Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification

Objectives: Shotgun proteomics is a generic method enabling detection of multiple viral species in one assay. The reliable and accurate identification of these viral species by analyzing peptides from MS-spectra is a challenging task. The aim of this study was to develop an easy accessible proteome analysis approach for the identification of...

Proteomics, an agnostic approach to detect emerging viruses - Poster -

The COVID-19 pandemic, but also MERS, SARS-1, monkeypox and other emerging biological threats have shown the pitfalls of diagnostics targeting only one or, at best, a limited number of pathogens. To overcome this, a next generation diagnostic platform that is causative-agent agnostic is developed. Moreover, the method is able to identify 1895...

Untargeted accurate identification of highly pathogenic bacteria directly from blood culture flasks

To improve the preparedness against exposure to highly pathogenic bacteria and to anticipate the wide variety of bacteria that can cause bloodstream infections (BSIs), a safe, unbiased and highly accurate identification method was developed. Our liquid chromatography-tandem mass spectrometry (LC–MS/MS)-based method can identify highly pathogenic...

Fecal Microbiome and Food Allergy in Pediatric Atopic Dermatitis: A Cross-Sectional Pilot Study

Background: Exposure to microbes may be important in the development of atopic disease. Atopic diseases have been associated with specific characteristics of the intestinal microbiome. The link between intestinal microbiota and food allergy has rarely been studied, and the gold standard for diagnosing food allergy (double-blind placebo...

Reversal of visceral hypersensitivity in rat by Menthacarin®, a proprietary combination of essential oils from peppermint and caraway, coincides with mycobiome modulation

Background: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder associated with altered gastrointestinal microflora and increased nociception to colonic distension. This visceral hypersensitivity can be reversed in our rat maternal separation model by fungicides. Menthacarin® is a proprietary combination of essential oils from...

Bacterial population dynamics and sensorial quality loss in modified atmosphere packed fresh-cut iceberg lettuce

The end of shelf life of fresh-cut iceberg lettuce packed in modified atmosphere (MA) is determined by its visual quality and by its microbial load. The total microbial load should not exceed 6–7 log CFU g−1 mesophilic counting and be free of human pathogens. Not much is known about specific interactions between the levels of specific spoilage...

Intestinal Fungal Dysbiosis Is Associated With Visceral Hypersensitivity in Patients With Irritable Bowel Syndrome and Rats

Background & Aims Visceral hypersensitivity is one feature of irritable bowel syndrome (IBS). Bacterial dysbiosis might be involved in the activation of nociceptive sensory pathways, but there have been few studies of the role of the mycobiome (the fungal microbiome) in the development of IBS. We analyzed intestinal mycobiomes of patients with...

Identification of microorganisms grown in blood culture flasks using liquid chromatography-tandem mass spectrometry

Aim: Bloodstream infections are a common cause of disease and a fast and accurate identification of the causative agent or agents of bloodstream infections would aid the start of adequate treatment. Materials & methods: A liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics method was developed for the identification of...

On the ecosystemic network of saliva in healthy young adults

A dysbiotic state is believed to be a key factor in the onset of oral disease. Although oral diseases have been studied for decades, our understanding of oral health, the boundaries of a healthy oral ecosystem and ecological shift toward dysbiosis is still limited. Here, we present the ecobiological heterogeneity of the salivary ecosystem and...

Deep learning for classification of dental plaque images

Organic acids produced by lactic acid bacteria (Leuconostoc sp.) contribute to sensorial quality loss in modified-atmosphere-packed fresh-cut iceberg lettuce

The shelf-life of fresh-cut lettuce packed in a modified atmosphere (MA) is determined by its "overall visual quality" (OVQ), being a measure of its general appearance based on colour and shape criteria. In addition to the OVQ, the development of off-flavour and acid off-smell reduces consumer acceptance of such products. Concomitant with these...

Feature selection via co-regularized sparse-group lasso

Effect of experimental gingivitis induction and erythritol on the salivary metabolome and functional biochemistry of systemically healthy young adults

Introduction: Understanding the changes occurring in the oral ecosystem during development of gingivitis could help improve prevention and treatment strategies for oral health. Erythritol is a non-caloric polyol proposed to have beneficial effects on oral health. Objectives: To examine the effect of experimental gingivitis and the effect of...

Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery

The human gut microbiome diet and health Post hoc non ergo propter hoc

The gastro-intestinal microbiome has become the subject of intensive research, which is beginning to elucidate its roles in human health. It is becoming increasingly recognised that gut microbiota plays a part in regulating human immune homeostasis and metabolism, which gives rise to novel opportunities for preventative and treatment strategies....

KeCo: Kernel-based online co-agreement algorithm

We propose a kernel-based online semi-supervised algorithm that is applicable for large scale learning tasks. In particular, we use a multi-view learning framework and a co-agreement strategy to take into account unlabelled data and to improve classification performance of the algorithm. Unlike the standard online methods our algorithm is...