Publications

The lactic acid bacterial (LAB) community dynamics of two wheat and two spelt sourdough fermentations that were daily back-slopped were monitored during a period of 10 days by hybridizing time-related RNA samples, representing the metatranscriptome, to an LAB functional gene microarray. To indicate the species present in each hybridized sample, annotation information for the 2,269 oligonucleotides on the microarray was used. The overall ...

Background The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver's effects on this environment is lacking because the impact ...

Dear Editors,

In their recent short communication, published in this journal, Nam and colleagues have described the use of their earlier developed genome-probing microarray (Bae et al., 2005) for so-called metagenome and metatranscriptome analysis of lactic acid bacteria during the fermentation of kimchi, a traditional Korean fermented vegetable product (Nam et al., 2009). In this study, the authors have isolated DNA and RNA from ...

The lactic acid bacterial (LAB) community dynamics of two wheat and two spelt sourdough fermentations that were daily back-slopped were monitored during a period of 10 days by hybridizing time-related RNA samples, representing the metatranscriptome, to an LAB functional gene microarray. To indicate the species present in each hybridized sample, annotation information for the 2,269 oligonucleotides on the microarray was used. The overall ...

Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, including sourdough-derived products. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Triggered by the considerable amount of LAB genomic information that became available during ...

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level ...

Bees are associated with a remarkable diversity of microorganisms, including unicellular parasites, bacteria, fungi, and viruses. The application of next-generation sequencing approaches enables the identification of this rich species composition as well as the discovery of previously unknown associations. Using high-throughput polyadenylated ribonucleic acid (RNA) sequencing, we investigated the metatranscriptome of eight wild bee species ...

Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, including sourdough-derived products. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Triggered by the considerable amount of LAB genomic information that became available during ...

Due to their rapid responses to environmental variation, planktonic organisms are used as bio-indicators of ecosystem changes. Most zooplankton monitoring studies focus mainly on variability in biodiversity, densities and biomass. Advances in practical, cost-effective molecular approaches can help overcome the issues with morphology-based biomonitoring. While molecular studies are growing in popularity, a fundamental challenge remains the ...

High-throughput sequencing technologies have advanced RNA virus genomics, but recovering viral genomes from mammalian tissues remains challenging due to the predominance of host RNA. We evaluated two metatranscriptomic workflows to address these challenges. Our results demonstrate that the methods differed significantly in performance, with Method B achieving a 5-fold increase in RNA yield and improved RNA integrity over Method A. These ...