The human gut microbiome encodes a large variety of antimicrobial peptides (AMPs), but the short lengths of AMPs pose a challenge for computational prediction. Here we combined multiple natural language processing neural network models, including LSTM, Attention and BERT, to form a unified pipeline...
Peptide based drugs have emerged as potential alternative cancer treatment tools due to their selectivity, ease of design and synthesis, safety profile, and low cost of manufacturing. In this study, we utilized the Red Sea metagenomics database, generated during AUC/KAUST...
The glycopeptide resistance gene vanU and the peptide resistance gene ugd were the two common phage/prophage ARGs found in all three groups of samples. Taking human fecal samples as an example, we found that the frequency of occurrence of each ARG among our samples was highly consistent with ...
De novo emergence of peptides that confer antibiotic resistance. mBio 10, e00837–19 (2019). Article PubMed PubMed Central CAS Google Scholar Brauner, A., Fridman, O., Gefen, O. & Balaban, N. Q. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat. ...
The metagenomics (in-situ incubations) and HT-qPCR data (ex-situ incubations) have also evidenced the occurrence of a clearly distinct set of ARGs between biofilms and planktonic microbiomes. Of particular note, some biofilm-related ARGs seemed to be more enriched on weathered LDPE than wood ...
We also analyzed enzymes associated with antibiotic production/resistance such as polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), antibiotic synthesis and antibiotic resistance. For every predicted ORFs, we use AAMG to align ORF to proteins from the UniProt database, and if ...
The marine environment is considered one of the most important ecosystems with high biodiversity. Microorganisms in this environment are variable and coexi
across 102 analysis-naïveP. aeruginosastrains (‘Validation Dataset’). Our approach, which we demonstrate far exceeds the performance to current AMR prediction software, provides a crucial steppingstone towards the routine clinical use of genomics and metagenomics to inform personalisedP. aeruginosaan...
Antimicrobial peptides (AMPs) are promising antimicrobials, however, the potential of bacterial resistance is a major concern. Here we systematically study the evolution of resistance to 14 chemically diverse AMPs and 12 antibiotics in Escherichia coli.
We noticed thatGilliamella, the Gram-negative core bee gut member, also encoded a distinct GCF of RiPPs, which are annotated as potential thiopeptides by antiSMASH (Fig.1a, b). These BGCs did not show connections with any reference clusters from the MIBiG database32, suggesting previously une...