Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

Published: 5 May 2015Background: The rapid expansion of 16S rRNA gene sequencing in challenging clinical contexts has resulted in a growing body of literature of variable quality. To a large extent, this is due to a failure to address spurious signal that is characteristic of samples with low levels of bacteria and high levels of non-bacterial DNA. We have developed a workflow based on the paired-end read Illumina MiSeq-based approach, which enables significant improvement in data quality, post-sequencing. We demonstrate the efficacy of this methodology through its application to paediatric upper-respiratory samples from several anatomical sites. Results: A workflow for processing sequence data was developed based on commonly available tools. Data generated from different sample types showed a marked variation in levels of non-bacterial signal and ‘contaminant’ bacterial reads. Significant differences in the ability of reference databases to accurately assign identity to operational taxonomic units (OTU) were observed. Three OTU-picking strategies were trialled as follows: de novo, open-reference and closed-reference, with open-reference performing substantially better. Relative abundance of OTUs identified as potential reagent contamination showed a strong inverse correlation with amplicon concentration allowing their objective removal. The removal of the spurious signal showed the greatest improvement in sample types typically containing low levels of bacteria and high levels of human DNA. A substantial impact of pre-filtering data and spurious signal removal was demonstrated by principal coordinate and co-occurrence analysis. For example, analysis of taxon co-occurrence in adenoid swab and middle ear fluid samples indicated that failure to remove the spurious signal resulted in the inclusion of six out of eleven bacterial genera that accounted for 80% of similarity between the sample types. Conclusions: The application of the presented workflow to a set of challenging clinical samples demonstrates its utility in removing the spurious signal from the dataset, allowing clinical insight to be derived from what would otherwise be highly misleading output. While other approaches could potentially achieve similar improvements, the methodology employed here represents an accessible means to exclude the signal from contamination and other artefacts.Jake Jervis-Bardy, Lex E X Leong, Shashikanth Marri, Renee J Smith, Jocelyn M Choo, Heidi C Smith-Vaughan, Elizabeth Nosworthy, Peter S Morris, Stephen O'Leary, Geraint B Rogers and Robyn L Mars

Stellar occultations enable milliarcsecond astrometry for Trans-Neptunian objects and Centaurs

Trans-Neptunian objects (TNOs) and Centaurs are remnants of our planetary system formation, and their physical properties have invaluable information for evolutionary theories. Stellar occultation is a ground-based method for studying these small bodies and has presented exciting results. These observations can provide precise profiles of the involved body, allowing an accurate determination of its size and shape. The goal is to show that even single-chord detections of TNOs allow us to measure their milliarcsecond astrometric positions in the reference frame of the Gaia second data release (DR2). Accurated ephemerides can then be generated, allowing predictions of stellar occultations with much higher reliability. We analyzed data from stellar occultations to obtain astrometric positions of the involved bodies. The events published before the Gaia era were updated so that the Gaia DR2 catalog is the reference. Previously determined sizes were used to calculate the position of the object center and its corresponding error with respect to the detected chord and the International Celestial Reference System (ICRS) propagated Gaia DR2 star position. We derive 37 precise astrometric positions for 19 TNOs and 4 Centaurs. Twenty-one of these events are presented here for the first time. Although about 68\% of our results are based on single-chord detection, most have intrinsic precision at the submilliarcsecond level. Lower limits on the diameter and shape constraints for a few bodies are also presented as valuable byproducts. Using the Gaia DR2 catalog, we show that even a single detection of a stellar occultation allows improving the object ephemeris significantly, which in turn enables predicting a future stellar occultation with high accuracy. Observational campaigns can be efficiently organized with this help, and may provide a full physical characterization of the involved object.Comment: 16 pages, 28 figures. The manuscript was accepted and is to be publishe

Congenital dyserythropoietic anaemia and dyskeratosis in Australian Poll Hereford calves

Congenital dyserythropoietic anaemia (CDA) is a heterogeneous group of rare genetic disorders that in humans is characterised by ineffective haematopoiesis with morphological abnormalities in erythroid precursor cells and secondary iron overload. In the 1990s, a syndrome of CDA with dyskeratosis and progressive alopecia was reported in Poll Hereford calves in Canada and the USA. We report the clinical and pathological findings in two Poll Hereford calves with this syndrome from separate properties in South Australia. The animals had a variably severe anaemia, associated with abnormal nucleated red blood cells in peripheral blood, and large numbers of rubricytes and metarubricytes with a characteristic nuclear ultrastructure in the bone marrow. Both calves were born with a wiry hair coat and a progressively ‘dirty-faced’ appearance associated with hyperkeratosis and dyskeratosis (apoptosis).AE Kessell, DM Hanshaw, JW Finnie and P Nosworth

A randomized, placebo-controlled, double-blind phase 2 study of docetaxel compared to docetaxel plus zosuquidar (LY335979) in women with metastatic or locally recurrent breast cancer who have received one prior chemotherapy regimen

Purpose: To determine if concomitant administration of docetaxel plus zosuquidar.3HC1 can prolong progression-free survival in patients with metastatic breast cancer. Methods: A randomized, double-blind, multicenter, placebo-controlled clinical trial comparing docetaxel plus 500 mg zosuquidar.3HCl (DZ) with docetaxel plus placebo (DP). Results: A total of 170 patients were enrolled and randomly assigned to treatment. The median age was 53 years (range, 31-74 years). 81.7% of patients had prior chemotherapy in the adjuvant setting and 18.3% in the neoadjuvant setting. The median progression-free survival time was statistically different between groups [7.2 months (DZ) vs. 8.3 months (DP)]. Once the stratification factor relative to progression following prior chemotherapy was considered, no significant treatment difference existed. Conclusion: The combination of zosuquidar.3HCl plus docetaxel is safe. The analysis of efficacy data is complex, but it can be concluded that there is no difference in progression-free survival, overall survival, or response rate in the study as a whole. © 2009 Springer-Verlag.Articl