The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining...

The use of next generation sequencing for improving food safety: Translation into practice

Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis...

Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome

Background: Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antibiotics. Little is known on the effect of this exposure on antibiotic resistance. In this study, we aimed to investigate the...

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota

Background: A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus-dominated vaginal...

The fungal composition of natural biofinishes on oil-treated wood

Background: Biofinished wood is considered to be a decorative and protective material for outdoor constructions, showing advantages compared to traditional treated wood in terms of sustainability and self-repair. Natural dark wood staining fungi are essential to biofinish formation on wood. Although all sorts of outdoor situated timber are...

Microbial metabolism shifts towards an adverse profile with supplementary iron in the TIM-2 in vitro model of the human colon

Oral iron administration in African children can increase the risk for infections. However, it remains unclear to what extent supplementary iron affects the intestinal microbiome. We here explored the impact of iron preparations on microbial growth and metabolism in the well-controlled TNO's in vitro model of the large intestine (TIM-2). The...

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....

Prebiotic mechanisms, functions and applications - A review

In October 2012, a group of scientists met at the 10th Meeting of the International Scientific Association of Probiotics and Prebiotics (ISAPP) in Cork, Ireland to discuss issues surrounding prebiotics and their development. This article summarises outputs from the meeting. Various prebiotic definitions were discussed and how the concept has...

The human gastrointestinal microbiota - An unexplored frontier for pharmaceutical discovery

The mammalian gastrointestinal tract (GIT) harbors microorganisms (the microbiota) of vast phylogentic, genomic, and metabolic diversity, and recent years have seen a rapid development in the techniques for studying these complex microbial ecosystems. It is increasingly apparent that the GIT microbiota plays an intricate role in host health and...

Beneficial microbes. Foreword.

The effect of the undigested fraction of maize products on the activity and composition of the microbiota determined in a dynamic in vitro model of the human proximal large intestine.

OBJECTIVE: To investigate the effect of 5 newly developed maize-based fibers on the activity and composition of the microbiota in the colon. The fibers tested were glucose-based and had variable structures, including 2 resistant starch preparations, soluble corn fiber, pullulan, and soluble fiber dextrin. METHODS: The fibers were predigested,...