Draft genome sequence of Paenibacillus algorifonticola sp. nov., an antimicrobial-producing strain.

Paenibacillus algorifonticola sp. nov. is isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region (China), a novel strain that can produce antimicrobial substance against human pathogenic bacteria and fungi, including Staphylococcus aureus and Candida albicans. Here we report a 7.60-Mb assembly of its genome sequence and other useful information, including the coding sequences (CDSs) responsible for the biosynthesis of antibacterial factors, anaerobic respiration and several immune-associated reactions. Also, prospective studies on P. algorifonticola sp. nov. in the cold spring might offer a potential source for the discovery of bioactive compounds with medical value. The data repository is deposited on the website http://www.ncbi.nlm.nih.gov/nuccore/LAQO00000000 and the accession number is LAQO00000000.

Direct link to deposited data

http://www.ncbi.nlm.nih.gov/nuccore/LAQO00000000

A large-scale metagenomic-based study revealed that the microbes with antibiotic resistance genes are abundant and diverse in nature [1]. However, the widespread misuse or abuse of antibiotics in clinical practice has led to a large number of antibiotic-resistant pathogenic bacteria such as Staphylococcus aureus and Candida albicans. Recently, our group has isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region (China) with a novel species of Paenibacillus algorifonticola sp. nov., named XJ259T(= CGMCC 1.10223T = JCM16598T), which can produce water-soluble constituents with the significant inhibitory activity against both S. aureus and C. albicans [2]. Comparisons with 16S rRNA gene sequences as shown in Fig. 1 revealed that the novel strain (1519 nt) had the highest similarity to Paenibacillus xinjiangensis B538T (96.6%) [3]. However, the phylogenetic distances from recognized species (Fig. 2) indicated that P. algorifonticola is not affiliated to any of these recognized species and the proportion of saturated straight-chain fatty acid C16:0 was relatively high [2]. We can therefore conclude that this strain represents a novel species of the genus Paenibacillus. In consequence, investigation of the genetic information and characteristics of P. algorifonticola is desired to further investigate its mechanism of metabolic regulation. Knowledge of the genome sequence and bioinformatics will be of great help in this regard.

Fig. 1

Multiple sequences alignment of Paenibacillus (P: Paenibacillus telluris; 2P: Paenibacillus sp. LNUB461; 3P: Paenibacillus telluris strain JS01-08; 4P: Paenibacillus xinjiangensis strain B538; 5P: Paenibacillus castaneae strain Ch-32; 6P: Paenibacillus algorifonticola).

Fig. 2

Phylogenetic tree analysis of Paenibacillus algorifonticola in this study and other strains belonging to the genus Paenibacillus (MEGA 3.1).

Here we present the draft genome sequence of strain P. algorifonticola XJ259T obtained using Illumina Hiseq 2000 system. The reads were assembled with SOAPdenovo [4], [5], the version is 2.04, and the sequence was annotated using the RAST annotation server (Fig. 3) [6], and the KEGG metabolic pathway was also constructed (Fig. 4). A library containing 500-bp inserts was constructed. Sequencing was performed based on the paired-end strategy of 478-bp reads to produce 1161 Mb of filtered sequences, representing a 132-fold coverage of the genome. The sequence of P. algorifonticola is 7,495,641 bases with a G + C content of 48.39%, which was assembled into 115 contigs and 101 scaffolds. It contains 7048 open reading frames (ORFs), 70 tRNA genes, and 4 rRNA genes (Table 1) identified by Glimmer 3.02 [7], Genemark [8], tRNAscan-SE [9], and RNAmmer [10].

Fig. 3

COG function classification of Paenibacillus algorifonticola (B: Chromatin structure and dynamics; C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; O: Posttranslational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolite biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms).

Fig. 4

KEGG metabolic pathway classification of Paenibacillus algorifonticola (A1: Organismal systems–Nervous system; A2: Organismal systems–Immune system; A3: Organismal systems–Excretory system; A4: Organismal systems–Environmental adaptation; A5: Organismal systems–Endocrine system; A6: Organismal systems–Digestive system; A7: Metabolism–Xenobiotics biodegradation and metabolism; A8: Metabolism–Nucleotide metabolism; A9: Metabolism–Metabolism of terpenoids and polyketides; A10: Metabolism–Metabolism of other amino acids; A11: Metabolism–Metabolism of cofactors and vitamins; A12: Metabolism–Lipid metabolisms; A13: Metabolism–Glycan biosynthesis and metabolism; A14: Metabolism–Enzyme metabolism; A15: Metabolism–Energy metabolism; A16: Metabolism–Amino acid metabolism; A17: Metabolism–Biosynthesis of other secondary metabolism; A18: Metabolism–Carbohydrate metabolism; A19: Human diseases–Neurodegenerative diseases; A20: Human diseases–Metabolic diseases; A21: Human diseases–Infectious diseases; A22: Human diseases–Immune system disease; A23: Human diseases–Cancers; A24: Genetic information processing–Translation; A25: Genetic information processing–Transcription; A26: Genetic information processing–Replication and repair; A27: Genetic information processing–Folding,sorting and degradation; A28: Environmental information processing–Signaling molecules and interaction; A29: Environmental information processing–Signal transduction; A30: Environmental information processing–Membrane transport; A31: Cellular processes–Transport and catabolism; A32: Cellular processes–Cell motility; A33: Cellular processes–Cell growth and death).

Table 1

General features of Paenibacillus algorifonticola sp. nov. draft genome.

Attributes	Value
Total sequence length (bp)	7,495,641
Gene number	7048
Gene length/Genome (%)	85.86
Gene average length (bp)	913
GC content (%)	48.39
N50 contig length (bp)	200,917
N90 contig length (bp)	57,078
Number of contig	115
Number of scaffolds	101
tRNAs	70
rRNAs (5S, 16S, 23S)	4
sRNA	5
Protein-coding genes	5364
Genes assigned to COGs	3376
Number of TFR	143

According to the genomic analysis of the strain P. algorifonticola, we identified 6 neutrophil extracellular traps (NETs)-associated proteins, including the calcium ion binding protein and cytoplasmic calprotecin protein complex (e.g., Mrp8/14-complex or S100A8/A9) with potent antimicrobial properties [11]. We also identified 6 ORFs relate to the immune-associated reactions, including the nucleotide-binding oligomerization domain(NOD)-like receptor signaling pathway, antigen processing and immune-responsive domain IPR011614. The strain P. algorifonticola can also utilize other complex immune responses that lead to production of soluble effectors, including 14 antimicrobial peptides (AMPs), or to activation of complement to inhibit activity of key metabolic enzymes (e.g., malate dehydrogenase and succinate dehydrogenase), which can directly damage the pathogen [12], [13]. Additionally, P. algorifonticola have the ability to keep alive in the anaerobic condition since there were 8 ORFs related to the anaerobic dehydrogenases and anaerobic regulatory protein. Except for the biosynthesis of antimicrobial substances, the trehalose, vitamin B12 and B2 biosynthesis were also annotated in P. algorifonticola, further studies will be performed to confirm their functions, and a complete genome sequence will be included in the future to reveal the unique molecular characteristics of strain P. algorifonticola.

Nucleotide sequence accession numbers

This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number LAQO00000000. The version described in this paper is the first version, with accession number LAQO01000000.

Conflict of interest

The authors declare that there is no conflict of interest on any work published in this paper.

Specifications
Organism/cell/tissue	Paenibacillus algorifonticola sp. nov.
Strain	XJ259T
Sequencer or array type	Illumina Hiseq 2000
Data format	Raw and processed
Experimental factors	DNA extracted from a wild-type strain, no treatment
Experimental features	Draft genome sequencing of Paenibacillus algorifonticola, assembly and annotation
Consent	N/A
Sample source location	a cold spring sample from Xinjiang Uyghur Autonomous Region (China)