IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

BACKGROUND

Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments.

FINDINGS

We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline, which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics that are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2.

CONCLUSION

The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.

Elaidic acid enhanced the simultaneous neurotoxicity attributable to the cerebral pathological lesion resulted from oxidative damages induced by acrylamide and benzo(a)pyrene

Acrylamide (ACR), benzopyrene [B(a)P] and trans-fatty acids (TFA) could be found to co-exist in many foods processed by high temperature. Our study investigated the effects of elaidic acid (ELA), a predominant TFA, on neuropathology induced by simultaneous exposure of ACR and B(a)P to mice. Results showed ELA enhanced the decrease of weight gains induced by simultaneous exposure of ACR and B(a)P (AB). Moreover, ELA enhanced ACR-induced increase of gait abnormality, B(a)P-induced damage to learning and memory, and AB-induced both of the damage above. Meanwhile, ELA enhanced B(a)Pinduced axonal degeneration in hippocamp, ACR- and AB-induced up-regulating of abnormal cerebellar Purkinje cells. ELA enhanced ACR-induced up-regulating of MDA in cerebrum and 8-OHdG in cerebrum and cerebellum; ELA enhanced B(a)P-induced up-regulating of MDA in cerebrum, PCO in cerebellum and 8-OHdG in cerebrum and cerebellum. Meanwhile, the enhancing role of ELA, on ACR-induced reduction of SOD activity in cerebrum and cerebellum, on B(a)P-induced reduction of GPx activity in cerebrum were found. Results suggested that ELA play a enhancing role on ACR-induced and B(a)P-induced oxidative damage, which attributable to the cerebral pathological lesion, and subsequent effect on gait abnormality and deficit on learning and memory in mice.