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

Abstract

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.

FIG. 1.

Percentage of 16S rRNA gene copies of the predominant fecal bacterial groups and species in relation to total bacterial 16S rRNA gene copies (relative abundance). The percentage was calculated for each individual, and the median was determined for each subject group. A nonparametric Mann-Whitney U test was used for pairwise comparison of the subject groups. Error bars represent the interquartile range. *, significant difference (P < 0.05) between groups H and P; §, significant difference (P < 0.05) between groups H and PAB; ‡, significant difference (P < 0.05) between groups P and PAB.

FIG. 2.

Percentage of 16S rRNA gene copies of less abundant fecal bacterial groups and species in relation to total bacterial 16S rRNA gene copies (relative abundance). The percentage was calculated for each individual, and the median was determined for each subject group. A nonparametric Mann-Whitney U test was used for pairwise comparison of the subject groups. Error bars represent the interquartile range. *, significant difference (P < 0.05) between groups H and P; §, significant difference (P < 0.05) between groups H and PAB; ‡, significant difference (P < 0.05) between groups P and PAB.