Genome sequence of Xanthomonas campestris JX, an industrially productive strain for Xanthan gum

A review of the key ingredients in industrial formulations of baby wet wipes

The skin of newborns is classified as sensitive, with a higher risk of skin barrier disruption and irritation of a diapered area. Despite dermatologist recommendations to use only water and a cloth for cleaning, most of the population still relies on the comforts of modern parenting, which includes intensive daily usage of baby wet wipes. Novel baby formulations are designed following the concept of infant skin health, containing a gentle cleanser, suitable emollient, and buffer system enabling a slightly acidic pH value and they are free of ethyl alcohol. Thus, it is important to understand the chemical background of such a complex liquid formulation, with emphasis on its safety. In line with this, the present paper discusses the scientific background of various chemical compounds found in baby wipe formulations to improve the understanding of wet wipe designs and direct them toward more skin-friendly solutions.

Exopolysaccharides Producing Bacteria: A Review

Bacterial exopolysaccharides (EPS) are essential natural biopolymers used in different areas including biomedicine, food, cosmetic, petroleum, and pharmaceuticals and also in environmental remediation. The interest in them is primarily due to their unique structure and properties such as biocompatibility, biodegradability, higher purity, hydrophilic nature, anti-inflammatory, antioxidant, anti-cancer, antibacterial, and immune-modulating and prebiotic activities. The present review summarizes the current research progress on bacterial EPSs including their properties, biological functions, and promising applications in the various fields of science, industry, medicine, and technology, as well as characteristics and the isolation sources of EPSs-producing bacterial strains. This review provides an overview of the latest advances in the study of such important industrial exopolysaccharides as xanthan, bacterial cellulose, and levan. Finally, current study limitations and future directions are discussed.

Bimetallic (Ag and MgO) nanoparticles, Aloe vera extracts loaded xanthan gum nanocomposite for enhanced antibacterial and in-vitro wound healing activity

We prepared nanocomposite (XG-AVE-Ag/MgO NCs) using the bimetallic Ag/MgO NPs, Aloe vera extract (AVE), and biopolymer (Xanthan gum (XG)) to archive a synergetic antibacterial and wound healing activity. The changes in XRD peaks at 20° of XG-AVE-Ag/MgO NCs indicated the XG encapsulation. The XG-AVE-Ag/MgO NCs showed the zeta potential and zeta size of 151.3 ± 3.14 d·nm and -15.2 ± 1.08 mV with a PDI of 0.265 while TEM showed an average size of 61.19 ± 3.89. The EDS confirmed the co-existence of Ag, Mg, carbon, oxygen, and nitrogen in NCs. XG-AVE-Ag/MgO NCs displayed higher antibacterial activity in terms of zone of inhibition, at 15.00 ± 0.12 mm for B. cereus and 14.50 ± 0.85 mm for E. coli. Moreover, NCs exhibited MICs of 2.5 μg/mL for E. coli, and 0.62 μg/mL for B. cereus. The in vitro cytotoxicity and hemolysis assays indicated the non-toxic properties of XG-AVE-Ag/MgO NCs. The higher wound closure activity was observed with the treatment of XG-AVE-Ag/MgO NCs (91.19 ± 1.87 %) compared to the control, untreated group (68.68 ± 3.54 %) at 48 h of incubation. These findings revealed that XG-AVE-Ag/MgO NCs was promising non-toxic, antibacterial, and wound-healing agent that deserved further in-vivo studies.

Advances in Xanthan Gum-Based Systems for the Delivery of Therapeutic Agents

In the last three decades, polymers have contributed significantly to the improvement of drug delivery technologies by enabling the controlled and sustained release of therapeutic agents, versatility in designing different delivery systems, and feasibility of encapsulation of both hydrophobic and hydrophilic molecules. Both natural and synthetic polymers have been explored for the delivery of various therapeutic agents. However, due to the disadvantages of synthetic polymers, such as lack of intrinsic biocompatibility and bioactivity, hydrophobicity, and expensive and complex procedure of synthesis, there is a move toward the use of naturally occurring polymers. The biopolymers are generally derived from either plants or microorganisms and have shown a wide range of applications in drug administration due to their hydrophilic nature, biodegradability, biocompatibility, no or low toxicity, abundance, and readily available, ease of chemical modification, etc. This review describes the applications of a biopolymer, xanthan gum (XG), in the delivery of various therapeutic agents such as drugs, genetic materials, proteins, and peptides. XG is a high molecular weight, microbial heteropolysaccharide and is produced as a fermented product of Gram-negative bacteria, Xanthomonas campestris. Traditionally, it has been used as a thickener in liquid formulations and an emulsion stabiliser. XG has several favourable properties for designing various forms of drug delivery systems. Furthermore, the structure of XG can be easily modified using different temperature and pH conditions. Therefore, XG and its derivatives have been explored for various applications in the food, pharmaceutical, and cosmetic industries.

Biomedical Applications of Bacteria-Derived Polymers

Plastics have found widespread use in the fields of cosmetic, engineering, and medical sciences due to their wide-ranging mechanical and physical properties, as well as suitability in biomedical applications. However, in the light of the environmental cost of further upscaling current methods of synthesizing many plastics, work has recently focused on the manufacture of these polymers using biological methods (often bacterial fermentation), which brings with them the advantages of both low temperature synthesis and a reduced reliance on potentially toxic and non-eco-friendly compounds. This can be seen as a boon in the biomaterials industry, where there is a need for highly bespoke, biocompatible, processable polymers with unique biological properties, for the regeneration and replacement of a large number of tissue types, following disease. However, barriers still remain to the mass-production of some of these polymers, necessitating new research. This review attempts a critical analysis of the contemporary literature concerning the use of a number of bacteria-derived polymers in the context of biomedical applications, including the biosynthetic pathways and organisms involved, as well as the challenges surrounding their mass production. This review will also consider the unique properties of these bacteria-derived polymers, contributing to bioactivity, including antibacterial properties, oxygen permittivity, and properties pertaining to cell adhesion, proliferation, and differentiation. Finally, the review will select notable examples in literature to indicate future directions, should the aforementioned barriers be addressed, as well as improvements to current bacterial fermentation methods that could help to address these barriers.

Pan Proteome of Xanthomonas campestris pv. campestris Isolates Contrasting in Virulence

Fully sequenced genomes of Xanthomonas campestris pv. campestris (Xcc) strains are reported. However, intra-pathovar differences are still intriguing and far from clear. In this work, the contrasting virulence between two isolates of Xcc - Xcc51 (more virulent) and XccY21 (less virulent) is evaluated by determining their pan proteome profiles. The bacteria are grown in NYG and XVM1 (optimal for induction of hrp regulon) broths and collected at the max-exponential growth phase. Shotgun proteomics reveals a total of 329 proteins when Xcc isolates are grown in XVM1. A comparison of both profiles reveals 47 proteins with significant abundance fluctuations, out of which, 39 show an increased abundance in Xcc51 and are mainly involved in virulence/adaptation mechanisms, genetic information processing, and membrane receptor/iron transport systems, such as BfeA, BtuB, Cap, Clp, Dcp, FyuA, GroEs, HpaG, Tig, and OmpP6. Several differential proteins are further analyzed by qRT-PCR, which reveals a similar expression pattern to the protein abundance. The data shed light on the complex Xcc pathogenicity mechanisms and point out a set of proteins related to the higher virulence of Xcc51. This information is essential for the development of more efficient strategies aiming at the control of black rot disease.

Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire

Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.

Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA

EFSA is requested to assess the safety of a broad range of biological agents in the context of notification for market authorisation as sources of food and feed additives, food enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic pre-assessment to support safety risk assessments performed by EFSA's scientific Panels. The safety of unambiguously defined biological agents (at the highest taxonomic unit appropriate for the purpose for which an application is intended), and the completeness of the body of knowledge are assessed. Identified safety concerns for a taxonomic unit are, where possible and reasonable in number, reflected as 'qualifications' in connection with a recommendation for a QPS status. The list of QPS recommended biological agents was reviewed and updated in the current opinion and therefore becomes the valid list. The 2016 update reviews previously assessed microorganisms including bacteria, yeasts and viruses used for plant protection purposes following an Extensive Literature Search strategy. The taxonomic units related to the new notifications received since the 2013 QPS opinion, were periodically evaluated for a QPS status and the results published as Statements of the BIOHAZ Panel. Carnobacterium divergens, Lactobacillus diolivorans, Microbacterium imperiale, Pasteuria nishizawae, Pediococcus parvulus, Bacillus flexus, Bacillus smithii, Xanthomonas campestris and Candida cylindracea were recommended for the QPS list. All taxonomic units previously recommended for the 2013 QPS list had their status reconfirmed as well their qualifications with the exception of Pasteuria nishizawae for which the qualification was removed. The exclusion of filamentous fungi and enterococci from the QPS evaluations was reconsidered but monitoring will be maintained and the status will be re-evaluated in the next QPS Opinion update. Evaluation of bacteriophages should remain as a case-by-case procedure and should not be considered for QPS status.

Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031

Here, we report the draft genome sequence of Xanthomonas campestris LMG 8031, for which nearly no genetic information is available, despite its good xanthan-producing properties. We performed an Illumina-based sequencing approach of LMG 8031. The genome revealed a 5.0-Mb chromosome having 4,434 coding sequences and a G+C content of 65%.

Dissection of exopolysaccharide biosynthesis in Kozakia baliensis

Background

Acetic acid bacteria (AAB) are well known producers of commercially used exopolysaccharides, such as cellulose and levan. Kozakia (K.) baliensis is a relatively new member of AAB, which produces ultra-high molecular weight levan from sucrose. Throughout cultivation of two K. baliensis strains (DSM 14400, NBRC 16680) on sucrose-deficient media, we found that both strains still produce high amounts of mucous, water-soluble substances from mannitol and glycerol as (main) carbon sources. This indicated that both Kozakia strains additionally produce new classes of so far not characterized EPS.

Results

By whole genome sequencing of both strains, circularized genomes could be established and typical EPS forming clusters were identified. As expected, complete ORFs coding for levansucrases could be detected in both Kozakia strains. In K. baliensis DSM 14400 plasmid encoded cellulose synthase genes and fragments of truncated levansucrase operons could be assigned in contrast to K. baliensis NBRC 16680. Additionally, both K. baliensis strains harbor identical gum-like clusters, which are related to the well characterized gum cluster coding for xanthan synthesis in Xanthomanas campestris and show highest similarity with gum-like heteropolysaccharide (HePS) clusters from other acetic acid bacteria such as Gluconacetobacter diazotrophicus and Komagataeibacter xylinus. A mutant strain of K. baliensis NBRC 16680 lacking EPS production on sucrose-deficient media exhibited a transposon insertion in front of the gumD gene of its gum-like cluster in contrast to the wildtype strain, which indicated the essential role of gumD and of the associated gum genes for production of these new EPS. The EPS secreted by K. baliensis are composed of glucose, galactose and mannose, respectively, which is in agreement with the predicted sugar monomer composition derived from in silico genome analysis of the respective gum-like clusters.

Conclusions

By comparative sugar monomer and genome analysis, the polymeric substances secreted by K. baliensis can be considered as unique HePS. Via genome sequencing of K. baliensis DSM 14400 + NBRC 16680 we got first insights into the biosynthesis of these novel HePS, which is related to xanthan and acetan biosynthesis. Consequently, the present study provides the basis for establishment of K. baliensis strains as novel microbial cell factories for biotechnologically relevant, unique polysaccharides.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0572-x) contains supplementary material, which is available to authorized users.

Influence of the xanthan gum addition on the technological and sensory quality of baking products during the freezing storage

The influence of the 0.16% xanthan gum addition in the recipe of the bread production and its influence on the baking and sensory quality of products was monitored during the process of our research. Prepared dough was inserted in the freezing box directly (-18°C) and it was stored for one, two, three, four, five and six months. When the baking process was finished, the products with xanthan gum and the products without it were compared and evaluated by both objective and subjective methods. It was found that freezing, cooling and storage of the products without xanthan gum addition influenced the volume, vaulting and general appearance of the products in a negative way and loaves of bread were evaluated as unacceptable after four months of freezing. The quality of experimental loaves of bread with xanthan gum was, even after six months of freezing storage, comparable with freshly baked products. Despite the freezing, the volume of the products had an increased value. After first month of freezing the volume increased by 28.6% and after two months of freezing it increased by 23.8% both compared to the control. The vaulting in products processed by freezing was in the required optimal level during the whole period of freezing. Sensory evaluation results of loaves of bread with xanthan gum were the best after three, four and five months of storage in a freezer, when 98 points were achieved. During the monitored period of freezing, the addition of 0.16% of xanthan gum markedly contributed to the preservation of sensory and baking quality of the frozen wheat dough.

Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome

BACKGROUND

The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani).

RESULTS

In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins.

CONCLUSIONS

This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.

Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16

Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The draft genome sequences of three strains (CN14, CN15, and CN16) that are highly aggressive on Arabidopsis have been determined. These genome sequences present an unexpected genomic diversity in X. campestris pv. campestris, which will be valuable for comparative analyses.

Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach

Xanthomonas campestris pv. campestris (Xcc) synthesizes huge amounts of the exopolysaccharide xanthan and is a plant pathogen affecting Brassicaceae, among them the model plant Arabidopsis thaliana. Xanthan is produced as a thickening agent at industrial scale by fermentation of Xcc. In an approach based on 2D gel electrophoresis, protein samples from different growth phases were characterized to initialize analysis of the Xanthomonas phosphoproteome. The 2D gels were stained with Pro-Q Diamond phosphoprotein stain to identify putatively phosphorylated proteins. Spots of putatively phosphorylated proteins were excised from the gel and analyzed by mass spectrometry. Three proteins were confirmed to be phosphorylated, the phosphoglucomutase/phosphomannomutase XanA that is important for xanthan and lipopolysaccharide biosynthesis, the phosphoenolpyruvate synthase PspA that is involved in gluconeogenesis, and an anti-sigma factor antagonist RsbR that was so far uncharacterized in xanthomonads. The growth phase in which the samples were collected had an influence on protein phosphorylation in Xcc, particular distinct in case of RsbR, which was phosphorylated during the transition from the late exponential growth phase to the stationary phase.

Genome sequences published outside of Standards in Genomic Sciences, October - November 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, July - October 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.