A human gut microbial gene catalogue established by metagenomic sequencing

Abstract

To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.

Modulation of the gut microbiota by prebiotic fibres and bacteriocins

“…Therefore, it is not possible to clearly define and classify the gut microbiota of each individual based on the enterotypes. Moreover, larger projects such as the US Human Microbiome Project [14] and the European Metagenomics of the Human Intestinal Tract [15], and many others [16], aim to identify healthy (normal) microbiota and have made considerable progress. However, in spite of the relatively well-organized structure of the main bacterial groups, it is difficult to define the composition of the normal or healthy microbiota owing to the complexity of the microbiota and its variation between and within individuals [17].…”

The gut microbiota and inflammatory noncommunicable diseases: Associations and potentials for gut microbiota therapies

“…While inflammation and the pathways to disease are multifactorial, the altered gut colonization patterns associated with declining microbial diversity is a central theme, and increasingly implicated in the physiological, immunological and metabolic dysregulation seen in many NCDs. The adult gut harbors as many as 100 trillion resident microbes called the microbiota and the corresponding genome (microbiome) has been estimated to contain 150-fold more genes than the host genome 3 . These complex communities have a symbiotic relationship with the host, and are involved in many aspects of host physiology.…”

Optimized Sample Handling Strategy for Metabolic Profiling of Human Feces

“…Although urine and blood are often used to investigate systemic responses of animals and humans to various environmental stimuli or therapeutic interventions 1 , the search for disease biomarkers in fecal samples and studies on host-microbial interactions have intensified over the last decade. The human intestinal tract harbors >100 trillion microbial cells 2 and these microbes exert their influences on the human host primarily by metabolic signaling and therefore optimized methodologies for the study of microbial metabolic footprint is crucial to this field. Mounting evidence shows that the microbial composition and its collective metabolic activity profoundly impacts host physiology and modulates the disease risk of the host 3 .…”