Samples and techniques highlighting the links between obesity and microbiota

Abstract

The composition of gut microbiota and its relationship to human health, particularly its links with obesity remain an ongoing challenge for scientists. The current gold standard for exploring human gut microbiota consists of using stool samples and only applying next generations sequencing techniques, which sometimes generate contradictory results. Here, we comprehensively describe nutrient absorption, fat digestion, carbohydrate and protein absorption, demonstrating that absorption of these diverse nutrients occurs mainly in the stomach and small intestine. Indeed, bariatric surgery, including Roux-en-Y, removes part of the upper intestine, resulting in weight loss, while colonic surgery is associated with a stable weight. However, most studies only use stool samples rather than small intestine samples because of the easy with which this can be accessed. Metagenomics studies are associated with several biases such as extraction and primer biases and depth bias, including the more modern platforms. High-throughput culture-dependent techniques, such as culturomics, which uses rapid identification methods such as MALDI-TOF, remain time-consuming, but have demonstrated their complementarity with molecular techniques. In conclusion, we believe that a comprehensive analysis of the relationships between obesity and gut microbiota requires large-scale studies coupling metagenomics and culture-dependent research, in order to analyse both small intestine and stool samples.

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic

“…Microbial gene richness was measured by counting the number of genes identified in a given sample using 11 million reads as performed in the original studies65.…”

Changes in the intestinal microbiota of superobese patients after bariatric surgery

“…A higher proportion of Firmicutes is associated with greater energy absorption, while more Bacteroidetes is associated with a decrease (5). Nevertheless, the participation of genera and species also seems important since the distribution of phyla between lean and obese individuals shows no difference in some studies (6).…”

Taxonogenomic description of four new Clostridium species isolated from human gut: ‘Clostridium amazonitimonense’ , ‘Clostridium merdae’ , ‘Clostridium massilidielmoense’ and ‘Clostridium nigeriense’

“…As showed by a remarkable number of studies, the human gut microbiota plays a tremendous role in human health and the homeostasis of the human body [1] , [2] , [3] . Conversely, an increasing number of links between the gut microbiota and several diseases has been uncovered; these diseases include nutritional disorders, metabolic diseases and pathologies of the intestine [1] , [4] , [5] , [6] . Techniques used in exploratory studies have evolved alongside technology from culture-based techniques in early studies to today's culture-independent techniques [7] .…”