Application of state-of-art sequencing technologies to indigenous food fermentations.

Abstract:

:Fermented foods and beverages are an integral part of the human diet globally. Understanding the microbial interactions within these fermenting ecosystems is required to deliver safe products with desirable consumer properties, and moreover, maintenance of these traditions. Effective tools are required for documentation of cultures in traditional and artisanal fermented products, for sensory quality and safety improvements, in some cases for starter culture design for commercialization and potentially for supporting sustainable food systems. Here we trace the developments of sequence-based molecular technologies for investigating the diversity and functionality of microbiota in traditional or indigenous fermented foods and beverages. The opportunities of phylobiomics, metagenomics and metatranscriptomics to enrich our knowledge of fermenting microbial ecosystems are presented.

journal_name

Curr Opin Biotechnol

authors

van Hijum SA,Vaughan EE,Vogel RF

doi

10.1016/j.copbio.2012.08.004

subject

Has Abstract

pub_date

2013-04-01 00:00:00

pages

178-86

issue

2

eissn

0958-1669

issn

1879-0429

pii

S0958-1669(12)00118-8

journal_volume

24

pub_type

杂志文章,评审
  • Use of cell wall-less bacteria (L-forms) for efficient expression and secretion of heterologous gene products.

    abstract::In spite of many efforts and achievements to optimize the prokaryotic expression systems, there are still general and specific problems in obtaining sufficient yields of the functionally active gene products. The main problems concern the formation of inclusion bodies, incorrect folding, toxicity for the producer cell...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(98)80037-2

    authors: Gumpert J,Hoischen C

    更新日期:1998-10-01 00:00:00

  • New methods for separation and recovery of biomolecules.

    abstract::New methods and applications in the separation of biomolecules are reviewed, with an emphasis on the large-scale recovery of proteins. Highlights include the advent of flow-through particles in perfusion chromatography, which allows for very high flow rates, while retaining a high chromatographic efficiency. ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(05)80148-x

    authors: Glad M,Larsson PO

    更新日期:1991-06-01 00:00:00

  • Antisense technology in molecular and cellular bioengineering.

    abstract::Antisense technology is finding increasing application not only in clinical development, but also for cellular engineering. Several types of antisense methods (e.g. antisense oligonucleotides, antisense RNA and small interfering RNA) can be used to inhibit the expression of a target gene. These antisense methods are b...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(03)00115-0

    authors: Lee LK,Roth CM

    更新日期:2003-10-01 00:00:00

  • Alternative bioseparation operations: life beyond packed-bed chromatography.

    abstract::Chromatography is undoubtedly the workhorse of downstream processes, affording high resolution for bioseparations. At the same time, it has the notoriety of being the single largest cost center in downstream processing and of being a low-throughput operation. Consequently, 'chromatography alternatives' are an attracti...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2004.08.008

    authors: Przybycien TM,Pujar NS,Steele LM

    更新日期:2004-10-01 00:00:00

  • DNA analysis in forensics, disease and animal/plant identification.

    abstract::During 1993, significant advances have been achieved in applications of DNA analysis to forensic science, disease assessment, and animal/plant identification. These advances include the development of simple and high sample-throughput techniques for highly informative personal identification, rapid screening for patho...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(05)80066-7

    authors: Alford RL,Caskey CT

    更新日期:1994-02-01 00:00:00

  • Decaying signals: will understanding bacterial-plant communications lead to control of soft rot?

    abstract::Soft rot pathogens cause significant losses worldwide in fruit and vegetable production during the growing season and after harvest. These pathogens engage in molecular interactions with their plant hosts via acyl-homoserine lactone (AHL) quorum sensing, pectin metabolites, phenolic acids, and auxin. The AHL-based int...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2009.01.005

    authors: Charkowski AO

    更新日期:2009-04-01 00:00:00

  • Biological approaches for controlling shellfish-associated pathogens.

    abstract::As the consumption of seafood and shellfish increases around the world, so is the incidence of associated outbreaks of illness. Various postharvest treatments are effective at killing seafood-associated bacteria, but most of these treatments also kill the mollusks. Because consumer preferences for raw live shellfish p...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.copbio.2009.03.001

    authors: Teplitski M,Wright AC,Lorca G

    更新日期:2009-04-01 00:00:00

  • Advances in cellulosic conversion to fuels: engineering yeasts for cellulosic bioethanol and biodiesel production.

    abstract::Cellulosic fuels are expected to have great potential industrial applications in the near future, but they still face technical challenges to become cost-competitive fuels, thus presenting many opportunities for improvement. The economical production of viable biofuels requires metabolic engineering of microbial platf...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2017.11.007

    authors: Ko JK,Lee SM

    更新日期:2018-04-01 00:00:00

  • In situ treatment of PCBs by anaerobic microbial dechlorination in aquatic sediment: are we there yet?

    abstract::The remediation of polychlorinated biphenyls (PCBs) in soils and sediments remains a particularly difficult problem to solve. The possibility of in situ degradation by microorganisms has been pursued for many years since this approach has the potential to provide a cost-effective and environmentally sustainable altern...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2012.10.004

    authors: Sowers KR,May HD

    更新日期:2013-06-01 00:00:00

  • Flux modeling for monolignol biosynthesis.

    abstract::The pathway of monolignol biosynthesis involves many components interacting in a metabolic grid to regulate the supply and ratios of monolignols for lignification. The complexity of the pathway challenges any intuitive prediction of the output without mathematical modeling. Several models have been presented to quanti...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2018.12.003

    authors: Wang JP,Matthews ML,Naik PP,Williams CM,Ducoste JJ,Sederoff RR,Chiang VL

    更新日期:2019-04-01 00:00:00

  • Nano-spectroscopic imaging of proteins with near-field scanning optical microscopy (NSOM).

    abstract::Understanding the hierarchical structure of proteins at their fundamental length scales is essential to get insights into their functions and roles in fundamental biological processes. Near-field scanning optical microscopy (NSOM), which overcomes the diffraction limits of conventional optics, provides a powerful anal...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2018.01.022

    authors: Yong YC,Wang YZ,Zhong JJ

    更新日期:2018-12-01 00:00:00

  • Current strategies for cell delivery in cartilage and bone regeneration.

    abstract::Several cell-based tissue-engineering therapies are emerging to regenerate damaged tissues. These strategies use autologous cells in combination with bioresorbable delivery materials. Major functions of a delivery scaffold are to provide initial mechanical stability, homogenous three-dimensional cell distribution, imp...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2004.08.010

    authors: Sittinger M,Hutmacher DW,Risbud MV

    更新日期:2004-10-01 00:00:00

  • Plastid biotechnology: prospects for herbicide and insect resistance, metabolic engineering and molecular farming.

    abstract::Transgene expression from the chloroplast (plastid) genome offers several attractions to plant biotechnologists, including high-level accumulation of foreign proteins, transgene stacking in operons and a lack of epigenetic interference with the stability of transgene expression. In addition, the technology provides an...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2006.12.001

    authors: Bock R

    更新日期:2007-04-01 00:00:00

  • Patient-derived xenografts (PDXs) as model systems for human cancer.

    abstract::Patient-derived xenografts (PDXs) are obtained by transplanting fragments of a patient's tumour into immunodeficient mice. Growth and propagation of PDXs allows correlating therapeutic response in vivo with extensive, multi-dimensional molecular annotation, leading to identification of predictive biomarkers. PDXs are ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2020.01.003

    authors: Invrea F,Rovito R,Torchiaro E,Petti C,Isella C,Medico E

    更新日期:2020-06-01 00:00:00

  • Novel perspectives for the engineering of abiotic stress tolerance in plants.

    abstract::Adverse environmental conditions pose serious limitations to agricultural production. Classical biotechnological approaches towards increasing abiotic stress tolerance focus on boosting plant endogenous defence mechanisms. However, overexpression of regulatory elements or effectors is usually accompanied by growth han...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2013.09.011

    authors: Cabello JV,Lodeyro AF,Zurbriggen MD

    更新日期:2014-04-01 00:00:00

  • Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli.

    abstract::Heterologous production of polyketide compounds, an important class of natural products with complex chemical structures, was first demonstrated with Streptomyces parvulus in 1984. Although Streptomyces strains are good first options for heterologous polyketide biosynthesis, their slow growth kinetics prompt other hos...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2011.12.029

    authors: Yuzawa S,Kim W,Katz L,Keasling JD

    更新日期:2012-10-01 00:00:00

  • Bacterial virulence as a target for antimicrobial chemotherapy.

    abstract::As bacterial resistance to currently used antibiotics increases, so too must efforts to identify novel agents and strategies for the prevention and treatment of bacterial infection. In the past, antimicrobial drug discovery efforts have focused on eradicating infection by either cidal or static agents, resulting in cl...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0958-1669(00)00155-5

    authors: Alksne LE,Projan SJ

    更新日期:2000-12-01 00:00:00

  • Computational methods for evaluation of cell-based data assessment--Bioconductor.

    abstract::Recent advances in miniaturization and automation of technologies have enabled cell-based assay high-throughput screening, bringing along new challenges in data analysis. Automation, standardization, reproducibility have become requirements for qualitative research. The Bioconductor community has worked in that direct...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2012.09.003

    authors: Le Meur N

    更新日期:2013-02-01 00:00:00

  • Towards synthetic microbial consortia for bioprocessing.

    abstract::The use of microbial consortia for bioprocessing has been limited by our ability to reliably control community composition and function simultaneously. Recent advances in synthetic biology have enabled population-level coordination and control of ecosystem stability and dynamics. Further, new experimental and computat...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2012.02.001

    authors: Shong J,Jimenez Diaz MR,Collins CH

    更新日期:2012-10-01 00:00:00

  • Microbial fuel cells: novel microbial physiologies and engineering approaches.

    abstract::The possibility of generating electricity with microbial fuel cells has been recognized for some time, but practical applications have been slow to develop. The recent development of a microbial fuel cell that can harvest electricity from the organic matter stored in marine sediments has demonstrated the feasibility o...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2006.04.006

    authors: Lovley DR

    更新日期:2006-06-01 00:00:00

  • New strategies to generate induced pluripotent stem cells.

    abstract::Direct reprogramming of somatic cells to a pluripotent state, substantiated only three years prior, is one of the most rapidly developing areas of stem cell research. The generation of patient-derived pluripotent cells applicable to disease modelling, drug screening, toxicology tests and, ultimately, autologous cell-b...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2009.09.005

    authors: O'Malley J,Woltjen K,Kaji K

    更新日期:2009-10-01 00:00:00

  • Single cell stable isotope probing in microbiology using Raman microspectroscopy.

    abstract::Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2016.04.018

    authors: Wang Y,Huang WE,Cui L,Wagner M

    更新日期:2016-10-01 00:00:00

  • Omics data input for metabolic modeling.

    abstract::Recent advancements in high-throughput large-scale analytical methods to sequence genomes of organisms, and to quantify gene expression, proteins, lipids and metabolites have changed the paradigm of metabolic modeling. The cost of data generation and analysis has decreased significantly, which has allowed exponential ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2015.10.010

    authors: Rai A,Saito K

    更新日期:2016-02-01 00:00:00

  • Engineered minichromosomes in plants.

    abstract::Genetic engineering for complex or combined traits requires the simultaneous expression of multiple genes, and has been considered as the bottleneck for the next generation of genetic engineering in plants. Minichromosome technology provides one solution to the stable expression and maintenance of multiple transgenes ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2007.09.005

    authors: Yu W,Han F,Birchler JA

    更新日期:2007-10-01 00:00:00

  • Plant secretory structures: more than just reaction bags.

    abstract::Plants have a remarkable capacity for the production of a wide range of metabolites. Much has been reported and reviewed on the diversity of these metabolites and how it is achieved, for example through the evolution of enzyme families. In comparison, relatively little is known on the extraordinary metabolic productiv...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2017.08.003

    authors: Tissier A

    更新日期:2018-02-01 00:00:00

  • Engineering nanoreactors using bacterial microcompartment architectures.

    abstract::Bacterial microcompartments (BMCs) are organelles that encapsulate enzymes involved in CO2 fixation or carbon catabolism in a selectively permeable protein shell. Here, we highlight recent advances in the bioengineering of these protein-based nanoreactors in heterologous systems, including transfer and expression of B...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2017.09.005

    authors: Plegaria JS,Kerfeld CA

    更新日期:2018-06-01 00:00:00

  • Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

    abstract::The recent technological advances in next generation sequencing have brought the field closer to the goal of reconstructing all genomes within a community by presenting high throughput sequencing at much lower costs. While these next-generation sequencing technologies have allowed a massive increase in available raw s...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2011.11.013

    authors: Scholz MB,Lo CC,Chain PS

    更新日期:2012-02-01 00:00:00

  • Engineering yeast for utilization of alternative feedstocks.

    abstract::Realizing the economic benefits of alternative substrates for commodity chemical bioproduction typically requires significant metabolic engineering of common model organisms, such as Saccharomyces cerevisiae. A growing toolkit is enabling engineering of non-conventional yeast that have robust native metabolism for xyl...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2017.12.003

    authors: Yaguchi A,Spagnuolo M,Blenner M

    更新日期:2018-10-01 00:00:00

  • Bacteriophage ecology in environmental biotechnology processes.

    abstract::Heterotrophic bacteria are an integral part of any environmental biotechnology process (EBP). Therefore, factors controlling bacterial abundance, activity, and community composition are central to the understanding of such processes. Among these factors, top-down control by bacteriophage predation has so far received ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2011.01.012

    authors: Shapiro OH,Kushmaro A

    更新日期:2011-06-01 00:00:00

  • Microfluidic platforms for the dynamic characterisation of synthetic circuitry.

    abstract::Generating novel functionality from well characterised synthetic parts and modules lies at the heart of synthetic biology. Ideally, circuitry is rationally designed in silico with quantitatively predictive models to predetermined design specifications. Synthetic circuits are intrinsically stochastic, often dynamically...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.copbio.2020.02.002

    authors: Prangemeier T,Lehr FX,Schoeman RM,Koeppl H

    更新日期:2020-06-01 00:00:00