Persistent Gut Microbiota Immaturity in Malnourished Bangladeshi Children

Sathish Subramanian; Sayeeda Huq; Tanya Yatsunenko; Rashidul Haque; Mustafa Mahfuz; Mohammed A Alam; Amber Benezra; Joseph DeStefano; Martin F Meier; Brian D Muegge; Michael J Barratt; Laura G VanArendonk; Qunyuan Zhang; Michael A Province; William A Petri; Tahmeed Ahmed; Jeffrey I Gordon

doi:10.1038/nature13421

. Author manuscript; available in PMC: 2014 Dec 19.

Published in final edited form as: Nature. 2014 Jun 4;510(7505):417–421. doi: 10.1038/nature13421

Persistent Gut Microbiota Immaturity in Malnourished Bangladeshi Children

Sathish Subramanian ¹, Sayeeda Huq ², Tanya Yatsunenko ¹, Rashidul Haque ², Mustafa Mahfuz ², Mohammed A Alam ², Amber Benezra ^1,³, Joseph DeStefano ¹, Martin F Meier ¹, Brian D Muegge ¹, Michael J Barratt ¹, Laura G VanArendonk ¹, Qunyuan Zhang ⁴, Michael A Province ⁴, William A Petri ⁵, Tahmeed Ahmed ², Jeffrey I Gordon ^1,^*

PMCID: PMC4189846 NIHMSID: NIHMS591059 PMID: 24896187

Abstract

Therapeutic food interventions have reduced mortality in children with severe acute malnutrition (SAM) but incomplete restoration of healthy growth remains a major problem^1,2. The relationships between the type of nutritional intervention, the gut microbiota, and therapeutic responses are unclear. In the current study, bacterial species whose proportional representation define a healthy gut microbiota as it assembles during the first two postnatal years were identified by applying a machine-learning-based approach to 16S rRNA datasets generated from monthly fecal samples obtained from a birth-cohort of children, living in an urban slum of Dhaka, Bangladesh, who exhibited consistently healthy growth. These age-discriminatory bacterial species were incorporated into a model that computes a ‘relative microbiota maturity index’ and ‘microbiota-for-age Z-score’ that compare development (defined here as maturation) of a child’s fecal microbiota relative to healthy children of similar chronologic age. The model was applied to twins and triplets (to test for associations of these indices with genetic and environmental factors including diarrhea), children with SAM enrolled in a randomized trial of two food interventions, and children with moderate acute malnutrition. Our results indicate that SAM is associated with significant relative microbiota immaturity that is only partially ameliorated following two widely used nutritional interventions. Immaturity is also evident in less severe forms of malnutrition and correlates with anthropometric measurements. Microbiota maturity indices provide a microbial measure of human postnatal development, a way of classifying malnourished states, and a parameter for judging therapeutic efficacy. More prolonged interventions with existing or new therapeutic foods and/or addition of gut microbes may be needed to achieve enduring repair of gut microbiota immaturity in childhood malnutrition and improve clinical outcomes.

Severe acute malnutrition and moderate acute malnutrition (MAM) are typically defined by anthropometric measurements: children are classified as having SAM if their weight-for-height Z-scores (WHZ) are below three standard deviations (-3 SD) from the median of the World Health Organization (WHO) reference growth standards, while those with WHZ scores between minus two and minus three SD are categorized as having MAM³. SAM and MAM typically develop between three and 24 months of life⁴. A standardized treatment protocol for SAM and its complications has been developed in Bangladesh¹. The result has been a reduction in mortality rate, although the extent to which this protocol results in long-term restoration of normal growth and development needs to be ascertained through longitudinal studies^5,6. There is similar lack of clarity about the long-term efficacy of nutritional interventions for MAM^7,8.

Food is a major factor that shapes the proportional representation of organisms present in the gut microbial community (microbiota), and its gene content (microbiome). The microbiota/microbiome in turn plays an important role in extracting and metabolizing dietary ingredients^9-14. Hypothesizing that healthy postnatal development (maturation) of the gut microbiota is perturbed in malnutrition¹², we followed 50 healthy Bangladeshi children monthly during the first two years of life (25 singletons, 11 twin pairs, 1 set of triplets; 996 monthly fecal samples collected, see Methods, Extended Data Tables 1-3). By identifying bacterial taxa that discriminate the microbiota of healthy children at different chronologic ages, we were able to test our hypothesis by studying 6-20 month old children presenting with SAM, just prior to, during, and after treatment 4 with two very different types of food intervention, as well as children with MAM. The results provide a different perspective about malnutrition - one involving disruption of a microbial facet of our normal human postnatal development.

Table ED1.

Metadata for 50 healthy Bangladeshi children sampled monthly during the first two years of life

Child ID	Family ID	Birth Cohort	Gender	Zygosity	WHZ	WAZ	HAZ	Age at first fecal sample collection (days)	Age at last fecal sample collection (days)	Number of fecal samples collected	Sampling interval (days) mean ± SD	Months of exclusive breastfeeding	Age at first introduction of solid food (months)	Number of diarrheal episodes / yr	% Days with diarrhea during sampling period	Fraction of samples collected where antibiotics had been consumed within prior 7 days	Training-Validation Set Subject Allocation

Bgsng7035	Bgsng7035	Healthy Singleton Birth Cohort	Male	NA	-0.5 ± 0.5	-1.7 ± 0.2	-1.7 ± 0.2	5	701	23	32 ± 11	0.0	1.2	3.6	1.9	0.2	Training
Bgsng7106	Bgsng7106	Healthy Singleton Birth Cohort	Male	NA	-0.4 ± 0.6	-0.9 ± 0.9	-0.9 ± 0.9	9	738	19	41 ± 19	4.4	9.4	4.0	3.9	0.1	Training
Bgsng7115	Bgsng7115	Healthy Singleton Birth Cohort	Male	NA	-1.6 ± 0.5	0.2 ± 0.4	0.2 ± 0.4	5	706	21	35 ± 19	0.9	6.2	5.2	5.9	0.1	Training
Bgsng7128	Bgsng7128	Healthy Singleton Birth Cohort	Female	NA	-1.4 ± 0.7	-1.3 ± 0.6	-1.3 ± 0.6	4	735	23	33 ± 12	3.3	9.8	4.5	5.0	0.1	Training
Bgsng7150	Bgsng7150	Healthy Singleton Birth Cohort	Male	NA	0.0 ± 1.2	0.0 ± 0.8	0.0 ± 0.8	5	701	22	33 ± 14	5.9	8.2	2.1	3.0	0.4	Training
Bgsng7155	Bgsng7155	Healthy Singleton Birth Cohort	Female	NA	-1.5 ± 1.3	-1.0 ± 1.3	-1.0 ± 1.3	5	701	24	30 ± 5	1.2	4.3	1.6	1.6	0.3	Training
Bgsng7177	Bgsng7177	Healthy Singleton Birth Cohort	Female	NA	0.9 ± 0.6	-0.9 ± 1.0	-0.9 ± 1.0	8	700	23	31 ± 6	6.4	7.3	3.7	4.3	0.2	Training
Bgsng7192	Bgsng7192	Healthy Singleton Birth Cohort	Female	NA	0.0 ± 0.8	-1.6 ± 0.7	-1.6 ± 0.7	4	704	24	30 ± 8	5.4	6.3	5.2	4.4	0.4	Training
Bgsng7202	Bgsng7202	Healthy Singleton Birth Cohort	Female	NA	-0.4 ± 1.8	0.1 ± 0.6	0.1 ± 0.6	6	714	23	32 ± 11	5.4	6.2	3.1	3.1	0.1	Training
Bgsng7204	Bgsng7204	Healthy Singleton Birth Cohort	Male	NA	-0.7 ± 1.7	-0.1 ± 0.6	-0.1 ± 0.6	5	708	24	31 ± 10	0.2	4.5	8.8	7.2	0.4	Training
Bgsng8064	Bgsng8064	Healthy Singleton Birth Cohort	Male	NA	0.9 ± 0.7	1.7 ± 0.7	1.7 ± 0.7	6	700	24	30 ± 4	3.0	6.0	3.1	3.6	0.1	Training
Bgsng8169	Bgsng8169	Healthy Singleton Birth Cohort	Male	NA	0.9 ± 1.5	1.1 ± 0.5	1.1 ± 0.5	6	737	22	35 ± 18	3.0	5.6	3.0	2.3	0.0	Training

Bgsng7018	Bgsng7018	Healthy Singleton Birth Cohort	Male	NA	-0.7 ± 0.7	-0.4 ± 0.9	-0.4 ± 0.9	3	710	21	35 ± 24	7.3	9.6	4.6	3.5	0.3	Validation
Bgsng7052	Bgsng7052	Healthy Singleton Birth Cohort	Male	NA	0.0 ± 1.1	-0.3 ± 1.2	-0.3 ± 1.2	7	715	20	37 ± 22	6.6	7.3	4.1	4.8	0.1	Validation
Bgsng7063	Bgsng7063	Healthy Singleton Birth Cohort	Male	NA	-0.4 ± 0.7	0.0 ± 0.9	0.0 ± 0.9	5	700	20	37 ± 17	0.2	9.2	2.1	1.6	0.0	Validation
Bgsng7071	Bgsng7071	Healthy Singleton Birth Cohort	Male	NA	0.5 ± 0.8	0.6 ± 0.7	0.6 ± 0.7	4	704	18	41 ± 11	6.3	8.4	8.8	8.0	0.3	Validation
Bgsng7082	Bgsng7082	Healthy Singleton Birth Cohort	Female	NA	-0.9 ± 1.4	-0.8 ± 0.7	-0.8 ± 0.7	5	724	18	42 ± 28	4.4	5.8	3.5	3.0	0.3	Validation
Bgsng7090	Bgsng7090	Healthy Singleton Birth Cohort	Male	NA	-0.4 ± 0.5	-0.3 ± 0.7	-0.3 ± 0.7	5	703	23	32 ± 12	3.4	4.7	7.3	5.1	0.4	Validation
Bgsng7096	Bgsng7096	Healthy Singleton Birth Cohort	Female	NA	-0.5 ± 0.4	-1.1 ± 0.6	-1.1 ± 0.6	15	706	23	31 ± 10	3.2	7.2	2.6	2.7	0.2	Validation
Bgsng7114	Bgsng7114	Healthy Singleton Birth Cohort	Male	NA	-0.9 ± 0.3	-0.7 ± 0.2	-0.7 ± 0.2	4	702	18	41 ± 18	3.1	4.3	0.5	0.1	0.0	Validation
Bgsng7131	Bgsng7131	Healthy Singleton Birth Cohort	Male	NA	-0.9 ± 0.5	-1.3 ± 0.8	-1.3 ± 0.8	10	717	23	32 ± 10	2.2	3.1	4.1	4.3	0.3	Validation
Bgsng7142	Bgsng7142	Healthy Singleton Birth Cohort	Male	NA	-0.7 ± 1.5	-0.8 ± 1.5	-0.8 ± 1.5	12	728	22	34 ± 13	0.4	4.6	3.0	4.1	0.3	Validation
Bgsng7149	Bgsng7149	Healthy Singleton Birth Cohort	Female	NA	-1.0 ± 0.4	-0.3 ± 0.4	-0.3 ± 0.4	5	704	22	33 ± 11	3.4	9.4	6.2	3.7	0.2	Validation
Bgsng7173	Bgsng7173	Healthy Singleton Birth Cohort	Male	NA	-0.5 ± 0.5	-1.2 ± 0.6	-1.2 ± 0.6	8	702	24	30 ± 9	1.6	4.0	7.8	10.8	0.5	Validation
Bgsng7178	Bgsng7178	Healthy Singleton Birth Cohort	Female	NA	0.6 ± 1.4	-0.9 ± 0.6	-0.9 ± 0.6	8	700	24	30 ± 6	5.3	6.3	4.7	4.3	0.3	Validation

Bgtw1.T1	Bgtw1	Healthy Twins & Triplets	Female	MZ	-0.5 ± 0.7	-2.3 ± 0.5	-3.1 ± 0.7	35	730	26	28 ± 7	0.0	4.1	2.0	2.7	0.4	Validation - Twins & Triplets
Bgtw1.T2	Bgtw1	Healthy Twins & Triplets	Female	MZ	-1.3 ± 0.8	-3.0 ± 0.3	-3.4 ± 0.7	34	729	24	30 ± 9	0.0	4.1	2.0	2.7	0.3	Validation - Twins & Triplets
Bgtw2.T1	Bgtw2	Healthy Twins & Triplets	Male	DZ	-1.2 ± 0.8	-3.8 ± 0.9	-4.7 ± 0.7	31	701	25	28 ± 8	1.0	3.1	0.5	0.7	0.1	Validation - Twins & Triplets
Bgtw2.T2	Bgtw2	Healthy Twins & Triplets	Female	DZ	-0.8 ± 1.0	-3.3 ± 0.9	-4.2 ± 0.4	31	701	25	28 ± 7	2.0	7.9	1.0	1.0	0.1	Validation - Twins & Triplets
Bgtw3.T1	Bgtw3	Healthy Twins & Triplets	Male	MZ	-0.6 ± 0.4	-1.4 ± 0.5	-1.6 ± 0.3	8	638	24	27 ± 12	0.0	7.1	2.9	5.0	0.0	Validation - Twins & Triplets
Bgtw3.T2	Bgtw3	Healthy Twins & Triplets	Male	MZ	-0.6 ± 0.5	-1.8 ± 0.6	-2.1 ± 0.6	8	639	26	25 ± 12	0.0	7.9	1.7	4.7	0.1	Validation - Twins & Triplets
Bgtw4.T1	Bgtw4	Healthy Twins & Triplets	Female	MZ co-twin in set of triplets	-0.2 ± 0.8	-2.4 ± 0.6	-3.4 ± 0.5	1	575	21	29 ± 10	0.0	9.1	1.3	0.3	0.1	Validation - Twins & Triplets
Bgtw4.T2	Bgtw4	Healthy Twins & Triplets	Female	MZ co-twin in set of triplets	-0.1 ± 0.8	-2.2 ± 0.9	-3.4 ± 0.6	1	581	19	32 ± 7	0.0	8.9	1.9	0.7	0.1	Validation - Twins & Triplets
Bgtw4.T3	Bgtw4	Healthy Twins & Triplets	Female	Fraternal co-twin in set of triplets	-1.7 ± 0.9	-2.9 ± 0.7	-2.6 ± 0.6	7	575	22	27 ± 9	0.0	8.9	3.8	3.8	0.1	Validation - Twins & Triplets
Bgtw5.T1	Bgtw5	Healthy Twins & Triplets	Male	DZ	-0.5 ± 0.8	-3.1 ± 0.9	-4.3 ± 0.8	31	638	21	30 ± 3	1.0	8.0	0.6	0.2	0.0	Validation - Twins & Triplets
Bgtw5.T2	Bgtw5	Healthy Twins & Triplets	Female	DZ	-0.1 ± 0.5	-2.5 ± 0.4	-4.0 ± 0.5	4	638	21	32 ± 7	0.1	7.0	1.7	1.1	0.0	Validation - Twins & Triplets
Bgtw6.T1	Bgtw6	Healthy Twins & Triplets	Male	DZ	-0.2 ± 0.6	-1.5 ± 1.8	-1.6 ± 1.7	6	286	9	35 ± 25	0.2	7.9	1.3	1.7	0.1	Validation - Twins & Triplets
Bgtw6.T2	Bgtw6	Healthy Twins & Triplets	Male	DZ	-0.6 ± 0.6	-2.5 ± 1.2	-2.6 ± 1.7	6	286	10	35 ± 11	0.2	9.4	0.0	0.3	0.1	Validation - Twins & Triplets
Bgtw7.T1	Bgtw7	Healthy Twins & Triplets	Female	DZ	0.5 ± 1.0	-2.3 ± 0.5	-3.8 ± 0.4	14	455	18	26 ± 8	0.0	9.0	0.8	0.4	0.2	Validation - Twins & Triplets
Bgtw7.T2	Bgtw7	Healthy Twins & Triplets	Female	DZ	0.5 ± 1.7	-2.8 ± 0.8	-4.3 ± 0.2	12	455	18	26 ± 7	0.4	9.1	3.2	2.0	0.2	Validation - Twins & Triplets
Bgtw8.T1	Bgtw8	Healthy Twins & Triplets	Female	DZ	-0.9 ± 0.7	-1.6 ± 0.3	-1.4 ± 0.4	15	364	14	27 ± 8	1.0	6.1	1.0	1.9	0.2	Validation - Twins & Triplets
Bgtw8.T2	Bgtw8	Healthy Twins & Triplets	Female	DZ	-1.4 ± 0.8	-2.6 ± 0.5	-2.3 ± 0.6	15	366	13	29 ± 5	1.0	6.1	0.0	0.0	0.5	Validation - Twins & Triplets
Bgtw9.T1	Bgtw9	Healthy Twins & Triplets	Female	MZ	0.1 ± 1.2	-3.1 ± 0.5	-4.0 ± 0.7	37	368	12	30 ± 3	2.1	6.9	3.0	1.4	0.3	Validation - Twins & Triplets
Bgtw9.T2	Bgtw9	Healthy Twins & Triplets	Female	MZ	0.8 ± 1.2	-2.6 ± 0.6	-4.0 ± 0.9	8	368	14	28 ± 7	2.3	6.9	2.0	2.2	0.1	Validation - Twins & Triplets
Bgtw10.T1	Bgtw10	Healthy Twins & Triplets	Female	MZ	-1.5 ± 0.8	-2.7 ± 0.5	-2.4 ± 0.4	4	366	17	23 ± 10	1.0	6.9	5.0	9.6	0.1	Validation - Twins & Triplets
Bgtw10.T2	Bgtw10	Healthy Twins & Triplets	Female	MZ	-1.0 ± 1.1	-2.8 ± 0.3	-2.8 ± 0.5	4	365	17	23 ± 11	1.1	6.9	4.0	9.3	0.1	Validation - Twins & Triplets
Bgtw11.T1	Bgtw11	Healthy Twins & Triplets	Female	not tested	-0.2 ± 0.3	-2.9 ± 0.4	-3.7 ± 0.4	1	336	12	30 ± 5	0.9	3.9	0.0	0.0	0.1	Validation - Twins & Triplets
Bgtw11.T2	Bgtw11	Healthy Twins & Triplets	Female	not tested	-0.7 ± 0.9	-2.6 ± 0.4	-2.9 ± 0.3	5	368	13	30 ± 11	1.1	4.0	0.0	0.0	0.0	Validation - Twins & Triplets
Bgtw12.T1	Bgtw12	Healthy Twins & Triplets	Male	DZ	1.2 ± 1.3	-2.3 ± 1.1	-4.4 ± 1.2	6	372	14	28 ± 6	1.0	8.5	1.0	1.6	0.4	Validation - Twins & Triplets
Bgtw12.T2	Bgtw12	Healthy Twins & Triplets	Female	DZ	-0.6 ± 2.0	-2.9 ± 1.2	-3.6 ± 0.9	6	372	13	31 ± 5	1.0	8.0	1.0	0.5	0.1	Validation - Twins & Triplets

Family ID	Person ID	Family membership	Fecal Sample ID	Age of subject at time of fecal sample collection, years	Age of subject’s children at the time of subject’s fecal sample collection, months	Age of subject’s children at the time of subject’s fecal sample collection, days	Number of high quality V4-16S rRNA sequences	16S rRNA Sequencing Run ID	Sample specific barcode sequence

Bgtw1	Bgtw1.F	Father	Bgtw1.F.m1	33.0	1	5	17,266	TCP2 (runs 1 and 2)	CGGATCGTAATAC
Bgtw1	Bgtw1.F	Father	Bgtw1.F.m4	33.3	4	93	13,599	T12	CGCTCGAAGATTC
Bgtw1	Bgtw1.F	Father	Bgtw1.F.m7	33.5	7	184	18,411	T12	GTTCTCCATCACA
Bgtw1	Bgtw1.F	Father	Bgtw1.F.m10	33.8	10	274	18,354	T12	CGCGTCCATGAAT
Bgtw1	Bgtw1.F	Father	Bgtw1.F.m12	34.0	12	369	33,506	T12	AGACTACCCGTTG
Bgtw1	Bgtw1.F	Father	Bgtw1.F.m16	34.3	16	459	22,406	T12	GAACCGCATAAGT
Bgtw2	Bgtw2.F	Father	Bgtw2.F.m4	26.3	4	95	14,837	T34	CATGCTGCAACAC
Bgtw2	Bgtw2.F	Father	Bgtw2.F.m10	26.5	10	276	9,185	T34	ATTCGATGCCGCA
Bgtw3	Bgtw3.F	Father	Bgtw3.F.m1	40.0	1	8	11,154	T12	ATAACGTGTGTGC
Bgtw3	Bgtw3.F	Father	Bgtw3.F.m4	40.3	4	92	10,854	T34	AGACGCACTAACT
Bgtw3	Bgtw3.F	Father	Bgtw3.F.m7	40.5	7	179	34,147	T78	TACCTGTCCTTTC
Bgtw3	Bgtw3.F	Father	Bgtw3.F.m10	40.8	10	274	15,316	TCP2 (runs 1 and 2)	TCTGTCAGTGACC
Bgtw3	Bgtw3.F	Father	Bgtw3.F.m13	41.0	13	367	22,178	T12	AGCAACACCATCC
Bgtw3	Bgtw3.F	Father	Bgtw3.F.m16	41.3	16	458	30,845	TCP2 (runs 1 and 2)	ACATACCGTGAGT
Bgtw4	Bgtw4.F	Father	Bgtw4.F.m1	23.0	1	5	27,558	T12	CGCTGTACGGATT
Bgtw4	Bgtw4.F	Father	Bgtw4.F.m4	23.3	4	92	18,137	T34	CACCTTACACCTT
Bgtw4	Bgtw4.F	Father	Bgtw4.F.m7	23.5	7	187	18,674	T34	CATAATTGCCGAG
Bgtw4	Bgtw4.F	Father	Bgtw4.F.m10	23.8	10	272	23,417	T56 (runs 1 and 2)	CGAATACCAAGTC
Bgtw4	Bgtw4.F	Father	Bgtw4.F.m13	24.0	13	365	23,890	T56 (runs 1 and 2)	CGAACACTTTGGA
Bgtw5	Bgtw5.F	Father	Bgtw5.F.m1	38.0	1	4	18,085	T12	TGCCTGTCTGCAA
Bgtw5	Bgtw5.F	Father	Bgtw5.F.m4	38.3	4	94	25,138	T56 (runs 1 and 2)	CGAGCCATCTGTA
Bgtw5	Bgtw5.F	Father	Bgtw5.F.m7	38.5	7	195	14,529	T34	CACTGACTTAAGG
Bgtw5	Bgtw5.F	Father	Bgtw5.F.m10	38.8	10	274	15,468	T12	GAGGTCCAAATCA
Bgtw5	Bgtw5.F	Father	Bgtw5.F.m13	39.0	13	366	17,789	T34	GTTCTGAGAGGTA
Bgtw6	Bgtw6.F	Father	Bgtw6.F.m1	29.0	1	2	14,873	T34	GCGACTCTAAACG
Bgtw6	Bgtw6.F	Father	Bgtw6.F.m4	29.3	4	92	19,520	TCP2 (runs 1 and 2)	GTTCTCTCGACAT
Bgtw6	Bgtw6.F	Father	Bgtw6.F.m7	29.5	7	181	16,345	TCP2 (runs 1 and 2)	CGTAAATTCAGGC
Bgtw6	Bgtw6.F	Father	Bgtw6.F.m10	29.8	10	286	9,139	T12	GCGGTCAATTGAC
Bgtw7	Bgtw7.F	Father	Bgtw7.F.m1	38.0	1	14	21,791	T34	ACGCCATTGTGCA
Bgtw7	Bgtw7.F	Father	Bgtw7.F.m4	38.3	4	91	12,730	TCP2 (runs 1 and 2)	ATGCCGTATGCCA
Bgtw7	Bgtw7.F	Father	Bgtw7.F.m7	38.5	7	190	13,123	T12	CGAACACTTTGGA
Bgtw8	Bgtw8.F	Father	Bgtw8.F.m1	40.0	1	18	14,289	TCP2 (runs 1 and 2)	ATCTGCACTGAGC
Bgtw8	Bgtw8.F	Father	Bgtw8.F.m4	40.3	4	92	18,075	TCP2 (runs 1 and 2)	TAGTGTTTCGGAC
Bgtw8	Bgtw8.F	Father	Bgtw8.F.m7	40.5	7	185	29,674	TCP2 (runs 1 and 2)	ATCGTGCGTGTTG
Bgtw8	Bgtw8.F	Father	Bgtw8.F.m13	41.0	13	374	29,593	TCP2 (runs 1 and 2)	GTACCGAAGGTAT
Bgtw9	Bgtw9.F	Father	Bgtw9.F.m1	28.0	1	8	16,769	T34	CTGGCTTTCTATC
Bgtw9	Bgtw9.F	Father	Bgtw9.F.m4	28.3	4	93	8,311	T12	CATTGACCGGTCA
Bgtw9	Bgtw9.F	Father	Bgtw9.F.m7	28.5	7	185	25,311	T56 (runs 1 and 2)	CAGCTATGTATGG
Bgtw9	Bgtw9.F	Father	Bgtw9.F.m10	28.8	10	278	20,809	T56 (runs 1 and 2)	CACTTCCAACTTC
Bgtw9	Bgtw9.F	Father	Bgtw9.F.m13	29.0	13	367	26,044	T56 (runs 1 and 2)	CATGGCTGTCAGT
Bgtw10	Bgtw10.F	Father	Bgtw10.F.m1	32.0	1	2	20,923	T12	TCTTAGGCATGTG
Bgtw10	Bgtw10.F	Father	Bgtw10.F.m4	32.3	4	92	14,148	T34	ATAAGGCATCGCT
Bgtw10	Bgtw10.F	Father	Bgtw10.F.m7	32.5	7	191	14,161	TCP2 (runs 1 and 2)	ATGGTCGCATCGT
Bgtw10	Bgtw10.F	Father	Bgtw10.F.m10	32.8	10	275	25,813	T56 (runs 1 and 2)	ACATCCCTCTACT
Bgtw10	Bgtw10.F	Father	Bgtw10.F.m13	33.0	13	365	38,175	T56 (runs 1 and 2)	TAGCGGAGGTTAG
Bgtw11	Bgtw11.F	Father	Bgtw11.F.m1	26.0	1	4	23,237	TCP2 (runs 1 and 2)	GCACTCATCATTC
Bgtw11	Bgtw11.F	Father	Bgtw11.F.m4	26.3	4	88	28,777	T56 (runs 1 and 2)	CTGCGCTGAATGT
Bgtw12	Bgtw12.F	Father	Bgtw12.F.m1	25.0	1	7	23,115	TCP2 (runs 1 and 2)	GACTTGGTGTAAG
Bgtw12	Bgtw12.F	Father	Bgtw12.F.m4	25.3	4	94	22,396	T56 (runs 1 and 2)	ATCCTCGAGCGAT
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m1	25.0	1	5	12,057	T34	GCCGAGGTATAAT
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m3	25.2	3	64	15,500	T34	CGCTGTGATTCGA
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m4	25.3	4	92	22,699	T34	TACGGCGTTATGT
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m5	25.3	5	124	14,512	T34	CTAACGCTGTGTG
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m6	25.5	6	167	15,921	T34	TACCCATACAGCC
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m7	25.5	7	188	19,137	T12	TACCATAGCTCCG
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m8	25.6	8	216	37,309	T56 (runs 1 and 2)	AGCGATATATCGC
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m9	25.7	9	243	18,428	T34	AGAGATCGCCTAT
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m10	25.8	10	274	15,102	T34	CATTGACCGGTCA
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m11	25.8	11	305	13,393	T34	CAATGACCTCGTG
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m12	25.9	12	338	19,050	T34	ACTGAAGGGCGAA
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m13	26.0	13	365	19,374	T12	GAAGACAGCTATC
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m14	26.1	14	397	19,439	T12	TCATTCGTGGCGT
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m15	26.2	15	426	22,949	TCP2 (runs 1 and 2)	AGGTTCGGTCCAT
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m16	26.2	16	456	10,227	T12	ATGCATACACTGG
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m17	26.3	17	488	23,442	T12	CTGGCTTTCTATC
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m18	26.4	18	519	18,496	T12	CATGGCTGTCAGT
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m19	26.5	19	551	18,563	T78	AGCTCTCCGTAGA
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m20	26.6	20	579	20,085	T78	ACGATGCTGTTGA
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m21	26.7	21	610	18,046	T78	GTGTAAGACTTGG
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m22	26.8	22	639	16,539	T78	CACGACTGCATAA
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m23	26.8	23	669	14,823	T78	GCGCAGATTAGTA
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m24	26.9	24	700	15,480	T56 (runs 1 and 2)	CGTACGATATGAC
Bgtw1	Bgtw1.M	Mother	Bgtw1.M.m25	27.0	25	730	35,842	T56 (runs 1 and 2)	CGTCACGGACATT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m1	22.0	1	1	14,645	TRX	AGCGTTCTAGCTG
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m2	22.1	2	31	20,841	T34	GCTCTGCCTAATT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m3	22.2	3	60	15,540	T12	CTCGGAATTAGAC
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m4	22.3	4	94	12,088	T12	TCCAATACGCCTG
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m5	22.3	5	123	17,342	T34	TGCATTCGGCGTT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m6	22.4	6	154	12,497	T34	CGTCGTCCAAATG
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m7	22.5	7	184	33,721	T56 (runs 1 and 2)	TATGGGTTCCGTC
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m8	22.6	8	214	13,669	T34	ACGGAGTAATCCT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m9	22.7	9	240	35,256	T56 (runs 1 and 2)	CGTAGATCGTGTA
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m10	22.8	10	275	14,594	T34	CGGCGATTTACGT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m11	22.8	11	302	13,499	T34	TGCCTGTCTGCAA
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m12	22.9	12	333	13,956	T34	GCTACGAAAGCCT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m13	23.0	13	367	11,822	T34	CGTACTGAAGATC
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m14	23.1	14	399	14,283	T34	ACCTGTCCTATCT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m15	23.2	15	426	21,608	T12	TGTCGCCGTACAT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m16	23.3	16	458	20,707	T34	TAAGGGCGCTGAA
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m17	23.3	17	491	21,304	T56 (runs 1 and 2)	CGTTGTTCTGGGA
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m18	23.4	18	518	18,054	TCP2 (runs 1 and 2)	CGATGTGGTGTTA
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m19	23.5	19	547	21,550	T56 (runs 1 and 2)	CTCAGTTCTCGTT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m20	23.6	20	581	24,239	T56 (runs 1 and 2)	CGTAAATTCAGGC
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m21	23.7	21	609	18,456	T78	CGTTCCTCCATTA
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m22	23.8	22	639	23,139	T56 (runs 1 and 2)	TAGCATGTCCCGT
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m23	23.8	23	668	18,401	T78	AGCACACCTGATA
Bgtw2	Bgtw2.M	Mother	Bgtw2.M.m24	23.9	24	702	22,541	T56 (runs 1 and 2)	ACTGCTATTCCTC
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m1	30.0	1	8	18,168	T56 (runs 1 and 2)	ACTCACAACCGTG
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m2	30.1	2	32	15,001	T34	ATATGAACGTCCG
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m3	30.2	3	61	12,832	T34	GACTTTGCTTTGC
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m4	30.3	4	92	15,985	T34	GAAGTGGCTATCC
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m5	30.3	5	123	17,652	T34	GCCAGATATAGCA
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m6	30.4	6	151	17,953	TCP2 (runs 1 and 2)	TCACTGGTGCATA
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m7	30.5	7	178	17,506	T34	GTTCTCCATCACA
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m8	30.6	8	213	7,341	T12	ACAACTCCCGTGA
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m9	30.7	9	240	16,599	T34	TCGAGCTGTTACC
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m10	30.8	10	274	24,901	T56 (runs 1 and 2)	CACGAGACTGATT
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m11	30.8	11	304	19,920	T34	AGCCGTAAACTTG
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m12	30.9	12	341	15,278	TCP2 (runs 1 and 2)	GCTGATCCATCTT
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m13	31.0	13	367	30,379	TCP2 (runs 1 and 2)	GCAGAAATGTGTC
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m14	31.1	14	400	26,537	TCP2 (runs 1 and 2)	AGCACACCTGATA
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m15	31.2	15	430	14,244	T12	ATCTCTACCACTC
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m16	31.3	16	459	22,655	T12	GATAACATGTGCG
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m17	31.3	17	487	32,562	T56 (runs 1 and 2)	CACTCCTTGTGTT
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m19	31.5	19	549	29,619	T56 (runs 1 and 2)	GCTGATCCATCTT
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m20	31.6	20	579	15,865	TCP2 (runs 1 and 2)	TGTTAAGCTGACC
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m21	31.7	21	609	17,611	TCP2 (runs 1 and 2)	CACTCCTTGTGTT
Bgtw3	Bgtw3.M	Mother	Bgtw3.M.m22	31.7	22	638	15,611	TCP2 (runs 1 and 2)	CGTCACGGACATT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m1	20.0	1	5	20,006	T34	TATTCGGTAGTGC
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m2	20.1	2	32	16,042	T34	ACGCACTACGCAT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m3	20.2	3	61	15,325	T34	ATCGCCGTGTACA
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m4	20.3	4	92	22,921	T12	AGAGCGTATCCAT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m5	20.3	5	123	13,727	T34	CGTTCCTCCATTA
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m6	20.4	6	151	25,198	T56 (runs 1 and 2)	AGTATCTGCGCGT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m7	20.5	7	181	20,259	T34	CGGAATTATCGGT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m8	20.6	8	211	15,493	T34	TGCCACGACTTAC
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m9	20.7	9	251	14,538	T34	CGCGTCCATGAAT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m10	20.8	10	277	16,851	T34	GCTTCCAACTCAT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m11	20.8	11	305	11,467	T34	TGGCTGCATACTC
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m12	20.9	12	334	32,997	T56 (runs 1 and 2)	CATCGCACAGTAA
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m13	21.0	13	364	20,722	T12	CAACTTTCAGGAG
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m14	21.1	14	395	13,616	T12	ACATCCCTCTACT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m15	21.2	15	425	21,943	T12	ATACGAGCCCTAA
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m16	21.3	16	458	22,991	T78	ACGGAGTAATCCT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m17	21.3	17	487	17,381	T78	ATCTGCACTGAGC
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m18	21.4	18	517	34,752	T56 (runs 1 and 2)	TACGGGTCATCAT
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m19	21.5	19	547	24,521	T56 (runs 1 and 2)	CTGTCGCAAATAG
Bgtw4	Bgtw4.M	Mother	Bgtw4.M.m20	21.6	20	575	44,125	T56 (runs 1 and 2)	AGCAACACCATCC
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m1	29.0	1	4	9,540	T34	CATTATCGTCCCT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m2	29.1	2	33	16,280	T34	CGATCATTCTCTC
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m3	29.2	3	61	23,552	TCP2 (runs 1 and 2)	ATACTCGGGAACT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m4	29.3	4	95	25,903	T12	TATGGGCGAATGG
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m5	29.3	5	123	15,880	T34	TAGGCACAGTAGG
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m6	29.4	6	152	16,214	T34	TACCTGTCCTTTC
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m7	29.5	7	181	20,984	T56 (runs 1 and 2)	CAACTAGTTCAGG
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m8	29.6	8	218	13,008	T34	CGAAATGCTACGT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m9	29.7	9	248	21,653	T34	GCATCAAGCATAG
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m10	29.8	10	277	13,582	T34	GCGAAACTACGTA
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m11	29.8	11	310	14,621	T12	CGGTTCCATTAGG
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m12	29.9	12	341	18,744	T34	TCGATAGGCCTTA
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m13	30.0	13	365	15,753	T34	GCAGTCGTTAAGA
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m14	30.1	14	396	21,882	T56 (runs 1 and 2)	CTCGACATCTCTT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m15	30.2	15	429	17,027	T12	CAGCAGAACATCT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m16	30.3	16	458	14,496	T78	GCACTCATCATTC
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m17	30.4	17	493	14,010	T78	ACGCTGTGGATTA
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m18	30.4	18	514	18,506	T78	TACCCATACAGCC
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m19	30.5	19	548	19,202	T56 (runs 1 and 2)	CAGCAGAACATCT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m20	30.6	20	578	22,358	T56 (runs 1 and 2)	ATCACCTCCTTGT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m21	30.7	21	613	41,854	T56 (runs 1 and 2)	TCATTCGTGGCGT
Bgtw5	Bgtw5.M	Mother	Bgtw5.M.m22	30.8	22	640	14,899	T78	ACCGTGACAACTC
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m1	18.0	1	6	21,134	T12	ATGTGGCTCGTGT
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m2	18.1	2	35	22,561	TCP2 (runs 1 and 2)	ACGATGCTGTTGA
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m3	18.2	3	63	12,071	TCP2 (runs 1 and 2)	ATGGGTCCCACAT
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m4	18.3	4	92	15,084	T12	CTTGGCTCTATTC
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m6	18.4	6	152	8,105	T12	TGGTCTCCTACAG
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m7	18.5	7	182	24,708	TCP2 (runs 1 and 2)	GTGCAGCAAGATT
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m8	18.6	8	212	25,775	T56 (runs 1 and 2)	ATGCAGTCCTCGA
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m9	18.7	9	246	31,301	TCP2 (runs 1 and 2)	CGAGAGCAACAGA
Bgtw6	Bgtw6.M	Mother	Bgtw6.M.m10	18.8	10	286	22,264	TCP2 (runs 1 and 2)	ATTAGAGCCATGC
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m1	32.0	1	12	12,620	T34	CGGTTCCATTAGG
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m2	32.1	2	32	12,895	T34	ATGTGGCTCGTGT
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m3	32.2	3	61	14,622	T34	CGCGTTGCAAACT
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m4	32.2	4	90	15,904	T12	TGAGAGTCCACTT
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m5	32.3	5	125	13,728	T34	ATTGGGCCACATA
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m6	32.5	6	167	25,899	TCP2 (runs 1 and 2)	CGATTATCGACGA
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m7	32.5	7	189	16,171	TCP2 (runs 1 and 2)	ATCCTCGAGCGAT
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m8	32.6	8	214	21,054	TCP2 (runs 1 and 2)	CGCAATTAGGTAC
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m9	32.7	9	244	16,054	TCP2 (runs 1 and 2)	CGCCAACAACCAT
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m10	32.8	10	275	16,972	T78	TAGTGTTTCGGAC
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m11	32.8	11	307	18,622	T78	TCGTACTCTCGAG
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m12	32.9	12	336	17,114	T56 (runs 1 and 2)	ATGCCGTATGCCA
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m13	33.0	13	364	24,908	TCP2 (runs 1 and 2)	AGCTCTCCGTAGA
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m14	33.1	14	397	25,642	T56 (runs 1 and 2)	AGCTCTCCGTAGA
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m15	33.2	15	427	34,912	T56 (runs 1 and 2)	GTGTGCGATAACA
Bgtw7	Bgtw7.M	Mother	Bgtw7.M.m16	33.2	16	455	26,763	T56 (runs 1 and 2)	TGCGAGCGAAGTA
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m2	35.1	2	35	14,743	T34	CTTATGGTACGGA
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m3	35.2	3	64	12,586	T34	GAACCAAACTCGA
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m4	35.2	4	90	15,905	T12	CACCAGTGACTCA
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m5	35.3	5	122	22,094	T56 (runs 1 and 2)	CGATGTTCGCTAG
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m6	35.4	6	157	11,955	T12	CTGCGCTGAATGT
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m7	35.5	7	185	12,986	T12	ATATACCGCTGCG
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m8	35.6	8	212	24,345	T56 (runs 1 and 2)	CATCAGTACTAGG
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m9	35.7	9	247	24,921	T56 (runs 1 and 2)	CAGCAACATTGCA
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m11	35.8	11	305	18,724	T56 (runs 1 and 2)	CGTGCAACCAATC
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m12	35.9	12	333	22,064	T56 (runs 1 and 2)	GATCTACCGAAGC
Bgtw8	Bgtw8.M	Mother	Bgtw8.M.m13	36.0	13	364	22,114	T78	TGTAGAGGTAGAG
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m2	20.1	2	38	21,305	TCP2 (runs 1 and 2)	TGTTATCGCATGG
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m3	20.2	3	65	11,004	T12	TCTCACCTAGGAA
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m4	20.3	4	93	17,898	T12	CTACACAAGTCGC
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m5	20.3	5	120	12,883	T12	CGGTGACTAGTTC
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m7	20.5	7	185	22,936	TCP2 (runs 1 and 2)	ACGTGCTTAGGCT
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m8	20.6	8	218	18,803	T78	GCAGAAATGTGTC
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m10	20.7	10	273	16,732	TCP2 (runs 1 and 2)	ATTGATCCGGTAG
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m12	20.9	12	336	29,995	T56 (runs 1 and 2)	ATGTAACGCCGAT
Bgtw9	Bgtw9.M	Mother	Bgtw9.M.m13	21.0	13	368	19,398	T56 (runs 1 and 2)	CTAGTATGCGCAA
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m1	30.0	1	3	22,263	TCP2 (runs 1 and 2)	AGCCTAGCCCAAT
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m2	30.1	2	33	18,615	T12	GCGACTCTAAACG
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m3	30.2	3	60	22,139	T12	GTGGTCAACGATA
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m4	30.3	4	93	19,762	TRX	ACGCTGTGGATTA
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m5	30.3	5	123	15,019	T78	TAGCTGTCAAGCT
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m6	30.4	6	154	24,658	T56 (runs 1 and 2)	CGTCGAATTTGCG
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m7	30.5	7	184	18,035	T78	AGGTTCGGTCCAT
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m8	30.6	8	212	19,391	T56 (runs 1 and 2)	CGTGTTAGATGTG
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m9	30.7	9	245	38,351	T56 (runs 1 and 2)	TAGCTGTCAAGCT
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m10	30.7	10	271	26,347	T56 (runs 1 and 2)	CTATCGACACAAG
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m11	30.8	11	303	31,076	T56 (runs 1 and 2)	TCTCACCTAGGAA
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m12	30.9	12	332	27,492	T56 (runs 1 and 2)	CACGATTCGAGTC
Bgtw10	Bgtw10.M	Mother	Bgtw10.M.m13	31.0	13	365	13,612	T78	CGTAAATTCAGGC
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m1	21.0	1	3	26,161	T56 (runs 1 and 2)	ACGCTACAACTCG
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m2	21.1	2	27	33,396	T56 (runs 1 and 2)	CGTATTTCGGACG
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m3	21.2	3	60	38,371	T56 (runs 1 and 2)	ACAACTCCCGTGA
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m4	21.2	4	88	18,784	T78	ATTGATCCGGTAG
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m5	21.3	5	120	31,702	T56 (runs 1 and 2)	TGCTTGAGCTTGA
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m6	21.4	6	151	27,234	TCP2 (runs 1 and 2)	GTGGCAAATCTAG
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m7	21.5	7	192	18,199	TCP2 (runs 1 and 2)	CAGTTGTAGTCCG
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m8	21.6	8	216	41,854	T56 (runs 1 and 2)	GACCGGTATGTAC
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m9	21.7	9	243	19,865	T56 (runs 1 and 2)	ACCTGCGAAGTAT
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m10	21.8	10	279	16,839	T78	CGCATAGCATCAA
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m11	21.8	11	306	20,396	T78	AGTTCACGCCCAA
Bgtw11	Bgtw11.M	Mother	Bgtw11.M.m12	21.9	12	334	17,489	T78	TACCAATCTCGGC
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m1	22.0	1	7	18,105	T56 (runs 1 and 2)	GTTAAGACAGTCG
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m2	22.1	2	31	38,175	T56 (runs 1 and 2)	CAGTTGAGGCATT
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m3	22.2	3	60	16,379	T78	CGGATCGTAATAC
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m4	22.2	4	91	40,446	T56 (runs 1 and 2)	ACATTATGGCGTG
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m5	22.3	5	125	12,674	T78	TCTGTCAGTGACC
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m6	22.4	6	158	41,746	T56 (runs 1 and 2)	TAAGGCGCTCCTT
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m7	22.5	7	187	21,437	T56 (runs 1 and 2)	CTAATACGGATCG
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m8	22.6	8	216	36,976	T56 (runs 1 and 2)	CACAATAGACACC
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m9	22.7	9	245	15,573	T78	CAGCAACATTGCA
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m10	22.8	10	280	16,713	T78	GCGTTCCTTGTTA
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m11	22.9	11	314	16,498	T78	CGGCGATTTACGT
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m12	22.9	12	341	15,881	TRX	AGCGATATATCGC
Bgtw12	Bgtw12.M	Mother	Bgtw12.M.m13	23.0	13	372	17,612	TRX	TCGTAAGATGCCT

		Hellinger Distance Metric					Unweighted UniFrac Distance Metric

	Factor	SumsOfSqs	MeanSqs	F.Model	R²	p-value	SumsOfSqs	MeanSqs	F.Model	R²	p-value
	Chronologic Age	0.6212	0.6212	108.364	0.19033	0.001	0.79963	0.79963	290.79	0.37721	0.001

Diet at time of fecal sample collection	Breastmilk	0.0549	0.0549	9.568	0.01681	0.001	0.03117	0.03117	11.336	0.01471	0.052
	Formula	0.0049	0.0049	0.848	0.00149	0.88	0.00939	0.00939	3.415	0.00443	0.184
	Solid foods	0.0205	0.0205	3.584	0.00629	0.08	0.03922	0.03922	14.263	0.0185	0.001

	Diarrhea	0.01	0.01	1.681	0.00295	0.18	0.01255	0.01255	4.563	0.00592	0.006
	Antibiotic Usage	0.002	0.002	0.294	0.00052	0.88	0.00421	0.00421	1.533	0.00199	0.154

16S rRNA OTU ID (as shown in Main Fig. 2b)	Relative abundance (%) during first month post-partum¹	Relative abundance (%) during subsequent months	FDR- corrected p value	Beta Coefficient²	Rank order of importance in Random Forests- based age- discriminatory model	RDP 2.4 Taxonomic Annotation (Phylum;Class;Order;Family;Genus;Species)

469873	12.27 ± 4.91	2.08 ± 0.45	0.033	+0.148	22	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium
72820	7.70 ± 3.33	0.64 ± 0.14	0.001	+0.13	5	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;Bifidobacterium_longum
348374	0.62 ± 0.60	0.00 ± 0.00	0.012	+0.028		Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides_thetaiotaomicron
158660	0.54 ± 0.46	0.02 ± 0.01	0.037	+0.025		Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides
194648	0.40 ± 0.13	0.11 ± 0.01	0.020	+0.024		Firmicutes;Clostridia;Clostridiales;unclassified_Clostridiales;Blautia;Blautia_sp_M25
528842	0.29 ± 0.26	0.02 ± 0.00	0.006	+0.023		Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;Streptococcus_parasanguinis
561483	0.15 ± 0.07	0.01 ± 0.00	< 0.0001	+0.019	8	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium
113558	0.19 ± 0.12	0.02 ± 0.00	0.027	+0.018		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
122816	0.16 ± 0.15	0.00 ± 0.00	0.007	+0.014		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Morganella;Morganella_morganii
259130	0.10 ± 0.09	0.00 ± 0.00	0.012	+0.011		Firmicutes;Clostridia;Clostridiales;Eubacteriaceae;Eubacterium;Eubacterium_limosum
259422	0.06 ± 0.05	0.00 ± 0.00	0.012	+0.008		Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus
192132	0.04 ± 0.03	0.00 ± 0.00	0.024	+0.007		Proteobacteria;Deltaproteobacteria;Desulfovibrionales;Desulfovibrionaceae;Bilophila;Bilophila_wadsworthia
44126	0.03 ± 0.02	0.00 ± 0.00	0.012	+0.007		Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus

Child ID	Gender	WHZ at enrollment	Food Intervention Assignment	Age at beginning of intervention (months)	Duration of food intervention (days)¹	WHZ at end of food intervention phase	Rate of weight gain (g/kg body weight/day)	Enteropathogens detected at enrollment	Months followed during post intervention period

Bgmal1	Male	-5.22	RUTF	7.43	28	-2.97	2.12	none detected	5.53
Bgmal5	Male	edema	RUTF	10.87	21	-4.18	8.07	none detected	5.97
Bgmal6	Male	-4	RUTF	11.7	17	-2.75	10.69	none detected	lost to follow-up
Bgmal7	Female	-3.92	RUTF	10.3	27	-2.72	12.47	none detected	3.04
Bgmal9	Female	-3.76	RUTF	11.27	8	-3.02	5.18	not done	lost to follow-up
Bgmal13	Female	-3.51	RUTF	6.67	3 (LAMA)	-3.78	4.63	none detected	lost to follow-up
Bgmal14	Male	-4.17	RUTF	14.2	17	-2.79	8.31	Vibrio cholerae	lost to follow-up
Bgmal15	Male	-4.03	RUTF	17.37	8	-2.49	17.23	none detected	2
Bgmal18	Male	-4.6	RUTF	14.97	17	-3.67	4.76	none detected	1.1
Bgmal20	Female	-3.38	RUTF	10.67	9 (LAMA)	-3.32	11.13	Shigella flexneri	lost to follow-up
Bgmal22	Male	-3.35	RUTF	9.27	8	-3.31	4.75	not done	6.17
Bgmal25	Male	-3.38	RUTF	6.77	18	-2.25	7.82	none detected	6
Bgmal26	Male	-4.97	RUTF	NA	3 (LAMA)	-5.23	16.2	none detected	lost to follow-up
Bgmal27	Male	-4.91	RUTF	9.07	16	-3.75	15.98	none detected	lost to follow-up
Bgmal29	Male	-4.07	RUTF	10.47	8	-2.63	16.87	none detected	0.13
Bgmal33	Female	-4.86	RUTF	8.33	21	-3.23	11.6	none detected	3.93
Bgmal34	Male	-4.73	RUTF	16.6	17	-3.3	14.7	none detected	3.04
Bgmal35	Male	-5.28	RUTF	7.87	15	-3.92	12.3	not done	4.9
Bgmal38	Male	-4.66	RUTF	14.13	1 (LAMA)	-4.66	no weight gain	none detected	lost to follow-up
Bgmal41	Female	-3.39	RUTF	18.8	17	-2.33	8.6	Shigella boydi	4.87
Bgmal42	Female	-3.4	RUTF	14.6	13	-2.58	10.7	Hafnia alvae	lost to follow-up
Bgmal43	Male	-5.3	RUTF	7.13	14	-4.07	15.3	none detected	5.9
Bgmal44	Male	-3.45	RUTF	7.77	14	-2.63	10.1	not done	5.9
Bgmal48	Male	-3.3	RUTF	16.1	13	-1.99	8.6	Vibrio cholerae	1.54
Bgmal49	Male	-4.09	RUTF	8.73	4 (LAMA)	-3.81	15.9	none detected	lost to follow-up
Bgmal52	Male	-5.3	RUTF	12.57	12 (LAMA)	-4.24	4.5	not done	lost to follow-up
Bgmal54	Female	-3.91	RUTF	10.53	14	-3.1	7.4	not done	2.93
Bgmal57	Male	-4.24	RUTF	17.33	12	-2.57	13.8	not done	6
Bgmal58	Male	-4.29	RUTF	11.07	11	-2.13	17.1	not done	7.27
Bgmal59	Male	-4.54	RUTF	14.77	9	-2.75	16.2	not done	6.06
Bgmal61	Male	-4.44	RUTF	14.27	13	-3.31	16.69	not done	0.54
Bgmal62	Male	-3.51	RUTF	7.33	20	-2.34	6.92	not done	1.5
Bgmal2	Female	-4.21	Khichuri-Halwa	12.13	21	-2.72	10.62	none detected	lost to follow-up
Bgmal3	Male	-4.4	Khichuri-Halwa	9.23	17	-3.09	10.1	Vibrio cholerae	3.76
Bgmal4	Male	-4.35	Khichuri-Halwa	9.13	29	-3.53	4.85	none detected	1.03
Bgmal8	Female	-3.29	Khichuri-Halwa	17.9	18	-1.7	8.57	none detected	2.07
Bgmal10	Male	-5.45	Khichuri-Halwa	15.57	13	-3.69	16.48	none detected	1.97
Bgmal11	Male	-3.84	Khichuri-Halwa	15.07	16	-3.13	1.95	none detected	lost to follow-up
Bgmal12	Female	-3.48	Khichuri-Halwa	19.77	9	-1.67	13.91	none detected	0.56
Bgmal16	Female	-3.94	Khichuri-Halwa	12.73	8	-2.12	16.42	none detected	0.16
Bgmal17	Male	-4.2	Khichuri-Halwa	na	2 (LAMA)	-4.16	3.78	none detected	lost to follow-up
Bgmal19	Male	edema	Khichuri-Halwa	7.8	25	-0.09	7.06	Aeromona hydrophila	1.17
Bgmal21	Male	-4.76	Khichuri-Halwa	8.83	22	-3.89	3.31	none detected	2.74
Bgmal23	Male	-3.15	Khichuri-Halwa	9.97	6 (LAMA)	-3.1	4	not done	lost to follow-up
Bgmal24	Male	-4.63	Khichuri-Halwa	8.43	14	-3.94	4.81	Shigella sonnei	0.46
Bgmal28	Female	-3.56	Khichuri-Halwa	15.87	18	-2.26	8.89	Shigella flexneri	5.94
Bgmal30	Female	-3.35	Khichuri-Halwa	9.2	13	-2.13	11.31	none detected	lost to follow-up
Bgmal31	Male	-4.47	Khichuri-Halwa	13.9	13	-3	12.5	none detected	5.67
Bgmal32	Male	-4.54	Khichuri-Halwa	19.9	15	-3.05	11.4	none detected	5.9
Bgmal36	Male	-3.96	Khichuri-Halwa	15.37	27	-2.61	5.9	none detected	3.4
Bgmal37	Male	-3.37	Khichuri-Halwa	13.13	26	3.01	2.6	none detected	5.43
Bgmal39	Female	-5.59	Khichuri-Halwa	14.13	10	-4.93	15.9	Salmonella enterica group C1	9.1
Bgmal40	Female	-4.21	Khichuri-Halwa	10.1	27	-3.76	3.3	not done	5.57
Bgmal45	Male	-5.32	Khichuri-Halwa	8.6	26	-4.58	5.6	none detected	5.9
Bgmal46	Female	-5.4	Khichuri-Halwa	18.5	15	-4.03	12.3	none detected	3.87
Bgmal47	Female	-4.76	Khichuri-Halwa	12.33	10	-3.91	10.8	Shigella flexneri	5.9
Bgmal50	Male	-3.79	Khichuri-Halwa	13.97	13	-2.23	12.9	not done	6.03
Bgmal51	Male	-4.03	Khichuri-Halwa	14.93	10	-2.22	14.7	Vibrio cholerae	1.96
Bgmal53	Male	-4.54	Khichuri-Halwa	14.53	11	-2.76	16.1	not done	lost to follow-up
Bgmal55	Male	-5.58	Khichuri-Halwa	8.4	4 (LAMA)	-4.9	23.2	not done	lost to follow-up
Bgmal56	Male	-3.35	Khichuri-Halwa	9	11	-1.87	13.5	not done	7.3
Bgmal60	Male	edema	Khichuri-Halwa	8.97	15	-0.71	11.7	not done	5.9
Bgmal63	Male	-3.02	Khichuri-Halwa	8.47	12	-1.59	14.74	not done	6
Bgmal64	Female	-3.1	Khichuri-Halwa	11.17	8	-1.55	19.77	not done	4.5

Child ID	Fecal Sample ID	Threshold for MAM Diagnosis	Age, days	Age, months	WHZ	HAZ	WAZ	Diet at time of fecal sample collection			Diarrhea at the time of sample collection	Antibiotics within 7 days prior to sample collection	Medications (Antibiotics and other)	Number of high quality V4-16S rRNA sequences	16S rRNA Sequencing Run ID	Sample specific barcode sequence
Child ID	Fecal Sample ID	Threshold for MAM Diagnosis	Age, days	Age, months	WHZ	HAZ	WAZ	Breast Milk	Solid Foods	Formula	Diarrhea at the time of sample collection	Antibiotics within 7 days prior to sample collection	Medications (Antibiotics and other)	Number of high quality V4-16S rRNA sequences	16S rRNA Sequencing Run ID	Sample specific barcode sequence

Bgsng7001	Bgsng7001.m19	MAM	552	18.1	-2.87	-2.9	-3.38	Yes	Yes	No	No	No	Chlorpheniramine Maleate, Paracetamol	18,860	7	GCCTGCAGTACT
Bgsng7013	Bgsng7013.m19	MAM	547	18.0	-2.54	-3.16	-3.31	Yes	Yes	No	Yes	No		18,634	7	TCTCGATAAGCG
Bgsng7031	Bgsng7031.m19	MAM	557	18.3	-2.08	-2.67	-2.86	Yes	Yes	No	No	No		15,771	7	GGAACGACGTGA
Bgsng7082	Bgsng7082.m19	MAM	551	18.1	-3.7	-0.83	-3.11	Yes	Yes	No	No	No		46,439	4	CACCGAAATCTG
Bgsng7094	Bgsng7094.m19	MAM	562	18.5	-2.1	-2.49	-2.78	Yes	Yes	No	No	No		21,799	5	GGCGAACTGAAG
Bgsng7109	Bgsng7109.m18	MAM	548	18.0	-2.62	-4	-3.78	Yes	Yes	No	No	No		25,516	6	GAACCTATGACA
Bgsng7110	Bgsng7110.m18	MAM	552	18.1	-2.72	-2.07	-3	Yes	Yes	No	No	No		21,546	6	ATCCTACGAGCA
Bgsng7116	Bgsng7116.m19	MAM	553	18.2	-2.7	-2.41	-3.05	Yes	Yes	No	No	Yes	Flucloxacillin Sodium, Chlorpheniramine Maleate, Multi Vitamin	20,166	5	GTCGCTTGCACA
Bgsng7123	Bgsng7123.m18	MAM	548	18.0	-2.95	-2.67	-3.46	Yes	Yes	No	No	No		27,214	7	TGCTCCGTAGAA
Bgsng7148	Bgsng7148.m19	MAM	551	18.1	-3.69	-2.32	-3.79	Yes	Yes	No	No	No		44,754	4	GTCAATTAGTGG
Bgsng7004	Bgsng7004.m19	Not MAM	557	18.3	-1.68	-3.63	-2.99	Yes	Yes	No	No	No		23,688	4	ACGGGATACAGG
Bgsng7018	Bgsng7018.m19	Not MAM	551	18.1	-1.6	-1.29	-1.78	Yes	Yes	No	No	Yes	Flucloxacillin Sodium	25,765	7	AATCAACTAGGC
Bgsng7040	Bgsng7040.m19	Not MAM	551	18.1	-0.1	-3.01	-1.56	Yes	Yes	No	No	No		49,576	7	AGACAAGCTTCC
Bgsng7050	Bgsng7050.m19	Not MAM	555	18.2	-0.2	-2.54	-1.37	Yes	Yes	No	No	No	Chlorpheniramine Maleate, Multi Vitamin	13,988	5	CTCTCATATGCT
Bgsng7052	Bgsng7052.m19	Not MAM	552	18.1	-1.05	-0.87	-1.2	Yes	Yes	No	No	No		25,364	5	AGCCTCATGATG
Bgsng7063	Bgsng7063.m19	Not MAM	553	18.2	-0.87	-0.85	-1.06	Yes	Yes	No	No	No		23,878	7	CGACTCTAAACG
Bgsng7071	Bgsng7071.m19	Not MAM	554	18.2	-0.04	0.02	-0.07	Yes	Yes	No	No	No	Paracetamol	21,695	5	CCAGTATCGCGT
Bgsng7074	Bgsng7074.m19	Not MAM	556	18.3	-1.82	-3.47	-2.99	Yes	Yes	No	Yes	No	Oral rehydration saline, Multi Vitamin	15,006	5	GTGTATCGCCAC
Bgsng7081	Bgsng7081.m19	Not MAM	551	18.1	-0.73	-2.25	-1.62	Yes	Yes	No	No	No		17,264	5	TTGACACACGAC
Bgsng7087	Bgsng7087.m19	Not MAM	551	18.1	-1.63	-2.5	-2.43	Yes	Yes	No	No	No		19,084	5	AGTACCTAAGTG
Bgsng7090	Bgsng7090.m19	Not MAM	552	18.1	-0.71	-0.75	-0.9	Yes	Yes	No	No	Yes	Amoxycillin trihydrate, Sulbutamol	20,562	5	GGTCTAGGTCTA
Bgsng7096	Bgsng7096.m19	Not MAM	560	18.4	-0.68	-1.98	-1.44	Yes	Yes	No	No	No		27,208	5	CCTGGAATTAAG
Bgsng7108	Bgsng7108.m18	Not MAM	548	18.0	-1.32	-2.51	-2.14	Yes	Yes	No	No	No		21,247	6	TGACGTAGAACT
Bgsng7130	Bgsng7130.m19	Not MAM	544	17.9	-1.89	-4.18	-3.43	Yes	Yes	No	No	No		26,268	5	GTACCTAGCCTG
Bgsng7131	Bgsng7131.m19	Not MAM	570	18.7	-1.63	-1.9	-2.07	Yes	Yes	No	No	No		39,288	5	AATATCGGGATC
Bgsng7133	Bgsng7133.m19	Not MAM	558	18.3	-1.64	-2.3	-2.33	Yes	Yes	No	Yes	Yes	Azithromycin Dihydrate, Oral rehydration saline, Chlorpheniramine Maleate	23,886	5	AAGCGTACATTG
Bgsng7135	Bgsng7135.m19	Not MAM	549	18.0	-0.96	-2.34	-1.84	Yes	Yes	No	No	No		18,644	5	GAGTTTACGGTC
Bgsng7145	Bgsng7145.m19	Not MAM	549	18.0	1.38	-4.18	-1.08	Yes	Yes	No	No	No		24,350	4	CTTGGAGGCTTA
Bgsng7149	Bgsng7149.m19	Not MAM	565	18.6	-1.05	-0.84	-1.16	Yes	Yes	No	No	No		21,384	4	GGTACCTGCAAT
Bgsng7152	Bgsng7152.m19	Not MAM	554	18.2	-1.5	-1.96	-2	Yes	Yes	No	No	No		22,772	4	CTCGGATAGATC
Bgsng7173	Bgsng7173.m19	Not MAM	556	18.3	0.14	-1.58	-0.63	Yes	Yes	No	No	Yes	Amoxicillin trihydrate + Clavulanic acid, Chloramphenicol, Sulbutamol	22,652	9	TCCACATTGGGTC
Bgsng7178	Bgsng7178.m19	Not MAM	560	18.4	0.72	-0.91	0.11	Yes	Yes	No	No	No		26,494	9	TGCGAAGTTGGGA
Bgsng7203	Bgsng7203.m19	Not MAM	551	18.1	0.16	-3.44	-1.55	Yes	Yes	No	No	No		15,174	7	TGACGCCTCCAA

(a) Training Set
Characteristics	Training

Weight-for-Height Z score	-0.32 ± 1
Male / Female	7 / 5
Number of fecal samples collected per child	22.7 ± 1.5
Age at first fecal sample collection (days)	6 ± 1
Age at last fecal sample collection (days)	712 ± 15
Mean sampling interval (days)	33 ± 3.0
Months of exclusive breastfeeding	3.2 ± 2.3
Age of first introduction of solid food (months)	6.3 ± 2.3
Number of diarrheal episodes per year	4.0 ± 1.9
% Days with diarrhea during sampling period	3.9 ± 1.7
Fraction within prior 7 days	0.2 ± 0.1

(b) Validation

Characteristics	Validation

Weight-for-Height Z score	-0.44 ± 0.8
Male / Female	9 / 4
Number of fecal samples collected per child	21.2 ± 2.2
Age at first fecal sample collection (days)	7 ± 4
Age at last fecal sample collection (days)	709 ± 9
Mean sampling interval (days)	35.1 ± 4.3
Months of exclusive breastfeeding	3.6 ± 2.3
Age of first introduction of solid food (months)	6.4 ± 6.4
Number of diarrheal episodes per year	4.6 ± 2.4
% Days with diarrhea during sampling period	4.3 ± 2.7
Fraction of samples collected where antibiotics had been consumed within prior 7 days	0.2 ± 0.2

(c) Validation - Twins & Triplets

Characteristics	Validation - Twins & Triplets

Weight-for-Height Z score	-0.46 ± 0.7
Male / Female	7 / 18
Number of fecal samples collected per child	17.9 ± 5.3
Age at first fecal sample collection (days)	13 ± 12
Age at last fecal sample collection (days)	497 ± 147
Mean sampling interval (days)	29 ± 3.1
Months of exclusive breastfeeding	0.7 ± 2.3
Age of first introduction of solid food (months)	7.0 ± 1.9
Number of diarrheal episodes per year	1.7 ± 1.3
% Days with diarrhea during sampling period	2.2 ± 2.6
Fraction of samples collected where antibiotics had been consumed within prior 7 days	0.1 ± 0.1

Study Subjects	V4-16S rRNA reads per sample (mean ± SD)	Number of fecal samples	Total number of high quality reads

50 Healthy Children (Singletons, Twins and Triplets)	25,288 ± 13,990	996	25,187,256
Mothers & Fathers	20,233 ± 7,120	243	4,916,630
Severe Acute Malnutrition Randomized Clinical Trial	21,545 ± 15,731	589	12,689,785
Moderate Acute Malnutrition Cross-Sectional Analysis	22,964 ± 8,713	22	505,207
Concordant Healthy Malawian Twins and Triplets	151,578 ± 65,521	47	7,124,158

		1897	50,423,036

(a) Relative microbiota maturity
Factor	Effect size on relative microbiota maturity	Standard Error	p-value

Diarrhea	-1.98	0.51	0.0001
Month following Diarrhea	-1.55	0.56	0.01
Formula	+0.75	0.34	0.03
Antibiotics	-0.42	0.39	0.27
Chronologic Age (months)	-0.05	0.02	0.06

	Log-likelihood ratio	Degrees of Freedom	p-value

random by-family intercepts	102.1	1	p<0.0001
nested random by-child intercepts within family-intercepts	3.29E-07	1	0.9995

(b) MAZ score
Factor	Effect size on MAZ	Standard Error	p-value

Diarrhea	-0.60	0.16	0.0002
Month following Diarrhea	-0.42	0.18	0.02
Formula	+0.22	0.11	0.04
Antibiotics	-0.08	0.12	0.52
Chronologic Age (months)	-0.04	0.01	<0.001

	Log-likelihood ratio	Degrees of Freedom	p-value

random by-family intercepts	102.1	1	<0.0001
nested random by-child intercepts within family-intercepts	3.29E-07	1	0.9995

(c) Age-adjusted Shannon Diversity Index
Factor	Effect size on ΔSDI:	Standard Error	p-value

Diarrhea	-0.44	0.15	0.0028
Month following Diarrhea	-0.37	0.16	0.0247
Formula	+0.11	0.10	0.2796
Antibiotics	-0.08	0.11	0.3987
Chronologic Age (months)	+0.01	0.01	0.296

	Log-likelihood ratio	Degrees of Freedom	p-value

random by-family intercepts	53.8	1	<.0001
nested random by-child intercepts within family-intercepts	1.31	1	0.2515

(a) Khichuri
Ingredient	Amount in 1 kg khichuri

Rice	120 g
Lentils (mashur dal)	60 g
Oil (soya)	70 ml
Potato	100 g
Pumpkin	100 g
Leafy vegetable (shak)	80 g
Onion (2 medium size)	50 g
Spices (ginger, garlic, turmeric and coriander powder)	50 g
Water	1000 ml

Total energy/kg	1,442 kcal
Total protein/kg	29.6 g

(b) Halwa
Ingredient	Amount in 1 kg halwa

Wheat flour (atta)	200 g
Lentils (mashur dal)	100 g
Oil (soya)	100 ml
Molasses (brown sugar or gur)	125 g
Water (to make a thick paste)	600 ml

Total energy/kg	2,404 kcal
Total protein/kg	50.5 g

(c) Milk suji & Milk suji ‘100’
Ingredient	Amount in 1 L Milk Suji	Amount in 1L Milk Suji ‘100’

Whole milk powder (g)	40	80
Rice powder (g)	40	50
Sugar (g)	25	50
Soya oil (g)	25	25
MgCl₂ (g)	0.5	0.5
KCl (g)	1	1
Calcium lactate/ calcium carbonate (g)	2	2

Total energy/L	670 kcal	1000 kcal
Total protein/L	14 g	26 g

Rank Order	16S rRNA OTU ID (as shown in Fig. 1)	Age discriminatory feature importance score (mean ± SD)	RDP 2.4 Taxonomic Annotation (Phylum;Class;Order;Family;Genus;Species)	Representative 16S rRNA Sequence of the 97% ID OTU cluster

1	326792	9.64 ± 0.29	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;Faecalibacterium_prausnitzii	AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGTAGCAAACAGG
2	189827	7.21 ± 0.38	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;Ruminococcus_sp_5_1_39BFAA	TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
3	470663	3.89 ± 0.22	Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;Lactobacillus_ruminis	TACGTAGGTGGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG
4	191687	3.27 ± 0.23	Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Dorea;Dorea_longicatena	TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCACGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGCTGAGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
5	72820	2.86 ± 0.14	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;Bifidobacterium_longum	TACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
6	194745	2.43 ± 0.19	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;Ruminococcus_sp_5_1_39BFAA	TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCCGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
7	15141	1.98 ± 0.12	Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;Lactobacillus_mucosae	TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTGATAAGTCTGATGTGAAAGCCTTTGGCTTAACCAAAGAAGTGCATCGGAAACTGTCAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG
8	561483	1.59 ± 0.10	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium	TACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGGAAGCGTGGGGAGCGAACAGG
9	217996	0.99 ± 0.06	Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Staphylococcus	TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAGATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG
10	364234	0.95 ± 0.12	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;Ruminococcus_sp_5_1_39BFAA	TACGTAGGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
11	287510	0.92 ± 0.08	Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Catenibacterium;Catenibacterium_mitsuokai	TACGTAGGTGGCGAGCGTTATCCGGAATCATTGGGCGTAAAGAGGGAGCAGGCGGCCGCAAGGGTCTGTGGTGAAAGACCGAAGCTAAACTTCGGTAAGCCATGGAAACCGGGCGGCTAGAGTGCGGAAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGGTCTGGGCCGCAACTGACGCTCATTCCCGAAAGCGTGGGGAGCAAATAGG
12	261912	0.88 ± 0.10	Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Dorea;Dorea_formicigenerans	TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCTGTGCAAGTCTGAAGTGAAAGGCATGGGCTCAACCTGTGGACTGCTTTGGAAACTGTGCAGCTAGAGTGTCGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
13	361809	0.61 ± 0.11	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;Ruminococcus_torques	TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGAGTGGCAAGTCTGATGTGAAAACCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTCAATCTAGAGTACCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
14	108747	0.52 ± 0.05	Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;Streptococcus_thermophilus	TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTGATAAGTCTGAAGTTAAAGGCTGTGGCTCAACCATAGTTCGCTTTGGAAACTGTCAAACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG
15	533785	0.51 ± 0.05	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium	TACGTAGGGCGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
16	9514	0.46 ± 0.06	Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;Haemophilus_parainfluenzae	TACGGAGGGTGCGAGCGTTAATCGGAATAACTGGGCGTAAAGGGCACGCAGGCGGTGACTTAAGTGAGGTGTGAAAGCCCCGGGCTTAACCTGGGAATTGCATTTCATACTGGGTCGCTAGAGTACTTTAGGGAGGGGTAGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAATACCGAAGGCGAAGGCAGCCCCTTGGGAATGTACTGACGCTCATGTGCGAAAGCGTGGGGAGCAAACAGG
17	561636	0.42 ± 0.05	Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus	TACGTAGGTCCCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
18	312461	0.42 ± 0.04	Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium	TACGTAGGGGGCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG
19	470139	0.40 ± 0.05	Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;unclassified_Erysipelotrichaceae;Clostridium_ramosum	TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGGGAGCAGGCGGCAGCAAGGGTCTGTGGTGAAAGCCTGAAGCTTAACTTCAGTAAGCCATAGAAACCAGGCAGCTAGAGTGCAGGAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGATCTGGCCTGCAACTGACGCTCAGTCCCGAAAGCGTGGGGAGCAAATAGG
20	181834	0.38 ± 0.08	Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium	TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCGATGCAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTATGGCTAGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTCAGGCTCGAAAGCGTGGGGAGCAAACAGG
21	148099	0.38 ± 0.05	Firmicutes;Bacilli;Lactobacillales;Leuconostocaceae;Weissella;Weissella_cibaria	TACGTATGTTCCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTATTTAAGTCTGAAGTGAAAGCCCTCAGCTCAACTGAGGAATTGCTTTGGAAACTGGATGACTTGAGTGCAGTAGAGGAAAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGTTGAGGCTCGAAAGTGTGGGTAGCAAACAGG
22	469873	0.36 ± 0.05	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium	TACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
23	185951	0.35 ± 0.06	Firmicutes;Clostridia;Clostridiales	TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGGACAAGTCTGATGTGAAAGGCTGGGGCTCAACCCCGGGACTGCATTGGAAACTGCCCGTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
24	212619	0.31 ± 0.04	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae	AACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGACCGGCAAGTTGGAAGTGAAAACTATGGGCTCAACCCATAAATTGCTTTCAAAACTGCTGGCCTTGAGTAGTGCAGAGGTAGGTGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGACCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCAAACAGG
25	469852	0.29 ± 0.05	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;Bifidobacterium_bifidum	TACGTAGGGCGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGCTCGTAGGCGGCTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCGATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
26	170124	0.28 ± 0.06	Firmicutes;Clostridia;Clostridiales;Eubacteriaceae;Eubacterium;Eubacterium_desmolans	TACGTAGGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGCAGGCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACATTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG
27	187010	0.28 ± 0.06	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;Faecalibacterium_prausnitzii	TACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAGCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGTAGCAAACAGG
28	303304	0.27 ± 0.05	Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella_copri	TACGGAAGGTCCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGTATCGAACAGG
29	470527	0.26 ± 0.03	Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;Lactobacillus_reuteri	TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG
30	210269	0.25 ± 0.04	Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae	TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG
31	182202	0.24 ± 0.03	Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium_glycolicum	TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGG
32	178122	0.23 ± 0.06	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;Ruminococcus_obeum	TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGACTGGCAAGTCTGATGTGAAAGGCGGGGGCTCAACCCCTGGACTGCATTGGAAACTGTTAGTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
33	540230	0.21 ± 0.04	Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus;Enterococcus_faecalis	TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
34	309068	0.18 ± 0.04	Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella_copri	TACGGAAGGTCCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGTATCGAACAGG
35	24773	0.16 ± 0.03	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium	TACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCGATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
36	554755	0.16 ± 0.03	Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus	TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG
37	305760	0.15 ± 0.04	Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia_coli	TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG
38	268604	0.15 ± 0.03	Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella	TACGGAAGGTCCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGGCGGACCTTTAAGTCAGCTGTGAAATACGGCGGCTCAACCGTCGAACTGCAGTTGATACTGGAGGTCTTGAGTGCACACAGGGATGCTGGAATTCATGGTGTAGCGGTGAAATGCTCAGATATCATGAAGAACTCCGATCGCGAAGGCAGGCATCCGGGGTGCAACTGACGCTGAGGCTCGAAAGTGCGGGTATCAAACAGG
39	188900	0.15 ± 0.04	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;Faecalibacterium_prausnitzii	AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGGAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGTAGCAAACAGG

16S rRNA OTU ID (as shown in Extended Data Fig. 6 & 7)	Unabbreviated OTU ID in deposited OTU table	FDR- corrected p value	Beta Coefficient	Rank order of importance in Random Forests- based age- discriminatory model	RDP 2.4 Taxonomic Annotation (Phylum;Class;Order;Family;Genus;Species)

142054	142054	0.000	0.0286		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
210269	210269	0.000	0.0278		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
9715	9715	0.000	0.0263		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
563485	563485	0.002	0.0236		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
436723	436723	0.000	0.0232		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
512914	512914	0.000	0.0215		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
310265	310265	0.000	0.0207		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
307981	307981	0.000	0.0174		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
307080	307080	0.000	0.0152		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia
305760	305760	0.000	0.0131		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia_coli
113558	113558	0.000	0.0115		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
280706	280706	0.000	0.0090		Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae
540230	540230	0.002	0.0079		Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus;Enterococcus_faecalis
15382	15382	0.027	0.0068		Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus
249155.c0	New.0.CleanUp.ReferenceOTU249155	0.027	0.0067		Firmicutes;Bacilli;Lactobacillales;Leuconostocaceae;Leuconostoc
316587	316587	0.007	0.0063		Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;Streptococcus_gallolyticus

469852	469852	0.000	-0.0163		Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;Bifidobacterium_bifidum
533785	533785	0.000	-0.0146	15	Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium
24773	24773	0.000	-0.0137		Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium
326792	326792	0.000	-0.0118	1	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;Faecalibacterium_prausnitzii
301004	301004	0.001	-0.0115		Actinobacteria;1760;Coriobacteriales;Coriobacteriaceae;Olsenella
181834	181834	0.000	-0.0112	20	Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium
261912	261912	0.000	-0.0109	12	Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Dorea;Dorea_formicigenerans
13823	13823	0.005	-0.0104		Firmicutes;Negativicutes;Selenomonadales;Veillonellaceae;Veillonella;Veillonella_ratti
188900	188900	0.000	-0.0103		Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;Faecalibacterium_prausnitzii
187010	187010	0.000	-0.0102		Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;Faecalibacterium_prausnitzii
131391	131391	0.000	-0.0098		Actinobacteria;1760;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium
576.d0	New.0.ReferenceOTU576	0.001	-0.0097		Actinobacteria;1760;Coriobacteriales;Coriobacteriaceae
162427	162427	0.020	-0.0096		Firmicutes;Negativicutes;Selenomonadales;Veillonellaceae;Megasphaera
303304	303304	0.000	-0.0094		Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella_copri
470663	470663	0.000	-0.0094	3	Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;Lactobacillus_ruminis
309068	309068	0.000	-0.0093		Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella_copri
186029	186029	0.000	-0.0092		Actinobacteria;1760;Coriobacteriales;Coriobacteriaceae;Collinsella;Collinsella_aerofaciens
145149	145149	0.001	-0.0090		Firmicutes;Negativicutes;Selenomonadales;Veillonellaceae;Veillonella
130663	130663	0.020	-0.0088		Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides_fragilis
194745	194745	0.000	-0.0088	6	Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;Ruminococcus_sp_5_1_39BFAA
212503	212503	0.000	-0.0088		Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium
184464	184464	0.001	-0.0085		Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella_copri

Child ID	Fecal Sample ID	Food Intervention Assignment	Phase of Study	Age of child at time of fecal sample collection (months)	Weight, kg	Height, cm	Weight-for-Height Z score (WHZ)	Height-for-Age Z score (HAZ)	Weight-for-age Z score (WAZ)	24 hour Dietary Recall	Antibiotics	Antibiotic type2	Diarrhea	Fever	Cough	Number of high quality V4-16S rRNA sequences	16S rRNA Sequencing Run ID	Sample specific barcode sequence

Bgmal1¹	Bgmal1.s1	RUTF	Acute Phase - Pre Antibiotics	7	4.35	61	-4.47	-3.7	-5.23	rice, lentil, cow’s milk	No		Yes	No	No	25,095	ACMAL_1 (runs 1 and 2)	TAGTCGTGCACAT
Bgmal1	Bgmal1.s2	RUTF	Acute Phase - Pre Antibiotics	7	4.35	61	-4.47	-3.7	-5.23	rice, lentil, cow’s milk	No		Yes	No	No	22,968	ACMAL_1 (runs 1 and 2)	TACCATAGCTCCG
Bgmal1	Bgmal1.s3	RUTF	Acute Phase - First Antibiotic	7.37	4.05	61	-5.22	-3.92	-5.74	milk suji	No		No	No	No	22,051	ACMAL_1 (runs 1 and 2)	CGATGTTCGCTAG
Bgmal1	Bgmal1.s4.RUTF	RUTF	RUTF	7.43	4.08	61	-5.15	-3.96	-5.72	RUTF	No		No	No	No	10,633	ACMAL_1 (runs 1 and 2)	CGCTCGAAGATTC
Bgmal1	Bgmal1.s5.RUTF	RUTF	RUTF	7.5	4.13	61	-5.02	-4	-5.66	RUTF	No		No	No	Yes	13,308	ACMAL_1 (runs 1 and 2)	GTAGGCATGCTTG
Bgmal1	Bgmal1.s7.RUTF	RUTF	RUTF	7.63	4.07	61.6	-5.43	-3.8	-5.78	RUTF	Yes	Azithromycin syrup	Yes	No	No	10,485	ACMAL_1 (runs 1 and 2)	GATCACCAGGTGT
Bgmal1	Bgmal1.s8.RUTF	RUTF	RUTF	7.7	3.96	61.6	-5.71	-3.84	-5.95	RUTF	Yes	Azithromycin syrup	No	No	No	11,310	ACMAL_1 (runs 1 and 2)	CGAATACCAAGTC
Bgmal1	Bgmal1.s9.RUTF	RUTF	RUTF	7.77	4.1	61.6	-5.36	-3.88	-5.77	RUTF	Yes	Azithromycin syrup	No	Yes	No	14,004	ACMAL_1 (runs 1 and 2)	AGTATCTGCGCGT
Bgmal1	Bgmal1.s10.RUTF	RUTF	RUTF - Last Antibiotic	8.27	4.32	63	-5.4	-3.53	-5.57	RUTF	Yes	Cefixime syrup	No	No	Yes	8,823	ACMAL_1 (runs 1 and 2)	CTCGACATCTCTT
Bgmal1	Bgmal1.s11	RUTF	Post intervention follow-up (months) < 1	8.83	not taken	not taken	na	na	na	powdered milk	Yes	Ceftazidime injection	No	Yes	No	6,976	ACMAL_1 (runs 1 and 2)	TCCAATACGCCTG
Bgmal1	Bgmal1.s12	RUTF	Post intervention follow-up (months) 1 to 2	9.27	5.41	63.2	-2.94	-3.98	-4.33	milk, leafy vegetable, dal	No		No	No	No	23,297	ACMAL_1 (runs 1 and 2)	CAGTTACGAGCTA
Bgmal1	Bgmal1.s13	RUTF	Post intervention follow-up (months) 1 to 2	9.43	5.74	63.4	-2.26	-3.97	-3.93	powdered milk	No		No	Yes	No	33,614	ACMAL_1 (runs 1 and 2)	TAAGGCGCTCCTT
Bgmal1	Bgmal1.s14	RUTF	Post intervention follow-up (months) 2 to 3	10.3	6	64	-1.97	-4.13	-3.78	powdered milk	No		No	No	No	21,826	ACMAL_1 (runs 1 and 2)	CTGTCGCAAATAG
Bgmal1	Bgmal1.s15	RUTF	Post intervention follow-up (months) 2 to 3	10.73	6.51	65.5	-1.57	-3.69	-3.22	Halwa	No		No	No	No	33,128	ACMAL_1 (runs 1 and 2)	TGTGTTGTCGTGC
Bgmal1	Bgmal1.s16	RUTF	Post intervention follow-up (months) 3 to 4	11.8	6.73	66.3	-1.47	-3.82	-3.17	Halwa	No		No	No	No	31,511	ACMAL_1 (runs 1 and 2)	ACGCTGTGGATTA
Bgmal1	Bgmal1.s17	RUTF	Post intervention follow-up (months) > 4	12.77	6.2	66.3	-2.52	-4.21	-4	Halwa	Yes	Amoxicillin syrup	No	Yes	Yes	22,182	ACMAL_1 (runs 1 and 2)	CGATTATCGACGA
Bgmal1	Bgmal1.s18	RUTF	Post intervention follow-up (months) > 4	13.8	5.89	66.3	-3.19	-4.6	-4.53	Halwa	Yes	Azithromycin syrup	No	No	Yes	16,103	ACMAL_1 (runs 1 and 2)	CACCTTACACCTT
Bgmal10¹	Bgmal10.s1	Khichuri-Halwa	Acute Phase - Pre Antibiotics	15.17	4.46	64	-5.45	-5.97	-6.36	Breast milk, rice, potato, lentil, milk	No		Yes	Yes	Yes	20,928	ACMAL_1 (runs 1 and 2)	TACCCAAGCGTTA
Bgmal10	Bgmal10.s3	Khichuri-Halwa	Acute Phase - First Antibiotic	15.43	4.46	64	-5.45	-6.05	-6.39	milk suji, Breast milk	Yes	Azithromycin syrup	No	No	Yes	23,831	ACMAL_1 (runs 1 and 2)	ATGAACCCTATGG
Bgmal10	Bgmal10.s4.khich	Khichuri-Halwa	Khichuri-Halwa	15.57	4.53	64	-5.29	-6.09	-6.32	Khichuri-Halwa, milk suji, Breast milk	Yes	Azithromycin syrup	No	No	Yes	18,550	ACMAL_1 (runs 1 and 2)	TGTTATCGCATGG
Bgmal10	Bgmal10.s5.khich	Khichuri-Halwa	Khichuri-Halwa	15.63	4.7	64	-4.91	-6.11	-6.14	Khichuri-Halwa, milk suji 100, Breast milk	No		No	No	No	25,485	ACMAL_1 (runs 1 and 2)	ATCTGCACTGAGC
Bgmal10	Bgmal10.s6.khich	Khichuri-Halwa	Khichuri-Halwa	15.7	4.75	64	-4.79	-6.12	-6.09	Khichuri-Halwa, Breast milk, milk suji 100	Yes	Ciprofloxacin syrup	No	Yes	No	22,302	ACMAL_1 (runs 1 and 2)	AGCCTAGCCCAAT
Bgmal10	Bgmal10.s7.khich	Khichuri-Halwa	Khichuri-Halwa	15.77	4.98	64	-4.27	-6.14	-5.83	Khichuri-Halwa, Breast milk, milk suji 100	Yes	Ciprofloxacin syrup	No	Yes	No	26,216	ACMAL_1 (runs 1 and 2)	TAGCTGTCAAGCT
Bgmal10	Bgmal10.s8.khich	Khichuri-Halwa	Khichuri-Halwa	15.83	5.22	64	-3.73	-6.16	-5.57	Khichuri-Halwa, Breast milk, milk suji 100	Yes	Ciprofloxacin syrup	No	No	No	17,248	ACMAL_1 (runs 1 and 2)	CATGTGTGTAGAC
Bgmal10	Bgmal10.s9.khich	Khichuri-Halwa	Khichuri-Halwa - Last Antibiotic	15.9	5.39	64	-3.35	-6.18	-5.38	Khichuri-Halwa, Breast milk, milk suji 100	No		No	No	No	16,982	ACMAL_1 (runs 1 and 2)	CAGCAACATTGCA
Bgmal10	Bgmal10.s10	Khichuri-Halwa	Post intervention follow-up (months) < 1	16.43	5.91	65	-2.61	-5.94	-4.86	Halwa, milk, rice, potato, biscuit, Breast milk	No		No	No	No	10,039	ACMAL_1 (runs 1 and 2)	CACAACACTCCGA
Bgmal10	Bgmal10.s11	Khichuri-Halwa	Post intervention follow-up (months) 1 to 2	16.9	6.39	65.8	-1.93	-5.76	-4.38	Halwa, Khichuri, milk, juice, biscuit, Breast milk	Yes	Amoxicillin syrup	No	No	Yes	17,518	ACMAL_1 (runs 1 and 2)	CGTAAATTCAGGC
Bgmal10	Bgmal10.s12	Khichuri-Halwa	Post intervention follow-up (months) 1 to 2	17.37	6.57	67	-2.05	-5.43	-4.24	Halwa, rice, meat, potato, banana, milk, Breast milk	No		No	No	No	17,437	ACMAL_1 (runs 1 and 2)	CTATCTATCCTGC
Bgmal10	Bgmal10.s13	Khichuri-Halwa	Post intervention follow-up (months) 2 to 3	17.87	6.32	68	-2.94	-5.18	-4.58	Khichuri, Breast milk, banana	No		No	No	No	15,864	ACMAL_1 (runs 1 and 2)	CGCCAACAACCAT
Bgmal11¹	Bgmal11.s1	Khichuri-Halwa	Acute Phase - Pre Antibiotics	14.8	6.78	74	-3.93	-1.87	-3.64	Breast milk, suji, cerelac, rice, milk, lentil	No		No	No	Yes	24,883	ACMAL_1 (runs 1 and 2)	ATGGGTCCCACAT
Bgmal11	Bgmal11.s3	Khichuri-Halwa	Acute Phase - First Antibiotic	15	6.83	74	-3.84	-1.95	-3.61	milk suji, Breast milk	No		No	No	No	21,894	ACMAL_1 (runs 1 and 2)	CACGATTCGAGTC
Bgmal11	Bgmal11.s4.khich	Khichuri-Halwa	Khichuri-Halwa	15.07	6.83	74	-3.84	-1.98	-3.62	Khichuri-Halwa, Breast milk, milk suji	Yes	Levofloxacin syrup	Yes	No	Yes	20,542	ACMAL_1 (runs 1 and 2)	CGATGTATGTGGT
Bgmal11	Bgmal11.s5.khich	Khichuri-Halwa	Khichuri-Halwa	15.13	7	74	-3.56	-2	-3.44	Khichuri-Halwa, Breast milk, milk suji 100	Yes	Levofloxacin syrup	No	No	Yes	19,400	ACMAL_1 (runs 1 and 2)	CGAGAGCAACAGA
Bgmal11	Bgmal11.s6.khich	Khichuri-Halwa	Khichuri-Halwa	15.2	7.02	74.5	-3.65	-1.83	-3.43	Khichuri-Halwa, Breast milk, milk suji 100	Yes	Levofloxacin syrup	No	No	Yes	18,534	ACMAL_1 (runs 1 and 2)	ACCTGCGAAGTAT
Bgmal11	Bgmal11.s7.khich	Khichuri-Halwa	Khichuri-Halwa	15.27	6.92	74.5	-3.82	-1.85	-3.55	Khichuri-Halwa, Breast milk, milk suji 100	No		No	No	No	20,747	ACMAL_1 (runs 1 and 2)	CGATGTGGTGTTA
Bgmal11	Bgmal11.s8.khich	Khichuri-Halwa	Khichuri-Halwa	15.33	6.97	74.5	-3.73	-1.88	-3.51	Khichuri-Halwa, Breast milk, milk suji 100	Yes	Azithromycin syrup	Yes	No	Yes	24,782	ACMAL_1 (runs 1 and 2)	ACGATGCTGTTGA
Bgmal11	Bgmal11.s9.khich	Khichuri-Halwa	Khichuri-Halwa - Last Antibiotic	15.37	6.82	74.5	-3.99	-1.89	-3.68	Khichuri-Halwa, Breast milk, milk suji 100	Yes	Azithromycin syrup	No	No	Yes	26,701	ACMAL_1 (runs 1 and 2)	TAGTGTTTCGGAC
Bgmal12	Bgmal12.s3	Khichuri-Halwa	Acute Phase	19.7	7.55	77.4	-2.79	-1.59	-2.82	milk suji, Breast milk	Yes	Amoxicillin syrup, Gentamicin injection	No	No	No	25,996	ACMAL_1 (runs 1 and 2)	AGGTTCGGTCCAT
Bgmal12	Bgmal12.s4.khich	Khichuri-Halwa	Khichuri-Halwa	19.77	7.77	77.4	-2.44	-1.61	-2.58	Khichuri-Halwa, Breast milk, milk suji	No		No	No	No	16,957	ACMAL_1 (runs 1 and 2)	CACTCCTTGTGTT

(a) ‘Gender by Food-intervention’
Gender	RUTF	Khichuri-Halwa	Total	p value

Male	24	21	45
Female	8	11	19

Total	32	32	64	0.59

(b) ‘Antibiotics by Food-intervention’ during nutritional rehabilitation
Antibiotics	RUTF	Khichuri-Halwa	Total	p value

Yes	84	79	163
No	55	90	145

Total	139	169	308	0.02

(c) ‘Antibiotics by Food-intervention’ during the post-intervention follow-up period
Antibiotics	RUTF	Khichuri-Halwa	Total	p value

Yes	22	23	45
No	78	80	158

Total	100	103	203	1

(d) RUTF (Plumpy Nut)¹
Ingredient	Amount in 1 kg RUTF

Skimmed milk powder	300 g
Sugar	280 g
Vegetable oil	154 g
Peanut paste	250 g
Mineral vitamin mix	16g

Total energy/kg	5300 – 5450 kcal
Total protein/kg	136g

(a) Effect size and significance of differences in microbiota maturation metrics between each treatment phase relative to healthy children
Relative microbiota maturity	Intervention Arm	Estimate	Std. Error	p value

Enrollment	RUTF	-5.62	0.78	<0.001
During		-5.09	0.68	<0.001
End of Intervention		-4.75	0.82	<0.001
< 1 month		-2.85	0.83	<0.01
1 - 2 months		-2.19	0.87	0.07
2 - 3 months		-0.31	1.03	1.00
3 - 4 months		-1.96	1.11	0.35
> 4 months		-3.43	0.96	<0.01

Enrollment	Khichuri-Halwa	-6.55	0.67	<0.001
During		-5.88	0.53	<0.001
End of Intervention		-5.63	0.72	<0.001
< 1 month		-3.98	0.74	<0.001
1 - 2 months		-1.72	0.79	0.18
2 - 3 months		-2.67	0.89	0.02
3 - 4 months		-1.58	1.05	0.59
> 4 months		-2.29	0.82	0.04

Microbiota-for-Age Z-score	Intervention Arm	Estimate	Std. Error	p value

Enrollment	RUTF	-1.63	0.26	<0.001
During		-1.49	0.23	<0.001
End of Intervention		-1.39	0.27	<0.001
< 1 month		-0.84	0.27	0.01
1 - 2 months		-0.75	0.28	0.04
2 - 3 months		-0.42	0.33	0.68
3 - 4 months		-0.73	0.35	0.19
> 4 months		-1.43	0.31	<0.001

Enrollment	Khichuri-Halwa	-1.80	0.23	<0.001
During		-1.68	0.19	<0.001
End of Intervention		-1.66	0.24	<0.001
< 1 month		-1.30	0.25	<0.001
1 - 2 months		-0.69	0.26	0.06
2 - 3 months		-1.05	0.29	<0.01
3 - 4 months		-0.56	0.34	0.46
> 4 months		-0.96	0.27	<0.01

Age-Adjusted Shannon Diversity Index	Intervention Arm	Estimate	Std. Error	p value

Enrollment	RUTF	-1.18	0.16	<0.001
During		-0.82	0.12	<0.001
End of Intervention		-0.89	0.17	<0.001
< 1 month		-0.56	0.18	0.01
1 - 2 months		-0.30	0.19	0.55
2 - 3 months		-0.46	0.24	0.32
3 - 4 months		-1.18	0.26	<0.001
> 4 months		-0.79	0.22	<0.01

Enrollment	Khichuri-Halwa	-1.03	0.15	<0.001
During		-0.95	0.11	<0.001
End of Intervention		-0.90	0.16	<0.001
< 1 month		-0.83	0.17	<0.001
1 - 2 months		-0.89	0.18	<0.001
2 - 3 months		-0.73	0.21	<0.01
3 - 4 months		-0.41	0.25	0.54
> 4 months		-0.58	0.19	0.02

(b) Effect size and significance of differences in microbiota maturation metrics between each treatment phase relative to enrollment
Relative microbiota maturity	Intervention Arm	Estimate	Std. Error	p value

During	RUTF	0.53	0.57	0.93
End of Intervention		0.87	0.73	0.80
< 1 month		2.77	0.74	<0.01
1 - 2 months		3.44	0.78	<0.001
2 - 3 months		5.31	0.96	<0.001
3 - 4 months		3.67	1.05	<0.01
> 4 months		2.20	0.88	0.08

During	Khichuri-Halwa	6.55	0.67	<0.001
End of Intervention		0.67	0.56	0.79
< 1 month		0.92	0.74	0.76
1 - 2 months		2.58	0.76	<0.01
2 - 3 months		4.83	0.81	<0.001
3 - 4 months		3.88	0.91	<0.001
> 4 months		4.97	1.07	<0.001

Microbiota-for-Age Z-score	Intervention Arm	Estimate	Std. Error	p value

During	RUTF	0.13	0.17	0.98
End of Intervention		0.24	0.22	0.88
< 1 month		0.79	0.23	<0.01
1 - 2 months		0.88	0.24	<0.01
2 - 3 months		1.21	0.30	<0.001
3 - 4 months		0.90	0.32	0.036
> 4 months		0.20	0.27	0.98

During	Khichuri-Halwa	0.12	0.17	0.99
End of Intervention		0.14	0.23	0.99
< 1 month		0.50	0.24	0.20
1 - 2 months		1.11	0.25	<0.001
2 - 3 months		0.75	0.28	0.05
3 - 4 months		1.24	0.33	0.001
> 4 months		0.84	0.26	0.01

Age- adjusted Shannon Diversity Index	Intervention Arm	Estimate	Std. Error	p value

During	RUTF	0.36	0.15	0.11
End of Intervention		0.29	0.19	0.56
< 1 month		0.62	0.20	0.01
1 - 2 months		0.88	0.21	<0.001
2 - 3 months		0.72	0.26	0.03
3 - 4 months		0.00	0.28	1.00
> 4 months		0.39	0.23	0.46

During	Khichuri-Halwa	0.07	0.14	1.00
End of Intervention		0.12	0.18	0.99
< 1 month		0.19	0.19	0.89
1 - 2 months		0.13	0.20	0.99
2 - 3 months		0.30	0.23	0.70
3 - 4 months		0.62	0.27	0.12
> 4 months		0.45	0.21	0.18

Family ID	Child ID	Fecal Sample ID	Age, months	WHZ	Number of high quality V4-16S rRNA sequences	16S rRNA Sequencing Run ID	Sample specific barcode sequence

h208	h208A	h208A.1	0.4	-1.73	133,515	Malawi89	GTCTCATGTAGG
h301	h301A	h301A.1	0.6	0.2	101,465	Malawi89	GTAGCTGACGCA
h301	h301B	h301B.1	0.6	-0.33	135,737	Malawi89	GTCGACTCCTCT
h257	h257A	h257A.1	2.3	-0.62	117,949	Malawi89	GTGTCTACATTG
h257	h257B	h257B.1	2.3	0.47	121,595	Malawi89	TACACGATCTAC
h181	h181A	h181A.1	2.6	0.36	221,464	Malawi7	TAACTCTGATGC
h181	h181B	h181B.1	2.6	-0.25	229,814	Malawi7	TACTAATCTGCG
h181	h181C	h181C.1	2.6	-0.99	216,056	Malawi7	TAGCCTCTCTGC
h259	h259A	h259A.2	3.2	1.86	197,189	Malawi7	GGCAGTGTATCG
h259	h259B	h259B.2	3.2	1.53	200,122	Malawi7	GTAGAGCTGTTC
h305	h305B	h305B.2	4.7	-1	131,898	Malawi89	GTGTGTGTCAGG
h305	h305C	h305C.2	4.7	-0.42	111,403	Malawi89	TACAGTCTCATG
h121	h121B	h121B.1	5.2	2.58	122,051	Malawi89	TAGCACACCTAT
h165	h165A	h165A.1	5.3	-0.58	230,639	Malawi7	TAGCGACATCTG
h165	h165B	h165B.1	5.3	-0.38	236,422	Malawi7	GGACGTCACAGT
h209	h209A	h209A.2	6.8	-0.18	101,469	Malawi89	TACACACATGGC
h209	h209B	h209B.2	6.8	-0.83	80,917	Malawi89	TACTGCGACAGT
h47	h47A	h47A.1	7.2	-0.93	64,752	Malawi6	GTCGCTGTCTTC
h47	h47B	h47B.1	7.2	-2.26	99,204	Malawi7	GTGAGGTCGCTA
h235	h235A	h235A.1	8.0	-1.09	118,988	Malawi89	GTCAACGCGATG
h235	h235B	h235B.1	8.0	-0.31	108,240	Malawi89	GTCTCTCTACGC
h128	h128A	h128A.1	9.1	-1.31	177,426	Malawi7	GGTGCGTGTATG
h264	h264A	h264A.2	9.6	0.01	122,455	Malawi89	GGCTATGACATC
h264	h264B	h264B.2	9.6	-0.33	246,575	Malawi7	GTCTGACAGTTG
h273	h273A	h273A.2	11.1	0.48	245,101	Malawi7	TACAGATGGCTC
h273	h273B	h273B.2	11.1	0.81	245,319	Malawi7	TACTTACTGCAG
h37	h37A	h37A.1	11.2	-1.07	141,448	Malawi89	GTTCGCGTATAG
h37	h37B	h37B.1	11.2	-0.27	142,827	Malawi89	TACGATGACCAC
h279	h279A	h279A.2	11.4	0.96	106,307	Malawi89	GGCGACATGTAC
h279	h279B	h279B.2	11.4	-1.01	110,396	Malawi89	GTAGATGCTTCG
h144	h144A	h144A.1	14.6	-0.74	230,465	Malawi7	GCTTCATAGTGT
h144	h144B	h144B.1	14.6	-1.96	289,895	Malawi7	GTACAAGAGTGA
h10	h10A	h10A.1	16.1	-0.32	130,876	Malawi89	GTTAGAGCACTC
h18	h18A	h18A.4	16.2	0.51	76,375	Malawi6	GCTGTAGTATGC
h18	h18B	h18B.4	16.2	0.08	70,390	Malawi6	GGTCACTGACAG
h68	h68A	h68A.4	20.4	-0.09	267,547	Malawi3	GCTTGCGAGACA
h68	h68B	h68B.4	20.4	0	70,403	Malawi3	GTACGGCATACG
h35	h35A	h35A.3	22.7	-2.16	46,022	Malawi6	GTAGTGTCTAGC
h78	h78A	h78A.4	22.7	-0.7	241,999	Malawi3	GTCTATCGGAGT
h78	h78B	h78B.4	22.7	0.95	216,988	Malawi3	GTGGCGATACAC
h186	h186A	h186A.1	24.2	0.09	120,553	Malawi89	GTAGCAACGTCT
h186	h186B	h186B.1	24.2	1.36	62,791	Malawi7	GTACGGCATACG
h186	h186C	h186C.1	24.2	-0.07	121,883	Malawi89	GTCATTCACGAG
h60	h60A	h60A.2	24.5	0.04	232,045	Malawi7	TAGATCCTCGAT
h60	h60B	h60B.2	24.5	-0.29	93,313	Malawi89	GCTGTGTAGGAC
h101	h101A	h101A.3	25.1	-0.55	111,821	Malawi89	GTCGTAGCCAGA
h101	h101B	h101B.3	25.1	-0.16	122,049	Malawi89	GTGATAGTGCCG

PERMALINK

Persistent Gut Microbiota Immaturity in Malnourished Bangladeshi Children

Sathish Subramanian

Sayeeda Huq

Tanya Yatsunenko

Rashidul Haque

Mustafa Mahfuz

Mohammed A Alam

Amber Benezra

Joseph DeStefano

Martin F Meier

Brian D Muegge

Michael J Barratt

Laura G VanArendonk

Qunyuan Zhang

Michael A Province

William A Petri

Tahmeed Ahmed

Jeffrey I Gordon

Abstract

Table ED1.

Table ED3.

Table ED6.

Figure 1. Bacterial taxonomic biomarkers for defining gut microbiota maturation in healthy Bangladeshi children during the first two years of life.

Table ED8.

Table ED9.

The effects of SAM on microbiota maturity

Table ED10.

Figure 2. Persistent immaturity of the gut microbiota in children with SAM.

Table ED15.

Table ED17.

Prospectus

Methods

Singleton birth cohort

Table ED2.

Twins/Triplets birth cohort

Severe Acute Malnutrition (SAM) study

Table ED11.

Anthropologic study

Characterizing the bacterial component of the gut microbiota by V4-16S rRNA sequencing

Defining maturation of the gut microbiota in healthy children using Random Forests

Alpha diversity comparisons

Detecting associations of bacterial taxa with nutritional status and other parameters

Enteropathogen testing

Table ED19.

Additional details regarding statistical methods

Extended Data

Extended Data Figure 1. Illustration of the equations used to calculate ‘relative microbiota maturity’ and ‘Microbiota-for-Age Z score’.

Extended Data Figure 2. Transient microbiota immaturity and reduction in diversity associated with diarrhea in healthy twins and triplets.

Extended Data Figure 3. Microbiota variation in families with twins and triplets during the first year of life.

Extended Data Figure 4. Anthropometric measures of nutritional status in children with SAM before, during and after both randomized food interventions.

Extended Data Figure 5. Persistent reduction of diversity in the gut microbiota of children with SAM.

Extended Data Figure 6. Heatmap of bacterial taxa significantly altered during the acute phase of treatment and nutritional rehabilitation in the microbiota of children with SAM compared to similarly aged healthy children.

Extended Data Figure 7. Heatmap of bacterial taxa altered during long-term follow-up in the fecal microbiota of children with SAM compared to similarly aged healthy children.

Extended Data Figure 8. Effects of antibiotics on the microbiota of children with SAM.

Extended Data Figure 9. Relative microbiota maturity and MAZ scores correlate with Weight-for-Height Z-scores (WHZ) in children with MAM.

Extended Data Figure 10. Cross-sectional assessment of microbiota maturity at 18 months of age in Bangladeshi children with and without MAM plus extension of Bangladeshi-based model of microbiota maturity to Malawi.

Table ED4.

Table ED5.

Table ED7.

Table ED12.

Table ED13.

Table ED14.

Table ED16.

Table ED18.

Supplementary Material

Acknowledgments

Footnotes

References

Associated Data

Supplementary Materials

ACTIONS

PERMALINK

RESOURCES

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