Intestinal tract represents one of the most complex ecosystems in nature. In this part of the human body, are concentrated a great number of known microorganisms groups. In addition, each individual ecosystem is peculiar with its own distinct characteristics and has the propriety to change during time. It is very important to known that we are talking about a dynamic ecosystem. Thus the knowledge of this ecosystem and its interactions with the host are still at the beginning. For many years the lack of adequate methodologies has influenced the analysis. Until now a great part of the intestinal microbiota information has been reached through analyzing colony isolates from faeces or intestinal materials and then cultured in lab. This approach is still the predominant one, in spite of the inability to reproduce the natural conditions exiting in GI tract in the lab and thus many microbes are left uncultivable. The explanations of this are not well understood, but some causes considered include: • some bacteria have obligate interactions with host or other microorganisms; • some bacteria require unknown growth conditions (Zoetendal et al., 1998); • some bacteria are in a physiological state which is not good for a direct culture from fresh faeces or fresh intestinal material. This leads to a method which is often not precise. That is also due to the scarce affinity of part of the microorganisms present in GI tract to the majority of the media commonly used. Since intestinal ecosystem is dominated by obligate anaerobes, it is easily understood why investigation by culture-dependent techniques is laborious and prone to misinterpretation. In spite of this, it is still important to have a classical isolation approach based on culture methods (non-selective and selective media) which can allow us to have basic information about the number and classification of the cultivable part of the microorganisms present in a specific GI tract. In case of culture methods the identification is based principally on phenotypic characteristics. Molecular techniques are useful to identify and classify the non cultivable microorganism fraction that seems to be the biggest part of the GI ecosystem. Those methods reveal that each individual harbours a specific bacterial intestinal community, but few dominant bacterial species may be present in many individuals (Zoetendal et al., 1998). Molecular techniques have improved precision, rapidity of analysis and sensibility and are also useful to calculate the evolutionary relatedness between microbial strains. In the end, the best approach is a combination of traditional techniques and molecular techniques. Further development of molecular techniques will reveal details still obscure about the GI tract microbiota composition.
Methods of analysis of the intestinal microbiota / Mattarelli P.; Tabanelli D.; Baffoni L.; Sgorbati B.; Biavati B.. - STAMPA. - (2010).
Methods of analysis of the intestinal microbiota
MATTARELLI, PAOLA;BAFFONI, LOREDANA;SGORBATI, BARBARA;BIAVATI, BRUNO
2010
Abstract
Intestinal tract represents one of the most complex ecosystems in nature. In this part of the human body, are concentrated a great number of known microorganisms groups. In addition, each individual ecosystem is peculiar with its own distinct characteristics and has the propriety to change during time. It is very important to known that we are talking about a dynamic ecosystem. Thus the knowledge of this ecosystem and its interactions with the host are still at the beginning. For many years the lack of adequate methodologies has influenced the analysis. Until now a great part of the intestinal microbiota information has been reached through analyzing colony isolates from faeces or intestinal materials and then cultured in lab. This approach is still the predominant one, in spite of the inability to reproduce the natural conditions exiting in GI tract in the lab and thus many microbes are left uncultivable. The explanations of this are not well understood, but some causes considered include: • some bacteria have obligate interactions with host or other microorganisms; • some bacteria require unknown growth conditions (Zoetendal et al., 1998); • some bacteria are in a physiological state which is not good for a direct culture from fresh faeces or fresh intestinal material. This leads to a method which is often not precise. That is also due to the scarce affinity of part of the microorganisms present in GI tract to the majority of the media commonly used. Since intestinal ecosystem is dominated by obligate anaerobes, it is easily understood why investigation by culture-dependent techniques is laborious and prone to misinterpretation. In spite of this, it is still important to have a classical isolation approach based on culture methods (non-selective and selective media) which can allow us to have basic information about the number and classification of the cultivable part of the microorganisms present in a specific GI tract. In case of culture methods the identification is based principally on phenotypic characteristics. Molecular techniques are useful to identify and classify the non cultivable microorganism fraction that seems to be the biggest part of the GI ecosystem. Those methods reveal that each individual harbours a specific bacterial intestinal community, but few dominant bacterial species may be present in many individuals (Zoetendal et al., 1998). Molecular techniques have improved precision, rapidity of analysis and sensibility and are also useful to calculate the evolutionary relatedness between microbial strains. In the end, the best approach is a combination of traditional techniques and molecular techniques. Further development of molecular techniques will reveal details still obscure about the GI tract microbiota composition.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
