The Genome Sequence of
            <i>Alcaligenes faecalis</i>
            NBIB-017 Contains Genes with Potentially High Activities against
            <i>Erwinia carotovora</i>

Liu, Xiaoyan; Huang, Daye; Wu, Jinping; Yu, Changlong; Zhou, Ran; Liu, Cuijun; Zhang, Wei; Jing-wu, Yao; Cheng, Miao; Guo, Suxia

doi:10.1128/genomea.00222-16

Cited by 8 publications

(6 citation statements)

References 11 publications

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“…As an oxidase-, catalase-, and citrate-positive bacteria, it is widely distributed in the soil, water, and elsewhere in the environment. Previous studies on A. faecalis focused mainly on its pollutant biodegradation/bioremediation capacity [ 1 – 3 ], induction of clinical infection [ 4 , 5 ], genome assembly [ 6 – 8 ], bioremediation of phenols [ 9 ], polynuclear aromatic hydrocarbons [ 10 ], drug residues [ 11 ], and pesticides [ 12 , 13 ]. Moreover, A. faecalis strains are widely used in agricultural and industrial processes [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies

Lang

Yang

et al. 2022

BMC Genomics

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Background Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment strategies. Long-read sequencing platforms such as the Oxford Nanopore sequencer can improve genome assembly efficiency particularly when they are combined with short-read sequencing data. Results Alcaligenes faecalis PGB1 was isolated and identified with resistance to penicillin and three other antibiotics. After being sequenced by Nanopore MinION and Illumina sequencer, its entire genome was hybrid-assembled. One chromosome and one plasmid was assembled and annotated with 4,433 genes (including 91 RNA genes). Function annotation and comparison between strains were performed. A phylogenetic analysis revealed that it was closest to A. faecalis ZD02. Resistome related sequences was explored, including ARGs, Insert sequence, phage. Two plasmid aminoglycoside genes were determined to be acquired ARGs. The main ARG category was antibiotic efflux resistance and β-lactamase (EC 3.5.2.6) of PGB1 was assigned to Class A, Subclass A1b, and Cluster LSBL3. Conclusions The present study identified the newly isolated bacterium A. faecalis PGB1 and systematically annotated its genome sequence and ARGs.

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Section: Introductionmentioning

confidence: 99%

Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies

Lang

Yang

et al. 2022

BMC Genomics

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“…Several Af genomes have been sequenced [11,[13][14][15][16][17][18]. However, the first comparative analysis of Af genomes was published only recently, focusing on the analysis of systems related to antibiotic, metal, and pollutant resistance [13].…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant

et al. 2020

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Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.

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“…Tolerance to heavy metals has been reported as well 9 , 10 . Nanoparticle production 11 , nematicidal 12 and biocontrol activity 13 has been reported in addition to production of chemicals 14 , detergent 15 , gum 16 , and bioplastics 17 . Despite such high applicability of Alcaligenes species in major spheres of research and prospective benefits in industry, agricultural and environmental domain, it remains underrepresented and understudied at whole genome level.…”

Section: Introductionmentioning

confidence: 99%

Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207

Basharat

Yasmin

et al. 2018

Sci Rep

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Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and traits of Alcaligenes species, the genome of a tannery effluent isolated Alcaligenes faecalis subsp. phenolicus MB207 was sequenced and assembled. The genome was compared to the whole genome sequences of genus Alcaligenes present in the National Centre for Biotechnology Information database. Core, pan and species specific gene sequences i.e. singletons were identified. Members of this genus did not portray exceptional genetic heterogeneity or conservation and out of 5,166 protein coding genes from pooled genome dataset, 2429 (47.01%) contributed to the core, 1193 (23.09%) to singletons and 1544 (29.88%) to accessory genome. Secondary metabolite forming apparatus, antibiotic production and resistance was also profiled. Alcaligenes faecalis subsp. phenolicus MB207 genome consisted of a copious amount of bioremediation genes i.e. metal tolerance and xenobiotic degrading genes. This study marks this strain as a prospective eco-friendly bacterium with numerous benefits for the environment related research. Availability of the whole genome sequence heralds an opportunity for researchers to explore enzymes and apparatus for sustainable environmental clean-up as well as important compounds/substance production.

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The Genome Sequence of Alcaligenes faecalis NBIB-017 Contains Genes with Potentially High Activities against Erwinia carotovora

Abstract: Alcaligenes faecalis NBIB-017, a Gram-negative bacterium, was isolated from soil in China. Here, we provide the complete genome sequence of this bacterium, which possesses a high number of genes encoding antibacterial factors, including proteins and small molecular peptides.

Cited by 8 publications

References 11 publications

Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies

Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies

Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant

Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207

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