The host genotype affects the bacterial community in the human gastrointestinal tract

The gastrointestinal (GI) tract is one of the most complex ecosystems consisting of microbial and host cells. It is suggested that the host genotype, the physiology of the host and environmental factors affect the composition and function of the bacterial community in the intestine. However, the relative impact of these factors is unknown. In this study, we used a culture-independent approach to analyze the bacterial composition in the GI tract. Denaturing gradient gel electrophoresis (DGGE) profiles of fecal bacterial 16S rDNA amplicons from adult humans with varying degrees of genetic relatedness were compared by determining the similarity indices of the profiles compared. The similarity between fecal DGGE profiles of monozygotic twins were significantly higher than those for unrelated individuals (ts = 2.73, p1-tail = 0.0063, df=21). In addition, a positive relationship (F1, 30 = 8.63, p = 0.0063) between the similarity indices and the genetic relatedness of the hosts was observed. In contrast, fecal DGGE profiles of marital partners, which are living in the same environment and which have comparable feeding habits, showed low similarity which was not significantly different from that of unrelated individuals (ts = 1.03, p1-tail = 0.1561, df=27). Our data indicate that factors related to the host genotype have an important effect on determining the bacterial composition in the GI tract

The host genotype affects the bacterial community in the human gastrointestinal tract

The gastrointestinal (GI) tract is one of the most complex ecosystems consisting of microbial and host cells. It is suggested that the host genotype, the physiology of the host and environmental factors affect the composition and function of the bacterial community in the intestine. However, the relative impact of these factors is unknown. In this study, we used a culture-independent approach to analyze the bacterial composition in the GI tract. Denaturing gradient gel electrophoresis (DGGE) profiles of fecal bacterial 16S rDNA amplicons from adult humans with varying degrees of genetic relatedness were compared by determining the similarity indices of the profiles compared. The similarity between fecal DGGE profiles of monozygotic twins were significantly higher than those for unrelated individuals (ts = 2.73, p1-tail = 0.0063, df=21). In addition, a positive relationship (F1, 30 = 8.63, p = 0.0063) between the similarity indices and the genetic relatedness of the hosts was observed. In contrast, fecal DGGE profiles of marital partners, which are living in the same environment and which have comparable feeding habits, showed low similarity which was not significantly different from that of unrelated individuals (ts = 1.03, p1-tail = 0.1561, df=27). Our data indicate that factors related to the host genotype have an important effect on determining the bacterial composition in the GI tract

Temperature and denaturating gradient gel electrophoresis analysis of 16S rRNA from human faecal samples

The gastrointestinal tract (GIT) of mammals harbours a complex community of obligate and facultative anaerobic bacteria. The composition of the GIT microbiota is dependent on the physiological condition, age, genetics, and diet of the host. During the past 5 years a number of molecular fingerprinting methods have been developed to characterise complex communities based on 16S rRNA sequence diversity. This paper describes the use of temperature and denaturing gradient gel electrophoresis (T/DGGE) of bacterial 16S rRNA/DNA in faecal samples from humans, in which special attention was given to the quantification of the sequence diversity. After birth the GIT community develops into a relatively simple community consisting of 1-8 major types within three months. Adults show more complex, but remarkably constant patterns. These patterns are hardly affected by changes in diet. Significant differences were observed between different individuals, particularly between genetically unrelated persons. In general, bacterial communities of faecal samples from genetically related adults (i.e. twins, brothers, sisters) show higher similarity of DGGE banding patterns than those from genetically unrelated individuals, although occasionally all persons in one family show highly similar profiles. The DGGE banding patterns of humans are significantly different from those of other mammals, such as pigs, gorillas and cats, indicating that genetic factors of the host affect the composition of the GI-tract flora. The major bacterial groups were identified by cloning and sequencing of the dominant 16S rDNA molecules. At least three sequences with highest homology to Ruminococcus obeum and Eubacterium halii and Fusobacterium prausnitzii were present in all human subjects and are likely to play a universal role in the GI-tract. Other sequences were found in variable ratios in different individuals

16S rRNA targeted DGGE fingerprinting of microbial communities

The past decades have seen the staggering development of molecular microbial ecology as a discipline that uses the detection of so-called biomarkers to monitor microbial communities in environment samples. A variety of molecules can be used as biomarkers, including cell-wall components, proteins, lipids, DNA or RNA. Especially, the application of small subunit ribosomal RNA (rRNA) and the corresponding genes have proven invaluable for advances in microbial ecology. Several types of fingerprinting methods have been developed for the description of microbial communities in environmental samples. Among the most commonly used approaches is denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments. DGGE allows separation of DNA fragment mixtures of equal length depending on their sequence. The separation is based on their sequence-specific melting point in a polyacrylamide gel with a gradient of a denaturant chemical (generally a combination of urea and formamide). DGGE allows for a rapid analysis and comparison of microbial communities. Compositional diversity can be visualized using DGGE where each band in principle represents a bacterial phylotype. After staining bands are visualized at each position in the gel where DNA molecules stopped migration. In principle, DGGE fingerprinting can resolve single base pair difference

Desulfobacca acetoxidans gen. nov., sp. nov., a novel acetate-degrading sulfate reducer isolated from sulfidogenic granular sludge

A mesophilic sulfate reducer, strain ASRB2(T), was isolated with acetate as sole carbon and energy source from granular sludge of a laboratory-scale upflow anaerobic sludge bed reactor fed with acetate and sulfate. The bacterium was oval-shaped, 1.3 x 1.9-2.2 μm, non-motile and Gram-negative. Optimum growth with acetate occurred around 37 °C in freshwater medium (doubling time: 1.7-2.2 d). Enzyme studies indicated that acetate was oxidized via the carbon monoxide dehydrogenase pathway. Growth was not supported by other organic acids, such as propionate, butyrate or lactate, alcohols such as ethanol or propanol, and hydrogen or formate. Sulfite and thiosulfate were also used as electron acceptors, but sulfur and nitrate were not reduced. Phylogenetically, strain ASRB2(T) clustered with the delta subclass of the Proteobacteria. Its closest relatives were Desulfosarcina variabilis, Desulfacinum infernum and Syntrophus buswellii, Strain ASRB2(T) is described as the type strain of Desulfobacca acetoxidans gen. nov., sp. nov