Routine probiotic supplementation with Bifiborm® (Lactobacillus rhamnosus and Bifidobacterium lactis) in infants with gestational age below 30 weeks was introduced in April 2010 at the Department of Neonatology, Rigshospitalet to reduce the risk of NEC. We aimed to investigate the presence of the probiotic agents as well as potential changes in the total microbiota in the stools collected in two cohorts of infants, before and after the introduction of routine probiotics.
Methods
The first cohort (“control cohort”) was recruited from September 2006 to January 2009; the second cohort (“probiotic cohort”) was recruited from May 2010 to October 2011. Stool samples were collected by nurses as part of routine care at postnatal day 0–5 (sample 1), day 10 (sample 2) and day 30 (sample 3). The total number of samples was 446 in the control cohort and 225 in the probiotic cohort. All the stool samples were examined by conventional culture, tested by PCR for the 16S DNA of the two probiotic agents, as well as denaturing gel gradient electrophoresis (DGGE). The band patterns from DGGE were subjected to principal component analysis (PCA).
Results
In the probiotic cohort 82% was PCR positive for L. rhamnosus, 34% was positive for B. lactis in contrast to 6% and 3% in the control cohort. The PCA from the DGGE results did discriminate the two groups with a p < 1–70. This was dominantly caused by a strong first component representing mainly the total of number of bands, with no dominant pattern. Culture showed also a higher number of organisms (pp < 1–22) with no specific bacteria.
Conclusion
L. rhamnosus and B. lactis are not naturally present in the stool of neonates. Administration of probiotics resulted in the presence of the probiotic organisms in the stools and more importantly a profound increase in diversity of the intestinal microbiota. No specific bacteria were seen to be favoured by the probiotic supplementation.
There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful. QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®.
To the Editor: The potential pathogenicity of common intestinal parasitic eukaryotes such as Blastocystis and Dientamoeba fragilis has increasingly been subjected to scrutiny. Blastocystis is proba...
Background and aim: Ulcerative colitis (UC) is a chronic inflammatory bowel disease. The probiotic bacterium Escherichia coli Nissle 1917 (EcN) has been used to maintain and induce clinical remission in UC. Our aim was to test the effect of Ciprofloxacin and/or orally administered EcN as add-on to conventional therapies in patients with active UC.
