Complete genome sequence of a phthalic acid esters degrading Mycobacterium sp. YC-RL4

Ren, Lei; Fan, Shuanghu; Wang, Junhuan; Nahurira, Ruth; Cheng, Qiao; Yang, Jia; Yan, Yanchun

doi:10.1016/j.bjm.2016.09.022

Cited by 10 publications

(3 citation statements)

References 15 publications

(15 reference statements)

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“…Moreover, despite several reports of Mycolicibacterium genomes [15][16][17][18][19][20][21][22][23][24][25][26], these studies rarely survey plasmids among their contigs. Thus, only a few plasmids have been reported in this genus, mainly from unrecognized genomes [2,14,[27][28][29][30]. Despite the reclassification of Mycobacterium, some Mycobacterium sp.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Morgado

Moreno-Vicente

2021

Microbial Genomics

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The mobilome plays a crucial role in bacterial adaptation and is therefore a starting point to understand and establish the gene flow occurring in the process of bacterial evolution. This is even more so if we consider that the mobilome of environmental bacteria can be the reservoir of genes that may later appear in the clinic. Recently, new genera have been proposed in the family Mycobacteriaceae , including the genus Mycolicibacterium , which encompasses dozens of species of agricultural, biotechnological, clinical and ecological importance, being ubiquitous in several environments. The current scenario in the Mycobacteriaceae mobilome has some bias because most of the characterized mycobacteriophages were isolated using a single host strain, and the few plasmids reported mainly relate to the genus Mycobacterium . To fill in the gaps in these issues, we performed a systematic in silico study of these mobile elements based on 242 available genomes of the genus Mycolicibacterium . The analyses identified 156 putative plasmids (19 conjugative, 45 mobilizable and 92 non-mobilizable) and 566 prophages in 86 and 229 genomes, respectively. Moreover, a contig was characterized by resembling an actinomycete integrative and conjugative element (AICE). Within this diversity of mobile genetic elements, there is a pool of genes associated with several canonical functions, in addition to adaptive traits, such as virulence and resistance to antibiotics and metals (mercury and arsenic). The type-VII secretion system was a common feature in the predicted plasmids, being associated with genes encoding virulent proteins (EsxA, EsxB, PE and PPE). In addition to the characterization of plasmids and prophages of the family Mycobacteriaceae , this study showed an abundance of these genetic elements in a dozen species of the genus Mycolicibacterium .

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Section: Introductionmentioning

confidence: 99%

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Morgado

Moreno-Vicente

2021

Microbial Genomics

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“…Three RPR homologs were annotated in M. austroafricanum and M. sp. YC-RL4 [ 51 ] (Fig. 6 ; Table S 10 b).…”

Section: Resultsmentioning

confidence: 99%

Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA

et al. 2022

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Background The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. Results We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. Conclusions Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.

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“…In this study, it was common for the Acidobacteria OTUs to be identi ed as keystone taxa because Acidobacteria can occupy a broad niche and have traits related to degrading soil organic carbon (Jiang et al, 2017;Mannisto et al, 2013). Additionally, half of the biomarkers were also tied to the soil carbon cycle, including Methylotenera, Gemmatimonas, Methylobacterium, Blastococcus and Mycobacterium (Guo et al, 2016;Kalyuzhnaya et al, 2012;Ren et al, 2017;Sanjenbam et al, 2020;Wang et al, 2020c). More notably, some keystone taxa were simultaneously identi ed by generalists and hub nodes, which might be explained by their particularly important ecological functions.…”

Section: Variations In Soil Bacterial Community Compositions Induced ...mentioning

confidence: 99%

Conservation tillage regulates the assembly, network structure and ecological function of the soil bacterial community in black soils

Liu

Liang

et al. 2022

Plant Soil

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Conventional tillage is a serious threat to the stability of soil ecosystems. Understanding the response mechanisms of soil microbial community assemblies to anthropogenic activities is a major topic of ecological research. MethodsHere, we investigated the bacterial community structures and assemblies in bulk and rhizosphere soils of soybeans grown with conventional tillage (moldboard plow, MP) and with conservation tillage that involved no-tillage (NT) or ridge tillage (RT) using high-throughput sequencing methods. ResultsWe found that soil bacterial community compositions, structures and assembly processes were primarily altered by tillage practices. Brie y, in comparison to MP, NT and RT increased the relative abundances of the nitrogen-xing bacteria Mesorhizobium sp., Bradyrhizobium sp. and Burkholderia sp., but decreased the abundance of soil carbon-degrading bacteria, especially Blastococcus sp., Streptomyces sp. and Sphingomonas sp. In addition, in comparison to MP, NT and RT resulted in more stable bacterial networks and more lower the relative contribution of homogenizing dispersal. Soil pH was the primary soil factor regulating both the bacterial community structures and assembly processes under the three tillage practices. ConclusionsThe altered functional bacteria under conservation tillage was mostly a liated with biomarkers and keystone taxa, inferring that conservation tillage might contribute to biological nitrogen xation and soil carbon sequestration.

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Complete genome sequence of a phthalic acid esters degrading Mycobacterium sp. YC-RL4

Cited by 10 publications

References 15 publications

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA

Conservation tillage regulates the assembly, network structure and ecological function of the soil bacterial community in black soils

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