Fecal samples were obtained from a cohort of 330 healthy Danish infants at 9, 18, and 36 months after birth, enabling characterization of interbacterial relationships by use of quantitative PCR targeting 31 selected bacterial 16S rRNA gene targets representing different phylogenetic levels. Nutritional parameters and measures of growth and body composition were determined and investigated in relation to the observed development in microbiota composition. We found that significant changes in the gut microbiota occurred, particularly from age 9 to 18 months, when cessation of breastfeeding and introduction of a complementary feeding induce replacement of a microbiota characterized by lactobacilli, bifidobacteria, andEnterobacteriaceaewith a microbiota dominated byClostridiumspp. andBacteroidesspp. Classification of samples by a proxy enterotype based on the relative levels ofBacteroidesspp. andPrevotellaspp. showed that enterotype establishment occurs between 9 and 36 months. Thirty percent of the individuals shifted enterotype between 18 and 36 months. The composition of the microbiota was most pronouncedly influenced by the time of cessation of breastfeeding. From 9 to 18 months, a positive correlation was observed between the increase in body mass index and the increase of the short-chain-fatty-acid-producing clostridia, theClostridum leptumgroup, andEubacterium hallii. Considering previously established positive associations between rapid infant weight gain, early breastfeeding discontinuation, and later-life obesity, the corresponding microbial findings seen here warrant attention.

This paper focuses on the practical aspects and implications of preprocessing chromatographic data to correct for undesirable time‐shifts. An approach to automate the alignment of chromatographic data based on peak alignment or warping is proposed. This approach deals with selection of the required parameters including selection of reference sample to warp towards, and chooses warping settings based on a new evaluation criterion for goodness of correction. The new criterion aims at quantifying goodness of alignment while at the same time penalising significant shape or area‐changes in the warped peaks. The entire selection procedure is automated using a discrete‐coordinates simplex‐like optimisation routine. Examples with simulated chromatographic data, GC‐FID and HPLC‐Fluorescence measurement series illustrate the potential of using this automated alignment tool. Copyright © 2007 John Wiley & Sons, Ltd.