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Sunday, July 7, 2019

Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01.

Komagataeibacter nataicola is an acetic acid bacterium (AAB) that can produce abundant bacterial cellulose and tolerate high concentrations of acetic acid. To globally understand its fermentation characteristics, we present a high-quality complete genome sequence of K. nataicola RZS01. The genome consists of a 3,485,191-bp chromosome and 6 plasmids, which encode 3,514 proteins and bear three cellulose synthase operons. Phylogenetic analysis at the genome level provides convincing evidence of the evolutionary position of K. nataicola with respect to related taxa. Genomic comparisons with other AAB revealed that RZS01 shares 36.1%~75.1% of sequence similarity with other AAB. The sequence data was also…

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Sunday, July 7, 2019

Gas fermentation: cellular engineering possibilities and scale up.

Low carbon fuels and chemicals can be sourced from renewable materials such as biomass or from industrial and municipal waste streams. Gasification of these materials allows all of the carbon to become available for product generation, a clear advantage over partial biomass conversion into fermentable sugars. Gasification results into a synthesis stream (syngas) containing carbon monoxide (CO), carbon dioxide (CO2), hydrogen (H2) and nitrogen (N2). Autotrophy-the ability to fix carbon such as CO2 is present in all domains of life but photosynthesis alone is not keeping up with anthropogenic CO2 output. One strategy is to curtail the gaseous atmospheric release…

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Sunday, July 7, 2019

Revealing the saline adaptation strategies of the halophilic bacterium Halomonas beimenensis through high-throughput omics and transposon mutagenesis approaches.

Studies on the halotolerance of bacteria are attractive to the fermentation industry. However, a lack of sufficient genomic information has precluded an investigation of the halotolerance of Halomonas beimenensis. Here, we describe the molecular mechanisms of saline adaptation in H. beimenensis based on high-throughput omics and Tn5 transposon mutagenesis. The H. beimenensis genome is 4.05 Mbp and contains 3,807 genes, which were sequenced using short and long reads obtained via deep sequencing. Sixteen Tn5 mutants with a loss of halotolerance were identified. Orthologs of the mutated genes, such as nqrA, trkA, atpC, nadA, and gdhB, have significant biological functions in…

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Sunday, July 7, 2019

Complete genome sequence and comparative analysis of Staphylococcus condimenti DSM 11674, a potential starter culture isolated from soy sauce mash.

Coagulase-negative staphylococci (CNS) are key players in the majority of food fermentation ecosystems, which are commonly found in the production of fermented meat and milk products (Blaiotta et al., 2005; Resch et al., 2008). Strains of CNS have been implicated in exerting desirable effects as components of a fermentation flora, such as color formation, aroma development, and shelf-life enhancement, and may therefore have the potential for future application as starter cultures (Zell et al., 2008). Staphylococcus condimenti is one of the most prominent species and has the potential for use in starter cultures for the production of fermented sausage and…

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Sunday, July 7, 2019

Whole-genome sequencing of Lactobacillus salivarius strains BCRC 14759 and BCRC 12574.

Lactobacillus salivarius BCRC 14759 has been identified as a high-exopolysaccharide-producing strain with potential as a probiotic or fermented dairy product. Here, we report the genome sequences of L. salivarius BCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The PacBio RSII sequencing platform was used to obtain high-quality assemblies for characterization of this probiotic candidate. Copyright © 2017 Chiu et al.

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Sunday, 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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Sunday, July 7, 2019

Complete genome sequence of Staphylococcus equorum KS1039 isolated from Saeu-jeotgal, Korean high-salt-fermented seafood.

Staphylococcus equorum KS1039 was isolated from a form of traditional Korean high-salt-fermented seafood called Saeu-jeotgal, and exhibited growth at a NaCl (w/v) concentration of 25%. Comparative genome analyses with two other strains revealed the presence of two potassium voltage-gated channel genes uniquely in KS1039, which might be involved in salt tolerance. This first complete genome sequence of the species will increase our understanding of the genetic factors allowing it to be safely consumed by humans and to inhabit high-salt environments. Copyright © 2015 Elsevier B.V. All rights reserved.

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Sunday, July 7, 2019

Dam and Dcm methylations prevent gene transfer into Clostridium pasteurianum NRRL B-598: development of methods for electrotransformation, conjugation, and sonoporation.

Butanol is currently one of the most discussed biofuels. Its use provides many benefits in comparison to bio-ethanol, but the price of its fermentative production is still high. Genetic improvements could help solve many problems associated with butanol production during ABE fermentation, such as its toxicity, low concentration achievable in the cultivation medium, the need for a relatively expensive substrate, and many more. Clostridium pasteurianum NRRL B-598 is non-type strain producing butanol, acetone, and a negligible amount of ethanol. Its main benefits are high oxygen tolerance, utilization of a wide range of carbon and nitrogen sources, and the availability of…

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Sunday, July 7, 2019

Complete genome sequence of Lactobacillus acidophilus MN-BM-F01.

Lactobacillus acidophilus MN-BM-F01 was originally isolated from a traditional fermented dairy product in China. The characteristics of this bacterium are its low post-acidification ability and high acid-producing rate. Here, we report the main genome features of L. acidophilus MN-BM-F01. Copyright © 2016 Yang et al.

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Sunday, July 7, 2019

Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis.

The hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on carbon monoxide (CO) and its H2 production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H2 productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H2 production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the…

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Sunday, July 7, 2019

The identification of novel diagnostic marker genes for the detection of beer spoiling Pediococcus damnosus strains using the BlAst Diagnostic Gene findEr.

As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well. We present BlAst Diagnostic Gene findEr (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG identification settings can be modified easily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about the DMG finding process, thus making it easy to evaluate the impact of chosen…

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Sunday, July 7, 2019

Complete genome sequence of Lactobacillus helveticus CAUH18, a potential probiotic strain originated from koumiss.

Here we report the complete genome sequence of Lactobacillus helveticus CAUH18, a new strain isolated from traditional fermented dairy product koumiss. Its genome has a circular 2.16Mb chromosome with no plasmid. The genome sequence indicated that this strain harbors a gene cluster involved in a novel exopolysaccharides (EPS) biosynthesis and a gene encoding cell-surface aggregation-promoting factors (APFs) to facilitate its colonization in gastrointestinal tract (GIT). This genome sequence provides a basis for further studies about its molecular genetics and probiotic functions. Copyright © 2016. Published by Elsevier B.V.

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Sunday, July 7, 2019

Complete genome sequence of Streptococcus thermophilus MN-BM-A01, a strain with high exopolysaccharides production.

Streptococcus thermophilus MN-BM-A01 (ST MN-BM-A01) (CGMCC No. 11383) was a strain isolated from Yogurt Block in Gansu, China. The yogurt fermented with this strain has good flavor, acidity, and viscosity. Moreover, ST MN-BM-A01 could produce a high level of EPS which can confer the yogurt with improved rheological properties. We reported the complete genome sequence of ST MN-BM-A01 that contains 1,876,516bp encoding 1704 coding sequences (CDSs), 67 tRNA genes and 6 rRNA operons. The genomic sequence indicated that this strain included a 35.3-kb gene cluster involved in EPS biosynthesis. Copyright © 2016. Published by Elsevier B.V.

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Sunday, July 7, 2019

Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.

Clostridium paradoxum strain JW-YL-7 is a moderately thermophilic anaerobic alkaliphile isolated from the municipal sewage treatment plant in Athens, GA. We report the near-complete genome sequence of C. paradoxum strain JW-YL-7 obtained by using PacBio DNA sequencing and Pilon for sequence assembly refinement with Illumina data. Copyright © 2016 Lancaster et al.

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