LUKAS birth cohort living-room floor dust sequencing

LUKAS study comprises two birth cohorts, LUKAS1 and LUKAS2. In LUKAS1 (N=214) equal numbers of pregnant mothers living in farms with livestock and mother's living in rural areas but not in farms were recruited in the major local hospitals in eastern and middle Finland (Kuopio, Iisalmi, Jyväskylä and Joensuu) between September 2002-May 2004. The inclusion criteria were maternal age =18 years, singleton pregnancy, native language Finnish, no plans to move from the study area, expected delivery in one of the study hospitals, siblings of the study child not participating in the study, parturition at =37 weeks of gestation, no congenital abnormalities in newborn and successful cord blood sampling. In LUKAS2 all pregnant women with estimated delivery at Kuopio University Hospital between May 2004 and May 2005 were invited to join the study without selection by occupation or area of living. Mothers living in apartments were excluded to maintain housing conditions comparable with LUKAS1. The living room floor dust samples were collected By vacuuming at index child age of 2 months. DNA was extracted from sieved dust using bead beating method. The bacterial/archaeal 16S rRNA gene V4 region was amplified using 515F/806R primers and fungal ITS region by ITS1F/ITS2 primers.These DNA amplicons were sequenced as 300 base pair paired-end reads with Illumina MiSeq V3 chemistry.

LUKAS研究包含两个出生队列，即LUKAS1与LUKAS2。LUKAS1队列（N=214）的招募工作于2002年9月至2004年5月间在芬兰东部及中部的多家主要地方医院（库奥皮奥、伊萨尔米、于韦斯屈莱、约恩苏）开展，共纳入数量均等的两类孕妇：一类居住在养殖畜禽的农场，另一类居住在农村地区但并非农场住户。该队列的入组标准包括：产妇年龄≥18岁、单胎妊娠、母语为芬兰语、无搬迁出研究区域的计划、预计在研究合作医院分娩、研究所涉儿童的同胞未参与本研究、妊娠满37周及以上分娩、新生儿无先天性畸形、脐带血采样成功。LUKAS2队列的招募范围为2004年5月至2005年5月间所有预计在库奥皮奥大学医院分娩的孕妇，无需按职业或居住区域进行筛选；为保证与LUKAS1队列的居住环境具有可比性，本队列排除了居住在公寓的孕妇。在研究目标儿童2月龄时，研究人员通过真空吸尘法采集其起居室地板的灰尘样本；采用珠磨法从过筛后的灰尘中提取脱氧核糖核酸（Deoxyribonucleic Acid, DNA），使用515F/806R引物扩增细菌/古菌的16S核糖体RNA（16S ribosomal RNA, rRNA）基因V4区域，使用ITS1F/ITS2引物扩增真菌内部转录间隔区（Internal Transcribed Spacer, ITS）；随后以300碱基对的双端读长模式，借助Illumina MiSeq V3测序试剂对上述DNA扩增产物进行测序。