As the catalogue of sequenced genomes and metagenomes continues to grow, massively parallel approaches for the comprehensive and functional analysis of gene products and regulatory elements are becoming increasingly valuable. Current strategies to synthesize or clone complex libraries of DNA sequences are limited by the length of the DNA targets, throughput and cost. Here, we show that long-adapter single-strand oligonucleotide (LASSO) probes can capture and clone thousands of kilobase DNA fragments in a single reaction. As a proof-of-principle, we simultaneously cloned >3,000 bacterial open reading frames (ORFs) from E. coli genomic DNA (spanning 400–5,000 bp targets). Targets were enriched up to a median of ~60-fold compared to non-targeted genomic regions. At a cutoff of 3 times the median non-target reads per kilobase of genetic element per million reads, ~75% of the targeted ORFs were successfully captured. We also show that LASSO probes can clone human ORFs from complementary DNA, and an ORF library from a human-microbiome sample. LASSO probes could be used for the preparation of long-read sequencing libraries and for massively multiplexed cloning.

The minimum inhibitory concentrations (MICs) of six antibiotics with activity against gram-positive bacteria (ampicillin, clindamycin, erythromycin, gentamicin, streptomycin, and tetracycline) were determined by microdilution and the Etest in 121 Lactobacillus plantarum strains of plant and dairy origin. MIC values for all antibiotics varied widely between strains. The analysis of both absolute MICs and their distribution was used to define new susceptibility-resistance cutoff values for all antibiotics, except for streptomycin. Based on these new cutoffs, the studied strains were nearly all identified as either susceptible (ampicillin, clindamycin, erythromycin, and gentamicin) or intrinsically resistant (streptomycin). The exceptions were four strains with MICs for tetracycline higher than the cutoff point (64 microg ml(1)); these were suspected to harbor acquired resistance determinants.

A total of 74 Streptococcus thermophilus isolates collected between 1948 and 2005 from different environments were investigated to assess erythromycin, clindamycin, streptomycin, gentamicin, tetracycline and ampicillin susceptibility by means of microdilution, Etest and disk diffusion methods. For this purpose a new S. thermophilus Susceptibility test Medium (SSM) was developed. This medium allowed a better identification of strains with atypical tetracycline resistance. The recipe is a mixed formulation of Iso-Sensitest medium (90% v/v) and M17 medium (10% v/v) supplemented with lactose (0.5% w/v). The overall agreement of the techniques was good with exception of tetracycline, for which Etest provided lower MICs than the microdilution method. Most strains were susceptible to all the antibiotics tested while a few erythromycin, tetracycline and streptomycin resistant strains were detected.