Acquisition, Evolution and Maintenance of the Normal Gut Microbiota

Abstract

The gut is sterile at birth, but is rapidly colonised by faecal and vaginal bacteria of maternal origin. Over the succeeding weeks, months and years, a complex microbiota develops that plays a major role in host physiology. While the digestive tract is colonised to varying degrees by micro-organisms throughout its length, due to acid pH and the short retention time of gastric contents, bacterial numbers in the stomach are usually low. The rapid passage of digestive materials through the upper gut does not provide time for significant bacterial growth to occur, but cell numbers increase considerably in the distal ileum. The rate of movement of intestinal contents slows in the colon, which facilitates the development of complex bacterial communities. The large intestine is an intricate ecosystem that contains a complex microbiota composed of several hundred different types of bacteria. The growth and metabolism of microbial communities in the large intestine are determined by many factors, such as diet, environment and host physiological processes, as well as the anatomic structure of the digestive tract, disease, immunity, host genetics, drugs and ageing. Modifications in diet and host immune system activity, as well as physiological changes in the digestive tract affect microbiota composition in older people. The elderly have fewer bifidobacteria and higher numbers of enterobacteria and clostridia than young adults. Increased antibiotic use in older people and simply going into hospital have been shown to change bacterial community structure in the colonic microbiota, although the metabolic significance of this is unclear.

The gut microbiota in conventional and serrated precursors of colorectal cancer

“…Our observation of global OTU-level composition shifts in distal, but not proximal, CA cases compared to controls is likely due to stool being a better proxy for the bacterial communities of the distal colon than of the proximal colon [39]. This was proposed in a recent metagenomic study of colorectal cancer, in which carcinoma-associated bacterial genes were more abundant in stool of distal CRC cases than proximal CRC cases [10].…”

“…There are known molecular distinctions between proximal and distal CRCs, most notably that proximal CRCs are more likely to be hypermethylated and to have elevated mutation rates [41]. Additionally, the luminal environment differs between proximal and distal colon sites: there are high levels of easily fermentable carbohydrate substrates in the proximal colon, which decrease distally through the colon [39, 42]; the mucus layer increases in thickness distally through the colon [42]; the number of bacterial cells increases distally through the colon [43]; and immune activity decreases distally through the colon [44]. These differences can result in site-specific bacterial communities and processes, which may contribute to CA development in distinct ways.…”

“…Members of these Clostridia families have in common the capacity to generate butyrate from fermentation of non-digestible plant fibers [45], which is beneficial to colonic health [46]. Depletion of butyrate-producing bacteria in the distal colon, where carbohydrate substrate supply is already compromised [39, 42], may allow for adenoma growth. The decreased normalized abundance of Clostridia we have observed here is consistent with our previous study of CRC, in which the relative abundance of class Clostridia was depleted in stool samples of CRC cases compared to controls [9].…”

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

“…The increased diversification and succession of the bacterial community structure reflect the development of the immature cecal microflora toward a more mature and stable flora, a characteristic demonstrated in the juveniles of many species, including mice and humans (30,31). Host physiology has been shown to have an impact on the development of the gastrointestinal microbiota (32). It is also likely that age-related differences arise due to a number of other factors, including resource competition between bacterial species, shifts in the host's diet, or agerelated variation in the chemical and physiological state of the gastrointestinal tract (33).…”

The renaissance of continuous culture in the post-genomics age

“…One of these compounds, moxifloxacin, also appeared to trigger increased resistance to this fluoroquinolone. In the clinical context it is pertinent to note that the elderly have larger gut populations of enterobacteria and clostridia than young adults [119] and the implications that antibiotic use and hospitalization may have for this cohort of patients. As in our discussions of ecophysiology it must be emphasized that in vitro chemostat models are but a mirror of reality; in this case the gut model does not mimic immunological or secretory events within the colon, but it is a reliable indicator of whether a drug may have a propensity to induce CDI in vivo.…”