Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas.

Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products' pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer (ITS) for library construction and further sequencing using Illumina technology. This approach was successfully used to estimate the relative abundance of AAB species in defined consortia. Further application of this method for the analysis of different vinegar and kombucha samples proves it suitable for assessing the relative abundance of AAB species when these bacteria represent a predominant part of a microbial community.

Bacterial nanocellulose loaded with bromelain and nisin as a promising bioactive material for wound debridement.

The bacterial nanocellulose (BnC) membranes were produced extracellularly by a novel aerobic acetic acid bacterium Komagataeibacter melomenusus. The BnC was modified in situ by adding carboxymethyl cellulose (CMC) into the culture media, obtaining a BnC-CMC product with denser fibril arrangement, improved rehydration ratio and elasticity in comparison to BnC. The proteolytic enzyme bromelain (Br) and antimicrobial peptide nisin (N) were immobilized to BnC matrix by ex situ covalent binding and/or adsorption. The optimal Br immobilization conditions towards the maximized specific proteolytic activity were investigated by response surface methodology as factor variables. At optimal conditions, i.e., 8.8 mg/mL CMC and 10 mg/mL Br, hyperactivation of the enzyme was achieved, leading to the specific proteolytic activity of 2.3 U/mg and immobilization efficiency of 39.1 %. The antimicrobial activity was observed against Gram-positive bacteria (S. epidermidis, S. aureus and E. faecalis) for membranes with immobilized N and was superior when in situ modified BnC membranes were used. N immobilized on the BnC or BnC-CMC membranes was cytocompatible and did not cause changes in normal human dermal fibroblast cell morphology. BnC membranes perform as an efficient carrier for Br or N immobilization, holding promise in wound debridement and providing antimicrobial action against Gram-positive bacteria, respectively.

Exploitation of microbial activities at low pH to enhance planetary health.

Awareness is growing that human health cannot be considered in isolation but is inextricably woven with the health of the environment in which we live. It is, however, under-recognized that the sustainability of human activities strongly relies on preserving the equilibrium of the microbial communities living in/on/around us. Microbial metabolic activities are instrumental for production, functionalization, processing, and preservation of food. For circular economy, microbial metabolism would be exploited to produce building blocks for the chemical industry, to achieve effective crop protection, agri-food waste revalorization, or biofuel production, as well as in bioremediation and bioaugmentation of contaminated areas. Low pH is undoubtedly a key physical-chemical parameter that needs to be considered for exploiting the powerful microbial metabolic arsenal. Deviation from optimal pH conditions has profound effects on shaping the microbial communities responsible for carrying out essential processes. Furthermore, novel strategies to combat contaminations and infections by pathogens rely on microbial-derived acidic molecules that suppress/inhibit their growth. Herein, we present the state-of-the-art of the knowledge on the impact of acidic pH in many applied areas and how this knowledge can guide us to use the immense arsenal of microbial metabolic activities for their more impactful exploitation in a Planetary Health perspective.

From Nature to Lab: Sustainable Bacterial Cellulose Production and Modification with Synthetic Biology.

Bacterial cellulose (BC) is a macromolecule with versatile applications in medicine, pharmacy, biotechnology, cosmetology, food and food packaging, ecology, and electronics. Although many bacteria synthesize BC, the most efficient BC producers are certain species of the genera Komagataeibacter and Novacetimonas. These are also food-grade bacteria, simplifying their utilization at industrial facilities. The basic principles of BC synthesis are known from studies of Komagataeibacter xylinus, which became a model species for studying BC at genetic and molecular levels. Cellulose can also be of plant origin, but BC surpasses its purity. Moreover, the laboratory production of BC enables in situ modification into functionalized material with incorporated molecules during its synthesis. The possibility of growing Komagataeibacter and Novacetimonas species on various organic substrates and agricultural and food waste compounds also follows the green and sustainable economy principles. Further intervention into BC synthesis was enabled by genetic engineering tools, subsequently directing it into the field of synthetic biology. This review paper presents the development of the fascinating field of BC synthesis at the molecular level, seeking sustainable ways for its production and its applications towards genetic modifications of bacterial strains for producing novel types of living biomaterials using the flexible metabolic machinery of bacteria.

Production efficiency and properties of bacterial cellulose membranes in a novel grape pomace hydrolysate by Komagataeibacter melomenusus AV436T and Komagataeibacter xylinus LMG 1518.

The microbial production of cellulose using different bacterial species has been extensively examined for various industrial applications. However, the cost-effectiveness of all these biotechnological processes is strongly related to the culture medium for bacterial cellulose (BC) production. Herein, we examined a simple and modified procedure for preparing grape pomace (GP) hydrolysate, without enzymatic treatment, as a sole growth medium for BC production by acetic acid bacteria (AAB). The central composite design (CCD) was used to optimise the GP hydrolysate preparation toward the highest reducing sugar contents (10.4 g/L) and minimal phenolic contents (4.8 g/L). The experimental screening of 4 differently prepared hydrolysates and 20 AAB strains identified the recently described species Komagataeibacter melomenusus AV436T as the most efficient BC producer (up to 1.24 g/L dry BC membrane), followed by Komagataeibacter xylinus LMG 1518 (up to 0.98 g/L dry BC membrane). The membranes were synthesized in only 4 days of bacteria culturing, 1 st day with shaking, followed by 3 days of static incubation. The produced BC membranes in GP-hydrolysates showed, in comparison to the membranes made in a complex RAE medium 34 % reduction of crystallinity index with the presence of diverse cellulose allomorphs, presence of GP-related components within the BC network responsible for the increase of hydrophobicity, the reduction of thermal stability and 48.75 %, 13.6 % and 43 % lower tensile strength, tensile modulus, and elongation, respectively. Here presented study is the first report on utilising a GP-hydrolysate without enzymatic treatment as a sole culture medium for efficient BC production by AAB, with recently described species Komagataeibacter melomenusus AV436T as the most efficient producer in this type of food-waste material. The scale-up protocol of the scheme presented here will be needed for the cost-optimisation of BC production at the industrial levels.

Probiotic Lactobacillus paragasseri K7 Nanofiber Encapsulation Using Nozzle-Free Electrospinning.

Probiotics are live microorganisms that can have beneficial effects on humans. Encapsulation offers them a better chance of survival. Therefore, nozzle-free electrospinning was introduced for their embedding in nanofibrous material. Probiotic Lactobacillus paragasseri K7 in lyophilized and fresh form, with and without inulin as prebiotic, was added to a polymer solution of sodium alginate (NaAlg) and polyethylene oxide (PEO). Conductivity, viscosity, pH, and surface tension were determined to define the optimal concentration and volume ratio for smooth electrospinning. The success of the formed nanoscale materials was examined by scanning electron microscope (SEM), while the entrapment of probiotics in the nanofibrous mats was detected by attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS). Spontaneous diffusion of bacteria from electrospun samples in PBS buffer pH 7.4 was studied by plate counting on MRS agar. By exposing polymer solutions containing L. paragasseri K7 and inulin to a high electric field, the nanofilm was formed on a polypropylene substrate, used as collecting material. When polymer solutions without inulin were used, the bead-like nanofibers may have become visible. The SEM results suggest that inulin, in addition to K7 strain, additionally lowers the conductivity of spinning macromolecular solution and hinders the nanofiber formation. The results of ATR-FTIR confirmed the presence of L. paragasseri K7 embedded in nanocomposites by the appearance of characteristic peaks. The samples containing the probiotic regardless of its form with inulin had similar surface composition, except that the sodium content was higher in the samples with fresh probiotic, probably due to greater and thus less easy embedding of the bacteria in NaAlg. Within 2 h, the largest amount of probiotic strain K7 was spontaneously released from the electrospun sample containing the inulin and probiotic in freeze-dried form (44%), while the amount released from the nanofibrous sample, which also contained the inulin and probiotic in fresh form, was significantly lower (21%). These preliminary results demonstrate the potential of nozzle-free electrospinning technology for the development of probiotic delivery systems for short-term use, such as feminine hygiene materials (tampons, pads, napkins).

GO-Enabled Bacterial Cellulose Membranes by Multistep, In Situ Loading: Effect of Bacterial Strain and Loading Pattern on Nanocomposite Properties.

This paper presents the results of research on the preparation and properties of GO/BC nanocomposite from bacterial cellulose (BC) modified with graphene oxide (GO) using the in situ method. Two bacterial strains were used for the biosynthesis of the BC: Komagataeibacter intermedius LMG 18909 and Komagataeibacter sucrofermentans LMG 18788. A simple biosynthesis method was developed, where GO water dispersion was added to reinforced acetic acid-ethanol (RAE) medium at concentrations of 10 ppm, 25 ppm, and 50 ppm at 24 h and 48 h intervals. As a result, a GO/BC nanocomposite membrane was obtained, characterized by tensile strength greater by 150% as compared with the pure BC (Ì´ 50 MPa) and lower volume resistivity of ~4 ∙ 109 Ω × cm. Moreover, GO addition increases membrane thickness up to ~10% and affects higher mass production, especially with low GO concentration. All of this may indicate the possibility of using GO/BC membranes in fuel cell applications.

Comparative Genomics and Phenotypic Characterization of Gluconacetobacter entanii, a Highly Acetic Acid-Tolerant Bacterium from Vinegars.

The bacterial species Gluconacetobacter entanii belongs to a group of acetic acid bacteria. In 2000, it was described as a primary species of submerged spirit vinegar-producing bioreactors with a strict requirement of acetic acid, ethanol, and glucose for growth. Over the years, the type-strain of G. entanii deposited in international culture collections has lost the ability for revitalization and is thus not available any more in a culturable form. Here, we have systematically characterized phenotypic features and genomes of recently isolated G. entanii strains and compared them with characteristics of the type-strain available from published data. Using the functional annotation, genes gmhB and psp were identified as unique for G. entanii genomes among species in the clade Novacetimonas. The genome stability of G. entanii was assessed after 28 and 43 months of preculturing the strain Gluconacetobacter entanii AV429 twice a week. The strain G. entanii AV429 did not accumulate giant insertions or deletions but a few gene mutations. To unify further research into acetic acid bacteria systematics and taxonomy, we propose G. entanii AV429 as the neotype strain.

Antimicrobial Resistance of Acetobacter and Komagataeibacter Species Originating from Vinegars.

Consumers' preference towards healthy and novel foods dictates the production of organic unfiltered bottled vinegar that still contains acetic acid bacteria. After ingesting vinegar, the bacteria come into close contact with the human microbiota, creating the possibility of horizontal gene transfer, including genetic determinants for antibiotic resistance. Due to the global spread of antimicrobial resistance (AMR), we analyzed the AMR of Acetobacter and Komagataeibacter species originating mainly from vinegars. Six antibiotics from different structural groups and mechanisms of action were selected for testing. The AMR was assessed with the disk diffusion method using various growth media. Although the number of resistant strains differed among the growth media, 97.4%, 74.4%, 56.4%, and 33.3% of strains were resistant to trimethoprim, erythromycin, ciprofloxacin, and chloramphenicol, respectively, on all three media. Moreover, 17.9% and 53.8% of all strains were resistant to four and three antibiotics of different antimicrobial classes, respectively. We then looked for antimicrobial resistance genes in the genome sequences of the reference strains. The most common genetic determinant potentially involved in AMR encodes an efflux pump. Since these genes pass through the gastrointestinal tract and may be transferred to human microbiota, further experiments are needed to analyze the probability of this scenario in more detail.

Polysaccharide-Based Bilayer Coatings for Biofilm-Inhibiting Surfaces of Medical Devices.

Chitosan (Chi) and 77KS, a lysine-derived surfactant, form polyelectrolyte complexes that reverse their charge from positive to negative at higher 77KS concentrations, forming aggregates that have been embedded with amoxicillin (AMOX). Dispersion of this complex was used to coat polydimethylsiloxane (PDMS) films, with an additional layer of anionic and hydrophilic hyaluronic acid (HA) as an outer adsorbate layer to enhance protein repulsion in addition to antimicrobial activity by forming a highly hydrated layer in combination with steric hindrance. The formed polysaccharide-based bilayer on PDMS was analyzed by water contact angle measurements, X-ray photoelectron spectroscopy (XPS), and surface zeta (ζ)-potential. All measurements show the existence and adhesion of the two layers on the PDMS surface. Part of this study was devoted to understanding the underlying protein adsorption phenomena and identifying the mechanisms associated with biofouling. Thus, the adsorption of a mixed-protein solution (bovine serum albumin, fibrinogen, γ-globulin) on PDMS surfaces was studied to test the antifouling properties. The adsorption experiments were performed using a quartz crystal microbalance with dissipation monitoring (QCM-D) and showed improved antifouling properties by these polysaccharide-based bilayer coatings compared to a reference or for only one layer, i.e., the complex. This proves the benefit of a second hyaluronic acid layer. Microbiological and biocompatibility tests were also performed on real samples, i.e., silicone discs, showing the perspective of the prepared bilayer coating for medical devices such as prostheses, catheters (balloon angioplasty, intravascular), delivery systems (sheaths, implants), and stents.

Bioactive Functional Nanolayers of Chitosan-Lysine Surfactant with Single- and Mixed-Protein-Repellent and Antibiofilm Properties for Medical Implants.

Medical implant-associated infections resulting from biofilm formation triggered by unspecific protein adsorption are the prevailing cause of implant failure. However, implant surfaces rendered with multifunctional bioactive nanocoatings offer a promising alternative to prevent the initial attachment of bacteria and effectively interrupt biofilm formation. The need to research and develop novel and stable bioactive nanocoatings for medical implants and a comprehensive understanding of their properties in contact with the complex biological environment are crucial. In this study, we developed an aqueous stable and crosslinker-free polyelectrolyte-surfactant complex (PESC) composed of a renewable cationic polysaccharide, chitosan, a lysine-based anionic surfactant (77KS), and an amphoteric antibiotic, amoxicillin, which is widely used to treat a number of infections caused by bacteria. We successfully introduced the PESC as bioactive functional nanolayers on the "model" and "real" polydimethylsiloxane (PDMS) surfaces under dynamic and ambient conditions. Besides their high stability and improved wettability, these uniformly deposited nanolayers (thickness: 44-61 nm) with mixed charges exhibited strong repulsion toward three model blood proteins (serum albumin, fibrinogen, and γ-globulin) and their competitive interactions in the mixture in real-time, as demonstrated using a quartz crystal microbalance with dissipation (QCM-D). The functional nanolayers with a maximum negative zeta potential (ζ: -19 to -30 mV at pH 7.4), water content (1628-1810 ng cm-2), and hydration (low viscosity and elastic shear modulus) correlated with the mass, conformation, and interaction nature of proteins. In vitro antimicrobial activity testing under dynamic conditions showed that the charged nanolayers actively inhibited the growth of both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria compared to unmodified PDMS. Given the ease of fabrication of multifunctional and charged biobased coatings with simultaneous protein-repellent and antimicrobial activities, the limitations of individual approaches could be overcome leading to a better and advanced design of various medical devices (e.g., catheters, prosthetics, and stents).

Acetan and Acetan-Like Polysaccharides: Genetics, Biosynthesis, Structure, and Viscoelasticity.

Bacteria produce a variety of multifunctional polysaccharides, including structural, intracellular, and extracellular polysaccharides. They are attractive for the industrial sector due to their natural origin, sustainability, biodegradability, low toxicity, stability, unique viscoelastic properties, stable cost, and supply. When incorporated into different matrices, they may control emulsification, stabilization, crystallization, water release, and encapsulation. Acetan is an important extracellular water-soluble polysaccharide produced mainly by bacterial species of the genera Komagataeibacter and Acetobacter. Since its original description in Komagataeibacter xylinus, acetan-like polysaccharides have also been described in other species of acetic acid bacteria. Our knowledge on chemical composition of different acetan-like polysaccharides, their viscoelasticity, and the genetic basis for their production has expanded during the last years. Here, we review data on acetan biosynthesis, its molecular structure, genetic organization, and mechanical properties. In addition, we have performed an extended bioinformatic analysis on acetan-like polysaccharide genetic clusters in the genomes of Komagataeibacter and Acetobacter species. The analysis revealed for the first time a second acetan-like polysaccharide genetic cluster, that is widespread in both genera. All species of the Komagataeibacter possess at least one acetan genetic cluster, while it is present in only one third of the Acetobacter species surveyed.

Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C.

The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.

A Cyclic di-GMP Network Is Present in Gram-Positive Streptococcus and Gram-Negative Proteus Species.

The ubiquitous cyclic di-GMP (c-di-GMP) network is highly redundant with numerous GGDEF domain proteins as diguanylate cyclases and EAL domain proteins as c-di-GMP specific phosphodiesterases comprising those domains as two of the most abundant bacterial domain superfamilies. One hallmark of the c-di-GMP network is its exalted plasticity as c-di-GMP turnover proteins can rapidly vanish from species within a genus and possess an above average transmissibility. To address the evolutionary forces of c-di-GMP turnover protein maintenance, conservation, and diversity, we investigated a Gram-positive and a Gram-negative species, which preserved only one single clearly identifiable GGDEF domain protein. Species of the family Morganellaceae of the order Enterobacterales exceptionally show disappearance of the c-di-GMP signaling network, but Proteus spp. still retained one diguanylate cyclase. As another example, in species of the bovis, pyogenes, and salivarius subgroups as well as Streptococcus suis and Streptococcus henryi of the genus Streptococcus, one candidate diguanylate cyclase was frequently identified. We demonstrate that both proteins encompass PAS (Per-ARNT-Sim)-GGDEF domains, possess diguanylate cyclase catalytic activity, and are suggested to signal via a PilZ receptor domain at the C-terminus of type 2 glycosyltransferase constituting BcsA cellulose synthases and a cellulose synthase-like protein CelA, respectively. Preservation of the ancient link between production of cellulose(-like) exopolysaccharides and c-di-GMP signaling indicates that this functionality is even of high ecological importance upon maintenance of the last remnants of a c-di-GMP signaling network in some of today's free-living bacteria.

Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar.

Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S-23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S-23S rRNA gene ITS of AV382 was to Komagataeibacter kakiaceti LMG 26206T (91.6%), of AV436 to Komagataeibacter xylinus LMG 1515T (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to K. kakiaceti (ANIb 88.2%) and AV436 to K. xylinus (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus Komagataeibacter. The strain AV382 can be differentiated from its closest relatives K. kakiaceti and Komagataeibacter saccharivorans by its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C19:0 cyclo ω8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relatives K. xylinus, Komagataeibacter sucrofermentans, and Komagataeibacter nataicola by its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C18:1ω7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382T and AV436T represent novel species of the genus Komagataeibacter, for which the names Komagataeibactermelaceti sp. nov. and Komagataeibacter melomenusus are proposed, respectively. The type strain of Komagataeibacter melaceti is AV382T (= ZIM B1054T = LMG 31303T = CCM 8958T) and of Komagataeibacter melomenusus AV436T (= ZIM B1056T = LMG 31304T = CCM 8959T).

Low Occurrence of Acinetobacter baumannii in Gulls and Songbirds.

Acinetobacter baumannii is a worldwide occurring nosocomial pathogen, the natural habitats of which remain to be defined. Recently, white stork nestlings have been described as a recurring source of A. baumannii. Here, we challenged the hypothesis of a general preference of A. baumannii for avian hosts. Taking advantage of campaigns to ring free-living birds, we collected cloacal swab samples from 741 black-headed gulls (Chroicocephalus ridibundus) in Poland, tracheal and cloacal swabs from 285 songbirds in Poland as well as tracheal swabs from 25 songbirds in Slovenia and screened those for the growth of A. baumannii on CHROMagarTM Acinetobacter. Of the 1,051 samples collected only two yielded A. baumannii isolates. Each carried one variant of the bla OXA-51-like gene, i.e. OXA-71 and OXA-208, which have been described previously in clinical isolates of A. baumannii. In conclusion, our data do not support a general preference of A. baumannii for avian hosts.Acinetobacter baumannii is a worldwide occurring nosocomial pathogen, the natural habitats of which remain to be defined. Recently, white stork nestlings have been described as a recurring source of A. baumannii. Here, we challenged the hypothesis of a general preference of A. baumannii for avian hosts. Taking advantage of campaigns to ring free-living birds, we collected cloacal swab samples from 741 black-headed gulls (Chroicocephalus ridibundus) in Poland, tracheal and cloacal swabs from 285 songbirds in Poland as well as tracheal swabs from 25 songbirds in Slovenia and screened those for the growth of A. baumannii on CHROMagarTM Acinetobacter. Of the 1,051 samples collected only two yielded A. baumannii isolates. Each carried one variant of the bla OXA-51-like gene, i.e. OXA-71 and OXA-208, which have been described previously in clinical isolates of A. baumannii. In conclusion, our data do not support a general preference of A. baumannii for avian hosts.

Bacterial Cellulose: Production, Modification and Perspectives in Biomedical Applications.

Bacterial cellulose (BC) is ultrafine, nanofibrillar material with an exclusive combination of properties such as high crystallinity (84%-89%) and polymerization degree, high surface area (high aspect ratio of fibers with diameter 20-100 nm), high flexibility and tensile strength (Young modulus of 15-18 GPa), high water-holding capacity (over 100 times of its own weight), etc. Due to high purity, i.e., absence of lignin and hemicellulose, BC is considered as a non-cytotoxic, non-genotoxic and highly biocompatible material, attracting interest in diverse areas with hallmarks in medicine. The presented review summarizes the microbial aspects of BC production (bacterial strains, carbon sources and media) and versatile in situ and ex situ methods applied in BC modification, especially towards bionic design for applications in regenerative medicine, from wound healing and artificial skin, blood vessels, coverings in nerve surgery, dura mater prosthesis, arterial stent coating, cartilage and bone repair implants, etc. The paper concludes with challenges and perspectives in light of further translation in highly valuable medical products.

Two FtsH Proteases Contribute to Fitness and Adaptation of Pseudomonas aeruginosa Clone C Strains.

Pseudomonas aeruginosa is an environmental bacterium and a nosocomial pathogen with clone C one of the most prevalent clonal groups. The P. aeruginosa clone C specific genomic island PACGI-1 harbors a xenolog of ftsH encoding a functionally diverse membrane-spanning ATP-dependent metalloprotease on the core genome. In the aquatic isolate P. aeruginosa SG17M, the core genome copy ftsH1 significantly affects growth and dominantly mediates a broad range of phenotypes, such as secretion of secondary metabolites, swimming and twitching motility and resistance to aminoglycosides, while the PACGI-1 xenolog ftsH2 backs up the phenotypes in the ftsH1 mutant background. The two proteins, with conserved motifs for disaggregase and protease activity present in FtsH1 and FtsH2, have the ability to form homo- and hetero-oligomers with ftsH2 distinctively expressed in the late stationary phase of growth. However, mainly FtsH1 degrades a major substrate, the heat shock transcription factor RpoH. Pull-down experiments with substrate trap-variants inactive in proteolytic activity indicate both FtsH1 and FtsH2 to interact with the inhibitory protein HflC, while the phenazine biosynthesis protein PhzC was identified as a substrate of FtsH1. In summary, as an exception in P. aeruginosa, clone C harbors two copies of the ftsH metallo-protease, which cumulatively are required for the expression of a diversity of phenotypes.

Genome sequences and description of novel exopolysaccharides producing species Komagataeibacter pomaceti sp. nov. and reclassification of Komagataeibacter kombuchae (Dutta and Gachhui 2007) Yamada et al., 2013 as a later heterotypic synonym of Komagataeibacter hansenii (Gosselé et al. 1983) Yamada et al., 2013.

Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors Komagataeibacter maltaceti LMG 1529T and Gluconacetobacter entanii LTH 4560T. Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S-23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus. Average nucleotide identity of T5K1 and AV446 draft genome sequences compared to other Komagataeibacter type strains was below 94% and at the same time, in-silico DNA-DNA hybridization was below 70%. Both strains on the other hand showed approximately 98% (average nucleotide identity) and 87% (in silico DNA-DNA hybridization) similarity to each other. Strains T5K1 and AV446 can be differentiated from other Komagataeibacter type strains based on their ability to produce 2-keto-d-gluconic acid and at the same time inability to produce 5-keto-d-gluconic acid. Furthermore, strains of the new species do not grow on Asai medium supplemented with d-glucose or d-mannitol. The growth is also absent (T5K1) or weak (AV446) on Hoyer-Frateur medium supplemented with afore mentioned sugars. Both strains produce cellulose. In addition, draft genome analysis revealed that strains T5K1 and AV446 possess genes involved in the synthesis of acetan-like extracellular heteropolysaccharide. We propose the name Komagataeibacter pomaceti sp. nov. for the new species with LMG 30150T [=CCM 8723T=ZIM B1029T] as the type strain. Data collected in this study and in a previous study also revealed that Komagataeibacter kombuchae is a later heterotypic synonym of Komagataeibacter hansenii.

Draft genome sequence of Chryseobacterium limigenitum SUR2T (LMG 28734T) isolated from dehydrated sludge

ABSTRACT The type strain SUR2 of the novel species Chryseobacterium limigenitum was isolated from a dehydrated sludge of the municipal sewage treatment plant in Dogoše near Maribor in Slovenia. The draft genome, with 60 contigs, 4,697,725 bp, 34.4% of G+C content, was obtained using the Illumina HiSeq 2500-1 platform. Joint Genome Institute Microbial Genome Annotation Pipeline (MGAP v.4) has identified 4322 protein-coding sequences including resistance genes against arsenic and other heavy metals. In addition, a subclass B3 metallo-β-lactamase, which confers resistance to penicillins, cephalosporins and carbapenems, was also present in the genome. The genome sequence provides important information regarding bioremediation potential and pathogenic properties of this newly identified species.