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There are as many gut bacteria cells as our own cells. Do these bugs help us or just cause problems? Have their impact on human health been overestimated, and are they just leftover remnants of our ancestors (cf. appendix)? Do humans encourage microbe growth or is there a perpetual war to contain and exclude the influence of the microbiome?
There is ample evidence we actively encourage certain types of microbes to inhabit our intestinal tracts. New mothers produce oligosaccharides in breast milk that can only be digested by commensal bacteria and not by the baby. Soluble fibre that would otherwise be excreted serves as food for some bugs who reciprocate by providing nutrients and energy for us. There is also growing evidence our normal residents educate our immune system and exclude pathogens from attacking us.
It is important to know what type of organisms inhabit our gut so that we can better understand how they interact with us and with each other. As such, an extensive Bacteria and archaea database has been created. This can be accessed through either the species search tool or the supporting data tables (below).
Search for a microbiome species:
The Pu•biome Database currently has over 2600 bacteria and archaea reported to have been isolated from - or detected in - human faeces, gut biopsies or gastrointestinal mucosa. Each organism has its own page containing information about its physiology, growth tolerances, diet, response to antibiotics and substrate utilisation. To understand the methodology and caveats regarding the development of the database, click on the link above.
In support of the database, an array of over 30 sortable tables covering available test data for all 2600 microbes has been added. This will allow readers to compare bugs against a related set of attributes.
The General Physiology table (without images, or with images) is often a good place to start.
Some compounds have traditionally been used by microbiologists to identify and characterise unknown microorganisms. Many of the substances used for testing occur naturally (e.g., glucose), but others are rare in nature (e.g., arbutin) or 'artificial' (e.g., D-tartrate) and are typically just used for the purposes of identification. The tables below quantify the gut microbes that use these compounds, their presence in food, and the likely human response when encountering them.
In the vast majority of cases, when an organism digests a complex substrate it consumes at least one of the breakdown products. The tables below demonstrate this for some common carbohydrates and the exceptions are noted.
All the information was created by many scientists over decades; as such, an extensive reference database has been created to recognise and appropriately attribute their work.
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Work in progress ... Information pages. The sidebar to the left will guide the reader to all aspects of topics related to the gut microbiome. These pages will be filled over the coming months (hopefully).