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July 7, 2019

Complete genome sequence of Lactobacillus plantarum JBE245 isolated from Meju

Lactobacillus plantarum is widely found in fermented foods and has various phenotypic and genetic characteristics to adapt to the environment. Here we report the complete annotated genome sequence of the L. plantarum strain JBE245 (= KCCM43243) isolated for malolactic fermentation of apple juice. The genome comprises a single circular 3,262,611 bp chromosome with 2907 coding regions, 45 pseudogenes, and 91 RNA genes. The genome contains 4 malate dehydrogenase genes, 3 malate permease genes and various types of plantaricin-synthesizing genes. These genetic traits meet the selection criteria of the strains that should prevent the spoilage of apple juice during fermentation and efficiently convert malate to lactic acid.

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July 7, 2019

Linear peptides are the major products of a biosynthetic pathway that encodes for cyclic depsipeptides.

Three new dentigerumycin analogues are produced by Streptomyces sp. M41, a bacterium isolated from a South African termite, Macrotermes natalensis. The structures of the complex nonribosomal peptide synthetase-polyketide synthase (NRPS/PKS) hybrid compounds were determined by 1D- and 2D-NMR spectroscopy, high-resolution mass spectrometry, and circular dichroism (CD) spectroscopy. Both cyclic and linear peptides are reported, and the genetic organization of the NRPS modules within the biosynthetic gene cluster accounts for the observed structural diversity.

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July 7, 2019

Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment.

Resource limitation and predation mortality are major determinants of microbial population dynamics, and optimization for either aspect is considered to imply a trade-off with respect to the other. Adaptation to these selective factors may, moreover, lead to disadvantages at rich growth conditions. We present an example of a concomitant evolutionary optimization to both, substrate limitation and predation in an aggregate-forming freshwater bacterial isolate, and we elucidate an underlying genomic mechanism. Bacteria were propagated in serial batch culture in a nutrient-restricted environment either with or without a bacterivorous flagellate. Strains isolated after 26 growth cycles of the predator-prey co-cultures formed as much total biomass as the ancestor at ancestral growth conditions, albeit largely reallocated to cell aggregates. A ~273?kbp genome fragment was lost in three strains that had independently evolved with predators. These strains had significantly higher growth yield on substrate-restricted media than others that were isolated from the same treatment before the excision event. Under predation pressure, the isolates with the deletion outcompeted both, the ancestor and the strains evolved without predators even at rich growth conditions. At the same time, genome reduction led to a growth disadvantage in the presence of benzoate due to the loss of the respective degradation pathway, suggesting that niche constriction might be the price for the bidirectional optimization.

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July 7, 2019

Glaucophyta

The Glaucophyta is by far the least species-rich phylum of the Archaeplastida comprising only four described genera, Glaucocystis, Cyanophora, Gloeochaete, and Cyanoptyche, and 15 species. However, recent molecular and morphological analyses reveal that glaucophytes are not as species poor as hitherto assumed with many novel lineages existing in natural environments. Glaucophytes are freshwater phototrophs of moderate to low abundance and retain many ancestral plastid traits derived from the cyanobacterial donor of this organelle, including the remnant peptidoglycan wall in their envelope. These plastids were originally named “cyanelles,” which was later changed to “muroplasts” when their shared ancestry with other Archaeplastida was recognized. The model glaucophyte, Cyanophora paradoxa, is well studied with respect to biochemistry, proteomics, and the gene content of the nuclear and organelle genomes. Investigation of the biosynthesis of cytosolic starch led to a model for the transition from glycogen to starch storage during plastid endosymbiosis. The photosynthetic apparatus, including phycobilisome antennae, resembles that of cyanobacteria. However, the carbon-concentrating mechanism is algal in nature and based on pyrenoids. Studies on protein import into muroplasts revealed a primordial Toc/Tic translocon. The peptidoglycan wall was elucidated with respect to composition, biosynthesis, and involvement of nuclear genes. The muroplast genome is distinct, not due to the number of encoded genes but, rather, because of the presence of unique genes not present on other plastid genomes. The mosaic nature of the gene-rich (27,000) nuclear genome came as a surprise, considering the relatively small genomes of unicellular red algae.

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July 7, 2019

Tracing origins of the Salmonella Bareilly strain causing a food-borne outbreak in the United States.

Using a novel combination of whole-genome sequencing (WGS) analysis and geographic metadata, we traced the origins of Salmonella Bareilly isolates collected in 2012 during a widespread food-borne outbreak in the United States associated with scraped tuna imported from India.Using next-generation sequencing, we sequenced the complete genome of 100 Salmonella Bareilly isolates obtained from patients who consumed contaminated product, from natural sources, and from unrelated historically and geographically disparate foods. Pathogen genomes were linked to geography by projecting the phylogeny on a virtual globe and produced a transmission network.Phylogenetic analysis of WGS data revealed a common origin for outbreak strains, indicating that patients in Maryland and New York were infected from sources originating at a facility in India.These data represent the first report fully integrating WGS analysis with geographic mapping and a novel use of transmission networks. Results showed that WGS vastly improves our ability to delimit the scope and source of bacterial food-borne contamination events. Furthermore, these findings reinforce the extraordinary utility that WGS brings to global outbreak investigation as a greatly enhanced approach to protecting the human food supply chain as well as public health in general. Published by Oxford University Press for the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

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July 7, 2019

Characterization of ESBL disseminating plasmids.

Bacteria producing extended-spectrum ß-lactamases (ESBLs) constitute a globally increasing problem that contributes to treatment complications and elevated death rates. The extremely successful dissemination by ESBL-producing Enterobacteriaceae during the latest decades is a result of the combination of mobilization, evolution and horizontal spread of ß-lactamase genes on plasmids. In parallel, spread of these plasmids to particularly well-adapted bacterial clones (outbreak clones) has expanded. In this review we describe ESBL-producing bacteria and the genetic mechanisms for dissemination of ESBL resistance. We describe available methodology for studying plasmids and the importance of including plasmids in epidemiological typing as natural parts of the organisms. Plasmids play a fundamental role in how resistance arises and disseminates.

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July 7, 2019

Microbial bioinformatics for food safety and production.

In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput ‘omics’ technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety. © The Author 2015. Published by Oxford University Press.

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July 7, 2019

Complete Sequences and Characterization of Two Novel Plasmids Carrying aac(6′)-Ib-cr and qnrS Gene in Shigella flexneri.

The complete sequences of two previously reported plasmids carrying plasmid-mediated quinolone resistance genes from Shigella flexneri in China have not been available. The present study using the p5-C3 assembly method revealed that (1) the plasmid pSF07201 with aac(6′)-Ib-cr had 75,335?bp with antibiotic resistance genes CTX-M-3, TEM-1, and FosA3; (2) seven fragments of pSF07201 had more than 99% homology with the seven corresponding plasmids; (3) the other plasmid pSF07202 with qnrS had 47,669?bp with antibiotic resistance gene TEM-1 and 99.95% homology with a segment of pKF362122, which has the qnrS gene from location 162,490 to 163,146. A conjugation and electrotransformation experiment suggested that these two plasmids might horizontally transfer between and coexist in Escherichia coli J53 and S. flexneri 2a 301. Either the aac(6′)-Ib-cr or qnrS gene contributed to, but only the coexistence of the two genes conferred to the resistance to ciprofloxacin in these two strains. To the best of our knowledge, this is the first report of the complete sequences of the aac(6′)-Ib-cr- and qnrS-positive plasmids in Shigella isolates. Our findings indicate that two genes probably evolve through horizontal plasmid transfer between the different bacterial types.

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July 7, 2019

Genetic and functional characterization of an extracellular modular GH6 endo-ß-1,4-glucanase from an earthworm symbiont, Cellulosimicrobium funkei HY-13.

The gene (1608-bp) encoding a GH6 endo-ß-1,4-glucanase (CelL) from the earthworm-symbiotic bacterium Cellulosimicrobium funkei HY-13 was cloned from its whole genome sequence, expressed recombinantly, and biochemically characterized. CelL (56.0 kDa) is a modular enzyme consisting of an N-terminal catalytic GH6 domain (from Val57 to Pro396), which is 71 % identical to a GH6 protein (accession no.: WP_034662937) from Cellulomonas sp. KRMCY2, together with a C-terminal CBM 2 domain (from Cys429 to Cys532). The highest catalytic activity of CelL toward carboxymethylcellulose (CMC) was observed at 50 °C and pH 5.0, and was relatively stable at a broad pH range of 4.0-10.0. The enzyme was capable of efficiently hydrolyzing the cellulosic polymers in the order of barley ß-1,3-1,4-D-glucan > CMC > lichenan > Avicel > konjac glucomannan. However, cellobiose, cellotriose, p-nitrophenyl derivatives of mono- and disaccharides, or structurally unrelated carbohydrate polymers including ß-1,3-D-glucan, ß-1,4-D-galactomannan, and ß-1,4-D-xylan were not susceptible to CelL. The enzymatic hydrolysis of cellopentaose resulted in the production of a mixture of 68.6 % cellobiose and 31.4 % cellotriose but barley ß-1,3-1,4-D-glucan was 100 % degraded to cellotriose by CelL. The enzyme strongly bound to Avicel, ivory nut mannan, and chitin but showed relatively weak binding affinity to lichenan, lignin, or poly(3-hydroxybutyrate) granules.

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July 7, 2019

First Azospirillum genome from aquatic environments: Whole-genome sequence of Azospirillum thiophilum BV-S(T), a novel diazotroph harboring a capacity of sulfur-chemolithotrophy from a sulfide spring.

Azospirillum thiophilum BV-S(T), isolated from a sulfide spring, is a novel nitrogen-fixing bacterium harboring sulfur-lithotrophy. In order to identify genetic characteristics with habitat- and metabolic features contrasting to those from terrestrial Azospirillum species, we present here the genome sequence of a novel species A. thiophilum BV-S(T), with a significance of first genome report in the aquatic Azospirillum species. The genome of strain BV-S(T) is comprised of 7.6Mb chromosome with a GC content of 68.2%. This information will contribute to expand understandings of sulfur-oxidizer microbes that preserve inherencies as a diazotroph, and further it will provide insights into genome plasticity of the genus Azospirillum for niche specific adaptations. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia.

To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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July 7, 2019

Protein O-linked glycosylation in the plant pathogen Ralstonia solanacearum.

Ralstonia solanacearum is one of the most lethal phytopathogens in the world. Due to its broad host range, it can cause wilting disease in many plant species of economic interest. In this work, we identified the O-oligosaccharyltransferase (O-OTase) responsible for protein O-glycosylation in R. solanacearum. An analysis of the glycoproteome revealed that 20 proteins, including type IV pilins are substrates of this general glycosylation system. Although multiple glycan forms were identified, the majority of the glycopeptides were modified with a pentasaccharide composed of HexNAc-(Pen)-dHex3, similar to the O antigen subunit present in the lipopolysaccharide of multiple R. solanacearum strains. Disruption of the O-OTase led to the total loss of protein glycosylation, together with a defect in biofilm formation and reduced pathogenicity towards tomato plants. Comparative proteomic analysis revealed that the loss of glycosylation is not associated with widespread proteome changes. Only the levels of a single glycoprotein, the type IV pilin, were diminished in the absence of glycosylation. In parallel, disruption of glycosylation triggered an increase in the levels of a surface lectin homologous to Pseudomonas PA-IIL. These results reveal the important role of glycosylation in the pathogenesis of R. solanacearum. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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July 7, 2019

Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli.

As a highly valued keto-carotenoid, astaxanthin is widely used in nutritional supplements and pharmaceuticals. Therefore, the demand for biosynthetic astaxanthin and improved efficiency of astaxanthin biosynthesis has driven the investigation of metabolic engineering of native astaxanthin producers and heterologous hosts. However, microbial resources for astaxanthin are limited. In this study, we found that the a-Proteobacterium Sphingomonas sp. ATCC 55669 could produce astaxanthin naturally. We used whole-genome sequencing to identify the astaxanthin biosynthetic pathway using a combined PacBio-Illumina approach. The putative astaxanthin biosynthetic pathway in Sphingomonas sp. ATCC 55669 was predicted. For further confirmation, a high-efficiency targeted engineering carotenoid synthesis platform was constructed in E. coli for identifying the functional roles of candidate genes. All genes involved in astaxanthin biosynthesis showed discrete distributions on the chromosome. Moreover, the overexpression of exogenous E. coli idi in Sphingomonas sp. ATCC 55669 increased astaxanthin production by 5.4-fold. This study described a new astaxanthin producer and provided more biosynthesis components for bioengineering of astaxanthin in the future. © 2015 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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