{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T05:31:42Z","timestamp":1763443902248,"version":"3.45.0"},"reference-count":34,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T00:00:00Z","timestamp":1763078400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nutrients"],"abstract":"<jats:p>Background\/Objectives: Stunting and weight faltering (WF) remain pressing public health challenges in low- and middle-income countries, with long-term consequences for child growth, development, and survival. While the role of gut health in early growth is increasingly recognized, evidence on how the gut microbiome and metabolome respond to nutritional interventions in WF infants is scarce. This study explored gut microbiome and metabolome changes in Indonesian infants aged 6\u201312 months who overcame WF following a one-month intervention. Methods: Infants were assigned to either a Nutritional Advice (NA) group or a Nutritional Advice plus Oral Nutritional Supplements (NAONS) group. Stool samples were collected before and after the intervention for microbiome (16S rRNA sequencing) and metabolome (LC-MS) analysis. Results: Significant shifts in gut microbial composition (beta diversity) and species richness (Chao1 index) were observed in both groups, suggesting enhanced microbial diversity and gut resilience. Within-group analysis revealed increases in beneficial genera such as Faecalibacterium and Peptostreptococcus, and a reduction in pro-inflammatory Fusobacterium in the NA group. The NAONS group showed a notable decrease in Proteus, a potentially pathogenic genus. Between-group comparisons indicated higher abundances of Lactococcus and Leuconostoc in the NAONS group, likely reflecting the influence of milk protein-rich supplements on microbial colonization, favoring lactic acid bacteria over SCFA-producing taxa, leading to better gut health. Metabolome analysis revealed significant changes in the NA group, increases in metabolites like Threonine, Tryptophan, and Xylose pointed to improved energy metabolism and gut health, while a decrease in Oxalic Acid suggested better metabolic efficiency. In contrast, the NAONS group, while benefiting from rapid weight gain, displayed a distinct metabolic profile influenced by high milk protein intake. No significant correlations were found between microbiome and metabolome changes, highlighting the complexity of gut-host interactions, suggesting that the interventions led to independent shifts in the aforementioned profiles. Conclusions: Overall, the findings suggest that nutritional interventions may enhance gut health and support recovery from weight faltering, providing insights into strategies that may contribute to restoring healthy growth trajectories and preventing stunting by modulating gut health.<\/jats:p>","DOI":"10.3390\/nu17223570","type":"journal-article","created":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T16:46:22Z","timestamp":1763138782000},"page":"3570","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Longitudinal Microbiome and Metabolome Shifts After Successful Intervention in Impending Stunting in Indonesian Infants"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0180-5129","authenticated-orcid":false,"given":"Conny","family":"Tanjung","sequence":"first","affiliation":[{"name":"Post Graduate School, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6195-441X","authenticated-orcid":false,"given":"Ryohei","family":"Shibata","sequence":"additional","affiliation":[{"name":"Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bahrul","family":"Fikri","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6788-7679","authenticated-orcid":false,"given":"Titis","family":"Prawitasari","sequence":"additional","affiliation":[{"name":"Department of Child Health, Dr. Cipto Mangunkusumo National Central Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4436-3906","authenticated-orcid":false,"given":"Andi Alfian","family":"Zainuddin","sequence":"additional","affiliation":[{"name":"Public Health and Community Medicine Department, Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aidah","family":"Juliaty","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dwi Sora","family":"Yullyana","sequence":"additional","affiliation":[{"name":"Institute of Research and Community, Microbiome Research Division, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9111-661X","authenticated-orcid":false,"given":"Tonny","family":"Sundjaya","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, Faculty of Public Health, University of Indonesia, Jakarta 16424, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hedi","family":"Kuswanto","sequence":"additional","affiliation":[{"name":"Public Health and Community Medicine Department, Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9199-8286","authenticated-orcid":false,"given":"Jessica","family":"Clarensia","sequence":"additional","affiliation":[{"name":"Graduate School of Medicine, Chiba University, Chiba 263-8522, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8076-0493","authenticated-orcid":false,"given":"Naoki","family":"Shimojo","sequence":"additional","affiliation":[{"name":"Center for Preventive Medical Sciences, Chiba University, Chiba 263-8522, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5345-7165","authenticated-orcid":false,"given":"Berthold","family":"Koletzko","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, LMU-Ludwig Maximilians Universit\u00e4t Munich, Dr. von Hauner Children\u2019s Hospital, 80337 Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8776-9661","authenticated-orcid":false,"given":"Hiroshi","family":"Ohno","sequence":"additional","affiliation":[{"name":"Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nasrum","family":"Massi","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,14]]},"reference":[{"key":"ref_1","unstructured":"De Sanctis, V., Soliman, A., Alaaraj, N., Ahmed, S., Alyafei, F., and Hamed, N. 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