Comparison of populations of human faecal bacteria before and after in vitro incubation with plant cell wall substrates

Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides

One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥ 97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.

Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota

Fecal bacteria were studied in healthy elderly volunteers (age, 63 to 90 years; n = 35) living in the local community, elderly hospitalized patients (age, 66 to 103; n = 38), and elderly hospitalized patients receiving antibiotic treatment (age, 65 to 100; n = 21). Group- and species-specific primer sets targeting 16S rRNA genes were used to quantitate intestinal bacteria by using DNA extracted from feces and real-time PCR. The principal difference between healthy elderly volunteers and both patient cohorts was a marked reduction in the Bacteroides-Prevotella group following hospitalization. Reductions in bifidobacteria, Desulfovibrio spp., Clostridium clostridiiforme, and Faecalibacterium prausnitzii were also found in the hospitalized patients. However, total 16S rRNA gene copy numbers (per gram of wet weight of feces) were generally lower in the stool samples of the two groups of hospitalized patients compared to the number in the stool samples of elderly volunteers living in the community, so the relative abundance (percentage of the group- and species-specific rRNA gene copies in relation to total bacterial rRNA gene copies) of bifidobacteria, Desulfovibrio spp., C. clostridiiforme, and F. prausnitzii did not change. Antibiotic treatment resulted in further reductions in the numbers of bacteria and their prevalence and, in some patients, complete elimination of certain bacterial communities. Conversely, the numbers of enterobacteria increased in the hospitalized patients who did not receive antibiotics, and due to profound changes in fecal microbiotas during antibiotic treatment, the opportunistic species Enterococcus faecalis proliferated.

Estimation of the fermentability of dietary fibre in vitro: a European interlaboratory study

Five European laboratories tested a simple in vitro batch system for dietary fibre fermentation studies. The inoculum was composed of fresh human faeces mixed with a carbonate-phosphate buffer complex supplemented with trace elements and urea. Five dietary fibre sources (cellulose, sugarbeet fibre, soyabean fibre, maize bran and pectin) were used by each laboratory on three occasions to determine pH, residual non-starch polysaccharides (NSP) and short-chain fatty acid production during fermentation. Cellulose and maize bran degradabilities were very low (7.2(SE 10.8) and 6.2 (SE 9.1)% respectively after 24 h), whereas pectin and soyabean fibre were highly degraded (97.4 (SE 4.4) and 91.1 (SE 3.4)% respectively after 24 h). Sugarbeet fibre exhibited an intermediate level of degradability (59.5 (SE 14.9)%). Short-chain fatty acid production was closely related to NSP degradation (r 0.99). Although each variable was ranked similarly by all laboratories, some differences occurred with respect to absolute values. However, the adaptation of donors to the experimental substrates was not an influential factor. Interlaboratory differences could be reduced either by adding less substrate during incubations or using less-diluted inocula. In vitro fermentations with inocula made from human faeces and from rat caecal contents gave similar results. There was a close correspondence between the data obtained in the present experiment and those previously published in in vivo studies in the rat using the same fibres. The in vitro batch system tested during the present study provides a rapid means of obtaining quantitative estimates of the fermentation and the estimation of the energy content of new sources of dietary fibre.

Dietary fiber, inulin, and oligofructose: a review comparing their physiological effects

Dietary fiber is a general term. It covers a wide variety of substances that belong to the family of carbohydrates that resist hydrolysis by human alimentary enzymes but are fermented by colonic microflora. The main physiological effects of dietary fiber are primarily on gastric emptying and small intestinal transit time, resulting in an improved glucose tolerance and a decreased digestion of starch: second, on colonic transit time and large bowel functions due to fermentation by ceco-colonic microbial flora or bulking action. The so-called soluble dietary fibers are fermented to a large extent by a wide variety of anaerobic bacteria that result in an increase in bacterial biomass, an increase in fecal mass, a change in intracolonic pH, and production of short chain fatty acids and various gases as metabolic end products. The insoluble fibers are only marginally fermented: they serve almost exclusively as bulking agents that result in shorter transit time and increased fecal mass. The short chain fatty acids resulting from the colonic fermentation of dietary fiber are largely absorbed via the portal blood and reach both the liver and the peripheral tissues. They induce changes in glucose and fat metabolism leading to post-prandial hypoglycemia and long-term hypolipidemia. Inulin and oligofructose are fructans with a degree of polymerization of 2 to 60 and 2 to 20, respectively. Due to the structural conformation of their osidic bridge (beta 2-1), they both resist the hydrolysis by human alimentary enzymes. Moreover, when reaching the colon, both inulin and oligofructose are almost quantitatively fermented almost exclusively by colonic bifidobacteria and bacteroides. Such an extensive fermentation causes an increase in fecal bacterial biomass, a decrease in ceco-colonic pH, and produces a large amount of fermentation products among which the short chain fatty acids that exert systemic effects on lipid metabolism. Thus, both inulin and oligofructose have most of the characteristics of a dietary fiber and the proposal is made to classify them as such. Moreover, they are bifidogenic factors, because, due to still unknown reasons, they are primarily fermented by bifidobacteria. It is concluded from this review that "nondigestible fructo-oligosaccharides," even though they are not included in the carbohydrate fraction that is quantified as dietary fiber by classic analytical methods, have most of the physiological effects of a dietary fiber.(ABSTRACT TRUNCATED AT 400 WORDS)

In vivo and in vitro models of the human colonic flora

The study of colonic flora composition and metabolism presents considerable methodological problems. Attempts to circumvent these problems have led to the development of numerous in vitro and in vivo models to simulate the human colon and its microbial population. In terms of in vivo models, conventional laboratory animals have many limitations. Data of greater relevance to man can be obtained by using germ-free rodents associated with human colonic bacteria. The applications of such animals to studies of toxicity of chemicals and gastrointestinal infections are discussed. The advantages and disadvantages of the various in vitro systems for studying gut microflora and its metabolic activity (from simple static cultures to the more sophisticated continuous and semicontinuous flow models) are reviewed. The apparatus involved is described together with practical information on media, running conditions, and sampling. The bacteriological and metabolic criteria for establishing the similarity of the models to the in situ colonic flora are also discussed. The final sections of the review are devoted to the major applications (current and future) of the models, including fermentation studies on dietary fiber, metabolism of nutrients and foreign compounds (including carcinogens) in food, and the investigation of colonization resistance.

Response of populations of human faecal bacteria to viscosity in vitro

The effects of viscosity on cultures of human faecal bacteria in vitro were studied. The composition of the microbial populations which developed during in vitro incubation were affected by viscosity. The proportion of Bacteroides species was decreased at high viscosities and it is concluded that the 'viscotolerance' of a bacterial population contributes towards its composition. Viscosity alters the enzyme activity of cultures. Cell-associated total, and specific, beta-galactosidase activities of cultures of human faecal bacteria were decreased at high viscosity.