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)

Lignocellulosic crop residue composting by cellulolytic nitrogen-fixing bacteria: A novel tool for environmental sustainability

Endproduct toxicity is a key bottleneck for biofuel/biochemical production. Biosynthesis of high-value derivatives that can easily separate would alleviate such toxicity and thus enhance bioproduction efficiency. As a proof of principle, biosynthesis (along with in-line extractive recovery) of fatty acid esters using clostridia was investigated in this study. We hypothesize that solventogenic clostridia are excellent platforms for ester production, because they co-produce acyl-CoAs (acetyl-CoA and butyryl-CoA), acids (acetate and butyrate), and alcohols (ethanol and butanol). Through rational screening for host strains and genes (encoding alcohol acyl transferases and lipase), systematic metabolic engineering, and elimination of putative prophages, we obtained strains that can produce 20.3 g/L butyl acetate and 1.6 g/L butyl butyrate respectively, which were both historically highest levels in microbial hosts. Our principle for engineering microorganisms to produce high-value and easy-recoverable endproducts is highly applicable to other bioprocesses, and could lead to breakthroughs in biofuel/biochemical production and general bioeconomy.

/pdf/renewable-fatty-acid-ester-production-in-clostridium-4n41vkfac8.pdf

Renewable Fatty Acid Ester Production in Clostridium

Bioproduction of renewable chemicals is considered as an urgent solution for fossil energy crisis. However, despite tremendous efforts, it is still challenging to generate microbial strains that can produce target biochemical to high levels. Here, we report an example of biosynthesis of high-value and easy-recoverable derivatives built upon natural microbial pathways, leading to improvement in bioproduction efficiency. By leveraging pathways in solventogenic clostridia for co-producing acyl-CoAs, acids and alcohols as precursors, through rational screening for host strains and enzymes, systematic metabolic engineering-including elimination of putative prophages, we develop strains that can produce 20.3 g/L butyl acetate and 1.6 g/L butyl butyrate. Techno-economic analysis results suggest the economic competitiveness of our developed bioprocess. Our principles of selecting the most appropriate host for specific bioproduction and engineering microbial chassis to produce high-value and easy-separable end products may be applicable to other bioprocesses. Esters can be used as fuels and specialty chemicals for food flavoring, cosmetic and pharmaceutical industries. Here, the authors systematically engineer clostridia, including discovery and deletion of prophages to increase strain stability, for the production of butyl acetate and butyl butyrate from corn stover at low cost.

/pdf/renewable-fatty-acid-ester-production-in-clostridium-1zmiq66ejf.pdf

Renewable fatty acid ester production in Clostridium.

Abstract Phages are regarded as powerful antagonists of bacteria, especially in industrial fermentation processes involving bacteria. While bacteria have developed various defense mechanisms, most of which are effective against a narrow range of phages and consequently exert limited protection from phage infection. Here, we report a strategy for developing phage-resistant Escherichia coli strains through the simultaneous genomic integration of a DNA phosphorothioation-based Ssp defense module and mutations of components essential for the phage life cycle. The engineered E. coli strains show strong resistance against diverse phages tested without affecting cell growth. Additionally, the resultant engineered phage-resistant strains maintain the capabilities of producing example recombinant proteins, D-amino acid oxidase and coronavirus-encoded nonstructural protein nsp8, even under high levels of phage cocktail challenge. The strategy reported here will be useful for developing engineered E. coli strains with improved phage resistance for various industrial fermentation processes for producing recombinant proteins and chemicals of interest. 

/pdf/systematic-strategies-for-developing-phage-resistant-2bxydpyy.pdf

Systematic strategies for developing phage resistant Escherichia coli strains

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

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

Clostridium hungatei is an obligate anaerobic and spore-forming bacterium, which was isolated from soil It ferments carbohydrates, such as cellulose or d-glucose C hungatei is able to fix nitrogen The draft genome consists of 1 chromosome (4902 Mb) with 4,246 predicted protein-coding genes

https://journals.asm.org/doi/pdf/10.1128/genomeA.00363-17

Miriam A Schüler

Papers

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

First Insights into the Genome Sequence of the Cellulolytic Bacterium Clostridium hungatei DSM 14427.