FoodMicrobionet  v1.0  web  visualisation:  user  manual    Disclaimer:   the  web  visualisation  has  a   limited  set  of  functions  and  has  the  sole  function  of  allowing  inexperienced  user  to  visually  explore  FoodMicrobionet  and  to  perform  a  few  basic  search  operations.  To   fully  explore  FoodMicrobionet   it   is  advisable  to   import   the  nodes  and  edges   tables   into   a   network   visualisation   and   analysis   software   such   as   Gephi  (http://www.cytoscape.org/)  or  Cytoscape  (http://www.cytoscape.org/).    Supplementary  files  and  nodes  and  edges  specifications  are  released  when  a  paper  describing  a  given  version  of  FoodMicrobionet  is  published.  Please  refer  to  this  page:  http://www2.unibas.it/parente/wordpress/?page_id=761  for  further  information.    The  web  visualisation  is  available  at:  http://www2.unibas.it/parente/fmbn1_0web/  Please  use  one  of  the  following  browsers:  Firefox  Google  Chrome  Safari    The  visualisation  was  created  from  a  Gephi  project  using  the  Sigmajs  exporter  plugin  (v1.1.1)  https://marketplace.gephi.org/plugin/sigmajs-­‐exporter/    Start  the  visualisation:  Access  this  URL  in  your  browser:  http://www2.unibas.it/parente/fmbn1_0web/    The   visualisation   will   load   typically   in   <10   seconds,   but   it   depends   on   the   speed   of   your  connection    

   Although  some  of  the  functions  are  rather  intuitive  please  read  the  instructions  below  before  exploring  the  graph.    

Edges  (connections  between  samples  and  OTU  nodes)  represent  the  %  occurrence  of  a  given  OTU  in  a  sample.  The  size  of  the  nodes  is  related  to  their  weighted  degree  (i.e.  to  the  sum  of  weights  of  all  connection  to  the  node)  in  the  whole  network.  Therefore,  large  nodes  represent  OTUs  which  are  "important"  in  all  the  dataset,  but  the  actual  abundance  of  a  given  OTU  in  a  given  sample  is  represented  by  the  width  of  the  edge.  The  colour  of  the  nodes  was  attributed  on  the  basis  of  the  content  of  field  <Custom  2>  which  stores  information  on  Family  (for  OTU  nodes)  or  food  subgroup  according  to  FoodEx  classification  (for  sample  nodes).  Please  refer  to  specifications  for  nodes  table.    A  Yfan  Hu  layout  algorithm  was  used  to  organize  the  graph.  This  pushes  to  the  borders  OTU  nodes  with   few  connections  or  with   connections  with   low  weights   (i.e.  OTU  which  occur  at  low  abundances)  and  brings  sample  nodes  close  to  the  OTUs  which  dominate  their  bacterial  community,  and  vice  versa.  As  a  consequence,   the  network   is,   to   some  degree,  organized   in  areas   which   are   dominated   by   nodes   corresponding   to   a   given   food   type   and   by   the   OTU  which  most  frequently  appear  in  that  food.    There  are  several  areas  in  the  visualisation:    

   Zooming   in   will   eventually   display   node   labels.   Nodes   can   be   selected   by   clicking:   all  connected  nodes  are  shown  and  specific  information  for  the  selected  node  are  displayed.  When   a   node   is   selected   an   information   pane   appears   on   the   right   of   the   screen.   Two  examples   for   a  OTU  node   (Pseudomonas   fragi)   and   a   sample   node   (a   raw  beef   sample)   are  shown  below.  Please  refer  to  nodes  and  edges  specifications   for   information.  Clickable   links  are   provided   to   NCBI   taxonomy   (for   OTU   nodes)   and   to   the   original   article   in   which   the  sample   was   described   (for   sample   nodes).   Please   beware:   the   size   of   the   nodes   is   not  adjusted   dynamically   after   the   selection   or   search   operations.   This   operation   can   only   be  performed   with   network   visualisation   software   such   as   Gephi   after   a   filtering   and  recalculation   operation.   Therefore   only   edge   width   provides   a   rough   estimate   of   the  abundance  of  an  OTU  in  a  given  sample.      

       In  addition,  a  clickable  list  of  nodes  connected  to  the  selected  node  is  provided  at  the  bottom  of  the  Information  pane  (scroll  down  to  visualise).    Search  operations.    Only   limited   search   operations   can  be   performed  with   the  web   visualisation.  One   option   is  typing   in   the  search   field  and  hitting  return.  This  performs  a   search  on   the   label   field  of  all  nodes.   At   least   three   characters   (position  within   the   label   is   not   relevant)   are   needed   and  wildcards  (*,  ?)  do  not  have  effect  on  search.  If  a  single  hit  is  found  the  result  is  equivalent  to  clicking  on  a  node   (see  above).   If   several  hits  are   found,  a   list   is  displayed  below  the  group  selection  area:    

   The  first  item  of  the  list  is  displayed  by  default.  Selecting  another  item  will  display  the  node  and  its  connections.  The  OTU  nodes  are  labelled  with  the  name  of  the  taxon  corresponding  to  their  identification  level.  If  the  node  was  identified  only  at  the  genus  name  only  the  genus  name  is  shown  etc.  The  sample  nodes  label  always  include  the  FoodID  of  the  FoodEx  classification  (please  refer  to  specifications  for  nodes  table).  FoodMicrobionet  currently  includes  the  following  FoodIDs:  A008K:  Naturally  leavened  bread  doughs  (Group  21)  

A01BP:  Olives  products  (Group  17)  A01QX:  Cow,  ox  or  bull  fresh  meat  (Group  24)  A024V:  Cured  ripened  raw  sausages  (Group  2)  A02LVNWC:  Cow  milk,  semi  skimmed  (half  fat)  +  starter  (Group  81)  A02LY:  Cow  milk,  whole  (Group  81)  A02MC:  Sheep  milk  (Group  64)  A02MD:  Buffalo  milk  (Group  135)  A02NV:  Kefir  (milk  and  grain)  (Group  11)  A02QJ:  Mozzarella,  high-­‐moisture  (cow's  milk,  water  buffalo  milk)  (Group  32)  A02TY:  Cheese,  Fontina    (curd,  cheese)  (Group  22)  A02YH:  Cheese,  Canestrato  Pugliese  (curd,  cheese)  (Group  20)  A02ZL:  Cheese,  Caciocavallo  (curd,  cheese)  (Group  34)  A02ZQ:  Cheese,  Grana  Padano  (curd,  cheese)  (Group  1)  A02ZS:  Cheese,  Parmigiano  Reggiano  (curd)  (Group  129)  A048Y:  Starter  cultures,  undefined  (Group  58,  Group  126)  A049S;  Bovine  minced  meat  (Group  18)  XX;  Olive  fermentation  brine  (Group  55)    The  Group   selector   can  be  used   to   select   for  members  of   the   same   family   (OTU  nodes)  or  food   samples   belonging   to   the   same   food   subgroup   on   the   basis   of   the   colour   of   the   node.  Unfortunately   the   current   version   of   the   SigmaJS   exporter   does   not   create   a   list   of   group  names.  A  list  of  the  sample  nodes,  by  FoodID,  is  shown  above.    

   A  clickable  list  of  nodes  belonging  to  a  given  group  is  shown  in  the  information  pane.      Enjoy!    The  FoodMicrobionet  team