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Widely used as drugs and agrochemicals, polyketides are a family of bioactive natural products, with diverse structures and functions. Polyketides are produced by megaenzymes termed as polyketide synthases (PKSs). PKS biosynthetic pathways are divided into the cis -AT PKSs and trans -AT PKSs; a division based mainly on the absence of an acyltransferase (AT) domain in the trans- AT PKS modules. In trans -AT biosynthesis, the AT activity is contributed via one or several independent proteins, and there are few other characteristics that distinguish trans -AT PKSs from cis -AT PKSs, especially in the formation of the β-branch. The trans -AT PKSs constitute a major PKS pathway, and many are found in Burkholderia species, which are prevalent in the environment and prolific sources of polyketides. This review summarizes studies from 1973 to 2017 on the biosynthesis of natural products by trans -AT PKSs from Burkholderia species.

The plant growth promoting rhizobacteria (PGPR) and plant growth regulators (PGRs) can be applied to improve the growth and productivity of plants, with potential to be used for genetic improvement of drought tolerance. However, for genetic improvement to be achieved, a solid understanding of the physiological and biochemical changes in plants induced by PGPR and PGR is required. The present study was carried out to investigate the role of PGPR and PGRs on the physiology and biochemical changes in chickpea grown under drought stress conditions and their association with drought tolerance. The PGPR, isolated from the rhizosphere of chickpea, were characterized on the basis of colony morphology and biochemical characters. They were also screened for the production of indole-3-acetic acid (IAA), hydrogen cyanide (HCN), ammonia (NH 3 ), and exopolysaccharides (EPS) production. The isolated PGPR strains, named P1, P2, and P3, were identified by 16S-rRNA gene sequencing as Bacillus subtilis, Bacillus thuringiensis, and Bacillus megaterium, respectively. The seeds of two chickpea varieties, Punjab Noor-2009 (drought sensitive) and 93127 (drought tolerant) were soaked for 2-3 h prior to sowing in 24 h old cultures of isolates. The salicylic acid (SA) and putrescine (Put) were sprayed (150 mg/L) on 25 day old chickpea seedlings. The results showed that chickpea plants treated with a consortium of PGPR and PGRs significantly enhanced the chlorophyll, protein, and sugar contents compared to irrigated and drought conditions. Leaf proline content, lipid peroxidation, and activities of antioxidant enzymes (CAT, APOX, POD, and SOD) all increased in response to drought stress but decreased due to the PGPR and PGRs treatment. An ultrahigh performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis was carried out for metabolic profiling of chickpea leaves planted under controlled (well-irrigated), drought, and consortium (drought plus PGPR and PGRs) conditions. Proline, L-arginine, L-histidine, L-isoleucine, and tryptophan were accumulated in the leaves of chickpea exposed to drought stress. Consortium of PGPR and PGRs induced significant accumulation of riboflavin, L-asparagine, aspartate, glycerol, nicotinamide, and 3-hydroxy-3-methyglutarate in the leaves of chickpea. The drought sensitive chickpea variety showed significant accumulation of nicotinamide and 4-hydroxy-methylglycine in PGPR and PGR treated plants at both time points (44 and 60 days) as compared to non-inoculated drought plants. Additionally, arginine accumulation was also enhanced in the leaves of the sensitive variety under drought conditions. Metabolic changes as a result of drought and consortium conditions highlighted pools of metabolites that affect the metabolic and physiological adjustments in chickpea that reduce drought impacts.

Objectives: This study reports the draft genome sequence of Xenophilus sp. E41, a strain resistant to multiple antimicrobials isolated from an activated sludge reactor treating wastewater with a high cephalexin concentration., Methods: Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. The generated sequence reads were assembled using MEGAHIT in combination with SOAPdenovo. Mauve and CompareM were used to align the Xenophilus sp. E41 genome to other draft genomes of the genus Xenophilus in order to determine their evolutionary relationships. The draft genome was annotated using the Rapid Annotation using Subsystem Technology (RAST) server and the nr database, whilst antimicrobial resistance genes (ARGs) were identified using the SARG 2.0 database, RAST server and nr database., Results: Xenophilus sp. E41, with a genome length of 5919552bp, harbours seven types of ARGs involving resistance to β-lactams, tetracycline, aminoglycosides, sulfonamides, chloramphenicol, teicoplanin and bleomycin. No virulence factors or plasmids were identified., Conclusion: The genome sequence reported here will provide useful information for a better understanding of antimicrobial resistance profiles in this strain and the genus Xenophilus., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

A Gram-negative, aerobic, motile, and rod-shaped bacterial strain designated CR182 T was isolated from freshwater of the Nakdong River, Republic of Korea. Optimal growth conditions for this novel strain were found to be: 25-30 °C, pH 6.5-8.5, and 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicates that the strain CR182 T belongs to type strains of genus Paucibacter. Strain CR182 T showed 98.0% 16S rRNA gene sequence similarity with Paucibacter oligotrophus CHU3 T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain CR182 T and P. oligotrophus CHU3 T was 78.4% and the genome-to-genome distance was 22.2% on average. The genomic DNA G+C content calculated from the genome sequence was 66.3 mol%. Predominant cellular fatty acids of strain CR182 T were summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) (31.2%) and C 16:0 (16.0%). Its major respiratory quinine was ubiquinone Q-8. Its polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified phospholipids. Its genomic DNA G+C content was 66.3%. Based on data obtained from this polyphasic taxonomic study, strain CR182 T represents a novel species belonging to genus Paucibacter, for which a name of P. aquatile sp. nov. is proposed. The type strain is CR182 T (= KCCM 90284 T  = NBRC 113032 T ).

The taxonomic positions of two moderately thermophilic bacteria, strains YIM 72259 T and YIM 72238 T , isolated from a hot spring sediment sample were determined using polyphasic taxonomic approaches. Pairwise comparison of the 16S rRNA gene sequences showed that strains YIM 72259 T and YIM 72238 T are closely related to Tepidimonas ignava SPS-1037 T (97.0 and 97.5%, respectively), Tepidimonas taiwanensis I1-1 T (96.5 and 97.3%), while sharing 98.0% sequence similarity with each other. The DNA-DNA relatedness values of strains YIM 72238 T with T. ignava SPS-1037 T and T. taiwanensis I1-1 T were determined to be 25.2 ± 1.2 and 24.6 ± 3.1%, respectively, while the two strains (YIM 72259 T and YIM 72238 T ) had a relatedness value of 38.3 ± 4.4% between themselves. The two strains were aerobic, Gram-stain negative, motile by means of a polar flagellum and formed non-pigmented colonies. The DNA G+C contents of strains YIM 72259 T and YIM 72238 T were determined to be 71.6 and 68.9 mol%, respectively. The major fatty acids in both strains were identified as (> 10%) C 16:0 , C 17:0 and summed feature 8, while the strain YIM 72238 T contained a moderately high amount of summed feature 3 as well. The polar lipid profiles for strains YIM 72259 T and YIM 72238 T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and several unidentified phospholipids. Besides the morphological and chemotaxonomic characteristics, phylogenetic analyses of the 16S rRNA gene sequences and the biochemical characteristics indicated that the two strains represented two novel members of the genus Tepidimonas, for which the name Tepidimonas sediminis sp. nov. [type strain YIM 72259 T (= NBRC 112410 T  = CGMCC 1.15971 T ) and Tepidimonas alkaliphilus sp. nov. [type strain YIM 72238 T (= KCTC 52717 T  = CCTCC AB 2017168 T )] are proposed.

In response to environmental changes, the photosynthetic bacterium Rubrivivax gelatinosus (Rvx.) can switch from a planktonic lifestyle to a phototrophic biofilm. Like in critical phenomena, the colonization and sedimentation of the cells is abrupt and hard to predict causally, and the underlying biophysics of the mechanisms involved is not known. Herein, we report basic experimental observations and quantitative explanations as keys to understanding microbial turnover of aggregates. (1) The moment of sedimentation can be controlled by the height of the tube of cultivation, by the concentrations of externally added Ficoll (a highly branched polymer) and/or of internally produced polysaccharides (constituents of the biofilm). (2) The observed translational diffusion coefficient of the planktonic bacteria is the sum of diffusion coefficients coming from random Brownian and twitching movements of the bacteria and amounts to 14 (μm) 2 /s. (3) This value drops hyperbolically with the association number of the cell aggregates and with the concentration of the exopolysaccharides in the biofilm. In the experiments described herein, their effects could be separated. (4) The critical conditions of colonization and sinking of the cells will be achieved if the height of the tube meets the scale height that is proportional to the ratio of the diffusion coefficient and the net mass of the bacterium. The decisive role of the web-like structure of a biofilm, the organization of bacteria from loose cooperativity to solid aggregation, and the possible importance of similar controls in other phototrophic microorganisms are discussed.

Background: Crohn's disease [CD] is known to be associated with gut microbial dysbiosis. Infliximab [IFX] is increasingly used to treat paediatric CD; however, it is not clear how the gut microbiota is modified during IFX treatment. The aim of this study was to characterise the faecal microbiota community composition in paediatric CD patients and to assess its dynamic changes during IFX therapy., Methods: A 16S rRNA sequencing approach was applied to determine the compositions of microbial communities in faecal samples. The composition and function of the faecal microbiota were compared between CD patients and healthy controls., Results: Characteristics of faecal microbiome composition in paediatric CD patients before IFX treatment were represented by a lower biodiversity, a gain in Enterococcus, and a significant loss in multiple short-chain fatty acid [SCFA]-producing bacteria, including Anaerostipes, Blautia, Coprococcus, Faecalibacterium, Lachnospira, Odoribacter, Roseburia, Ruminococcus, and Sutterella. Additionally, alterations were observed in metabolic functions of the gut microbial community in CD. IFX treatment increased the biodiversity of gut microbiota and shifted its composition as well as its functional capabilities in the paediatric CD patients toward a healthy status. However, multiple SCFA-producing taxa were not significantly expanded. The sustained response of paediatric CD patients to IFX was associated with abundance of SCFA-producing bacteria., Conclusions: A lower biodiversity with alterations in the composition and function of faecal microbial community, characterising gut microbial dysbiosis, was observed in Chinese paediatric CD patients. IFX diminished the CD-associated gut microbial dysbiosis but was deficient in increasing certain SCFA-producing taxa., (Copyright © 2017 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com)

Softwood hemicellulose hydrolysates are a cheap source of sugars that can be used as a feedstock to produce polyhydroxybutyrates (PHB), which are biobased and compostable bacterial polyesters. To assess the potential of the hemicellulosic sugars as a carbon source for PHB production, synthetic media containing softwood hemicellulose sugars (glucose, mannose, galactose, xylose, arabinose) and the potentially inhibitory lignocellulose degradation products (acetic acid, 5-hydroxymethylfurfural (HMF), furfural, and vanillin) were fermented with the model strain Paraburkholderia sacchari IPT 101. Relative to pure glucose, individual fermentation for 24 h with 20 g/L mannose or galactose exhibited maximum specific growth rates of 97% and 60%, respectively. On the other hand, with sugar mixtures of glucose, mannose, galactose, xylose, and arabinose, the strain converted all sugars simultaneously to reach a maximum PHB concentration of 5.72 g/L and 80.5% PHB after 51 h. The addition of the inhibitor mixture at the following concentration, sodium acetate (2.11 g/L), HMF (0.67 g/L), furfural (0.66 g/L), and vanillin (0.93 g/L), to the sugar mixture stopped the growth entirely within 24 h. Individually, the inhibitors either had no effect or only reduced growth. Moreover, it was found that a bacterial inoculum with high initial cell density (optical density, OD ≥ 5.6) could overcome the growth inhibition to yield an OD of 13 within 24 h. Therefore, softwood hemicellulose sugars are viable carbon sources for PHB production. Nevertheless, real softwood hemicellulose hydrolysates need detoxification or a high inoculum to overcome inhibitory effects and allow bacterial growth.

PET hydrolase (PETase), which hydrolyzes polyethylene terephthalate (PET) into soluble building blocks, provides an attractive avenue for the bioconversion of plastics. Here we present the structures of a novel PETase from the PET-consuming microbe Ideonella sakaiensis in complex with substrate and product analogs. Through structural analyses, mutagenesis, and activity measurements, a substrate-binding mode is proposed, and several features critical for catalysis are elucidated.

Previous studies suggested a close relationship between ruminant gut microbes and the mammary gland. In this study, shotgun metagenomic sequencing was used to reveal the differences in the intestinal microbiome potentially related to milk components in Murrah buffaloes and Chinese Holstein cattle. A PCoA based on the weighted Unifrac distances showed an apparent clustering pattern in the structure of intestinal microbiota between buffalo and cattle. We could attribute the structural difference to the genera of Sutterella, Coprococcus and Dorea. A further analysis of microbial functional features revealed that the biosynthesis of amino acids (including lysine, valine, leucine and isoleucine), lipopolysaccharide biosynthesis and cofactor/vitamin biosynthesis were enriched in the buffalo. In contrast, dairy cattle had higher levels of pyruvate metabolism and carbon fixation in photosynthetic organisms. A further correlation analysis based on different milk components and the typical microbiome uncovered a significant positive correlation between milk protein and the microbial biosynthesis of amino acids, which was also positively correlated in the genera of Parabacteroides, Dorea and Sutterella. This study will expand our understanding of the intestinal microbiome of buffalo and cattle as representative ruminants, as well as provide new views about how to improve the production and nutritional qualities of animal milk., Competing Interests: The authors declare no competing financial interests.