Lifestyles in transition: evolution and natural history of the genus Lactobacillus

RM Duar, XB Lin, J Zheng, ME Martino… - FEMS microbiology …, 2017‏ - academic.oup.com
Lactobacillus species are found in nutrient-rich habitats associated with food, feed, plants,
animals and humans. Due to their economic importance, the metabolism, genetics and …

Past, present and future of the boundaries of the Pseudomonas genus: proposal of Stutzerimonas gen. nov

J Lalucat, M Gomila, M Mulet, A Zaruma… - Systematic and applied …, 2022‏ - Elsevier
Pseudomonas is one the best studied bacterial genera, and it is the genus with the highest
number of species among the gram-negative bacteria. Pseudomonas spp. are widely …

Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

R Riesco, ME Trujillo - International Journal of Systematic …, 2024‏ - microbiologyresearch.org
The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary
classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics …

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

D Kim, S Park, J Chun - Journal of Microbiology, 2021‏ - Springer
The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and
multiple studies have proposed its application in prokaryotic taxonomy and related …

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

R Lücking, MC Aime, B Robbertse, AN Miller… - IMA fungus, 2020‏ - Springer
True fungi (Fungi) and fungus-like organisms (eg Mycetozoa, Oomycota) constitute the
second largest group of organisms based on global richness estimates, with around 3 …

A new genomic blueprint of the human gut microbiota

A Almeida, AL Mitchell, M Boland, SC Forster, GB Gloor… - Nature, 2019‏ - nature.com
The composition of the human gut microbiota is linked to health and disease, but knowledge
of individual microbial species is needed to decipher their biological roles. Despite …

Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species

Z Zhou, C Zhang, P Liu, L Fu, R Laso-Pérez, L Yang… - Nature, 2022‏ - nature.com
The methanogenic degradation of oil hydrocarbons can proceed through syntrophic
partnerships of hydrocarbon-degrading bacteria and methanogenic archaea,–. However …

Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics

AT Vincent, O Schiettekatte, C Goarant… - PLoS neglected …, 2019‏ - journals.plos.org
The causative agents of leptospirosis are responsible for an emerging zoonotic disease
worldwide. One of the major routes of transmission for leptospirosis is the natural …

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

Y Zou, W Xue, G Luo, Z Deng, P Qin, R Guo… - Nature …, 2019‏ - nature.com
Reference genomes are essential for metagenomic analyses and functional characterization
of the human gut microbiota. We present the Culturable Genome Reference (CGR), a …

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

I Lagkouvardos, TR Lesker, TCA Hitch, EJC Gálvez… - Microbiome, 2019‏ - Springer
Background Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse
gut microbiota and detected in the intestine of other animals. Because they had not been …