UMGAP: the Unipept MetaGenomics Analysis Pipeline

Background

Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools.

Results

Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools.

Conclusions

UMGAP’s protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-022-08542-4).

Enhanced biodegradation of chlortetracycline via a microalgae-bacteria consortium

Microbial removal of Chlortetracycline (CTC) at low CTC concentrations (in the order of 10-20 mg/L) has been reported. In this study, a novel microalgae-bacteria consortium was developed for effective CTC biodegradation at higher concentrations (up to 80 mg/L). The microalgae-bacteria consortium is resistant to up to 80 mg/L CTC, while the pure microalgal culture could only tolerate 60 mg/L CTC. CTC removal in the initial 12 h was primarily via biosorption by the microalgae-bacteria consortium and the adsorption capacity increased from 61.71 to 102.53 mg/g biomass in 12 h. Further, CTC biodegradation by the microalgae-bacteria consortium was catalyzed by extracellular enzymes secreted under antibiotic stress. The symbiotic bacterial diversity was analyzed by high throughput sequencing. The aerobic bacteria Porphyrobacter and Devosia were the dominant genera in the consortium. In the presence of CTC, a microbial community shift occurred with Chloroptast, Spingopyxis, and Brevundimonas being the dominant genera.

DNA barcoding to fishes: current status and future directions

DNA barcoding appears to be a promising approach for taxonomic identification, characterization, and discovery of newer species, facilitating biodiversity studies. It helps researchers to appreciate genetic and evolutionary associations by collection of molecular, morphological, and distributional data. Fish DNA barcoding, based on the sequencing of a uniform area of Cytochrome C Oxidase type I (COI) gene, has received significant interest as an accurate tool for species identification, authentication, and phylogenetic analysis. The aim of this review article was to investigate recent global status, approaches, and future direction of DNA barcoding in fisheries sectors. We have tried to highlight its possible impacts, complications, and validation issues at species levels for biodiversity analysis. Moreover, an effort has been put forward to understand issues related to various marker genes associated with barcode process as primer sequences and have concluded barcode promotion as an indispensable tool of molecular biology for the development of taxonomic support systems.