Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

M García-López, JP Meier-Kolthoff, BJ Tindall… - Frontiers in …, 2019 - frontiersin.org
Although considerable progress has been made in recent years regarding the classification
of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify …

Environmental superbugs: The case study of Pedobacter spp.

AT Viana, T Caetano, C Covas, T Santos… - Environmental Pollution, 2018 - Elsevier
The environment is one of the main reservoirs of antibiotic resistance genes (ARGs) but
multidrug resistant (MDR) environmental isolates are barely characterised. As suggested by …

Efficient DNA sequence compression with neural networks

M Silva, D Pratas, AJ Pinho - GigaScience, 2020 - academic.oup.com
Background The increasing production of genomic data has led to an intensified need for
models that can cope efficiently with the lossless compression of DNA sequences. Important …

The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study

G Figueiredo, M Gomes, C Covas, S Mendo… - Microbial ecology, 2022 - Springer
Research on secondary metabolites (SMs) has been mostly focused on Gram-positive
bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics …

[HTML][HTML] Characterisation of the bacterial microbiota of a landfill-contaminated confined aquifer undergoing intrinsic remediation

D Abiriga, A Jenkins, K Alfsnes, LS Vestgarden… - Science of the Total …, 2021 - Elsevier
Literature on microbiomes of landfill leachate-contaminated aquifers is scarce despite
groundwater contaminations from landfills being common globally. In this study, a …

Succession, replacement, and modification of chicken litter microbiota

T Kubasova, M Faldynova, M Crhanova… - Applied and …, 2022 - Am Soc Microbiol
Chickens are in constant interaction with their environment, eg, bedding and litter, and their
microbiota. However, how litter microbiota develops over time and whether bedding and …

Selective Isolation of Multidrug-Resistant Pedobacter spp., Producers of Novel Antibacterial Peptides

J Bjerketorp, JJ Levenfors, C Nord, B Guss… - Frontiers in …, 2021 - frontiersin.org
Twenty-eight multidrug-resistant bacterial strains closely related or identical to Pedobacter
cryoconitis, Pedobacter lusitanus and Pedobacter steynii were isolated from soil samples by …

Membrane lipid adaptation of soil Bacteroidetes isolates to temperature and pH

E Hellequin, S Collin, M Seder-Colomina… - Frontiers in …, 2023 - frontiersin.org
3-hydroxy fatty acids (3-OH FAs) are characteristic components of the Gram-negative
bacterial membrane, recently proposed as promising temperature and pH (paleo) proxies in …

JARVIS2: a data compressor for large genome sequences

D Pratas, AJ Pinho - 2023 Data Compression Conference …, 2023 - ieeexplore.ieee.org
Reducing data storage and its associated costs is one of the major bottlenecks in large-
scale genomic projects. In this paper, we present a new method for efficient reference-free …

The Pangenome of Gram-Negative Environmental Bacteria Hides a Promising Biotechnological Potential

C Covas, G Figueiredo, M Gomes, T Santos, S Mendo… - Microorganisms, 2023 - mdpi.com
Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various
health and environmental challenges. Researchers are employing advanced bioinformatic …