Joining Illumina paired-end reads for classifying phylogenetic marker sequences

Background

Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are limited, one can simply use only first reads for taxonomy annotation, but that wastes information in the second reads. Presumably, including second reads should improve taxonomy annotation. However, a rigorous investigation of how best to do this and how much can be gained has not been reported.

Results

We evaluated two methods of joining as opposed to merging PE reads into single reads for taxonomy annotation using simulated data with sequencing errors. Our rigorous evaluation involved several top classifiers (RDP classifier, SINTAX, and two alignment-based methods) and realistic benchmark datasets. For most classifiers, read joining ameliorated the impact of sequencing errors and improved the accuracy of taxonomy predictions. For alignment-based top-hit classifiers, rearranging the reference sequences is recommended to avoid improper alignments of joined reads. For word-counting classifiers, joined reads could be compared to the original reference for classification. We also applied read joining to our own real MiSeq PE data of nasal microbiota of asthmatic children. Before joining, trimming low quality bases was necessary for optimizing taxonomy annotation and sequence clustering. We then showed that read joining increased the amount of effective data for taxonomy annotation. Using these joined trimmed reads, we were able to identify two promising bacterial genera that might be associated with asthma exacerbation.

Conclusions

When mergeable PE reads are limited, joining them into single reads for taxonomy annotation is always recommended. Reference sequences may need to be rearranged accordingly depending on the classifier. Read joining also relaxes the constraint on primer selection, and thus may unleash the full capacity of Illumina PE data for taxonomy annotation. Our work provides guidance for fully utilizing PE data of a marker gene when mergeable reads are limited.

Vitamin D plasma concentration and vitamin D receptor genetic variants confer risk of asthma: A comparison study of Taiwanese and Mongolian populations

Background

Recent reports have suggested that lower vitamin D serum levels are associated with susceptibility to and severity of asthma in different white populations, which may be due to a lack of sunlight exposure, genetic polymorphism of vitamin D pathway genes, and dietary intake. We investigated the associations between vitamin D concentration, genetic polymorphism of the vitamin D receptor (VDR), and asthma traits in Mongolian and Taiwanese populations that inhabited two different geographical areas.

Methods

In total, 328 Han Taiwanese subjects and 381 Mongolian subjects were enrolled, and their vitamin D serum levels assayed. Genomic DNA of 178 Han Taiwanese subjects and 90 Mongolian subjects was obtained from blood samples. Single-nucleotide polymorphisms (SNPs) of VDR, ApaI (rs7975232), TaqI (rs731236), BsmI (rs1544410) and FokI (rs2228570), were selected for genotyping. Logistic regression analyses were performed to detect an association between allergic asthma status and the interaction of the VDR SNP and serum vitamin D concentration in the case–control samples.

Results

We observed a significantly lower vitamin D level in the Mongolian subjects as compared with the Taiwanese population. In particular, in the population under 14 years of age, the serum vitamin D level was significantly higher in the Taiwanese population, in both non-asthmatic and asthmatic subjects, than in the Mongolian non-asthmatic and asthmatic subjects, respectively (P < 0.01). Moreover, the vitamin D level in the asthmatic children was significantly lower than that in the non-asthmatic children in both the Taiwanese and Mongolian populations (P < 0.01, respectively). Furthermore, we found that the rs2228570 genotype (OR, 3.763) of the VDR SNP and the vitamin D concentration (lower than 40 ng/ml, OR: 38.938) both contribute to increased susceptibility to bronchial asthma.

Conclusion

Our results demonstrated an association between vitamin D concentration and the risk of asthma in two populations of differing ethnicity living in different geographical areas. This information implies a potential role of vitamin D in the prevention and treatment of asthma worldwide.

Longitudinal pattern of multiplexed immunoglobulin E sensitization from prenatal stage to the first year of life

BACKGROUND

The longitudinal pattern of allergen-specific IgE levels from the prenatal stage to early life has remained largely unexplored.

METHODS

One-hundred and three mother-infant pairs, which were part of an ongoing population-based prospective birth cohort study of early childhood allergic diseases in Tainan, Taiwan, were included in this study. We examined the relationship of 20 allergen-specific IgE levels with blood samples of mothers, cord blood, and infants at 12 months of age using Spearman rank correlation, Kenal τ and McNemar test, respectively.

RESULTS

Certain degree of IgE sensitization against most 20 examined specific allergens was observed in blood samples of mothers, cord blood, and infants at 12 months of age. When we further examined the association between allergy-related risk factors and atopy in infants at the first year of life, we found positive association between colic pain and atopy in infants at 12 months of age [adjusted odds ratios (AOR) = 3.51; 95% confidence interval (CI): 1.13-10.96; p = 0.03], and borderline significance between wheezing and atopy in infants at 12 months of age (AOR = 4.58; 95% CI: 0.89-23.50; p = 0.07).

CONCLUSION

The findings from this study suggest that influence of maternal allergen-specific IgE levels on infant immune response might occur at birth and then wane in infants at 12 months of age. Positive association of colic pain and wheezing with atopy in infants at 12 months of age provides supportive evidence for the 'Allergy March' theory of allergy development in an Asian birth cohort.