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.

Isolation and purification of nucleic acids DNA reassociation experiments DNA-rRNA hybridization and methods DNA sequencing in bacterial systematics direct sequence analysis of small RNAs 16S/23S rRNA sequencing the polymerase chain reaction development and application of nucleic acid probes DNA fingerprinting from macromolecules to trees.

Nucleic acid techniques in bacterial systematics

An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids

Menaquinones were the only isoprenoid quinones found in 48 corynebacteria and actinomycete strains examined. Dihydromenaquinones having nine isoprene units were the main components isolated from Gordona, Mycobacterium, Corynebacterium bovis, Corynebacterium glutamicum and a strain labelled Nocardia farcinica, but dihydromenaquinones having eight isoprene units were characteristic of other Corynebacterium species and representatives of the 'rhodochrous' complex. Tetrahydromenaquinones having six and eight isoprene units were found in Nocardia strains and in a single strain of Micropolyspora brevicatena, which also contained mycolic acids similar in chain length to those of Nocardia. Menaquinones having nine isoprene units with from one to five double bonds hydrogenated were the main components in Actinomadura madurae, Actinomadura pelletieri, Micropolyspora faeni, Oerskovia turbata and Streptomyces strains. Actinomadura dassonvillei strains had a characteristic pattern of di-, tetra- and hexahydromenaquinones with 10 isoprene units which was slightly different from the pattern in mixtures of similar quinones from Actinomyces israelii and Actinomyces viscosus.

Distribution of Menaquinones in Actinomycetes and Corynebacteria

Four hundred and seventy-five strains, which included 394 type cultures of Streptomyces and representatives of 14 other actinomycete genera, were studied. Overall similarities of these strains for 139 unit characters were determined by the SSM and SJ coefficients and clustering by the UPGMA algorithm. Test error and overlap between the phena defined were within acceptable limits. Cluster-groups were defined by the SSM coefficient at the 70.1% similarity (S) level and by the SJ coefficient at the 50% S-level. Clusters were distinguished at the 77.5% SSM and 63% SJ S-levels. Groupings obtained with the two coefficients were generally similar, but there were some changes in the definition and membership of cluster-groups and clusters. The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while Intrasporangium, Nocardioides and Streptoverticillium remained as distinct genera in the family Streptomycetaceae. Nocardiopsis dassonvillei also showed strong phenetic affinity to Streptomyces, despite its chemotaxonomic differences. Actinomadura sensu stricto was phenetically distinguishable from Streptomyces and 'Nocardia' mediterranea was recognized as a taxon distinct from both these genera and from Nocardia sensu stricto. Most of the Streptomyces type cultures fell into one large cluster-group. At the 77.5% SSM S-level, they were recovered in 19 major and 40 minor clusters, with 18 strains recovered as single member clusters. The status of the latter as species was therefore confirmed. Most of the minor clusters, consisting of two to five strains, can also be regarded as species. The major clusters varied in size (from 6 to 71 strains) and in there homogeneity. Therefore, it is suggested that they be regarded as species-groups until further information is available. The results provide a basis for the reduction of the large number of Streptomyces species which have been described. They also demonstrate that the previous use of a limited number of subjectively chosen characters to define species-groups or species has resulted in artificial classifications.

Numerical Classification of Streptomyces and Related Genera

Les actinomycetes sont tres largement distribues dans les ecosystemes terrestres et les ecosystemes aquatiques. Ils incluent aussi des zoopathogenes et des phytopathogenes

Michael Goodfellow

Papers

Nucleic acid techniques in bacterial systematics

An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids

Distribution of Menaquinones in Actinomycetes and Corynebacteria

Numerical Classification of Streptomyces and Related Genera

Ecology of actinomycetes