Determination and molecular analysis of antibiotic resistance in Gram-negative enteric bacteria isolated from Pelophylax sp. in the Eastern Black Sea Region

PanPA: generation and alignment of panproteome graphs

Motivation

Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space are still challenging due to this high diversity. In contrast, amino acid sequences have higher similarity due to evolutionary constraints, whereby a single amino acid may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, panproteomes present an attractive alternative leveraging the higher sequence similarity while not losing much of the genome in non-coding regions.

Results

We present PanPA, a method that takes a set of multiple sequence alignments of protein sequences, indexes them, and builds a graph for each multiple sequence alignment. In the querying step, it can align DNA or amino acid sequences back to these graphs. We first showcase that PanPA generates correct alignments on a panproteome from 1350 Escherichia coli. To demonstrate that panproteomes allow comparisons at longer phylogenetic distances, we compare DNA and protein alignments from 1073 Salmonella enterica assemblies against E.coli reference genome, pangenome, and panproteome using BWA, GraphAligner, and PanPA, respectively; with PanPA aligning around 22% more sequences. We also aligned a DNA short-reads whole genome sequencing (WGS) sample from S.enterica against the E.coli reference with BWA and the panproteome with PanPA, where PanPA was able to find alignment for 68% of the reads compared to 5% with BWA.

Availalability and implementation

PanPA is available at https://github.com/fawaz-dabbaghieh/PanPA.

Microplastic prevalence in anatolian water frogs (Pelophylax spp.)

Frogs are on the verge of extinction due to various biotic and abiotic stressors. Rivers, lakes, ponds, wetlands, and ditches that make up their habitats are exposed to different anthropogenic pollutants. Today, plastics stand out among these pollutants due to their widespread use; however, the information on microplastic (MP) accumulation in frogs is insufficient. In the present study, adult frog samples were collected from 19 different stations in Türkiye, including marsh frogs (Pelophylax ridibundus) from 18 stations and levantine frogs (Pelophylax bedriagae) from 1 station. MP was found in 147 (82.4%) of the 176 frogs that were analyzed. MP abundance in frogs varied between 0.20 and 18.93 MP individual^-1. The characterization of MPs was determined predominantly as follows; PET (70.1%) in polymer type, fiber (92.2%) in shape, navy blue/blue (76.1%) in color, and >90% were smaller than 300 μm. No significant relationship with frog's weight (correlation coefficient = 0.01, P = 0.812) or length (correlation coefficient = 0.06, P = 0.473) and MP abundance was detected. The outcomes of this survey might be a baseline to assess the ecological risks posed by MPs and to guide future experimental research.

Bioaccumulation of Trace Elements and Health Risk Predictions in Edible Tissues of the Marsh Frog

Certain amphibian species have long served as a valuable protein source for humans, in addition to being good bioindicators for environmental pollutants. Hence, to investigate the consumption outcomes leading to potential health risks, we determined the trace element (TE) levels in the hind leg and liver tissues of marsh frogs (Pelophylax ridibundus), one of the delicacies of several cuisines today. The sediment, water, and frog tissue samples were collected from 15 different locations of NE Turkey and analyzed to determine the arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), vanadium (V), and zinc (Zn) concentrations. The TE concentrations in the sediment, water, and individuals were detected to show significant variations among sampling stations (p < 0.05). Yet, Cd and Pb concentrations of the hind legs cooked and enjoyed in the diets were determined below the European Commission's permitted levels. Furthermore, based on the TEs in edible tissues, consumption of the marsh frog did not appear to pose a risk to humans in terms of provisional tolerable weekly intake (PTWI), target hazard coefficient (THQ), and hazard index (HI).