Supplementary Figure 1 Multicenter Randomised Control Trial 2746 Randomised

Home , Colpodella, Conoidasida, Eugregarinorida, Gregarinasina, Neogregarinorida, Syndiniales

Supplementary Figure 1 Multicenter randomised control trial 2746 randomised

947 control 910 MNP without zinc 889 MNP with zinc

223 lost to follow up 219 lost to follow up 183 lost to follow up 34 refused 29 refused 37 refused 16 died 12 died 9 died 3 excluded 4 excluded 1 excluded

671 in follow-up 646 in follow-up 659 in follow-up at 24mo of age at 24mo of age at 24mo of age

Selection for Microbiome sequencing 516 paired samples unavailable 469 paired samples unavailable 497 paired samples unavailable 69 antibiotic use 63 antibiotic use 67 antibiotic use 31 outside of WLZ criteria 37 outside of WLZ criteria 34 outside of WLZ criteria 6 diarrhea last 7 days 2 diarrhea last 7 days 7 diarrhea last 7 days

39 WLZ > -1 at 24 mo 10 WLZ < -2 at 24mo 58 WLZ > -1 at 24 mo 17 WLZ < -2 at 24mo 48 WLZ > -1 at 24 mo 8 WLZ < -2 at 24mo available for selection available for selection available for selection available for selection available for selection1 available for selection1

14 selected 10 selected 15 selected 14 selected 20 selected1 7 selected1

1 Two subjects (one in the reference WLZ group and one undernourished) had, at 12 months, no diarrhea within 1 day of stool collection but reported diarrhea within 7 days prior. red (undernourished)andblack(referenceWLZ)lines. by values areshown,withmediansforparticipantsprofiledincurrentstudyindicated quantile into clinicaltrialNCT00705445duringthefirst24monthsoflife.Medianand Supplementary Figure2. Length, cm Length (left) and weight (right) z-scores of children recruited Length(left)andweight(right)z-scoresofchildren

Weight, kg Protozoa, rarefied to 1000

80 reference WLZ undernourished

60 hness 40 Ri c

0 CTL MNP MNP + Zn

Supplementary Figure 3. Protozoan richness in stool samples, grouped by nutritional status and micronutrient supplementation. Samples were rarefied to 1000 reads. a age (p<0.001) nutritional status b 12 month reference WLZ (rarefied to 25,000) 2.00 24 month undernourished 1.7 reference WLZ 1.75 undernourished 1.6 3 1.50 1.5

1.25 1.4 Shannon diversity (H’) Shannon diversity (H’)

0 10000 20000 30000 40000 50000 0 10000 20000 30000 40000 50000 2 Read depth Read depth

supplementation site CTL rural MNP 1.7 urban

MNP+Zn Shannon diversity (H') 1.8 1 1.6 1.6 1.5 1.4 1.4 Shannon diversity (H’) Shannon diversity (H’) 1.2 0 0 10000 20000 30000 40000 50000 0 10000 20000 30000 40000 50000 Urban Rural Read depth Read depth

c (Bray-Curtis) ns ns ns ns ns 0.8 ns

0.7

0.6

0.5 Distance to centroid 0.4

CTL MNP CTL MNP MNP+Zn MNP+Zn 12 month 24 month

Supplementary Figure 4. Bacterial evenness and beta diversity. a, Rarefaction curves comparing species evenness (H′) by age group, micronutrient supplementation arm, nuritional status and site. Shaded regions represent standard error. Significance was tested at 25,000 read depth using a generalized linear model with stewise AIC-based model selection to identify significant variables. b, Boxplots comparing bacterial evenness by nutritional status and site. c, Variance among Bray-Curtis dissimilarities, calculated as distance to the centroid, between samples (n=150) by treatment arm and age group. 12 month CTL MNP MNP + Zn

Actinomucor Incertae Corynebacterium Cercozoa Lactobacillus Rhizopus Rothia Rhizomucor Lactobacillus ● ● Lactobacillus Rhizopus ● Candida−Lodderomyces clade ● ● ● ● ● Trichosporon Cercomonas ● ● Actinomyces Enterococcus Pichia ● ● ● Bifidobacterium ● ● ● Pediococcus Lactobacillus Wallemia Gemmiger Senegalimassilia ● Wallemia Blastobotrys Cryptosporida ● ● Toxoplasma ActinomucorTrichosporon ● ● Blautia ● ● Colpodella ● Blautia Clostridium_XlVb ● Terrisporobacter ● ● ● ● ● Dorea Pseudomonas ● ● ● Kodamaea Wallemia Eugregarinorida−distant−branch ● Rothia Romboutsia Eggerthella ● ● Conoidasida ● Enterococcus ● ● Romboutsia ● ● Flavonifractor● ● ●Clostridium_sensu_stricto Bifidobacterium● Blautia ● Kluyveromyces ● Trichomonascus ● Intestinibacter ● Candida Corynebacterium ● ● ● Senegalimassilia Saccharomyces Collinsella BlastobotrysAmoebozoa_unknown_group1 ● Pichia ● ● ● ● Lysinibacillus Acinetobacter ● ● ● ● Actinomyces ● ● ● ● Bacillus Collinsella ● ● StreptococcusLichtheimia Bifidobacterium CryptosporidiumSaccharomyces Lachnospiracea_incertae_sedis ● ● Clostridium_XlVb Bifidobacterium Streptococcus Bacillus StenotrophomonasLysinibacillus ● Colpodella ● ● ● ● ● ● ● ● ● ● ● Lactobacillus ● Lachnospiracea_incertae_sedis Ruminococcus2 ● Amylomyces Weissella Syndiniales● ● Trichomonascus ● Dorea Actinomyces Lactobacillus Dorea ● Streptococcus Candida ● ● ● Gregarina−distant−branch ● ● ● Paenibacillus Acinetobacter Eugregarinorida● Gregarinasina Clostridium_sensu_stricto Lachnospiracea_incertae_sedis ● Gregarinasina−distant−branch Gregarina ● Eggerthella ● ● Clostridium_XVIII Cercomonas ● Prevotella Dorea ● ● ● Olsenella Enterocytozoon ● ● Pseudomonas Rhizopus ● Actinomyces ● Bifidobacterium Streptococcus ● ● ● ● ● Anaerostipes ● Intestinibacter ● Bifidobacterium Bifidobacterium Clostridium_sensu_stricto ● ● Syndiniales ● Heteromita Actinomyces Anaerostipes ● ● ● ● ● FaecalibacteriumCandida−Lodderomyces clade ● ● Gemella ● Blastobotrys ● ● Neogregarinorida Actinomyces Collinsella ● ● Lachnospi● racea_incertae_sedis ● ● IncertaeKluyveromyces Lachnospiracea_incertae_sedis Actinomyces Bifidobacterium ● ● Conoidasida ● ● MegasphaeClostridium_XlVbra Faecalibacterium ● ● Lactobacillus Kodamaea ● Bacillus Penicillium Cryptomycota ● ● ● Streptococcus ● Clostridium_sensu_stricto ● Streptococcus ● ● Senegalimassilia Lichtheimiaceae Lichtheimia Eggerthella ● ● ● ● ● ● ● ● ● Pseudomonas ● Candida−Lodderomyces clade Lachnospiracea_incertae_sedisSlackia G●regarina−distant−branch Streptococcus Lachnospiracea_incertae_sedis Tritrichomonas● ● ● ● Urban Alveolata Colpodella Cryptosporidium ● Lachnospiracea_incertae_sedis● ● Lachnospiracea_incertae_sedis Gregarinasina Tritrichomonas ● ● Anaerococcus ● ● Streptococcus Gregarinasina Dorea ● Olsenella Holdemanella ● ● ● ● Lactobacillus ● ● Bromeliothrix ● ● ● ● ● Clostridium_XVIII Acinetobacter ● Bifidobacterium Pseudomonas Ruminococcus2 ● Lactobacillus Penicillium ● ● ● Streptococcus Clostridium_XI Collinsella ● Pediococcus ● Cryptosporidium Dorea Streptococcus ● ● ● ● ● ● Gregarinasina−distant−bCollinsellaranch Fusicatenibacter ● Streptococcus ● ● ● Enterococcus ● ● ● ● ● ● Streptococcus Varibaculum ● Faecalibacterium ● ● Lachnospiracea_incertae_sedis Alveolata ● Clostridium_XI uncultured ● Lactobacillus ● ● ● ● ● Prevotella● Bifidobacterium ● ● ● ● Lactobacillus Penicillium Lactobacillus ● Incertae Mucor Lactobacillus Lactobacillus ● ● ● Streptococcus Lachnospiracea_incertae_sedis Lichtheimia Streptococcus Anaerostipes Akkermansia Lactobacillus ● ● Rhizomucor ● Neogregarinorida● ● ● ● Collinsella Stenotrophomonas Bifidobacterium● Talaromyces ● Cryptosporida Cercozoa ● Lactobacillus Corynebacterium Pediococcus Gregarina Roseburia Lichtheimiaceae● ● ● ● Eubacterium ● ● Collinsella Pediococcus Alveolata Gemmiger ● ● ● Actinomyces ● Ruminococcus2 ● ● Clostridium_sensu_stricto Blautia Pediococcus ● ● Actinomucor ● Clostridium_XVIII ● ● ● Gregarina−distant−branch Blautia ● Pseudomonas ● ● ● ● Clostridium_sensu_stricto ● ● Roseburia ● Finegoldia Enterococcus uncultured Amylomyces ● ● ● ● ● Olsenella Flavonifractor Fusicatenibacter Prevotella ● ● ● Anaerococcus ● Streptococcus ● ● ● ● Paenibacillus ● ● ● ● ● Clostridium_sensu_stricto Saccharomyces Lichtheimiaceae ● Prevotella Flavonifractor Pichia Intestinibacter Finegoldia ● ● Mogibacterium Lactobacillus Blautia Lactobacillus Bifidobacterium ● Clostridium_XVIII Mucor ● ● ● ● ● ● AmylomycesAnaerostipes ● ● ● ● Hanseniaspora ● ● Lactobacillus ● ● ● ● Enterococcus ● ● Streptococcus Clostridium_XVIII Enterococcus ● Clostridium_XVIII Rhizomucor ● Lachnospiracea_incertae_sedis● ● ● ● ● (5) ● (10) ● (9)

Saccharomyces AkkermansiaClostridium_XlVb BifidobacteriumRhizomucor Streptococcus Nakaseomyces−Candida clade Gemella Pseudomonas Lactobacillus ● ● Stenotrophomonas Pichia ● ● ● Dorea Bacillus ● ● Mucor Rhizopus ● ● Collinsella ● Penicillium ● CollinsellaAlveolata−distant−branch ● ● BifidobacteriumBifidobacterium ● Blautia Dorea Lactobacillus ● Clostridium_sensu_stricto● ● Pseudomonas Streptococcus ● ● ● ● Olsenella Cryptomycota ● Rothia ● ● Eugregarinorida−distant−branch ● PseudomonasEugregarinorida−distant−b● ranch ● ● ● Bifidobacterium CercomonasClostridium_XVIII ● Atopobium ● Geotrichum● Candida−Lodderomyces clade ● ● Blautia ● ● ● Neogregarinorida Syndiniales Stenotrophomonas Actinomyces Lactobacillus ● Cercozoa● PucciniaEugregarinorida−distant−branch Varibaculum ● ● ● Lactobacillus ● ● ● ● Lichtheimiaceae Lactobacillus Trichomonascus ● ● Lactobacillus Heteromita Geotrichum ● Lichtheimia ● ● Talaromyces Actinomyces● Lactobacillus● ● Streptococcus ● Actinomucor ● WallemiaSaccharomyces Cercomonas ● Lactobacillus● Euglyphida ● ● Atopobium ● ● Holdemanella Anaerococcus Lactobacillus Hanseniaspo● r●a ● ● ● Prevotella● ● Cercomonas ● ● ActinomycesPenicillium● ● ● ● LactobacillusCandida−Lodderomyces clade Gregarina Actinomyces ●LactobacillusPediococcus Lactobacillus ● Wicherhamiella−Candida clade Eugregarinorida ● ● ● ● Weissella● Streptococcus● Gregarinasina−distant−branch uncultured ● Incertae ● ● Amylomyces ● ● Lactobacillus Amoebozoa_unknown_group3 ● Romboutsia ● ● ● Prevotella Pediococcus ConoidasidaAnaerostipes ● Neogregarinorida ● Gemella Eugregarinorida Clostridium_XlVb Toxoplasma Gordonibacter Alveolata−distant−branch ● Mucor Collinsella● ● ● ● Enterococcus ● ● Eggerthella Gemmiger Lactobacillus ● ● ● ● Actinomyces Candida Weissella ● Hanseniaspora Alveolata−distant−branch ● ● ● Amoebozoa_unknown_group1 ● Enterococcus Bifidobacterium Rothia● Alveolata ● Rhizopus Mogibacterium ● ● ● AkkermansiaGregarina−distant−branch Trichomonascus ● Pichia ● Blastobotrys ● ● Cercomonadidae ● ● Lactobacillus Cryptomycota Clostridium_XlVb ● ● Longamoebia Streptococcus● ● Corynebacterium ● Enterococcus Rhizomucor ● Slackia Holdemanella Enterococcus● Lichtheimiaceae Cryptosporidium Weissella ● Collinsella ● ● ● Gregarinasina Trichomonascus Bifidobacterium Enterocytozoon ● Colpodella Clostridium_sensu_stricto● Anaerostipes ● ● Streptococcus ● Streptococcus ● ● Blautia ● ● ● Enterococcus● ● ● ● Cercomonadidae Flavonifractor● Lichtheimia ● ● Prevotella Megasphaera Streptococcus Heteromita Clostridium_XlVb Cryptomycota ● ● Cercomonadidae Olsenella Lactobacillus ● Apicompl● exa Actinomyces ● Streptococcus Clostridium_XVIII ● Streptococcus ● Cryptosporida ● ● Lachnospiracea_incertae_sedis Streptococcus Colpodella uncultured Weissella ● ● Ruminococcus2 Streptococcus ● Faecalibacterium Conoidasida ● ● Wicherhamiella−Candida clade ● Bifidobacterium Atopobium ● Clostridium_XlVb Amoebozoa_unknown_group3 ● ●Slackia Heteromita ● Lysinibacillus ● Lachnospiracea_incertae_sedis ● CandidaBromeliothrixGemmiger ● ● ● ● Bacillus Lactobacillus Rhizomucor ● Eubacterium Pediococcus ● ● ● LaStcreptococcushnospiracea_incertae_sedis SenegalimassiliaColpodella Intestinibacter Streptococcus Gregarina−distant−branch ● ● Paenibacillus Collinsella Kodamaea ● ● Pichia ●Finegoldia Candida−Lodderomyces clade ● Enterocytozoon● ● Streptococcus Gregarinasina Lachnospiracea_incertae_sedis Wallemia ● ● ● Nakaseomyces−Candida● clade ● ● ● Rural Streptococcus ● Clostridium_sensu_strictoAnaerococcusSlackia ● Eubacterium Lactobacillus ● ● ● ● Mogibacterium Naganishia ● ● Pediococcus Clostridium_sensu_stricto Lactobacillus ● Lachnospiracea_incertae_sedis Actinomucor ● Actinomyces ● Roseburia Clostridium_XlVb Amylomyces ● ● Senegalimassilia Gregarina−distant−branch Lactobacillus Lachnospiracea_incertae_sedisRuminococcus2 ● ● ● Lactobacillus Collinsella Dorea ● Eubacterium ● Blautia ● Gregarinasina−distant−brancLactobacillush Euglyphida Eggerthella ● Lactobacillus Ruminococcus2 CorynebacteriumRomboutsia Streptococcus ● Rothia ● Clostridium_XI Fusicatenibacter Lactobacillus ● Cercozoa ● ● Intestinibacter● Incertae ● Blautia● ● Streptococcus ● ● Lactobacillus● ● Gregarinasina● Lachnospiracea_incertae_sedis ● ● Anaerostipes Lactobacillus Actinomyces ● Lactobacillus Terrisporobacter ● Lactobacillus● Wallemia ● ● Colpodella LactobacillusBlautia Geotrichum ● Bifidobacterium Amylomyces ● Bifidobacterium ● Anaerostipes ● Conoidasida Romboutsia ● Eggerthella Fusicatenibacter Clostridium_XVIII Blautia ● ● Gregarina−distant−branch ● Bacillus ● ● Actinomyces ● Apicomplexa Toxoplasma Lactobacillus ● ● ● ● ● Lactobacillus ● Senegalimassilia ● FaecalibacteriumBifidobacterium● Pediococcus Faecalibacterium Puccinia Lachnospi● racea_incertae_sedisHoldemanella ● ● Flavonifractor ● Flavonifractor Alveolata ● ● ● Finegoldia Tritrichomonas ● ● Anaerostipes ● ● Cryptosporidium Trichosporon ● ● Bifidobacterium Paenibacillus● ● Clostridium_sensu_stricto ● Clostridium_XVIII Pediococcus Tritrichomonas Lysinibacillus ● Gordonibacter Intestinibacter Bromeliothrix Lactobacillus Blautia Longamoebia Anaerostipes● Clostridium_XlVbMogibacterium Gregarina−distant−branch ● ● ● Bromeliothrix Dorea Actinomucor● DoreaGregarina Amoebozoa_unknown_group1 Trichosporon Cryptosporida● Saccharomyces ● ● Olsenella Tritrichomonas Gemmiger ● Roseburia ● Acinetobacter ● ● ● ● ● ● ● ● ● Lactobacillus ● Mucor ● Dorea ● ● Colpodella● ● Neogregarinorida ● ● Lactobacillus ● ● ●● Lichtheimia ●Longamoebia Finegoldia ● ● Toxoplasma ● Clostridium_XVIII EnterocytozoonClostridium_sensu_strictoClostridium_XlVb LichtheimiaceaeAmoebozoa_unknown_group1 Acinetobacter ● Bifidobacterium ● ● ● ● Corynebacterium ● ● Gregarina● Lachnospiracea_incertae_sedis ● Blautia ● Weissella Enterococcus Incertae Clostridium_sensu_stricto● ● ● ● Bacillus Syndiniales Clostridium_sensu_stricto Clostridium_XVIII Terrisporobacter Naganishia Clostridium_XlVb ● Weissella ● ● ● ● ● ● ● ● ● ● ● ● Lactobacillus AcinetobacterPseudomonasVaribaculum Pseudomonas Cryptosporidium Kluyveromyces Paenibacillus● Lactobacillus ● Alveolata● Clostridium_sensu_stricto Akkermansia ● Lysinibacillus ● ● ● (16) ● ● ● (14) ● ● Gregarina−distant−branch (14) ● ● ● Lactobacillus● ● ●

● bacteria ● protozoa ● fungi

Supplementary Figure 5. Graphic representations of microbial networks representing predicted microbial interactions in 12 month old children, grouped by place of residence and micronutrient supplementation arm. Nodes represent bacterial OTUs (yellow) and protozoan and fungal genera (red and grey, respectively), scaled by betweenness centrality scores. Edges represent significant positive (grey) and negative (blue) correlations among microbiota. Taxa with no predicted interactions have been removed. Numbers of samples used to generate each network are indicated within brackets.