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)

Production of exopolysaccharides (EPS) is one of the unique features of Lactobacillus genus. EPS not only have many physiological roles such as in stress tolerance, quorum sensing and biofilm formation, but also have numerous applications in the food and pharmaceutical industries. In this study, we identified and compared EPS biosynthesis gene clusters in 106 sequenced Lactobacillus genomes representing 27 species. Of the 146 identified clusters, only 41 showed the typical generic organization of genes as reported earlier. Hierarchical clustering showed highly varied nature of the clusters in terms of the gene composition; nonetheless, habitat-wise grouping was observed for the gene clusters from host-adapted and nomadic strains. Of the core genes required for EPS biosynthesis, epsA, B, C, D and E showed higher conservation, whereas gt, wzx and wzy showed high variability in terms of the number and composition of the protein families. Analysis of the distribution pattern of the protein families indicated a higher proportion of mutually exclusive families in clusters from host-adapted and nomadic strains, whereas those from the free-living group had very few unique families. Taken together, this analysis highlights high variability in the EPS gene clusters amongst Lactobacillus with some of their properties correlated to the habitats.

https://www.mdpi.com/2076-2607/7/10/444/pdf

A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes.

We present the newest version of CoryneRegNet, the reference database for corynebacterial regulatory interactions, available at www.exbio.wzw.tum.de/coryneregnet/
 . The exponential growth of next-generation sequencing data in recent years has allowed a better understanding of bacterial molecular mechanisms. Transcriptional regulation is one of the most important mechanisms for bacterial adaptation and survival. These mechanisms may be understood via an organism’s network of regulatory interactions. Although the Corynebacterium genus is important in medical, veterinary and biotechnological research, little is known concerning the transcriptional regulation of these bacteria. Here, we unravel transcriptional regulatory networks (TRNs) for 224 corynebacterial strains by utilizing genome-scale transfer of TRNs from four model organisms and assigning statistical significance values to all predicted regulations. As a result, the number of corynebacterial strains with TRNs increased twenty times and the back-end and front-end were reimplemented to support new features as well as future database growth. CoryneRegNet 7 is the largest TRN database for the Corynebacterium genus and aids in elucidating transcriptional mechanisms enabling adaptation, survival and infection.

CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks.

Corynebacterium diphtheriae is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic C. diphtheriae infections. Here, a C. diphtheriae strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of C. diphtheriae revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24% to 95.39%) with the C. diphtheriae NCTC 11397T reference genome than all other C. diphtheriae genomes (>98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new C. diphtheriae subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: C. diphtheriae subsp. lausannense subsp. nov. (instead of lineage-2), regrouping strains CHUV2995, CCUG 5865 and CMCNS703, and C. diphtheriae subsp. diphtheriae subsp. nov, regrouping all other C. diphtheriae in the dataset (instead of lineage-1). Interestingly, members of subspecies lausannense displayed a larger genome size than subspecies diphtheriae and were enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, they lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, the CHUV2995 genome is particularly enriched in mobility genes and harbours several prophages. The genome encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks csn2 or cas4, which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer.

/pdf/distinct-genomic-features-characterize-two-clades-of-41ki763404.pdf

Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov.

Actinobacteria constitute one of the largest phyla in the bacterial domain, with many species known for their large genome sizes and high G + C content. Members of this phylum exhibit a wide range of morphological, physiological, and metabolic properties and are ubiquitously distributed in diverse ecological niches. The phylum includes pathogens, symbionts of plants and invertebrates, gastrointestinal commensals, and free-living bacteria. Many species are well known for their ability to produce a plethora of natural products relevant to agriculture, biotechnology, and medicine, including majority of naturally derived antibiotics widely used in clinics. In this chapter, we discuss recent advances that highlight the role of horizontal gene transfer (HGT) in the evolutionary history, genomic structure, and ecological diversity of Actinobacteria, with emphasis on HGT between species and between phyla. We highlight genome studies that describe how HGT has contributed to the success of promiscuous antibiotic producers as well as the pathogens that they target. We conclude with how methods in population genomics can be used to elucidate the impacts of selective pressures and environmental changes on rates and patterns of HGT in various Actinobacteria species and populations.

Horizontal Gene Transfer and Genome Evolution in the Phylum Actinobacteria

Corynebacterium pseudotuberculosis is a Gram-positive, pleomorphic, facultative intracellular pathogen that causes Oedematous Skin Disease (OSD) in buffalo. To better understand the pathogenic mechanisms of OSD, we performed a comparative genomic analysis of 11 strains of C. pseudotuberculosis isolated from different buffalo found to be infected in Egypt during an outbreak that occurred in 2008. Sixteen previously described pathogenicity islands (PiCp) were present in all of the new buffalo strains, but one of them, PiCp12, had an insertion that contained both a corynephage and a diphtheria toxin gene, both of which may play a role in the adaptation of C. pseudotuberculosis to this new host. Synteny analysis showed variations in the site of insertion of the corynephage during the same outbreak. A gene functional comparison showed the presence of a nitrate reductase operon that included genes involved in molybdenum cofactor biosynthesis, which is necessary for a positive nitrate reductase phenotype and is a possible adaptation for intracellular survival. Genomes from the buffalo strains also had fusions in minor pilin genes in the spaA and spaD gene cluster (spaCX and spaYEF), which could suggest either an adaptation to this particular host, or mutation events in the immediate ancestor before this particular epidemic. A phylogenomic analysis confirmed a clear separation between the Ovis and Equi biovars, but also showed what appears to be a clustering by host species within the Equi strains.

/pdf/comparative-genomic-analysis-between-corynebacterium-1p3ep4ob3y.pdf

Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo.

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Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo.