followed by manured soil (38 MAGs) and soil (29 MAGs). High-quality MAGs were predominantly obtained from manure (6 high-quality, 21 putative high-quality), compared to manured soil (3 high-quality, 12 putative high-quality) and soil (1 high-quality, 14 putative high-quality). By providing their MAGs, this dataset offers a valuable resource for researchers investigating the genomic characteristics associated with the survival, environmental dispersal and ecological role of potentially hazardous NFGNB species in soil, particularly following the application of antibiotic-treated animal manure, and for comparative genomics studies in related environments.
本数据报告展示了从富集非发酵革兰氏阴性菌（NFGNB）后的微观世界中的粪便、土壤和施肥土壤样本中重建的111个宏基因组组装基因组（MAG）。进行了两项独立的微观世界实验，以研究在抗生素预防措施下，奶牛新鲜粪便中的NFGNB向两个有机农场的牧场土壤中的传播情况。在第2天、14天和28天对微观世界进行采样后，将粪便和土壤样本一式两份接种在用于NFGNB富集的CHROMagar不动杆菌培养基上，并在28°C下孵育24小时。从培养物中提取DNA，并使用Illumina NovaSeq 6000平台进行测序，读取150bp的双端读数。读数分别通过metaSPAdes单独组装和共同组装。使用MetaBAT、MaxBin、SemiBin2、COMEbin和AVAMB重建MAG，然后使用dRep在>95%ANI（成对比较）下进行去重复。总共获得了111个至少中等质量（MIMAG标准）的MAG。其中包括10个高质量MAG（完整性>90%，污染率<5%，至少18种氨基酸的rRNA基因和tRNA）、47个推定的高质量MAG（完整性>90%，污染率<5%）和54个中等质量MAG（完整性>50%，污染率<10%）。MAG的FASTA文件及其分类鉴定、完整性和污染情况、来源、基因组统计信息和rRNA序列在Zenodo数据集中公开可用，并且这些基因组也可在NCBI数据库中获取。大多数MAG（99个）被归类为假单胞菌门，主要是（28个MAG）、（20个MAG）和（18个MAG），而其余12个MAG属于拟杆菌门。大多数MAG（44个）来自粪便，其次是施肥土壤（38个MAG）和土壤（29个MAG）。与施肥土壤（3个高质量，12个推定高质量）和土壤（1个高质量，14个推定高质量）相比，高质量MAG主要从粪便中获得（6个高质量，21个推定高质量）。通过提供其MAG，该数据集为研究人员提供了宝贵的资源，用于调查与潜在有害的NFGNB物种在土壤中的生存、环境扩散和生态作用相关的基因组特征，特别是在施用抗生素处理的动物粪便之后，以及用于相关环境中的比较基因组学研究。
