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.

Three acidophilic actinobacteria, isolates LSCA2, FGG8 and HSCA14T, recovered from spruce litter were examined using a polyphasic approach. Chemotaxonomic and morphological properties of the isolates were found to be consistent with their classification in the genus Streptacidiphilus. The isolates were shown to have identical 16S rRNA gene sequences and were most closely related to Streptacidiphilus neutrinimicus DSM 41755T (99.9 % similarity). However, DNA:DNA relatedness between isolate HSCA14T and the type strain of S. neutrinimicus was found to be low at 44.0 (±14.1) %. A combination of phenotypic features, including degradative and nutritional characteristics were shown to distinguish the isolates from their nearest phylogenetic neighbours. Data from this study show that the isolates form a novel species in the genus for which the name S. hamsterleyensis sp. nov. is proposed. The type strain is HSCA 14T (=DSM 45900T = KACC 17456T = NCIMB 14865T).

/pdf/streptacidiphilus-hamsterleyensis-sp-nov-isolated-from-a-u5b5l86nfi.pdf

Streptacidiphilus hamsterleyensis sp. nov., isolated from a spruce forest soil

Differentiation of nocardioform actinomycetes by lysozyme sensitivity.

One hundred and seventeen streptosporangia from soil were compared with marker strains of the familyStreptosporangiaceae for many phenotypic properties The data were examined using the Jaccard, pattern and simple matching coefficients with clustering achieved using average, complete and single linkage algorithms Particular confidence was placed in the product of the pattern, average linkage analysis given the sharp definition of aggregate groups and clusters and a combination of low test error and high cophenetic correlation values The test strains were assigned to five aggregate groups that were equated with the generaStreptosporangium (group A),Microbispora (group B),Planobispora andPlanomonospora (Group C),Kutzneria (neeStreptosporangium viridogriseum (group D), andMicrotetraspora (group E) The streptosporangia, both isolates and marker strains, were assigned to 5 major, 7 minor and 18 single membered clusters Representative streptosporangia examined for chemical markers were characterised by the presence ofmeso-diaminopimelic acid in whole-organism hydrolysates, complex mixtures of straight- and branched chain fatty acids, di- and tetrahydrogenated menaquinones as predominant isoprenologues, and complex polar lipid patterns containing diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and uncharacterised components The chemical and numerical data support the taxonomic integrity of the validly described species ofStreptosporangium and suggest that the genus is markedly underspeciated

Numerical and chemical classification of Streptosporangium and some related actinomycetes.

Two acidophilic actinobacteria, isolates NA14 and NF37T, were the subject of a polyphasic taxonomic study. Chemotaxonomic and morphological properties of the isolates were characteristic of the genus Streptacidiphilus. The isolates were shown to have identical 16S rRNA gene sequences and to be closely related to Streptacidiphilus neutrinimicus DSM 41755T (>99.9 %). However, DNA:DNA relatedness between isolate NF37T and the type strain of S. neutrinimicus was found to be low at 11.1 (±3.5) %. A broad range of phenotypic features were shown to distinguish the isolates from their close phylogenetic neighbours. These data shown that the isolates form a novel species of Streptacidiphilus for which the name Streptacidiphilus toruniensis sp. nov. is proposed. The type strain is NF37T (= DSM 102291T = NCIMB 15025T).

/pdf/streptacidiphilus-toruniensis-sp-nov-isolated-from-a-pine-22wyh94tpq.pdf

Streptacidiphilus toruniensis sp. nov., isolated from a pine forest soil.

A polyphasic study was undertaken to establish the taxonomic position of a non-chromogenic, rapidly growing 
Mycobacterium
strain that had been isolated from sputum. The strain, CECT 8775T, has chemotaxonomic and cultural properties consistent with its classification in the genus 
Mycobacterium
and was distinguished from the type strains of closely related mycobacterial species, notably from 
Mycobacterium paraense
DSM 46749T, its nearest phylogenetic neighbour, based on 16S rRNA, hsp65 and rpoB gene sequence data. These organisms were also distinguished by a broad range of chemotaxonomic and phenotypic features and by a digital DNA–DNA relatedness value of 22.8 %. Consequently, the strain is considered to represent a novel species of 
Mycobacterium
for which the name Mycobacterium eburneum sp. nov is proposed; the type strain is X82T (CECT 8775T=DSM 44358T).

Michael Goodfellow

Papers

Streptacidiphilus hamsterleyensis sp. nov., isolated from a spruce forest soil

Differentiation of nocardioform actinomycetes by lysozyme sensitivity.

Numerical and chemical classification of Streptosporangium and some related actinomycetes.

Streptacidiphilus toruniensis sp. nov., isolated from a pine forest soil.

Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum.