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.

Effects of strains and growth conditions on autolytic activity and survival to freezing and lyophilization of Lactobacillus delbrueckii ssp. lactis isolated from cheese

Characterization of Yeasts Associated with Camel Milk using Phenotypic and Molecular Identification Techniques

In-home fortification of infants with micronutrient powders (MNPs) containing 12.5 mg iron may increase morbidity from infections; therefore, an efficacious low-dose iron-containing MNP might be advantageous. Effects of iron-containing MNPs on infant growth are unclear. We assessed the efficacy of a low-iron MNP on iron status and growth and monitored safety in a randomised, controlled, double-blind 1-year trial in 6-month-old infants (n = 287) consuming daily a maize porridge fortified with either a MNP including 2.5 mg iron as NaFeEDTA (MNP + Fe) or the same MNP without iron (MNP - Fe). At baseline, after 6 and 12 months, we determined haemoglobin (Hb), iron status [serum ferritin (SF), soluble transferrin receptor (sTfR) and zinc protoporphyrin (ZPP)], inflammation [C-reactive protein (CRP)] and anthropometrics. We investigated safety using weekly morbidity questionnaires asking for diarrhoea, cough, flu, bloody or mucus-containing stool and dyspnoea, and recorded any other illness. Furthermore, feeding history and compliance were assessed weekly. At baseline, 71% of the infants were anaemic and 22% iron deficient; prevalence of inflammation was high (31% had an elevated CRP). Over the 1 year, Hb increased and SF decreased in both groups, without significant treatment effects of the iron fortification. At end point, the weight of infants consuming MNP + Fe was greater than in the MNP - Fe group (9.9 vs. 9.5 kg, P = 0.038). Mothers of infants in the MNP + Fe group reported more infant days spent with cough (P = 0.003) and dyspnoea (P = 0.0002); there were no significant differences on any other of the weekly morbidity measures. In this study, low-dose iron-containing MNP did not improve infant's iron status or reduce anaemia prevalence, likely because absorption was inadequate due to the high prevalence of infections and the low-iron dose.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mcn.12163

In-home fortification with 2.5 mg iron as NaFeEDTA does not reduce anaemia but increases weight gain: a randomised controlled trial in Kenyan infants.

To increase the yield of heterologous production of the class II bacteriocin DvnRV41 with Escherichia coli Origami (DE3) (pLysS/pCR03), induction of bacteriocin gene expression was optimized by varying the inducer isopropyl β-d-thiogalactopyranoside (IPTG) concentration (0–2 mM), and controlled batch and fed-batch cultures were tested on a 2-L scale. A concentration of 0.5 mM IPTG was found to be optimal for cell growth and bacteriocin production. Shake flask cultivation of E. coli Origami (DE3) (pLysS/pCR03) gave biomass and bacteriocin yields of 1.54 ± 0.06 g cdw/l and 18 ± 1 mg DvnRV41/l, respectively. Biomass (2.70 ± 0.06 and 6.8 ± 0.6 g cdw/l, respectively) and bacteriocin yields (30 and 74 mg DvnRV41 per liter, respectively) were both increased with batch and fed-batch compared to shake flask cultures. Bacteriocin yields reported in this study are among the highest published for other heterologous expression systems in shake flasks.

/pdf/production-of-recombinant-bacteriocin-divercin-v41-by-high-26vxzl3izw.pdf

Production of recombinant bacteriocin divercin V41 by high cell density Escherichia coli batch and fed-batch cultures.

This study characterized the microflora of three Mexican fresh cheeses with (Oaxaca) or without starter culture (Panela and cottage cheese). The cheeses were produced without chemical preservatives from pasteurized milk in a single plant at industrial-scale in Mexico and stored for 20 days at 10 °C, simulating high market handling temperatures not suitable for consumption. Microbiological counts were determined on PC agar and 6 selective media and randomly selected isolates were identified by biochemical or molecular methods. Lactic acid bacteria were predominant at levels of log 5 to 8 cfu/g cheese on KFS, MRS, and M17 agar. Identification confirmed enterococci and lactobacilli on KFS agar and MRS agar, respectively. On M17 agar, Streptococcus thermophilus, Lactococcus sp., and Leuconostoc sp. were observed as most prevalent isolates. Beyond, typical contaminants such as Enterobacteriaceae and fungi (yeasts and molds) were determined at levels of log 3 to 7 cfu/g cheese with a predominance of Enterobacter amnigenus and Klebsiella oxytoca, Candida guilliermondii and Candida tropicalis, and Penicillium sp. No Listeria were found in any of the tested cheeses. These contaminants potentially involved in the spoilage of fresh non-preserved Mexican cheeses may serve as targets for the development of new biopreservation methods.

Christophe Lacroix

Papers

Effects of strains and growth conditions on autolytic activity and survival to freezing and lyophilization of Lactobacillus delbrueckii ssp. lactis isolated from cheese

Characterization of Yeasts Associated with Camel Milk using Phenotypic and Molecular Identification Techniques

In-home fortification with 2.5 mg iron as NaFeEDTA does not reduce anaemia but increases weight gain: a randomised controlled trial in Kenyan infants.

Production of recombinant bacteriocin divercin V41 by high cell density Escherichia coli batch and fed-batch cultures.

Characterization of the microflora of industrial Mexican cheeses produced without added chemical preservatives