Differences in the composition of the gut microbiota have been associated with a range of diseases using culture-independent methods. Reliable extraction of nucleic acid is a key step in identifying the composition of the faecal microbiota. Five widely used commercial deoxyribonucleic acid (DNA) extraction kits (QIAsymphony® Virus/Bacteria Midi Kit (kit QS), ZR Fecal DNA MiniPrep™ (kit Z), QIAamp® DNA Stool Mini Kit (kit QA), Ultraclean® Fecal DNA Isolation Kit (kit U) and PowerSoil® DNA Isolation Kit (kit P)) were evaluated, using human faecal samples. Yield, purity and integrity of total genomic DNA were compared spectrophotometrically and using gel electrophoresis. Three bacteria, commonly found in human faeces were quantified using real time polymerase chain reaction (qPCR) and total bacterial diversity was studied using denaturing gradient gel electrophoresis (DGGE) as well as terminal restriction fragment length polymorphism (T-RFLP). The measurements of DNA yield and purity exhibited variations between the five kits tested in this study. Automated kit QS exhibited the best quality and highest quantity of DNA. All kits were shown to be reproducible with CV values ≤ 0.46 for DNA extraction. qPCR results showed that all kits were uniformly efficient for extracting DNA from the selected target bacteria. DGGE and T-RFLP produced the highest diversity scores for DNA extracted using kit Z (H′ = 2.30 and 1.27) and kit QS (H′ = 2.16 and 0.94), which also extracted the highest DNA yields compared to the other kits assessed.

BackgroundFindings from animal studies indicate that the early gut bacteriome is a potential mechanism linking maternal prenatal stress with health trajectories in offspring. However, clinical studies are scarce and the associations of maternal psychological profiles with the early infant faecal bacteriome is unknown. This study aimed to investigate the associations of prenatal stressors and distress with early infant faecal bacterial profiles in a South African birth cohort study.MethodsAssociations between prenatal symptoms of depression, distress, intimate partner violence (IPV) and posttraumatic stress-disorder (PTSD) and faecal bacterial profiles were evaluated in meconium and subsequent stool specimens from 84 mothers and 101 infants at birth, and longitudinally from a subset of 69 and 36 infants at 4–12 and 20–28 weeks of age, respectively in a South African birth cohort study.ResultsInfants born to mothers exposed to high levels of IPV had significantly higher proportions of unclassified genera within the family Enterobacteriaceae detected at birth; higher proportions of the genus Weissella at 4-12 weeks; and increased proportions of genera within the family Enterobacteriaceae over time (birth to 28 weeks of life). Faecal specimens from mothers exposed to IPV had higher proportions of the family Lactobacillaceae and lower proportions of Peptostreptococcaceae at birth. Maternal psychological distress was associated with decreased proportions of the family Veillonellaceae in infants at 20-28 weeks and a slower decline in Gammaproteobacteria over time. No changes in beta diversity were apparent for maternal or infant faecal bacterial profiles in relation to any of the prenatal measures for psychological adversities.ConclusionIPV during pregnancy is associated with altered bacterial profiles in infant and maternal faecal bacteria. These findings may provide insights in the involvement of the gut bacteria linking maternal psychological adversity and the maturing infant brain.

qualitative data only. Results: Fourteen eligible studies were identified, of which seven met the inclusion criteria for the meta-analysis. There were no eligible adult studies. The meta-analysis results showed that Clostridium difficile was significantly associated with increased odds of wheezing (Odds Ratio (OR) = 1.50; 95% confidence interval (CI) = 1.19, 1.89). In addition, C. difficile was associated with increased odds of asthma (OR = 2.06; 95% CI = 1.16, 3.64), although a meta-analysis was not performed. Eligible studies reported that vaginal delivery and breastfeeding was significantly associated with changes in Clostridia and Bifidobacteria, respectively. A single study reported that factors significantly influencing both asthma and the composition of gut microbiota were mode and place of delivery.Conclusion: These results confirm the likely role of C. difficile with childhood wheezing illness. Large-scale longitudinal birth cohort studies, implementing massively parallel sequencing of the 16S rRNA gene of faecal bacteria or culturomics, are needed to better determine the role of faecal microbial profiles in the development of asthma or wheezing illness. Quantitative analysis is essential in association studies seeing that the relative species abundance contributes to the overall composition of the gut microbiota and eventually to disease states.

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