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.

A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.

/pdf/new-genus-specific-primers-for-pcr-identification-of-4m2m7d6i1w.pdf

New genus-specific primers for PCR identification of Rubrobacter strains

A novel sulphate-reducing, Gram-stain-negative, anaerobic strain, isolate XJ01T, recovered from production fluid at the LiaoHe oilfield, PR China, was the subject of a polyphasic study. The isolate together with Desulfovibrio oxamicus NCIMB 9442T and Desulfovibrio termitidis DSM 5308T formed a distinct, well-supported clade in the Desulfovibrionaceae 16S rRNA gene tree. The taxonomic status of the clade was underscored by complementary phenotypic data. The three isolates comprising the clade formed distinct phyletic branches and were distinguished using a combination of physiological features and by low average nucleotide identity and digital DNA-DNA hybridization values. Consequently, it is proposed that isolate XJ01T represents a novel genus and species for which the name Cupidesulfovibrio liaohensis gen. nov., sp. nov. is proposed with the type strain XJ01T (=CGMCC 1.5227T=DSM 107637T). It is also proposed that D. oxamicus and D. termitidis be reclassified as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov., respectively.

Cupidesulfovibrio liaohensis gen. nov., sp. nov., a novel sulphate-reducing bacterium isolated from an oil reservoir and reclassification of Desulfovibrio oxamicus and Desulfovibrio termitidis as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov.

Summary The antigenicity and cross-reactivity of glycolipids from strains of bovine fancy and the Mycobacterium chelonae-M. fortuitum complex were analyzed using the ELISA technique. Purified alkali-stable glycopeptidolipids (GPLs) with a characteristic dimethylrhamnosyl sugar unit extracted from M. abscessus, M. chelonae, M. peregrinum and M. senegalense, gave very strong reactions with sera against members of the same four species. Particularly strong cross-reactions were evident between M. peregrinum and M. senegalense. These GPLs reacted more weakly with antisera against the other mycobacteria tested, though clear reactions were noticed with M. farcinogenes and M. fortuitum and also with M. bovis BCG, M. phlei, and M. tuberculosis strains. Alkali-labile diacyl trehalose (DAT) and triacyl trehalose (TAT) from M. fortuitum reacted with homologous sera, and with that against M. tuberculosis. Traces of uncharacterized acyl trehaloses isolated from two strains of M. farcinogenes gave comparatively weak reactions. Mycobacteria labeled M. farcinogenes and M. senegalense produced glucosylated trehalose-based glycolipids (GTs) and the studies showed that the major type was antigenic. These glycolipids cross-reacted strongly with M. senegalense NCTC 4524 but not with the type strain of M. senegalense. On the basis of the chemical patterns and the antigenicity of the GPLs it is evident that M. peregrinum and M. senegalense are particularly closely related and these species show a very close affinity to M. abscessus -M. chelonae.

Serotaxonomic analysis of glycolipids from Mycobacterium chelonae-M. fortuitum complex and bovine farcy strains.

Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics.
This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries.

New Approaches to Prokaryotic Systematics

The ?golden age? of antibiotic therapy is threatened by new, existing, emerging and re-emerging pathogens. Since the first penicillin-resistant Staphylococcus aureus was noted in 1951, a half-century of successful anti-infective therapy has been built on the discovery of new antibiotics and their second, third and fourth generation derivatives.

Michael Goodfellow

Papers

New genus-specific primers for PCR identification of Rubrobacter strains

Cupidesulfovibrio liaohensis gen. nov., sp. nov., a novel sulphate-reducing bacterium isolated from an oil reservoir and reclassification of Desulfovibrio oxamicus and Desulfovibrio termitidis as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov.

Serotaxonomic analysis of glycolipids from Mycobacterium chelonae-M. fortuitum complex and bovine farcy strains.

New Approaches to Prokaryotic Systematics

Taxonomy as a roadmap for search and discovery