The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The demand for fossil derivate fuels and chemicals has increased, augmenting concerns on climate change, global economic stability, and sustainability on fossil resources. Therefore, the production of fuels and chemicals from alternative and renewable resources has attracted considerable and growing attention. Ethanol is a promising biofuel that can reduce the consumption of gasoline in the transportation sector and related greenhouse gas (GHG) emissions. Lignocellulosic biomass is a promising feedstock to produce bioethanol (cellulosic ethanol) because of its abundance and low cost. Since the conversion of lignocellulose to ethanol is complex and expensive, the cellulosic ethanol price cannot compete with those of the fossil derivate fuels. A promising strategy to lower the production cost of cellulosic ethanol is developing a biorefinery which produces ethanol and other high-value chemicals from lignocellulose. The selection of such chemicals is difficult because there are hundreds of products that can be produced from lignocellulose. Multiple reviews and reports have described a small group of lignocellulose derivate compounds that have the potential to be commercialized. Some of these products are in the bench scale and require extensive research and time before they can be industrially produced. This review examines chemicals and materials with a Technology Readiness Level (TRL) of at least 8, which have reached a commercial scale and could be shortly or immediately integrated into a cellulosic ethanol process.

/pdf/a-review-on-commercial-scale-high-value-products-that-can-be-22ttee469w.pdf

A review on commercial-scale high-value products that can be produced alongside cellulosic ethanol.

Anaerobic bacterial gas fermentation gains broad interest in various scientific, social, and industrial fields. This microbial process is carried out by a specific group of bacterial strains called acetogens. All these strains employ the Wood–Ljungdahl pathway but they belong to different taxonomic groups. Here we provide an overview of the metabolism of acetogens and naturally occurring products. Characteristics of 61 strains were summarized and selected acetogens described in detail. Acetobacterium woodii, Clostridium ljungdahlii, and Moorella thermoacetica serve as model organisms. Results of approaches such as genome-scale modeling, proteomics, and transcriptomics are discussed. Metabolic engineering of acetogens can be used to expand the product portfolio to platform chemicals and to study different aspects of cell physiology. Moreover, the fermentation of gases requires specific reactor configurations and the development of the respective technology, which can be used for an industrial application. Even though the overall process will have a positive effect on climate, since waste and greenhouse gases could be converted into commodity chemicals, some legislative barriers exist, which hamper successful exploitation of this technology.

Bacterial Anaerobic Synthesis Gas (Syngas) and CO2+H2 Fermentation.

Gas fermentation is a microbial process that contributes to at least four of the sustainable development goals (SDGs) of the United Nations. The process converts waste and greenhouse gases into commodity chemicals and fuels. Thus, world's climate is positively affected. Briefly, we describe the background of the process, some biocatalytic strains, and legal implications.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.12763

Gas fermentation for commodity chemicals and fuels.

Sustainable production of biofuels has provided an attractive alternative to fossil fuels, which has relieved the concern regarding energy supply and global climate change. Currently, interest in metabolic engineering of yeasts as microbial cell factories for biofuel production, which varies from short-chain ethanol to long-chain fatty acid-derived molecules, is growing. The commercial production of new energy-dense biofuels using yeasts and new synthetic biology tools is now possible due to recent developments in metabolic engineering. Here, it is attempted to comprehensively and critically review the latest advances in metabolism-targeted strategies and the production of different types of biofuels using yeasts. Furthermore, the key challenges and perspectives have been discussed for improving yeast biorefineries for the production of biofuels, such as host compatibility of heterologous genes, substrate extension for alternative feedstocks, better tools for reprogramming cell metabolism, host robustness for tolerating or alleviating toxicity induced by end products, and new design principles with predictable behaviors for the constructed biological systems.

Yeasts as microbial cell factories for sustainable production of biofuels

The genus Clostridium consists of a diverse group of pathogenic and non-pathogenic bacteria The non-pathogenic clostridia contain several solventogenic members of industrial importance, such as Clostridium acetobutylicum or C beijerinckii In the process of acetone-butanol-ethanol (ABE) fermentation, these strains are used in large scale fermentation plants since almost 100 years Soon after establishment of the first plants, the fermentation processes suffered from different bacteriophage infections worldwide A limited set of studies addressing bacteriophages in solventogenic clostridia have been conducted since then In this study, we present the genome sequence of the temperate bacteriophage TBP2 of the solventogenic strain C saccharoperbutylacetonicum N1-4 (HMT) that is used for ABE fermentation The phage genome consists of 38 039 bp and includes 48 open reading frames Sequence analysis indicates that the genome encloses random parts of the bacterial genome in addition to its own DNA It represents the first fully sequenced genome of a temperate bacteriophage infecting solventogenic clostridia

Benjamin A. Stegmann

Papers

Genome sequence analysis of the temperate bacteriophage TBP2 of the solvent producer Clostridium saccharoperbutylacetonicum N1-4 (HMT, ATCC 27021).

Host Organisms: Clostridium acetobutylicum/Clostridium beijerinckii and Related Organisms