b6 mice carrying myd88 and tlr mutations were backcrossed 10 - 12 times to nod / ltj males and intercrossed to produce ko and heterozygous animals .
gf animals were re - derived from nod / ltj females impregnated by nod.myd88ko males and kept gf at taconic farms , germantown , ny , the university of chicago and washington university ( st .
asf was introduced to gf nod.myd88ko mice by adding cecal contents from donor mice to sterile drinking water .
wild - type gf mice were colonized with microbiota from spf nod.myd88ko animals by co - housing gf nod females and newborn progeny with spf myd88.ko females .
damage to the islets was scored in a blinded fashion , and graded as follows : 0 no visible infiltration ; i  periinsulitis ; ii - insulitis with < 50% and iii  with > 50% islet infiltration ( supplemental fig .
at least 100 islets in each group of 5 to 12 animals were scored . in microbiota transfer experiments
20 sections per pancreas cut at 40m intervals ( 10 islets / section ) were examined and scored ( combining grades ii and iii ) .
610 splenocytes alone , or 210 lymph node cells mixed with 410 irradiated splenocytes from b6.nod-(d17mit21-d17mit10)/ltj ( b6.g7 ) mice , per well of 96-well plates pretreated with anti - ifn- antibodies were incubated overnight with listed peptides .
lymphocytes were stained with antibodies against cd4 and cd8 to calculate the frequency of peptide - specific cells per 10 cd4 or cd8 t cells .
16s rrna gene sequences were edited and assembled into consensus sequences using phred and phrap , aided by xplorseq23 , and bases with a phrap quality score of < 20 were trimmed .
sequences were aligned using the nast online alignment tool ( http://greengenes.lbl.gov/cgi-bin/nph-index.cgi ) , and checked for chimeras using the online greengenes server ( http://greengenes.lbl.gov/cgi-bin/nph-bel3_interface.cgi ) with a window size of 300 and using the nast - aligned sequences31 .
b6 mice carrying myd88 and tlr mutations were backcrossed 10 - 12 times to nod / ltj males and intercrossed to produce ko and heterozygous animals .
gf animals were re - derived from nod / ltj females impregnated by nod.myd88ko males and kept gf at taconic farms , germantown , ny , the university of chicago and washington university ( st .
asf was introduced to gf nod.myd88ko mice by adding cecal contents from donor mice to sterile drinking water .
wild - type gf mice were colonized with microbiota from spf nod.myd88ko animals by co - housing gf nod females and newborn progeny with spf myd88.ko females .
damage to the islets was scored in a blinded fashion , and graded as follows : 0 no visible infiltration ; i  periinsulitis ; ii - insulitis with < 50% and iii 
at least 100 islets in each group of 5 to 12 animals were scored . in microbiota transfer experiments
20 sections per pancreas cut at 40m intervals ( 10 islets / section ) were examined and scored ( combining grades ii and iii ) .
610 splenocytes alone , or 210 lymph node cells mixed with 410 irradiated splenocytes from b6.nod-(d17mit21-d17mit10)/ltj ( b6.g7 ) mice , per well of 96-well plates pretreated with anti - ifn- antibodies were incubated overnight with listed peptides .
lymphocytes were stained with antibodies against cd4 and cd8 to calculate the frequency of peptide - specific cells per 10 cd4 or cd8 t cells .
16s rrna gene sequences were edited and assembled into consensus sequences using phred and phrap , aided by xplorseq23 , and bases with a phrap quality score of < 20 were trimmed .
sequences were aligned using the nast online alignment tool ( http://greengenes.lbl.gov/cgi-bin/nph-index.cgi ) , and checked for chimeras using the online greengenes server ( http://greengenes.lbl.gov/cgi-bin/nph-bel3_interface.cgi ) with a window size of 300 and using the nast - aligned sequences31 .
 type 1 diabetes ( t1d ) is a debilitating autoimmune disease that results from t cell - mediated destruction of insulin - producing  cells . 
 its incidence has increased during the past several decades in developed countries 1 , 2 , suggesting that changes in the environment ( including human microbial environment ) may influence disease pathogenesis . 
 the incidence of spontaneous t1d in non - obese diabetic ( nod ) mice can be affected by the microbial environment in the animal housing facility3 or by exposure to microbial stimuli , such as injection with mycobacteria or various microbial products 4,5 . here we show that specific - pathogen free ( spf ) nod mice lacking myd88 protein ( an adaptor for multiple innate immune receptors that recognize microbial stimuli ) do not develop t1d . 
 the effect is dependent on commensal microbes as germ - free ( gf ) myd88-negative nod mice develop robust diabetes , whereas colonization of these gf nod.myd88-negative mice with a defined microbial consortium ( representing bacterial phyla normally present in human gut ) attenuates t1d . 
 we also find that myd88-deficiency changes the composition of the distal gut microbiota , and that exposure to the microbiota of spf nod.myd88-negative donors attenuates t1d in gf nod recipients . 
 together , these findings indicate that interaction of the intestinal microbes with the innate immune system is a critical epigenetic factor modifying t1d predisposition . 
Methods Summary
Mice
Histopathology of diabetes
Elispot analysis
Sequence and phylogenetic analysis
Supplementary Material