New paper

Featured

The paper describing FoodMicrobionet v 3.1 is now available:

Parente, E., De Filippis, F., Ercolini, D., Ricciardi, A., Zotta, T., 2019. Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database. International Journal of Food Microbiology, 305 (September 2019): 108249 DOI: 10.1016/j.ijfoodmicro.2019.108249.

Check it out, there are several important novelties. Don’t forget to read the supplementary material and to access the datasets and scripts on Mendeley datasets.

You can download it for free at https://authors.elsevier.com/a/1ZDuwcF3i1Aey until August 3 2019.

FMBN 3.2.3 version details

  • FoodMicrobionet now includes 104 studies and 5335 samples
  • minor changes to lineages for some taxa
  • corrected a few inconsistencies in the study table
  • added food codes to study description for version 3.1
  • added surname and email field for the corresponding author of studies
  • corrected a mismatch in row numbers and sample ids for the sample table (and corrected edges). This was probably due to deletion of a sample from a previous version and was causing errors in selection with the Shiny app after sample with id 1572.

FMBN includes an impressive variety of food types, with data on both foods and food environments:

  • Animal and vegetable fats and oils and primary derivatives thereof 53
  • Composite dishes 115
  • Eggs and egg products 21
  • Fish, seafood, amphibians, reptiles and invertebrates 362
  • Fruit and fruit products 252
  • Grains and grain-based products 149
  • Major isolated ingredients, additives, flavours, baking and processing aids 72
  • Meat and meat products 1086
  • Milk and dairy products 2516
  • Vegetables and vegetable products 537
  • Sugar and similar, confectionery and water-based sweet desserts 42
  • Alcoholic beverages 30
  • Starchy roots or tubers and products thereof, sugar plants 17
  • Legumes, nuts, oilseeds and spices 65
  • Seasoning, sauces and condiments 18

This version will be not made public (but parts of it will be released as supplementary material for review articles). We are however willing to discuss collaboration opportunities with other research groups.

ShinyFMBN 2.1.2 is available for download

The development version of ShinyFMBN 2.1.2 (I had time only for limited testing) is available for download. The app includes access to records of FoodMicrobionet 3.1 and a new version of the manual is available. If you have time to test it please do and let me know:

  • if you find a bug provide enough information to reproduce the error
  • if your testing is successful (i.e. everything seems to work smoothly) please let me know which machine, operating system, browser and R version you have used for testing (see examples on page 11 of the manual)

New graphs in the app!

Now ShinyFMBN (v2.1.2) can produce directly a number of useful exploratory graphs, including prevalence and abundance plots, bar plots of taxa abundance and box/violin plots for taxa abundance. All the graphs can be personalised.

a stacked bar plot for OTU abundance
a box plot of the most abundant and prevalent taxa
A violin plot of the most abundant and prevalent taxa: the level of aggregation can be personalised and the taxa to be displayed can be selected from a menu.

The new app will be released in February 2020.

4000!

There are more than 4000 samples in version 3.2 of FoodMicrobionet.

More will be added until the end of September. After that, development will be stopped for lack of funding and time and the new version is scheduled to be released on February 14th, 2020, together with a revised app and a few service scripts.

Food type (L1)Count
Animal and vegetable fats and oils and primary derivatives thereof52
Composite dishes115
Eggs and egg products21
Fish, seafood, amphibians, reptiles and invertebrates183
Fruit and fruit products135
Grains and grain-based products54
Major isolated ingredients, additives, flavours, baking and processing aids72
Meat and meat products899
Milk and dairy products2048
Vegetables and vegetable products427

A new version is in development

I am working on version 3.2 of FoodMicrobionet (which will include 70+ studies and 3500+ samples) and version 2 of the Shiny app. However, these versions will not be made public anytime soon and will only be shared with partners with whom I have research collaborations. If you are interested in collaborating in the development of FoodMicrobionet or in the submissions of research projects related to FoodMicrobionet contact me.

FMBN2MBanalyst

This is a new script for converting *_agg.RDS or *_physeq.Rdata files created using the ShinyFMBN app (v1.1 or later) in OTU, taxonomy and sample metadata tables suitable for use with the Marker Data Profiling analysis pipeline of Microbiome Analyst (https://www.microbiomeanalyst.ca). Click here to download. Please beware: I am too old to be willing to write foolproof scripts and try to predict the vagaries of lazy users. If you are a fool (and/or don’t read/follow the instructions provided as comments in the script) the script will not work. Period.