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is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. is the only identified species in the genus , but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of . For this, we used 12 newly sequenced, assembled, and curated genomes of , which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters-A, B, and C-composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to , but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609107 | PMC |
http://dx.doi.org/10.3389/fmicb.2017.01790 | DOI Listing |
Parasit Vectors
December 2024
Global Health and Tropical Medicine- Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Rua da Junqueira 100, 1349-008, Lisbon, Portugal.
Background: Tick-borne rickettsioses (TBR) are emerging, neglected, zoonoses, caused by intracellular α-proteobacteria of the genus Rickettsia, that pose a growing public health concern. The aim of the present study was to evaluate rickettsial infections in questing ticks collected from four different ecological areas in mainland Portugal.
Methods: Over a two-year period, a total of 707 questing ticks were collected.
Bot Stud
December 2024
Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacky University, Šlechtitelů 11, 779 00, Olomouc, Czech Republic.
Background: The genus Allium is known for its high chromosomal variability, but most chromosome counts are based on a few individuals and genome size (GS) reports are limited in certain taxonomic groups. This is evident in the Allium sect. Codonoprasum, a species-rich (> 150 species) and taxonomically complex section with weak morphological differences between taxa, the presence of polyploidy and frequent misidentification of taxa.
View Article and Find Full Text PDFAntonie Van Leeuwenhoek
December 2024
All-Russian Collection of Microorganisms (VKM), Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, 142290, Russia.
Four salt-tolerant and aromatics degrading strains used in this study were isolated from polluted technogenic soil on the territory of the Verkhnekamsk potash deposit (Russia). The strains were aerobic, Gram-stain-positive, non-motile, non-endospore-forming irregular rods, exhibiting a marked rod-coccus growth cycle. They contained lysine-based peptidoglycan, teichulosonic acid and poly(glycosyl phosphate) polymers in the cell walls.
View Article and Find Full Text PDFAntonie Van Leeuwenhoek
December 2024
GIPhy - Genome Informatics and Phylogenetics, Biological Resource Center of Institut Pasteur, Institut Pasteur, Université de Paris, 75015, Paris, France.
A Gram-staining-positive, aerobic bacterium, designated strain JJ-181, was isolated from the root surface of soybean. Based on the 16S rRNA gene sequence similarities, strain JJ-181 was grouped into the genus Cohnella, most closely related to Cohnella hashimotonis F6_2S_P_1 (98.85%) and C.
View Article and Find Full Text PDFAntonie Van Leeuwenhoek
December 2024
Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, South Korea.
A Gram-stain-negative, aerobic, non-spore-forming, non-motile, coccus-shaped, and red-pigmented bacterial strain designated as CJ14 was isolated from lettuce cultivation soil in Yong-In, South Korea. Strain CJ14 grew optimally on Luria-Bertani agar at 37 ℃ and pH 7.0 in the absence of NaCl.
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