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)

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese ob/ob mice, lean ob/+ and wild-type siblings, and their ob/+ mothers, all fed the same polysaccharide-rich diet. Although the majority of mouse gut species are unique, the mouse and human microbiota(s) are similar at the division (superkingdom) level, with Firmicutes and Bacteroidetes dominating. Microbial-community composition is inherited from mothers. However, compared with lean mice and regardless of kinship, ob/ob animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes. These changes, which are division-wide, indicate that, in this model, obesity affects the diversity of the gut microbiota and suggest that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals.

/pdf/obesity-alters-gut-microbial-ecology-31owgafp2h.pdf

Obesity alters gut microbial ecology

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

An artificial neural network was trained to distinguish between three putatively novel species of Streptomyces using normalised, scaled pyrolysis mass spectra from three representative strains of each of the taxa, each sampled in triplicate. Once trained, the artificial neural network was challenged with spectral data from the original organisms, the ‘training set’, from additional members of the putative novel taxa and from over a hundred strains representing six other actinomycete genera. All of the streptomycetes were correctly identified but many of the other actinomycetes were mis-identified. A modified network topology was developed to recognise the mass spectral patterns of the non-streptomycete strains. The resultant neural network correctly identified the streptomycetes, whereas all of the remaining actinomycetes were recognised as unknown organisms. The improved artificial neural network provides a rapid, reliable and cost-effective method of identifying members of the three target streptomycete taxa.

Rapid identification of streptomycetes by artificial neural network analysis of pyrolysis mass spectra

Curie-point pyrolysis mass spectrometry was used to evaluate the taxonomic integrity of three subclusters, provisionally labelled S. albidoflavus, S. anulatus and S. halstedii, which formed a species-group in an extensive numerical phenetic survey of the genus Streptomyces. Excellent agreement was found between the results of the triplicate analyses of each strain while the duplicated strains clustered adjacent to one another. Sequential principal component-canonical variates analysis of the experimental data collected on the 32 representative organisms showed that the S. albidoflavus strains formed a distinct group. This result taken together with earlier chemical, molecular and numerical taxonomic data indicates that the S. albidoflavus subcluster corresponds to a distinct species. In contrast, the subclusters equated with S. anulatus and S. halstedii were found to be heterogeneous and hence in need of further study. However, it is evident from the present investigation that Curie-point pyrolysis mass spectrometry provides a rapid and reproducible way of evaluating the taxonomic integrity of Streptomyces species-groups.

Evaluation of Streptomyces Species-Groups by Pyrolysis Mass Spectrometry

Strains of Listeria denitrificans (E2), Psendomonas fluorescens (C37 and C92), and Xanthomonas campestris (D119), isolated from the phylloplane of Lolium perenne (S24), were antagonistic to Drechsl...

Antagonistic interactions of phylloplane bacteria with Drechslera dictyoides (Drechslera) Shoemaker.

Diversity and geographical distribution of members of the Streptomyces violaceusniger 16S rRNA gene clade detected by clade‐specific PCR primers

The polar lipids of Actinomadura dassonvillei, Actinomadura madurae, and Actinomadura pelletieri were analysed by two-dimensional thin-layer chromatography. A. madurae and A. pelletieri had a simple pattern consisting essentially of diphosphatidylglycerol, phosphatidylinositol, and monoacyl phosphatidylinositol dimannoside, but A. dassonvillei strains contained diphosphatidylglycerol, phosphatidylglycerol, a lipid which co-chromatographed with phosphatidylcholine, and a chromatographically mobile unknown phospholipid. Two A. dassonvillei strains had substantial proportions of uncharacterised glycolipids and phosphoglycolipids. Low proportions of lipids co-chromatographing with, and having the same staining reactions as, phosphatidylethanolamine, phosphatidylinositol, and diacyl phosphatidylinositol dimannoside were detected in several strains of A. dassonvillei.

/pdf/polar-lipid-composition-in-the-classification-of-some-343nrfnp7a.pdf

Michael Goodfellow

Papers

Rapid identification of streptomycetes by artificial neural network analysis of pyrolysis mass spectra

Evaluation of Streptomyces Species-Groups by Pyrolysis Mass Spectrometry

Antagonistic interactions of phylloplane bacteria with Drechslera dictyoides (Drechslera) Shoemaker.

Diversity and geographical distribution of members of the Streptomyces violaceusniger 16S rRNA gene clade detected by clade‐specific PCR primers

Polar Lipid Composition in the Classification of Some Actinomadura Species