Eczema was considered atopic if it was associated with positive skin prick test(s) at 6 and/or 24 -month study visit. None of the study subjects
included in present study suffered from asthma or allergic rhinitis. Also, all the TSA HDAC cell line infants were normal weight at the age of 6 and 18 months of age. The study protocol was approved by the Ethics Committee of the Hospital District of Southwest Finland and subjects were enrolled in the study after written informed consent was obtained. Faecal samples and DNA extraction The faecal samples were taken from children at age of 6 and 18 months. The samples were aliquoted and frozen immediately after collection, and stored in −80°C. DNA was extracted from faecal samples using the repeated bead-beating method as described previously [31, 32]. 16S rRNA gene microarray analysis The composition of total microbiota was assessed by using the phylogenetic Human Intestinal Tract chip (HITChip) as described previously [28, 33], except for the amplification step, where 25 cycles of end-point PCR were used. Microarray analysis of all samples were performed in at least two independent hybridizations until satisfactory reproducibility was achieved (>96%). This study reports results
of more than 150 independent microarray hybridizations. The HITChip is a custom-made Agilent microarray (Agilent Technologies, Palo Alto, CA, USA) designed to comprehensively cover the diversity of the human intestinal microbiota. The array contains selleckchem 3699 unique oligonucleotide probes targeting the V1 and V6 hypervariable regions of the 16S rRNA gene and
covering over 1100 intestinal bacterial phylotypes. The HITChip allows the analysis at three phylogenetic levels: phylum-like level (level 1), genus-like level (level 2) and phylotype level (species-like, level 3). The details of the HITChip have previously been described, including its validation for phylogenetic fingerprinting and quantification . Microarray data extraction and microbiota diversity assessment Data were extracted from microarray images using the Agilent Feature Extraction software, version 9.5.1 (http://www.agilent.com). Normalization Tenofovir research buy of microarray data was performed as described earlier [28, 34]. Further data processing was performed by using a custom designed relational database running under the MySQL database management system (http://www.mysql.com) using R-based scripts . Quantitative PCR Quantitative PCR (qPCR) analysis of Bifidobacterium genus and species was carried out in an Applied Biosystems 7300 Fast Real-Time PCR System in a 96-well format and by using SYBR Green chemistry (SYBR Green PCR Master Mix, Applied Biosystems, USA). The www.selleckchem.com/products/apo866-fk866.html primers and their specificities are presented in Additional file 2. The PCR reactions and thermocycling conditions were as reported earlier [35, 36].