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correspond to known species. However, the 15 prominent bands were identified as belonging within different Clostridium clusters. In addition, the common biotypes found in virtually all subjects' TGGE patterns were identified as Ruminococcus obeum, Eubacterium hallii and Fusobacterium prausnitzii (reclassified as Faecalibacterium prausnitzii) (56).

More recent studies by this group have shown a positive linear relationship between host genetic relatedness and the similarity index of PCR-DGGE profiles (Table 4) (62). Higher similarity was seen between profiles obtained for monozygotic twins living apart than that seen for married couples. In addition, similarity was highest between monozygotic twin individuals than between pairs of twins. No correlation was shown between similarity index and gender or living arrangements of unrelated individuals, suggesting these factors did not significantly impact upon the bacterial composition. Inclusion of samples collected from four different primates (chimpanzee, gorilla, macaque, and orangutan) and subsequent analysis demonstrated that PCR-DGGE profiles of unrelated humans showed significantly greater similarity than that between humans and other primates. This work has indicated that host genotype factors have an important impact upon the bacterial composition of the gut microbiota (62).

A number of studies have also evaluated the application of PCR-DGGE to monitor the composition and dynamics of particular components of the human gut microbiota (60,61,64). To date, such research has concentrated on the lactic acid bacteria (LAB), as well as bifidobacteria. Each of these studies has displayed evidence of the ability to use PCR-DGGE for group- or genus-specific investigations. Overall, these studies demonstrated inter-individual variation within specific bacterial populations (Table 4). Differences were seen regarding the dynamics of different bacterial groups over time: fluctuations were seen in the LAB of two New Zealand adults over 6 months (61); the bifidobacteria! population of five Finnish adults remained relatively stable over 4 weeks (60); Lactobacillus spp. PCR-DGGE of several healthy adults displayed varying stability over 20 months (stable for certain individuals and more dynamic for others) (64). The study by Heilig and colleagues (64) also monitored the lactobacilli diversity in one baby boy, from birth to 5 months of age. No Lactobacillus spp. PCR product was obtained for the first 55 days (suggesting this population was either absent or below the detection limit). Subsequently, two prominent amplicons were seen to persist throughout the study period (64). These were identified as belonging to the species Lactobacillus rhamnosus and Lactobacillus casei. In addition, this work displayed bacterial succession of the lactobacilli corresponding to the introduction of solid foods (~ 3 months of age), from which time a third prominent amplicon was observed (Lactobacillus salivarius). Two of these studies further investigated the usefulness of this technique in probiotic feeding trials (61,64). Both groups demonstrated the ability to identify probiotic-specific amplicons within the group-specific bacterial profiles.

Favier and colleagues (63) performed a pilot study with two infants investigating the feasibility of DGGE profiling to monitor bacterial succession during the first 10-12 months of life. One infant was exclusively breast-fed prior to weaning, whilst the other was breast-fed for a fortnight and then mixed-fed (both formula- and breast-milk) until weaning. The results demonstrated a simple fecal microbiota initially, which progressively diversified with time. Bifidobacterial amplicons were predominant in the fecal microbiota of both infants during the first 6 months. Alterations in diet, such as the supplementation of breast-feeding with formula-milk and introduction of solid foods (weaning), was associated with changes in the bacterial profiles. The shift in bacterial profiles seen following weaning, was more pronounced in the exclusively breast-fed infant (compared to the mixed-fed infant)—although this may be a reflection of the relative simplicity of the pre-weaning profile of this infant (compared to the more complex pre-weaning profile of the mixed-fed infant, comprised of multiple dominant amplicons) (63).

PCR-DGGE has also been used to compare the microbial component of biopsy samples taken from different regions of the colon, both with each other and the fecal microbiota (65). Inter-individual variation was shown for both fecal and biopsy samples. Interestingly, the biopsy samples taken from three distinct regions of the colon (ascending, transverse, and descending colon) of the same individual provided extremely similar DGGE profiles (total community). Significant differences were evident in the total community PCR-DGGE of fecal and biopsy samples. This is by no means alarming, as one can readily appreciate the distinction of the two ecological niches (i.e., the luminal microbiota and mucosally associated community), and the numbers within the species are likely to differ and result in different profiles. However, Lactobacillus spp. PCR-DGGE patterns from fecal and biopsy samples were very similar in 6/10 subjects. Minor differences were seen in the Lactobacillus spp. PCR-DGGE profiles of the different biopsy samples from three of the 10 individuals. Overall, no differences were noted in the mucosally associated lactobacilli of different individuals based on host health (i.e., healthy versus diseased tissues).

In summary, molecular methods enabling community analysis of the human fecal microbiota have demonstrated that a large proportion of the predominant microbial component are novel or unknown species—which have not yet been cultivated. Interindividual variation and intra-individual stability are consistent features of studies of the prominent members of the total community. However, investigations of specific bacterial groups or genera indicate varying levels of stability, with fluctuations seen in some cases. Host genetic factors appear to play an important role in the microbial composition of healthy human adults, though it is as yet undetermined what impact bacterial acquisition and succession during childhood plays.

Pregnancy And Childbirth

Pregnancy And Childbirth

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