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Auto Tag: Industrial biotechnology

July 7, 2019

Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function.

Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species. Results show that a major evolutionary event leading to the clade of the infant-adapted species is linked to carbohydrate metabolism, but it is not the only factor responsible for the adaptation of bifidobacteria to the gut. The genome of B. longum subsp. infantis, a typical bifidobacterium in the gut of breast-fed infants, encodes proteins associated with several kinds of species-specific metabolic pathways, including urea metabolism and biosynthesis of riboflavin and lantibiotics. Our results demonstrate that these metabolic features, which are associated with the probiotic function of bifidobacteria, are species-specific and highly correlate with their phylogeny. Copyright © 2016 Elsevier GmbH. All rights reserved.

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July 7, 2019

Development of Streptomyces sp. FR-008 as an emerging chassis

Microbial-derived natural products are important in both the pharmaceutical industry and academic research. As the metabolic potential of original producer especially Streptomyces is often limited by slow growth rate, complicated cultivation profile, and unfeasible genetic manipulation, so exploring a Streptomyces as a super industrial chassis is valuable and urgent. Streptomyces sp. FR-008 is a fast-growing microorganism and can also produce a considerable amount of macrolide candicidin via modular polyketide synthase. In this study, we evaluated Streptomyces sp. FR-008 as a potential industrial-production chassis. First, PacBio sequencing and transcriptome analyses indicated that the Streptomyces sp. FR-008 genome size is 7.26 Mb, which represents one of the smallest of currently sequenced Streptomyces genomes. In addition, we simplified the conjugation procedure without heat-shock and pre-germination treatments but with high conjugation efficiency, suggesting it is inherently capable of accepting heterologous DNA. In addition, a series of promoters selected from literatures was assessed based on GusA activity in Streptomyces sp. FR-008. Compared with the common used promoter ermE*-p, the strength of these promoters comprise a library with a constitutive range of 60–860%, thus providing the useful regulatory elements for future genetic engineering purpose. In order to minimum the genome, we also target deleted three endogenous polyketide synthase (PKS) gene clusters to generate a mutant LQ3. LQ3 is thus an “updated” version of Streptomyces sp. FR-008, producing fewer secondary metabolites profiles than Streptomyces sp. FR-008. We believe this work could facilitate further development of Streptomyces sp. FR-008 for use in biotechnological applications.

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July 7, 2019

Complete genome sequence of Lactobacillus plantarum LZ227, a potential probiotic strain producing B-group vitamins.

B-group vitamins play an important role in human metabolism, whose deficiencies are associated with a variety of disorders and diseases. Certain microorganisms such as Lactic acid bacteria (LAB) have been shown to have capacities for B-group vitamin production and thus could potentially replace chemically synthesized vitamins for food fortification. A potential probiotic strain named Lactobacillus plantarum LZ227, which was isolated from raw cow milk in this study, exhibits the ability to produce B-group vitamins. Complete genome sequencing of LZ227 was performed to gain insights into the genetic elements involved in B-group vitamin production. The genome of LZ227 contains a circular 3,131,750-bp chromosome, three circular plasmids and two predicted linear plasmids. LZ227 also contains gene clusters for biosynthesis of both riboflavin and folate. This genome sequence provides a basis for further elucidation of its molecular genetics and probiotic functions, and will facilitate its applications as starter cultures in food industry. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of the proteorhodopsin-containing marine flavobacterium Dokdonia donghaensis DSW-1T, isolated from seawater off Dokdo in the East Sea (Sea of Korea).

Dokdonia spp. have been used for investigating the lifestyles of proteorhodopsin-containing photoheterotrophs and for understanding marine photobiology. Here, we report the complete genome sequence of Dokdonia donghaensis DSW-1(T) using the PacBio sequencing platform. It should provide a valuable resource for comparative genomic studies of marine life harboring microbial rhodopsins among others. Copyright © 2016 Kim et al.

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July 7, 2019

Genome sequence of Arenibacter algicola strain TG409, a hydrocarbon-degrading bacterium associated with marine eukaryotic phytoplankton.

Arenibacter algicola strain TG409 was isolated from Skeletonema costatum and exhibits the ability to utilize polycyclic aromatic hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 5,550,230 bp with 4,722 genes and an average G+C content of 39.7%. Copyright © 2016 Gutierrez et al.

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July 7, 2019

Complete genome sequence of Streptomyces parvulus 2297, integrating site-specifically with actinophage R4

Streptomyces parvulus 2297, which is a host for site-specific recombination according to actinophage R4, is derived from the type strain ATCC 12434. Species of S. parvulus are known as producers of polypeptide antibiotic actinomycins and have been considered for industrial applications. We herein report for the first time the complete genome sequence of S. parvulus 2297. Copyright © 2016 Nishizawa et al.

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July 7, 2019

Complete genome sequence of a potential probiotic, Lactobacillus pentosus MP-10, isolated from fermented Aloreña table olives.

We report here a 3,698,214-bp complete genome sequence of a potential probiotic Lactobacillus pentosus strain, MP-10, isolated from brines of naturally fermented Aloreña green table olives; it is considered the largest sequenced genome among lactobacilli to date. The annotated genome sequence revealed the presence of 3,558 open reading frames (ORFs) and 87 structural RNAs. Copyright © 2016 Abriouel et al.

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July 7, 2019

Genome sequence of the oral probiotic Streptococcus salivarius JF.

Streptococcus salivarius is a nonpathogenic Gram-positive bacterium and the predominant colonizer of the oral microbiota. It finds a wide application in the prevention of upper respiratory tract infections, also reducing the frequency of other main pathogens. Here, we present the complete genome sequence of the oral probiotic S. salivarius JF. Copyright © 2016 Jia.

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July 7, 2019

Complete genome sequence of Lactobacillus oris J-1, a potential probiotic isolated from the human oral microbiome.

Lactobacilli can exert health-promoting effects in the human oral microbiome through many mechanisms, including pathogen inhibition, maintenance of microbial balance, immunomodulation, and enhancement of the epithelial barrier function. Here, we present the complete genome sequence of a potential probiotic, Lactobacillus oris J-1, that was isolated from the oral cavity of a health child. Copyright © 2016 Jia.

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July 7, 2019

Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses.

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.

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