Draft Genome Sequence of Paludibacter jiangxiensis NM7T, a Propionate-Producing Fermentative Bacterium

Abstract

ABSTRACT

We report here a high-quality draft genome sequence of Paludibacter jiangxiensis strain NM7^T, a mesophilic, anaerobic, propionate-producing fermentative bacterium within the family Porphyromonadaceae of the phylum Bacteroidetes. The genome comprises 3,664,884 bp in four contigs, has a G+C content of 42.92%, and contains 2,949 protein-coding sequences and 62 RNAs.

GENOME ANNOUNCEMENT

Paludibacter jiangxiensis strain NM7^T (JCM 17480^T, CGMCC 1.5150^T, KCTC 5844^T) is a mesophilic, anaerobic, propionate-producing fermentative bacterium (1) and represents one of two currently described species of the genus Paludibacter in the family Porphyromonadaceae. Strain NM7^T shares 91.4% 16S rRNA gene sequence identity with P. propionicigenes strain WB4, the type species of the genus Paludibacter (2). Both P. jiangxiensis strain NM7^T and P. propionicigenes strain WB4^T were isolated from plant residue in anoxic rice paddy field soil and characterized as strictly anaerobic, rod-shaped, and nonmotile bacteria (1, 2). Phenotypic differences exist between both species in terms of their substrate utilization and temperature growth range: P. jiangxiensis can utilize sucrose and lactose as sole substrates, whereas P. propionicigenes cannot; growth of P. jiangxiensis occurs optimally at 37°C, while P. propionicigenes grows optimally at 30°C and fails to grow at 37°C (1, 2). Here, we report a high-quality draft genome sequence of P. jiangxiensis NM7^T to complement the genome sequence of P. propionicigenes WB4^T reported previously (3).

Pure culture genomic DNA was obtained by phenol-chloroform extraction, and Illumina sequencing libraries were prepared using a Nextera XT DNA library prep kit (400- to 600-bp inserts) and a Nextera mate-pair library preparation kit (1- to 14-kb inserts). The Illumina NextSeq 500 platform with the mid-output kit (300 cycles) was used for sequencing, at coverages of 843× and 105× for the paired-end and mate-pair libraries, respectively. Raw reads were quality filtered using Trimmomatic version 0.32 (4). Filtered paired-end reads were merged with FLASH version 1.2.11 (5), and mate-pair reads were further processed with NextClip version 1.3.1 (6), recovering reads in categories A, B, and C. Assembly was performed using SPAdes version 3.6.0 (7), followed by scaffolding and refinement of the assembly as described previously (8). Annotation of the genome was performed within the Integrated Microbial Genomes (IMG) platform (9).

The final genome assembly of P. jiangxiensis NM7^T contains four contigs and has an estimated coverage of 948×. The total assembly size is 3,664,884 bp, which is similar to the genome size of P. propionicigenes WB4^T (3,685,504 bp, NC_014734.1). The genome’s G+C content is 42.92%, which is slightly higher than that of P. propionicigenes WB4^T (38.86%). Annotation predicted 2,949 protein-coding genes and 62 RNA genes. The majority of the protein-coding genes (74.6%) could be assigned a putative function, and three complete sets of rRNAs were identified. Of note is that while genome annotation indicated that strain NM7^T harbors genes encoding lipoproteins required for gliding motility in the phylum Bacteroidetes (such as GldC, GldE, GldH), motility was not observed in our previous study (1). We anticipate that the availability of a high-quality draft genome sequence of P. jiangxiensis strain NM7^T, together with genomes of other Porphyromonadaceae bacteria, will shed light on the metabolic potential and possible ecological role of members of the family Porphyromonadaceae in different ecosystems.

Accession number(s).

The draft genome sequence of P. jiangxiensis NM7^T has been deposited at DDBJ/EMBL/GenBank under accession number BDCR00000000 (BioProject PRJDB4691). The version described in this paper is the first version, BDCR01000000.