Phenotypical properties of Enterobacter agglomerans (Pantoea agglomerans) from human, animal and plant sources

Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734

Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P. agglomerans DAPP-PG 734 was sequenced and annotated. The complete genome had a total size of 5′396′424 bp, containing one circular chromosome and four large circular plasmids. The aim of this study was to identify genomic features that could play a potential role in the interaction between P. agglomerans DAPP-PG 734 and P. savastanoi pv. savastanoi DAPP-PG 722. For this purpose, a comparative genomic analysis between the genome of P. agglomerans DAPP-PG 734 and those of related Pantoea spp. was carried out. In P. agglomerans DAPP-PG 734, gene clusters for the synthesis of the Hrp-1 type III secretion system (T3SS), type VI secretion systems (T6SS) and autoinducer, which could play an important role in a plant-pathogenic community enhancing knot formation in olive trees, were identified. Additional gene clusters for the biosynthesis of two different antibiotics, namely dapdiamide E and antibiotic B025670, which were found in regions between integrative conjugative elements (ICE), were observed. The in-depth analysis of the whole genome suggested a characterization of the P. agglomerans DAPP-PG 734 isolate as endophytic bacterium with biocontrol activity rather than as a plant pathogen.

Lipopolysaccharide and the gut microbiota: Considering structural variation

Systemic inflammation is associated with chronic disease and is purported to be a main pathogenic mechanism underlying metabolic conditions. Microbes harbored in the host gastrointestinal tract release signaling byproducts from their cell wall, such as lipopolysaccharides (LPS), which can act locally and, after crossing the gut barrier and entering circulation, also systemically. Defined as metabolic endotoxemia, elevated concentrations of LPS in circulation are associated with metabolic conditions and chronic disease. As such, measurement of LPS is highly prevalent in animal and human research investigating these states. Indeed, LPS can be a potent stimulant of host immunity but this response depends on the microbial species' origin, a parameter often overlooked in both preclinical and clinical investigations. Indeed, the lipid A portion of LPS is mutable and comprises the main virulence and endotoxic component, thus contributing to the structural and functional diversity among LPSs from microbial species. In this review, we discuss how such structural differences in LPS can induce differential immunological responses in the host.

Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov

Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3C^T = DOAB 1063^T = CECT 30248^T = LMG 32139^T), Pseudomonas triticumensis sp. nov. (type strain 32L3A^T = DOAB 1067^T = CECT 30249^T = LMG 32140^T) and Pseudomonas foliumensis sp. nov. (type strain 10L4B^T = DOAB 1069^T = CECT 30250^T = LMG 32142^T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.

Effects of feeding a Lactobacillus plantarum JL01 diet on caecal bacteria and metabolites of weaned piglets

Currently, knowledge is limited concerning the impact of a Lactobacillus plantarum JL01 diet for weaned piglets on caecal bacteria and metabolite profiles. In our experiments, 24 weaned piglets were randomly divided into two groups; each piglet in the treatment groups (Cec-Lac) was fed a basic diet and administered 10 ml of L. plantarum JL01 (1·0 × 10⁹  CFU per ml) every day. The control group (Cec-Con) was fed a basic diet. After feeding for 28 days, we analysed the parameters of the caecal digesta of weaned piglets. We used 16S rDNA gene sequencing and mass spectrometry (MS)-based metabolomics techniques to investigate the effect of a L. plantarum JL01 diet on intestinal microbial composition and its metabolite profiles in the caecum contents of weaned piglets. The results showed that the richness estimators (ACE and Chao indices) in the caecal bacteria increased in the Cec-Lac group. Prevotella_2 and Desulfovibrio decreased significantly, while Pantoea and Rectale_group increased in the caecum of weaned piglets in the Cec-Lac group. Furthermore, Pearson's correlation analysis revealed that the genus Rectale_group was positively correlated with indole-3-acetic acid (P < 0·05), and the genus Pantoea had the same correlation with 1-palmitoyl lysophosphatidic acid. The metabolomics analysis revealed that the L. plantarum JL01 diet supplementation had significant effects on tryptophan metabolism and fat digestion and absorption. The results indicated that the L. plantarum JL01 dietary supplementation not only altered the microbial composition but also mediated tryptophan metabolism and fat digestion and absorption in the caecum, factors that may further affect the health of the host.

Efficacy of continuous ingestion of dewaxed brown rice on the cognitive functions of the residents of elderly welfare facilities: A pilot test using crossover trial

Compared with regular brown rice, dewaxed brown rice (DBR), prepared by excluding only the wax layer in the outermost layer of brown rice using a new rice milling technique, has improved water absorbency, digestibility, and taste. Dewaxed brown rice has a nutritional value close to that of brown rice and contains a large amount of lipopolysaccharides (LPS), which are known to improve the cognitive function of mice. In this study, we examined the effect of continuous DBR ingestion on the cognitive function of elderly people. A crossover comparison test was performed, in which elderly people who moved into an elderly welfare facility were divided into two groups and ingested DBR or polished white rice for three meals a day for 6 months, followed by a change in test meals for the next 6 months. Cognitive function was assessed using Revised Hasegawa's Dementia Scale (HDS-R) before starting the test and 6 months after ingesting each test meal. No subjects withdrew or discontinued DBR intake during the study period, and all subjects continued the test for 6 months. In subjects with low cognitive function (defined as subjects with HDS-R total score of ≥1 but <10 at the start of the study), there was a significant association between continuous DBR ingestion and cognitive function improvement (increase in total HDS-R score). Our findings suggest that the long-term DBR ingestion as a staple food could be useful for preventing cognitive decline in elderly; it offers an easily implemented option as a daily diet for preventing cognitive decline.

Cultivable microbiota and pulmonary lesions in polymicrobial bovine pneumonia

In the present study, the spectrum of bacterial pathogens in the nasal shedding during disease process and in pneumonic lungs of dead animals was studied. A total of 288 clinical samples from cattle and buffaloes comprising of nasal swabs, blood, tracheal swabs, heart blood and lung tissue samples were collected from diseased (n = 190) and dead animals (n = 98). The recovered bacterial isolates were characterized by biochemical reactions, Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI TOF-MS) and the 16S rRNA sequence analysis. The predominant bacterial isolates associated were Pasteurella multocida, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus. The emerging pathogens causing bovine pneumonia identified were Leclercia spp., Stenotrophononas maltophila and Staphylococcus sciuri. Bacteriological examination of pneumonic lungs samples revealed 96.9% samples to be positive for polymicrobial isolation. Macroscopical lesions of lungs exhibited various stages and types of pneumonia with variable degree of haemorrhages, oedema and emphysema. Histopathologically, the fibrinous bronchopneumonia was observed to be the most frequent lesions seen in bovine pneumonia. Multi-drug resistance (MDR) was observed in 10% of P. multocida isolates. The resistance was seen for penicillin, cephalosporins and fluoroquinolones. Multi-drug resistance was seen in 90% of the E.coli tested. K. pneumoniae, E. hormaechei, E. cloacae, P. putida and Leclercia spp. identified were found to be multi-drug resistant. Understanding the etiological diversity of bacterial pathogens of bovine pneumonia may provide information for the better choice of therapeutics and health management.

Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species

The genus Pantoea contains a broad range of plant-associated bacteria, including some economically important plant pathogens as well as some beneficial members effective as biological control agents of plant pathogens. The most well-characterized representatives of biological control agents from this genus generally produce one or more antimicrobial compounds adding to biocontrol efficacy. Some Pantoea species evaluated as biocontrol agents for fire blight disease of apple and pear produce a histidine-reversible antibiotic. Three commonly studied histidine-reversible antibiotics produced by Pantoea spp. are herbicolin O, MccEh252, and pantocin A. Pantocin A is a novel ribosomally encoded and post-translationally modified peptide natural product. Here, we review the current knowledge on the chemistry, genetics, biosynthesis, and incidence and environmental relevance of pantocin A and related histidine-reversible antibiotics produced by Pantoea.

Oral administration of Pantoea agglomerans-derived lipopolysaccharide prevents development of atherosclerosis in high-fat diet-fed apoE-deficient mice via ameliorating hyperlipidemia, pro-inflammatory mediators and oxidative responses

Pantoea agglomerans (P. agglomerans) is a Gram-negative bacterium that grows symbiotically with various edible plants, and the oral or sublingual administration of lipopolysaccharide derived from P. agglomerans (LPSp) have been suggested to contribute to prevention of immune-related diseases. Our previous study indicated that orally administered LPSp was shown to exhibit an LDL-lowering effect in hyperlipidemic volunteers; however, a preventive effect of LPSp on atherosclerosis is unclear. The present study attempted to evaluate the anti-atherosclerotic effect by LPSp in a mouse model of high-fat diet (HFD)-induced atherosclerosis. For 16 weeks, apoE-deficient mice were fed an HFD and received drinking water containing LPSp (0.3 or 1 mg/kg body weight/day). The results showed that the orally administered LPSp decreased body weight. A significant reduction in atherosclerotic plaque deposition was observed even with the lower dose of LPSp. The biochemical analyses showed that LPSp markedly improved glucose tolerance and reduced plasma LDL and oxidized LDL levels. In addition, LPSp significantly reduced the production of pro-inflammatory mediators including MCP-1 (in the plasma), TNF-α and IL-6 (in the colon), and decreased the oxidative burst activities in the peripheral blood sample. Taken together, these results suggest the possibility that oral administration of LPSp can effectively ameliorate HFD-induced hyperlipidemia and inflammatory/oxidative responses to prevent atherosclerosis and related metabolic disorders.

Carbapenem Resistance among Enterobacter Species in a Tertiary Care Hospital in Central India

Objective. To detect genes encoding carbapenem resistance among Enterobacter species in a tertiary care hospital in central India. Methods. Bacterial identification of Enterobacter spp. isolates from various clinical specimens in patients admitted to intensive care units was performed by routine conventional microbial culture and biochemical tests using standard recommended techniques. Antibiotic sensitivity test was performed by standard Kirby Bauer disc diffusion technique. PCR amplification and automated sequencing was carried out. Transfer of resistance genes was determined by conjugation. Results. A total of 70/130 (53.84%) isolates of Enterobacter spp. were found to exhibit reduced susceptibility to imipenem (diameter of zones of inhibition ≤13 mm) by disc diffusion method. Among 70 isolates tested, 48 (68.57%) isolates showed MIC values for imipenem and meropenem ranging from 32 to 64 mg/L as per CLSI breakpoints. All of these 70 isolates were found susceptible to colistin in vitro as per MIC breakpoints (<0.5 mg/L). PCR carried out on these 48 MBL (IP/IPI) E-test positive isolates (12 Enterobacter aerogenes, 31 Enterobacter cloacae, and 05 Enterobacter cloacae complex) was validated by sequencing for beta-lactam resistance genes and result was interpreted accordingly. Conclusion. The study showed MBL production as an important mechanism in carbapenem resistance in Enterobacter spp. and interspecies transfer of these genes through plasmids suggesting early detection by molecular methods.

Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4

Nonpathogenic Pantoea spp. have been shown to confer biofertilizer and biocontrol activities, indicating their potential for increasing crop yield. Herein, we provide the high-quality genome sequence of Pantoea sp. strain AS-PWVM4, a Gram-negative motile plant growth-promoting rhizobacterium isolated from a pomegranate plant. The 4.9-Mb genome contains genes related to plant growth promotion and the synthesis of siderophores.

Genome sequence of Pantoea agglomerans strain IG1

Pantoea agglomerans is a gram-negative bacterium that grows symbiotically with various plants. Here we report the 4.8-Mb genome sequence of P. agglomerans strain IG1. The lipopolysaccharides derived from P. agglomerans IG1 have been shown to be effective in the prevention of various diseases, such as bacterial or viral infection, lifestyle-related diseases. This genome sequence represents a substantial step toward the elucidation of pathways for production of lipopolysaccharides.

Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3

A 530-kb megaplasmid pPag3 contributing 10.8% of the total genome of Pantoea vagans biocontrol strain C9-1 was sequenced. A rare nonpigmented variant C9-1W was obtained and shown to have lost pPag3, but retained all other plasmids (pPag1, pPag2). Phenotypic characterization of the variant confirmed the function of several annotated genes that may influence ecological fitness and efficacy. Metabolic profiling revealed important plasmid-based carbon utilization phenotypes. Plasmid loss resulted in thiamine auxotrophy, absence of carotenoid pigmentation, desferrioxamine diffusible siderophore biosynthesis, inherent ampicillin resistance and expression of AI-1 quorum-sensing signaling. This confirmed the functional expression of the corresponding genes located on pPag3 in P. vagans.

Applications of lipopolysaccharide derived from Pantoea agglomerans (IP-PA1) for health care based on macrophage network theory

Innate immunity is a universal prophylactic system which all multi-cellular animals possess. Macrophages are the cells that play the central role in the innate immune system. In 1991, we discovered a substance in a water extract of wheat flour that activated macrophages after oral or intradermal administration. The active substance was lipopolysaccharide (LPS), which is derived from the cell walls of Pantoea agglomerans, gram-negative bacteria that grows symbiotically with wheat. We named the substance IP-PA1 (immuno potentiator from P. agglomerans, former name: LPSp). The IP-PA1 is considered to be useful in various fields such as health food (to prevent and improve metabolic syndromes), skincare products (to maintain healthy skin, to improve atopic dermatitis, and to resist aging), and as active ingredients in feeds for stockbreeding and aquaculture (to act as a defense against infection). In this manuscript, we discuss the significance of activation of macrophages through oral or intradermal administration, the discovery of IP-PA1 as a macrophage-activating substance, the chemical structure of IP-PA1, the use of IP-PA1 to improve various disorders, the mechanism of action, and the possibility of application of IP-PA1 to various fields.

Recommended test panel for differentiation of Klebsiella species on the basis of a trilateral interlaboratory evaluation of 18 biochemical tests

Klebsiella pneumoniae and Klebsiella oxytoca are the two most frequently encountered Klebsiella species giving rise to infections in humans, but other Klebsiella species can also be found in clinical specimens: Klebsiella ozaenae, Klebsiella rhinoscleromatis, Klebsiella terrigena, Klebsiella planticola, Klebsiella ornithinolytica, and Enterobacter aerogenes (Klebsiella mobilis). However, many of these species are indistinguishable by the conventional methods employed routinely in the clinical microbiological laboratory. Several investigators have suggested various additional tests, but as yet there is no standardized test panel for identifying all Klebsiella species and subspecies. In the present study, performed in three national Klebsiella reference laboratories, we have evaluated a test panel consisting of 18 biochemical tests on 242 strains comprising all Klebsiella species and subspecies. The test panel was designed to identify organisms preliminarily identified as belonging to the genus Klebsiella on the basis of conventional methods or automated identification systems. With the described test panel it is possible to find one or more positive test results differentiating any Klebsiella species, except Klebsiella rhinoscleromatis, from its closest relative.

Molecular epidemiology of a nosocomial outbreak due to Enterobacter cloacae and Enterobacter agglomerans in Campinas, São Paulo, Brazil

A total of 73 isolates (57 Enterobacter cloacae and 16 Enterobacter agglomerans), recovered during an outbreak of bacteremia in the Campinas area, São Paulo, Brazil, were studied. Of these isolates, 61 were from parenteral nutrition solutions, 9 from blood cultures, 2 from a sealed bottle of parenteral nutrition solution, and one was of unknown origin. Of the 57 E. cloacae isolates, 54 were biotype 26, two were biotype 66 and one was non-typable. Of 39 E. cloacae isolates submitted to ribotyping, 87.2% showed the same banding pattern after cleavage with EcoRI and BamHI. No important differences were observed in the antimicrobial susceptibility patterns among E. cloacae isolates exhibiting the same biotype, serotype and ribotype. All E. agglomerans isolates, irrespective of their origin, showed same patterns when cleaved with EcoRI and BamHI. The results of this investigation suggest an intrinsic contamination of parenteral nutrition solutions and incriminate these products as a vehicle of infection in this outbreak.

Enterobacter spp.: pathogens poised to flourish at the turn of the century

Knowledge of the genus Enterobacter and its role in human disease has expanded exponentially in recent years. The incidence of infection in the hospital and the community has increased. New clinical syndromes have been recognized. Enterobacter spp. have also been implicated as causes of other syndromes that traditionally have been associated almost exclusively with more easily treatable pathogens, such as group A streptococci and staphylococci. Rapid emergence of multiple-drug resistance has been documented in individual patients during therapy and in populations and environments with strong selective pressure from antimicrobial agents, especially the cephalosporins. Therapeutic options for patients infected with multiply resistant strains have become severely limited. Carbapenems or, alternatively, fluoroquinolones are the most predictively active options, although resistance to both classes has been observed on rare occasions. Enterobacter spp. appear well adapted for survival and even proliferation as the turn of the century approaches.

Beta-lactamases and detection of beta-lactam resistance in Enterobacter spp

Enterobacter spp. are becoming increasingly frequent nosocomial pathogens, and beta-lactam-resistant strains are on the increase, especially among isolates recovered from intensive care units. Therefore, a study was designed to characterize the beta-lactamases produced by 80 isolates of E. cloacae, E. aerogenes, E. taylorae, E. gergoviae, E. sakazakii, E. asburiae, and E. agglomerans by induction studies, spectrophotometric hydrolysis assays, and isoelectric focusing. The ability of broth microdilution and disk diffusion susceptibility tests to detect resistance to 16 beta-lactam antibiotics among these species was also assessed. All species except E. agglomerans, E. gergoviae, and some isolates of E. sakazakii were found to produce a Bush group 1 cephalosporinase that was expressed inducibly or constitutively at high levels. In addition, some strains also produced a Bush group 2 beta-lactamase. In comparisons of broth microdilution and disk diffusion tests, disk diffusion tests failed to detect resistance in 1 of 25 isolates resistant to aztreonam and 2 of 30 isolates resistant to ceftazidime. These results indicate that species of Enterobacter can possess a variety of beta-lactamases that are responsible for beta-lactam resistance in this genus and that the disk diffusion test may occasionally miss resistance in some strains.