Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases

Abstract

Strains 335427T and 234509T, isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427T and 234509T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129T and Nocardia abscessus NBRC 100374T were 99.5% and 100%, respectively. Digital DNA–DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427T and 234509T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427T has C16:0, C18:1 ω9c, C18:0 and C18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52–54 carbon atoms. However, only C18:1 ω9c was detected for isolate 234509T, which had mycolic acids with 44–56 carbon. Based on phenotypic and genetic data, strains 335427T (DSM 109819T = CECT 9924T) and 234509T (DSM 111366T = CECT 30129T) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis, including experimentally verified virulence genes in humans related to tuberculosis. The narGHIJ (nitrate reduction pathway) and gvpAFGOJLMK (gas vesicles) genetic maps of strains 335427T, 234509T, NBRC 100129T and NBRC 100374T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

Mycobacteriaceae Mineralizes Micropolyethylene in Riverine Ecosystems

“…Two putative mPE-degrading genera, Mycobacterium and Nocardia , contain both pathogens that cause severe human diseases , and nonpathogenic strains. , Because not all members are pathogenic, investigation of the virulence factors was necessary to determine whether the plastisphere-colonizing Mycobacteriaceae are pathogens . Although multiple virulence factors were identified, many of these functions, such as amino acid and purine metabolism and cholesterol catabolism, perform essential metabolisms for survival in bacteria . In contrast, several gene clusters have been considered as true virulence factors that were either incomplete or completely absent in the eight reconstructed Mycobacteriaceae -associated MAGs in this study.…”

“…In contrast, several gene clusters have been considered as true virulence factors that were either incomplete or completely absent in the eight reconstructed Mycobacteriaceae -associated MAGs in this study. For instance, the mbtBDFCE cluster (which produces sidophores to scavenge iron from hosts), mce operons (whose products facilitate pathogen transportation into host cells), plcABCD (which produces Phospholipases C that interacts with host fatty acids), and mycolactone production ( mlsA1 , mlsA2 , and mlsB , a toxin that causes host cell lesion) ,,− were missing in these MAGs. Thus, it is presumed that the mPE-inhabiting Mycobacteriaceae identified in the current study may not be pathogenic.…”

Nocardia noduli sp. nov., a novel actinobacterium with biotechnological potential

“…Strain ncl1 T and N. aurea DSMZ 103986 T were examined for a range of phenotypic features; notably for their ability to use sole carbon and nitrogen sources; to grow at various pH values and in the presence of antibiotics and inorganic inhibitory compounds using GENIII microplates and an Omnilog device (Biolog Inc., Hayward, CA, USA), as described by Nouioui et al ( 2020 ). The resultant data were analysed using opm package version 1.3.36 (Vaas et al 2013 ).…”

“…Data acquired from polyphasic taxonomic and genome-based studies led to marked improvements in the classification of the genus Nocardia and related mycolic acid-containing bacteria (Nouioui et al 2018 ) which had previously been classified using a few subjectively weighted features. The genus forms a monophyletic clade within the family Nocardiaceae (Goodfellow and Maldonaldo 2012 ) and encompasses 120 validly published species ( https://lpsn.dsmz.de/genus/nocardia ) most of which have been recognized using combinations of genotypic and phenotypic properties (Nouioui et al 2020 ) though the steady flow of new species shows that the genus remains underspeciated (Goodfellow and Maldonaldo 2012 ; Nouioui et al 2020 ).…”

Nocardia sputi sp. nov. isolated from the sputum of patients with pulmonary infection

“…Also, the nitrate reductase gene cluster, which is present upstream of the gvp gene cluster, encodes nitrate reductase subunits α, β, γ and δ and facilitates the survival of dormant pathogenic bacteria (e.g., Mycobacterium tuberculosis) under hypoxic conditions [32,33].It remains unclear whether these two syntenic gene clusters are co-expressed in the infection process. Further studies are thus warranted to examine their role in infections caused by species of the genus Nocardia [31].…”