Examining horizontal gene transfer in microbial communities
IL Brito - Nature Reviews Microbiology, 2021 - nature.com
Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables
an organism to rapidly adapt to changing environmental conditions, provides a competitive …
an organism to rapidly adapt to changing environmental conditions, provides a competitive …
Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy
M Shintani, ZK Sanchez, K Kimbara - Frontiers in microbiology, 2015 - frontiersin.org
Plasmids are important “vehicles” for the communication of genetic information between
bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant …
bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant …
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Millions of new viral sequences have been identified from metagenomes, but the quality and
completeness of these sequences vary considerably. Here we present CheckV, an …
completeness of these sequences vary considerably. Here we present CheckV, an …
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
PS Krawczyk, L Lipinski… - Nucleic acids research, 2018 - academic.oup.com
Plasmids are mobile genetics elements that play an important role in the environmental
adaptation of microorganisms. Although plasmids are usually analyzed in cultured …
adaptation of microorganisms. Although plasmids are usually analyzed in cultured …
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
DH Parks, M Imelfort, CT Skennerton… - Genome …, 2015 - genome.cshlp.org
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has
been made possible by advances in computational methods and substantial reductions in …
been made possible by advances in computational methods and substantial reductions in …
Metagenomic data assembly–the way of decoding unknown microorganisms
AL Lapidus, AI Korobeynikov - Frontiers in Microbiology, 2021 - frontiersin.org
Metagenomics is a segment of conventional microbial genomics dedicated to the
sequencing and analysis of combined genomic DNA of entire environmental samples. The …
sequencing and analysis of combined genomic DNA of entire environmental samples. The …
Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance
Plasmid acquisition is an important mechanism of rapid adaptation and niche expansion in
prokaryotes. Positive selection for plasmid-coded functions is a major driver of plasmid …
prokaryotes. Positive selection for plasmid-coded functions is a major driver of plasmid …
Genomic characterization of nontuberculous mycobacteria
T Fedrizzi, CJ Meehan, A Grottola, E Giacobazzi… - Scientific reports, 2017 - nature.com
Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the
primary species of the genus Mycobacterium of clinical and microbiological interest. The …
primary species of the genus Mycobacterium of clinical and microbiological interest. The …
<? mode longmeta?> IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They
drive horizontal gene transfer, impacting ecological and evolutionary processes within …
drive horizontal gene transfer, impacting ecological and evolutionary processes within …
Plasmid-mediated transfer of antibiotic resistance genes in soil
M Meng, Y Li, H Yao - Antibiotics, 2022 - mdpi.com
Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes
(ARGs) are found in human hosts, plants, and animals and virtually all natural environments …
(ARGs) are found in human hosts, plants, and animals and virtually all natural environments …