Draft Genome Sequencing of Pseudoalteromonas tetraodonis Strain kknpp56, a Potent Biofilm-Forming Bacterium Isolated from Early-Stage Marine Biofilm

Pseudoalteromonas tetraodonis strain kknpp56 is an exopolysaccharide (EPS)-producing marine bacterium that forms potent biofilm. To determine the biosynthesis pathways involved in the EPS production of this bacterium, whole-genome sequencing was performed. The complete genome comes from one chromosome containing 3.72 Mbp of DNA with a G+C content of 41%.

Draft Genome Sequencing of Stenotrophomonas indicatrix BOVIS40 and Stenotrophomonas maltophilia JVB5, Two Strains with Identifiable Genes Involved in Plant Growth Promotion

Here, plant growth-promoting Stenotrophomonas strains isolated from the sunflower root endosphere were studied, yielding molecular insights. Bacterial DNA was sequenced on Illumina’s NextSeq platform. The gene prediction reveals diverse functional genes involved in plant growth promotion from each bacterial genome. The exploration of bacterial resources as bioinoculants is promising for agricultural biotechnology.

Characterization and description of Faecalibacterium butyricigenerans sp. nov. and F. longum sp. nov., isolated from human faeces

Exploiting a pure culture strategy to investigate the composition of the human gut microbiota, two novel anaerobes, designated strains AF52-21T and CM04-06T, were isolated from faeces of two healthy Chinese donors and characterized using a polyphasic approach. The two strains were observed to be gram-negative, non-motile, and rod-shaped. Both strains grew optimally at 37 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains clustered with species of the genus Faecalibacterium and were most closely related to Faecalibacterium prausnitzii ATCC 27768T with sequence similarity of 97.18% and 96.87%, respectively. The two isolates shared a 16S rRNA gene sequence identity of 98.69%. Draft genome sequencing was performed for strains AF52-21T and CM04-06T, generating genome sizes of 2.85 Mbp and 3.01 Mbp. The calculated average nucleotide identity values between the genomes of the strains AF52-21T and CM04-06T compared to Faecalibacterium prausnitzii ATCC 27768T were 83.20% and 82.54%, respectively, and 90.09% when comparing AF52-21T and CM04-06T. Both values were below the previously proposed species threshold (95–96%), supporting their recognition as novel species in the genus Faecalibacterium. The genomic DNA G + C contents of strains AF52-21T and CM04-06T calculated from genome sequences were 57.77 mol% and 57.51 mol%, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, we conclude that both strains represent two new Faecalibacterium species, for which the names Faecalibacterium butyricigenerans sp. nov. (type strain AF52-21T = CGMCC 1.5206T = DSM 103434T) and Faecalibacterium longum sp. nov. (type strain CM04-06T = CGMCC 1.5208T = DSM 103432T) are proposed.

Integrated Genetic and Phenotypic Analysis for the Capsulars from Different Serotype of Campylobacter jejuni

Background: Serotyping is one of the important typing scheme for Campylobacter jejuni (C. jejuni). However, this method is time-consuming and labor-intensive. Nowadays, genotypic analysis of the capsular polysaccharide (CPS) loci for the different serotype strains has been developed based on the unique sequences in specific serotypes. In order to establish the correlation between the genotypes and serotype characteristics, the genetic and phenotypic analysis was conducted in this study. Results: Draft-genome sequencing, followed by PCR, was performed to obtain the integrated CPS loci. Totally, the CPS loci from 26 C. jejuni isolates belonging to 9 genotypes were obtained, of which 15 serotypeable strains belonging to 10 serotypes. The main genetic polymorphisms of CPS loci are substitutions and variations in poly-G or poly-A tracts from the same genotype or serotype strains. A serotypic analysis was performed with different antigens, including the whole cell lysates, CPS and lipooligosaccharide (LOS), extracted from different strains. Compared to the results of the agglutination reaction with antiserum, similar typing results could be obtained using the CPS extract and LOS extracts did not cause serotype-specific passive agglutination.Conclusion: The genotyping results based on unique sequences were not always consistent with the phenotypic characteristics. The genotyping method based on unique sequences could not replace the serotyping but might be a supplement for genotyping of the non-serotypeable strains. Moreover, the present study supported that the determinant substance for Penner serotyping scheme is the CPS from C. jejuni instead of LOS.

Nicotinamide mononucleotide production by fructophilic lactic acid bacteria

Nicotinamide mononucleotide (NMN), an intermediate in nicotinamide adenine dinucleotide biosynthesis, is recently attracting much attention for its pharmacological and anti-aging efficacies. However, current commercial products containing NMN are very high-priced because efficient and facile methods for industrial NMN production are limited. In this study, aiming for its nutraceutical application, we attempted to screen lactic acid bacteria for intracellular and/or extracellular NMN production. Using a bioassay system with an auxotrophic yeast that requires nicotinamide riboside (NR; dephosphorylated NMN), three candidates were obtained from a library of 174 strains of facultative anaerobic lactic acid bacteria. All three candidates belonged to the genus Fructobacillus and produced NR in the culture media (0.8–1.5 mg/l). Lactic acid bacteria of the genus Fructobacillus are known to use d-fructose as an electron acceptor in anaerobic lactic acid fermentation; addition of d-fructose to the medium caused intracellular accumulation of NMN and NR, but no extracellular production of these compounds was observed. Draft genome sequencing for one of the candidates suggested that nicotinamide phosphoribosyltransferase, which exists commonly in mammals but is less reported in microorganisms, is a key enzyme for NMN and NR production in the fructophilic bacteria.

Draft Genome Sequence of Herminiimonas contaminans Strain CCM 7991T, a Biopharmaceutical Contaminant

ABSTRACT Herminiimonas contaminans was described as a new bacterial species, a contaminant isolated from a biopharmaceutical production process in Sweden. Since the genome sequence was not available, we performed draft genome sequencing. The genome of strain CCM 7991T (=CCUG 53591T = DSM 28178T = Marseille-Q4544T) was 4,038,814 bp long, with a G+C content of 53.9%; a total of 3,860 genes were identified, along with 3 rRNAs, 44 tRNAs, and 4 noncoding RNAs (ncRNAs).