1. Search for Microbiota Entries
In the field of “Search for Microbiota Entries”, users can find microbes by searching microbe species name, MC ID, microbiota-derived metabolites & component (MDM&MDC) name, microbiota-secreted proteins (MSP) name, epigenetic molecule name, MDM&MDC ID (MT ID), MSP ID (PT ID), EM ID among the entire textual component of MIAOME. Query can be submitted by entering keywords into the main searching frame. The resulting webpage displays profiles of all the Microbiota directly related to the search term, including MC ID, MIC Name, phylum, and MIC options. By clicking the hyperlink “MIC Info”, the details of microbes, which include general information of microbiota, the metabolites & component derived by this microbiota, the proteins secreted by this microbiota, and the epigenetic modifications affected by these microenvironmental factors will be displayed. Also, you can get the details of epigenetic modifications affected by MDM&MDC by clicking the hyperlink “Meta Info” and get the details of epigenetic modifications affected by MSP by clicking the hyperlink “Pro Info”. To facilitate a more customized input query, the wild characters of “*” and “?” are also supported in MIAOME.
1. If search: “Lactobacillus acidophilus”, find several MIC entries which are named as “Lactobacillus acidophilus ATCC 4796”, “Lactobacillus acidophilus NCFM”, “Lactobacillus acidophilus”, etc;
2. If search: “MC1011”, find corresponding MIC “Lactobacillus acidophilus” with this MC ID;
3. If search: “Resveratrol”, find 2 microbes produced this metabolite;
4. If search: “Rv2966c”, find 2 microbe that produced this protein;
5. If search: “EIF3A”, find 2 microbes affect this gene;
6. If search: “Candida?”, find a variety of microbes belonging to the Candida genus. Here“?” represents any single character;
7. If search: “Candida *”, find all microbes whose names have this word. Here “*” represents an arbitrary string.
For example: if you want to know the detailed information of “Lactobacillus acidophilus”, you can search it by typing “Lactobacillus acidophilus” in the “Search for MIC Entries” field. Brief information on Escherichia coli will be provided.
By clicking the “MIC Info” button, the detailed information page of “Lactobacillus acidophilus” will be displayed. Details of Microbe Species (MIC) is divided into three parts, “General Information of MIC”, “Full List of Metabolites&components derived by This MIC”, The general information of “Lactobacillus acidophilus” including its “MIC Name”, “Synonyms”, “Lineage”, “Oxygen Sensitivity”, “Microbial Metabolism”, “Gram”, “Host Relationship” and “External Links”. If you want to know more about “Lactobacillus acidophilus”, you can link to other related databases by clicking the hyperlinks in the “External Links” field.
“Full List of Metabolites&components derived by This MIC” includes the metabolites derived by “Lactobacillus acidophilus”, and the epigenetic modifications affected by these microbiota-derived metabolites. By clicking on the specific metabolites, the general information will be displayed.
By clicking on the “Meta Info” hyperlink, the details of this microbiota-derived metabolite will be displayed.
By clicking on the “EM Info” hyperlink, the details of this specific gene which was nidificated by this metabolite will be displayed.
2. Search for MIC Entries by MIC Name based on Taxonomic Phylum
Alternatively, in the field of “Search for MIC Entries by MIC Name based on Taxonomic Phylum”, users can find MIC entries by searching phylum-MIC name pair among the entire textual component of MIAOME. First, users should select a phylum from the drop-down list in the first column. Then corresponding MIC name options will become available after a short period. By clicking the “Search” button, the brief information of the selected MIC will be shown.
For example, if you want to know the detailed information of microbiota, you can select “Bacteroidetes” in the “Step 1 column and then select “Bacteroides fragilis” in the Step 2 drop-down list. After clicking the “Search” button, brief information on “Bacteroides fragilis” will be provided.
By clicking the “MIC Info” button, the detailed information page of “Bacteroides fragilis” will be displayed.
3. Search for MIC Entries by MIC Name based on Metabolite
Alternatively, in the field of “Search for MIC Entries by MIC Name based on Metabolite”, users can find MIC entries by the name of microbiota-derived metabolites (MDM) pair among the entire textual component of MIAOME. First, users should select a metabolite from the drop-down list in the first column. Then a list of microbe names under the selected type will be available for selection. By clicking the “Search” button, the brief information of the selected MIC will be provided.
For example, if you want to know the epigenetic modification affected by metabolite, you can select “Butyrate” in the Step 1 column and then select “Fusobacterium nucleatum” in the Step 2 drop-down list. After clicking the “Search” button, brief information on “Fusobacterium nucleatum” will be provided.
By clicking the “MIC Info” button, the detailed information page of Fusobacterium nucleatum will be displayed.
4.Search for MIC Entries by MIC Name based on Protein
Alternatively, in the field of “Search for MIC Entries by MIC Name based on Protein”, users can find MIC entries by the name of microbiota-secreted proteins pair among the entire textual component of MIAOME. First, users should select a protein name from the drop-down list in the first column. Then a list of protein names under the selected type will be available for selection. By clicking the “Search” button, the brief information of the selected MIC will be provided.
For example, if you want to know the epigenetic modification affected by microbiota-secreted protein, you can select “Rv1988” in the “Step 1 column and then select “Mycobacterium bovis” in the Step 2 drop-down list. After clicking the “Search” button, brief information on “Mycobacterium bovis” will be provided.
By clicking the “MIC Info” button, the detailed information page of Mycobacterium bovis will be displayed.
5.Search for the microbiota-derived metabolites that influence the epigenome.
In this field, users can find interactions between MIC and Host Epigenome by searching metabolite name, MT ID, MIC name, MC ID, Epigenetic molecule among the entire textual component of MIAOME. The query can be submitted by entering keywords into the main searching frame. The resulting webpage displays profiles of all the metabolites directly related to the search term, including MT ID, Unify Name, Synonym, Formula and the epigenetic modification information of this metabolite. By clicking the hyperlink “Meta Info”, the details of this metabolite in MIAOME will be displayed. “The epigenetic modification information of this metabolite” includes the epigenetic modification information affected by the searched metabolite. “The microbes that produce this metabolite” includes the microbe information produced by the searched metabolite. To facilitate a more customized input query, the wild characters of “*” and “?” are also supported.
1. If search: “Folate”, find the single entry of metabolite “Folate”;
2. If search: “MT062”, find a single entry of metabolite “Hydrogen sulfide (H2S)” with this MT ID;
3. If search: “Escherichia coli”, find various entries of metabolites produced by the microbe “Escherichia coli”;
4. If search: “MC0083”, find various entries of metabolites produced by this MC ID;
5. If search: “H3”, find various entries of metabolites that influenced this Epigenetic molecule.
6. Search for Metabolite Entries by the Name of Metabolite based on Metabolite Type
Alternatively, in the field of “Search for Metabolite Entries by the Name of Metabolite based on Metabolite Type”, users can find metabolite based on metabolite type pair among the entire textual component of MIAOME. First, users should select the metabolite type from the drop-down list in the first column. Then a list of metabolite names under the selected type will be available for selection after a short time. By clicking the “Search” button, the brief information of the selected metabolite will be shown.
For example, if you want to know the detailed information of metabolite reprogramming the host epigenome, you can select “Short-chain fatty acids (SCFAs)” in the Step1 column and then select “Acetate” in the Step 2 drop-down list. After clicking the “Search” button, brief information on “Acetate” will be provided.
By clicking the “Meta Info” button, the details of acetate reprogramming the host epigenome will display.
7. Search for Metabolite Entries by the Name of Metabolite based on Microbiota
Alternatively, in the field of “Search for Metabolite Entries by the Name of Metabolite based on Microbiota”, users can find metabolite based on microbe among the entire textual component of MIAOME. First, users should select the microbiota name from the drop-down list in the first column. Then a list of metabolite names under the selected microbe will be available for selection after a short time. By clicking the “Search” button, the brief information of the selected metabolite will be shown.
For example, if you want to know the metabolite detailed information of produced by microbiota, you can select “Bacteroides fragilis” in the Step 1 column and then select “Propionate” in the Step 2 drop-down list. After clicking the “Search” button, the brief information on “Propionate” will be provided.
By clicking the “Meta Info” button, the details of acetate reprogramming the host epigenome will display.
8. Search for the microbiota-secreted proteins that influence the epigenome
In this field, users can find interactions between MIC and Host Epigenome by searching protein name, PT ID, MIC name, MC ID, Epigenetic molecule among the entire textual component of MIAOME. The query can be submitted by entering keywords into the main searching frame. The resulting webpage displays profiles of all the proteins directly related to the search term, including PT ID, Unify Name, Synonym, Protein Entry and the epigenetic modification information of this protein. By clicking the hyperlink “Pro Info”, the details of this protein in MIAOME will be displayed. “The epigenetic modification information of this protein” includes the epigenetic modification information affected by the searched protein. “The microbes that produce this protein” includes the microbe information produced by the searched protein. To facilitate a more customized input query, the wild characters of “*” and “?” are also supported.
1. If search: “CagA”, find a single entry of protein “CagA”;
2. If search: “PT004”, find a single entry of Protein Entry “ESAT-6” with this PT ID;
3. If search: “Helicobacter pylori”, find various entries of proteins produced by the microbe “Helicobacter pylori”;
4. If search: “MC0083”, find various entries of proteins produced by this MC ID;
5. If search: “Histone H3”, find various entries of proteins that influenced this epigenetic molecule.
9. Search for Protein Entries by the Name of Protein based on Microbiota
Alternatively, in the field of “Search for Protein Entries by the Name of Protein based on Microbiota”, users can find protein based on microbe among the entire textual component of MIAOME. First, users should select the microbiota name from the drop-down list in the first column. Then a list of protein names under the selected microbe will be available for selection after a short time. By clicking the “Search” button, brief information on the selected protein will be shown.
For example, if you want to know the metabolite detailed information produced by microbiota, you can select “Salmonella enterica” in the “Step 1 column and then select “Acetyltransferase” in the Step 2 drop-down list. After clicking the “Search” button, brief information on “Acetyltransferase” will be provided.
By clicking the “Meta Info” button, the details of acetate reprogramming the host epigenome will display.
10. Search for Microbiota Entries
In the field of “Search for Microbiota Entries”, users can find microbes by searching microbe species name, MC ID, molecule name, EM ID among the entire textual component of MIAOME. The query can be submitted by entering keywords into the main searching frame. The resulting webpage displays profiles of all the Microbiota directly related to the search term, including MC ID, MIC Name, and MIC options. By clicking the hyperlink “MIC Info”, the details of epigenetic modifications affected by this microbiota will be displayed.
1. 1.If search: “Escherichia coli”, find several MIC entries which are named as “Escherichia coli”, “Escherichia coli Nissle 1917”;
2. If search: “MC0083”, find corresponding MIC “Escherichia coli” with this MC ID;
3. If search: “AB1”, find a microbe that influences this gene;
For example, if you want to know the microbiota detailed information of body site , in the Step 1: Please Select a body site name“ blood” column and then select “Firmicutes” in the drop-down list of Step 2 . After clicking the “Search” button, the brief information on “Firmicutes” will be provided.
11. Search for Epigenetic Molecule Entries
In the field of “Search for Epigenetic Molecule Entries”, users can find Epigenetic molecules by searching microbe species name, MC ID, microbiota-derived metabolites (MDM) name, microbiota-secreted proteins (MSP) name, MDM ID, MSP ID among the entire textual component of MIAOME. The query can be submitted by entering keywords into the main searching frame. The resulting webpage displays profiles of the Epigenetic molecule directly related to the search term, including EM ID, EM name, EM type, and EM option. By clicking the hyperlink “EM Info”, the details of the Epigenetic molecule, which include general information of the Epigenetic molecule, the metabolites that influence this epigenetic modification, and the proteins that influence this epigenetic modification. Also, you can get the details of epigenetic modifications affected by MDM by clicking the host genetic factor hyperlink “Meta Info” and get the details of epigenetic modifications affected by MSP by clicking the hyperlink “Pro Info”. To facilitate a more customized input query, the wild characters of “*” and “?” are also supported in MIAOME.
1. If search: “Histone H2B”, find EM entry which is named as “Histone H2B”;
2. If search: “EM01743”, find corresponding Epigenetic molecule “ARL4C” with this EM ID;
3. If search: “Folate (B9)”, find 8 Epigenetic molecules influenced by this metabolite;
4. If search: “NuE”, find 3 Epigenetic molecules influenced by this protein;
5. If search: “Eubacterium hallii”, find dozens of Epigenetic molecules influenced by this microbe.
12. Search for Epigenetic Molecule Entries by the Name of Epigenetic Molecule based on ICD11 Code
In this field, users can search epigenetic molecule information by selecting a certain ICD code from the drop-down list. For example, if search “IF84:Opisthorchiasis”, and chose “AACS” gene, users can access the basic information of AACS associated with the opisthorchiasis disease. If you want to know more about this gene, you can click the corresponding “EM Info” button.
13. Download the Full Data of MIAOME from A Variety of Customized Links
MIAOME provides functions for downloading all MIAOME data from various customized links.
(1) Data of human microbiome reprogram the host epigenome data: (i) Data of host epigenome reprogramed by human microbiota metabolites; (ii) Data of host epigenome reprogramed by human microbiota proteins.
(2) Data of microbes, microbiota metabolites, microbiota proteins information: (i) Microbes data (microbe species name / lineage / metabolism / genome statistics / external links, etc.); (ii) Microbiota-derived metabolites data (metabolites name / formula / synonyms / description / external links, etc.); (iii) Microbial surface antigens & secreted proteins data (proteins name / length / location / external links, etc.); (iiii) Specific Epigenetic molecules data (Epigenetic molecules name / gene type / chromosome information / external links, etc.).
