Diversity of the human gastrointestinal tract microbiota revisited

Abstract

SummarySince the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of highthroughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.

Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces

“…Prior to this investigation, the eukaryotic members of the human gut microbial community have been primarily assessed using cultivation-based methods, and this has led to the belief that they are not widely distributed or abundant in the human microbiota (Rajilic-Stojanovic et al, 2007). This statement is indeed true for the cultivable fraction of the community, but through the application of cultivation-independent techniques, such as DNA extraction and PCR, this study provides evidence that stable eukaryotic communities are widespread in the healthy human gut.…”

Human gut microbiota: does diet matter?

“…Each individual harbours at least 160 such species (11,12) . Under normal circumstances, predominant intestinal microbiota of an adult individual is fairly stable.…”

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

“…The GI tract is colonized with approximately 1000 microbial species, commonly called the microbiota, and may harbor more than nine million unique genes (Zoetendal et al, 2008;Yang et al, 2009). Culture-independent approaches such as ribosomal RNA (rRNA) targeting technologies have revealed that the microbiota is stable in time in healthy adults, and host-and location specific (Rajilić-Stojanović et al, 2007;Zoetendal et al, 2008). Random metagenomic analysis of fecal microbiota suggested that it complements human physiology with a range of essential functions that were canonically encountered in different adults, and that a potential link between microbiota-derived gene pool and health and disease exists (Gill et al, 2006;Kurokawa et al, 2007;Turnbaugh et al, 2009;Qin et al, 2010).…”