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)

Technology development for the production of biobased products from biorefinery carbohydrates—the US Department of Energy’s “Top 10” revisited

http://www.umassmed.edu/globalassets/immunology-and-microbiology/documents/papers-for-bbs821-2015/nov-24-reviewfor-general-info.pdf

Role of the Microbiota in Immunity and Inflammation

Liposomes, sphere-shaped vesicles consisting of one or more phospholipid bilayers, were first described in the mid-60s. Today, they are a very useful reproduction, reagent, and tool in various scientific disciplines, including mathematics and theoretical physics, biophysics, chemistry, colloid science, biochemistry, and biology. Since then, liposomes have made their way to the market. Among several talented new drug delivery systems, liposomes characterize an advanced technology to deliver active molecules to the site of action, and at present, several formulations are in clinical use. Research on liposome technology has progressed from conventional vesicles to ‘second-generation liposomes’, in which long-circulating liposomes are obtained by modulating the lipid composition, size, and charge of the vesicle. Liposomes with modified surfaces have also been developed using several molecules, such as glycolipids or sialic acid. This paper summarizes exclusively scalable techniques and focuses on strengths, respectively, limitations in respect to industrial applicability and regulatory requirements concerning liposomal drug formulations based on FDA and EMEA documents.

/pdf/liposome-classification-preparation-and-applications-48dnv7t3nr.pdf

Liposome: classification, preparation, and applications

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life.

A simple model is proposed to estimate freezing times of foodstuffs of simple shapes (infinite flat slabs, infinite cylinders and spheres). This model combines Plank's equation for the phase change period with unsteady state heat transfer solutions for the cooling periods before and after phase change. The total freezing time is obtained by the determination and the summation of the pre-cooling, phase change and tempering times. The results produced are at least as accurate as, or better than, any of the previous methods, including regression formulae and finite difference computations. All calculations are easily programmable on scientific calculators such as HP 41 C, allowing simple, fast and accurate prediction of freezing times of foodstuffs.

Simple Method for Freezing Time Calculations for Infinite Flat Slabs, Infinite Cylinders and Spheres

Development of a reversible binding process for in situ removal of 3-hydroxypropionaldehyde during biotechnological conversion of glycerol

Bifidobacterium infantis immobilized in κ-carrageenan - locust bean gum gel beads (1.0–2.0 mm diameter) was used to ferment. 10% reconstituted skim milk supplemented with 1% yeast extract in a continuous stirred tank reactor. Cell release rate from the gel beads into the milk and growth of free cells in the bioreactor allowed for a steady inoculation of the feed, with cell counts in the outflow varying from 1.0 to 2.2 × 109 CFU/mL for dilution rates in the range 0,5 to 1,0 h-1. High mechanical stability of the gel beads was observed in milk.

Continuous fermentation of a supplemented milk with immobilized Bifidobacterium infantis

Streptococcus infantarius subsp. infantarius, a member of the Streptococcus bovis/Streptococcus equinus complex, is highly prevalent in artisanal dairy fermentations in Africa. Here the complete genome sequence of the dairy-adapted S. infantarius subsp. infantarius CJ18 strain—a strain predominant in traditionally fermented camel milk (suusac) from Kenya—is presented.

https://journals.asm.org/doi/pdf/10.1128/JB.00160-12

Complete Genome Sequence of the African Dairy Isolate Streptococcus infantarius subsp. infantarius Strain CJ18

Culture-independent methods based on the 16S ribosomal RNA molecule are nowadays widely used for assessment of the composition of the intestinal microbiota, in relation to host health or probiotic efficacy. Because Bifidobacterium thermophilum was only recently isolated from human faeces until now, no specific real-time PCR (qPCR) assay has been developed for detection of this species as component of the bifidobacterial community of the human intestinal flora. Design of specific primers and probe was achieved based on comparison of 108 published bifidobacterial 16S rDNA sequences with the recently published sequence of the human faecal isolate B. thermophilum RBL67. Specificity of the primer was tested in silico by similarity search against the sequence database and confirmed experimentally by PCR amplification on 17 Bifidobacterium strains, representing 12 different species, and two Lactobacillus strains. The qPCR assay developed was linear for B. thermophilum RBL67 DNA quantities ranging from 0.02 ng/μl to 200 ng/μl and showed a detection limit of 105 cells per gram faeces. The application of this new qPCR assay allowed to detect the presence of B. thermophilum in one sample from a 6-month old breast-fed baby among 17 human faecal samples tested. Additionally, the specific qPCR primers in combination with selective plating experiments led to the isolation of F9K9, a faecal isolate from a 4-month old breast-fed baby. The 16S rDNA sequence of this isolate is 99.93% similar to that of B. thermophilum RBL67 and confirmed the applicability of the new qPCR assay in faecal samples. A new B. thermophilum-specific qPCR assay was developed based on species-specific target nucleotides in the 16S rDNA. It can be used to further characterize the composition of the bifidobacterial community in the human gastrointestinal tract. Until recently, B. thermophilum was considered as a species of animal origin, but here we confirm with the application of this new PCR assay the presence of B. thermophilum strains in the human gut.

/pdf/pcr-and-real-time-pcr-primers-developed-for-detection-and-3urhacimlq.pdf

Christophe Lacroix

Papers

Simple Method for Freezing Time Calculations for Infinite Flat Slabs, Infinite Cylinders and Spheres

Development of a reversible binding process for in situ removal of 3-hydroxypropionaldehyde during biotechnological conversion of glycerol

Continuous fermentation of a supplemented milk with immobilized Bifidobacterium infantis

Complete Genome Sequence of the African Dairy Isolate Streptococcus infantarius subsp. infantarius Strain CJ18

PCR and real-time PCR primers developed for detection and identification of Bifidobacterium thermophilum in faeces.