Phylogenetic studies of the rRNA group II pseudomonads based on 16S rRNA gene sequences

Nearly complete sequences of 16S rRNA genes were determined for eight bacterial strains representing five species of the rRNA homology group II pseudomonads that are members of the beta subclass of the class Proteobacteria. Comparative analysis with published sequence data indicated that Pseudomonas andropogonis, Ps. caryophylli, Ps. gladioli pv. gladioli and Ps. cepacia aggregate in one coherent cluster at 94·2% sequence similarity; Ps. solanacearum and Ps. pickettii shared 95·3% and 92·8% similarity with Alcaligenes eutrophus in another cluster. Both clusters joined at 87·8% similarity, which is similar to that for genera in this subclass of Proteobacteria. Based on this study and on comparison with other works we suggest that these species are separated from authentic pseudomonads and constitute a new genus or possibly two related genera accommodating Ps. andropogonis, Ps. caryophylli, Ps. gladioli, Ps. cepacia, and Ps. solanacearum, Ps. pickettii and A. eutrophus, respectively. Four strains of Ps. solanacearum representing Biovars 1, 2, 3 and 4 were subdivided into two clusters at 99·1% sequence similarity, in agreement with other published phenotypic and genotypic studies. The two clusters may be potentially regarded as subspecies

Isolation and identification of an Eikelboom type 1863 strain as Acinetobacter johnsonii

Type 1863 strain RT2 was isolated by micromanipulation techniques from an activated sludge sewage treatment plant in Rome. The isolate is a coccobacillus which grows in chains. It is a strict aerobe that is oxidase negative and catalase positive, exhibits chemoorganotrophic metabolism and grows on acetate as the sole carbon source but does not grow on carbohydrates. Strain RT2 is a member of the genus Acinetobacter by the transformation assay. The 16S rDNA sequence of RT2 was determined and used to phylogenetically place the strain in the gamma subclass of the proteobacteria as Acinetobacter johnsonii. Type 1863 strain RT2 was isolated by micromanipulation techniques from an activated sludge sewage treatment plant in Rome. The isolate is a coccobacillus which grows in chains. It is a strict aerobe that is oxidase negative and catalase positive, exhibits chemoorganotrophic metabolism and grows on acetate as the sole carbon source but does not grow on carbohydrates. Strain RT2 is a member of the genus Acinetobacter by the transformation assay. The 16S rDNA sequence of RT2 was determined and used to phylogenetically place the strain in the gamma subclass of the proteobacteria as Acinetobacter johnsonii

Isolation and characterization of a Clostridium sp with cinnamoyl esterase activity and unusual cell envelope ultrastructure

Microorganisms that hydrolyse the ester linkages between phenolic acids and polysaccharides in plant cell walls are potential sources of enzymes for the degradation of lignocellulosic waste. An anaerobic, mesophilic, spore-forming, xylanolytic bacterium with high hydroxy cinnamic acid esterase activity was isolated from the gut of the grass-eating termite Tumilitermes pastinator. The bacterium was motile and rod-shaped, stained gram-positive, had an eight-layered cell envelope, and.formed endospores. Phylogenetic analysis based on 16S rRNA indicated that the bacterium is closely related to Clostridium xylanolyticum and is grouped with polysaccharolytic strains of clostridia. A wide range of carbohydrates were fermented, and growth was stimulated by either xylan or cellobiose as substrates. The bacterium hydrolysed and then hydrogenated the hydroxy cinnamic acids (ferulic and p-coumaric acids), which are esterified to arabinoxylan in plant cell walls. Three cytoplasmic enzymes with hydroxy cinnamic acid esterase activity were identified using non-denaturing gel electrophoresis. This bacterium possesses an unusual multilayered cell envelope in which both leaflets of the cytoplasmic membrane, the peptidoglycan layer and the S layer are clearly discernible. The fate of all these components was easily followed throughout the endospore formation process. The peptidoglycan component persisted during the entire morphogenesis. It was seen to enter the septum and to pass with the engulfing membranes to surround the prespore. It eventually expanded to form the cortex, verification for the peptidoglycan origin of the cortex. Sporogenic vesicles, which are derived from the cell wall peptidoglycan, were associated with the engulfment process. Spore coat fragments appeared early, in stage II, though spore coat formation was not complete until after cortex formation

Pediatrics international : official English journal of the Japan Pediatric Society

A primary-structure analysis of the 16S rRNA gene was performed with 10 strains representing five described and one unidentified species of the genus Microcystis. The phylogenies determined illustrate the evolutionary affiliations among Microcystis strains, other cyanobacteria, and related plastids and bacteria. A cluster of 10 strains that included hepatotoxic isolates identified as Microcystis aeruginosa formed a monophyletic group. However, the genus Microcystis appeared to be polyphyletic and contained two strains that clustered with unicellular cyanobacteria belonging to the genus Synechococcus. The clustering of related Microcystis strains, including strains involved in the production of the cyclic peptide toxin microcystin, was consistent with cell morphology, gas vacuolation, and the low G+C contents of the genomes. The Microcystis lineage was also distinct from the lineage containing the unicellular genus Synechocystis and the filamentous, heterocyst-forming genus Nostoc. The secondary structure of a Microcystis 16S rRNA molecule was determined, and genus-specific sequence signatures were used to design primers that permitted identification of the potentially toxic cyanobacteria belonging to the genus Microcystis via DNA amplification

Diversity of the human gastrointestinal tract microbiota revisited

Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Propionate is produced in the human large intestine by microbial fermentation and may help maintain human health. We have examined the distribution of three different pathways used by bacteria for propionate formation using genomic and metagenomic analysis of the human gut microbiota and by designing degenerate primer sets for the detection of diagnostic genes for these pathways. Degenerate primers for the acrylate pathway (detecting the lcdA gene, encoding lactoyl-CoA dehydratase) together with metagenomic mining revealed that this pathway is restricted to only a few human colonic species within the Lachnospiraceae and Negativicutes. The operation of this pathway for lactate utilisation in Coprococcus catus (Lachnospiraceae) was confirmed using stable isotope labelling. The propanediol pathway that processes deoxy sugars such as fucose and rhamnose was more abundant within the Lachnospiraceae (based on the pduP gene, which encodes propionaldehyde dehydrogenase), occurring in relatives of Ruminococcus obeum and in Roseburia inulinivorans. The dominant source of propionate from hexose sugars, however, was concluded to be the succinate pathway, as indicated by the widespread distribution of the mmdA gene that encodes methylmalonyl-CoA decarboxylase in the Bacteroidetes and in many Negativicutes. In general, the capacity to produce propionate or butyrate from hexose sugars resided in different species, although two species of Lachnospiraceae (C. catus and R. inulinivorans) are now known to be able to switch from butyrate to propionate production on different substrates. A better understanding of the microbial ecology of short-chain fatty acid formation may allow modulation of propionate formation by the human gut microbiota

Safety of hospital discharge before return of bowel function after elective colorectal surgery

Background: Ileus is common after colorectal surgery and is associated with an increased risk of postoperative complications. Identifying features of normal bowel recovery and the appropriateness for hospital discharge is challenging. This study explored the safety of hospital discharge before the return of bowel function.Methods: A prospective, multicentre cohort study was undertaken across an international collaborative network. Adult patients undergoing elective colorectal resection between January and April 2018 were included. The main outcome of interest was readmission to hospital within 30 days of surgery. The impact of discharge timing according to the return of bowel function was explored using multivariable regression analysis. Other outcomes were postoperative complications within 30 days of surgery, measured using the Clavien-Dindo classification system.Results: A total of 3288 patients were included in the analysis, of whom 301 (9.2 per cent) were discharged before the return of bowel function. The median duration of hospital stay for patients discharged before and after return of bowel function was 5 (i.q.r. 4-7) and 7 (6-8) days respectively (P < 0.001). There were no significant differences in rates of readmission between these groups (6.6 versus 8.0 per cent; P = 0.499), and this remained the case after multivariable adjustment for baseline differences (odds ratio 0.90, 95 per cent c.i. 0.55 to 1.46; P = 0.659). Rates of postoperative complications were also similar in those discharged before versus after return of bowel function (minor: 34.7 versus 39.5 per cent; major 3.3 versus 3.4 per cent; P = 0.110).Conclusion: Discharge before return of bowel function after elective colorectal surgery appears to be safe in appropriately selected patients