Gut Microbiota and Stunting During the First 1,000 Days of Life: Mechanisms of Dysbiosis and Comprehensive Intervention Strategies
Main Article Content
Shalvira Purnama
The first 1,000 days of life (1,000 days of life) represent a critical period that determines the quality of a child’s growth and development. One of the key factors during this period is the gut microbiota, which influences nutrient absorption, energy metabolism, and immune function. An imbalance in the gut microbiota, known as dysbiosis, has been shown to contribute to stunting through impaired intestinal function and chronic inflammation. This literature review aims to describe the role of gut microbiota during the first 1,000 days of life in the development of stunting and to examine microbiota-based intervention strategies from pregnancy through the first two years of life. This study employed a narrative review approach by analyzing 60 scientific articles obtained from PubMed, Scopus, Google Scholar, ScienceDirect, and Consensus AI. The selected articles were published within the past ten years and were relevant to stunting and gut microbiota during the first 1,000 days of life. The review showed that stunted children have lower microbial diversity, decreased abundance of Bifidobacterium and Lactobacillus, and increased levels of potentially pathogenic bacteria, including Proteobacteria, Escherichia coli, and Desulfovibrio. Dysbiosis may lead to reduced short-chain fatty acid (SCFA) production, intestinal mucosal damage, and impaired nutrient absorption. Comparisons between stunted and non-stunted children indicate that healthy microbial diversity also contributes to metabolic efficiency and nutritional status. Preventive interventions targeting dysbiosis should begin during pregnancy through the maintenance of maternal nutritional status and probiotic supplementation, followed by exclusive breastfeeding and diversification of complementary foods rich in fiber and prebiotics. A microbiota-based approach may serve as a comprehensive and sustainable strategy for reducing the burden of stunting in Indonesia.
Organization WH. Joint Child Malnutrition Estimates, 2023 Edition. 2023.
Kementerian Kesehatan Republik Indonesia. Results of the 2024 Indonesian Nutrition Status Survey (SSGI). 2024.
RI SWP. Indonesia’s Stunting Prevalence Decreased to 19.8%. 2025.
Andriani H, Arsyi M, Sutrisno AE, Waits A, Rahmawati ND. Projecting the impact of a national strategy to accelerate stunting prevention in East Nusa Tenggara, Indonesia, using the Lives Saved Tool. Narra J. 2025 Jan 10;5(1):1462.
Purnamasari KD, Ningrum WM, Fatimah S. Training Posyandu Cadres to Prevent Stunting during the First 1000 Days of Life in Cidolog District. J SOLMA. 2025 Mar 31;14(1):42–50.
Marni M, Ratnasari NY. Counseling on Stunting Risk Prevention during the First 1000 Days of Life among the Younger Generation. Indones J Community Serv. 2021 Nov 23;3(2):116.
Hidayatunnikmah N, Rahmawati N, Nuraini SR, Setyani ETA, Aulia RA, Anggraini D, et al. Assistance with Providing Pumpkin Pudding Complementary Foods to Prevent Stunting in Children. As-Sidanah J Pengabdi Masy. 2024 Apr 30;6(1):193–204.
Dewi SK, Fuad A, Nurlia E. Counseling on the Dulur Penting Program (Donors of Eggs Caring for Stunting) in Muruy Village, Menes, Pandeglang. J Pengabdi Pada Masy. 2023 Sep 30;8(4):901–8.
Mulyaningsih E, Ningsih SS. The Effect of Health Education on Pregnant Women’s Knowledge about the First 1000 Days of Life. Malahayati Nurs J. 2024 Jun 1;6(6):2223–33.
Bappenas. National Medium-Term Development Plan (RPJMN) 2020–2024. 2020.
Kementerian Koordinator Bidang Pembangunan Manusia dan Kebudayaan. National Strategy for the Acceleration of Stunting Reduction 2021–2024 Type: Report. 2021.
Pratama MAE, Hendra S, Ngemba HR, Nur R, Azhar R, Laila R. Comparison of Machine Learning Algorithms for Predicting Stunting Prevalence in Indonesia. J Sisfokom (Sistem Inf dan Komputer). 2024 Jun 10;13(2):200–9.
Robertson RC, Manges AR, Finlay BB, Prendergast AJ. The Human Microbiome and Child Growth – First 1000 Days and Beyond. Trends Microbiol. 2019 Feb;27(2):131–47.
Rinanda T, Riani C, Artarini A, Sasongko L. Correlation between gut microbiota composition, enteric infections and linear growth impairment: a case–control study in childhood stunting in Pidie, Aceh, Indonesia. Gut Pathog. 2023 Nov 9;15(1):54.
Hidayah N, Marwan M. Community Empowerment Efforts to Create a Nutrition-Aware Generation of Millennials Free from Stunting through 1000 HPK Activities. J Community Engagem Heal. 2020 Mar 1;3(1):86–93.
Widhi BA, Abdussamad Z, Muhid A, Miswaty TC, Yuliana I, Patty ENS, et al. Community Empowerment Strategies for Stunting Management: Understanding, Prevention, and Intervention. INDRA J Pengabdi Kpd Masy. 2025 Apr 30;6(1):5–9.
Sayiati NQ, Firmansyah F. The Relationship between Energy and Protein Intake and Stunting in Children Aged 12–36 Months. Nutr J. 2025 Apr 27;9(1):11.
Apriluana G, Fikawati S. Analysis of Risk Factors for Stunting among Children Aged 0–59 Months in Developing Countries and Southeast Asia. Media Penelit dan Pengemb Kesehat. 2018 Dec 31;28(4):247–56.
Komalasari K, Supriati E, Sanjaya R, Ifayanti H. Factors Causing Stunting in Children Under Five. Maj Kesehat Indones. 2020 Oct 7;1(2):51–6.
Sarinastiti W, Murdaningtyas CD, Harvani Y. Design of an Explainer Video for Stunting Prevention in Children Under Five Using Skill Level Animation. ANDHARUPA J Desain Komun Vis Multimed. 2023 Jan 27;8(3):385–98.
Rokhaidah R, Hidayattullah R. Maternal Knowledge and Family Support as Efforts to Prevent Stunting in Children Under Five. J Ilm Kesehat Masy Media Komun Komunitas Kesehat Masy. 2022 Oct 4;14(3):141–6.
Kwartawaty NN, W ST, Sari DV. Stunting Prevention Literacy and the Effects of Formula Milk Provision in Stunted Children in Tawangmas Urban Village. J Kreat Pengabdi Kpd Masy. 2023 Nov 1;6(11):4655–68.
Eriyani T, Mardhiyah A, Fitria N, Yosep I. Family Empowerment in Early Growth Detection and Intervention for Stunting Prevention. J Kreat Pengabdi Kpd Masy. 2024 Feb 1;7(2):774–83.
Almira NG, Syafa’atulloh MY. Socialization and Screening of Stunting among Children Under Five in the Community of Sambikerep District, Sambikerep Urban Village, Surabaya City. J Kreat Pengabdi Kpd Masy. 2023 Mar 1;6(3):907–19.
Pakpahan S, Simbolon GAH, Panggabean H, Sitompul ES. Early Detection of Growth and Development and Stunting Prevention among Children Under Five in Pearung Silali Village, Paranginan District, Humbang Hasundutan Regency. J Kreat Pengabdi Kpd Masy. 2024 Jun 14;7(7):2837–50.
Matijašić M, Meštrović T, Paljetak HČ, Perić M, Barešić A, Verbanac D. Gut microbiota beyond bacteria-mycobiome, virome, archaeome, and eukaryotic parasites in IBD. Int J Mol Sci. 2020;21(8):1–21.
Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol. 2021 Jan 4;19(1):55–71.
Paul JK, Azmal M, Haque ASNB, Meem M, Talukder OF, Ghosh A. Unlocking the secrets of the human gut microbiota: Comprehensive review on its role in different diseases. World J Gastroenterol. 2025 Feb 7;31(5).
Al Bander Z, Nitert MD, Mousa A, Naderpoor N. The Gut Microbiota and Inflammation: An Overview. Int J Environ Res Public Health. 2020 Oct 19;17(20):7618.
Wang L, Wang S, Zhang Q, He C, Fu C, Wei Q. The role of the gut microbiota in health and cardiovascular diseases. Mol Biomed. 2022 Oct 11;3(1):30.
Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017 Jun 1;474(11):1823–36.
Young VB. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ. 2017 Mar 15;j831.
Rezkillah AR, Bahar H, Paridah P. Description of Pregnant Women’s Knowledge, Attitudes, and Practices Regarding the Importance of Balanced Nutrition during the First 1000 Days of Life (HPK) in the Working Area of Abeli Community Health Center, Kendari City, 2021. J Gizi dan Kesehat Indones. 2022 Jun 7;3(1).
Robertson RC, Edens TJ, Carr L, Mutasa K, Gough EK, Evans C, et al. The gut microbiome and early-life growth in a population with high prevalence of stunting. Nat Commun. 2023 Feb 14;14(1):654.
Hardjo J, Selene NB. Stunting and Gut Microbiota: A Literature Review. Pediatr Gastroenterol Hepatol Nutr. 2024;27(3):137.
Hutapea AD, Nova F, Panjaitan T, Clementine G, Angelina A. First 1000 Days of Life: Child Nutrition and Growth and Development. J Kreat Pengabdi Kpd Masy. 2022 Aug 1;5(8):2436–47.
Widyahening IS, Aufa MA, Alhas MF, Widodo AB, Friska D. Knowledge, Attitude, and Practice of Mothers on the First 1000 Days of Life. eJournal Kedokt Indones. 2021 Sep 1;9(2):129.
Siburian UD, Ritonga PT, Sembiring RNS. The Importance of Monitoring Nutritional Status in Pregnant Women and the First 1000 Days of Life in Stunting Prevention in Sangkaran Village, North Tapanuli Regency. J Kreat Pengabdi Kpd Masy. 2024 Jun 7;7(7):2822–36.
Puteri NJ, Fitria L. Access to Sanitation and Its Impact on Stunting in Toddlers in EastNusa Tenggara, Indonesia. Unnes J Public Heal. 2025 May 4;14(1):14–21.
Shen Y, Fan N, Ma SX, Cheng X, Yang X, Wang G. Gut Microbiota Dysbiosis: Pathogenesis, Diseases, Prevention, and Therapy. MedComm. 2025 May;6(5):e70168.
Helmyati S, Yuliati E, Wisnusanti SU, Maghribi R, Juffrie M. Gastrointestinal Microbiota in Elementary School Children Experiencing Stunting in West Lombok. J Gizi dan Pangan. 2017;12(1):55–60.
Surono IS, Venema K, Martosudarmo S, Kusumo PD. Effect of a 6-Month Functional Food Intervention on the Microbiota of Stunted Children in East Nusa Tenggara, Indonesia—A Randomized Placebo-Controlled Parallel Trial. Foods. 2025 Jun 24;14(13):2218.
Chen RY, Kung VL, Das S, Hossain MS, Hibberd MC, Guruge J, et al. Duodenal Microbiota in Stunted Undernourished Children with Enteropathy. N Engl J Med. 2020 Jul 23;383(4):321–33.
Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA. Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Curr Opin Microbiol. 2018 Aug;44:34–40.
Simanjuntak BY, Annisa R, Saputra AI. Literature Review: Is Gut Microbiota Associated with Stunting in Children Under Five? Amerta Nutr. 2022;6(1SP):343–51.
Blanton L V, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, et al. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science. 2016 Feb 19;351(6275).
Kumar M, Ji B, Babaei P, Das P, Lappa D, Ramakrishnan G, et al. Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling. Metab Eng. 2018 Sep;49:128–42.
Subramanian S, Blanton L V., Frese SA, Charbonneau M, Mills DA, Gordon JI. Cultivating Healthy Growth and Nutrition through the Gut Microbiota. Cell. 2015 Mar;161(1):36–48.
Grech A, Collins CE, Holmes A, Lal R, Duncanson K, Taylor R, et al. Maternal exposures and the infant gut microbiome: a systematic review with meta-analysis. Gut Microbes. 2021 Jan 12;13(1).
Bogaert D, van Beveren GJ, de Koff EM, Lusarreta Parga P, Balcazar Lopez CE, Koppensteiner L, et al. Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites. Cell Host Microbe. 2023 Mar;31(3):447-460.e6.
Gardner WM, Razo C, McHugh TA, Hagins H, Vilchis-Tella VM, Hennessy C, et al. Prevalence, years lived with disability, and trends in anaemia burden by severity and cause, 1990–2021: findings from the Global Burden of Disease Study 2021. Lancet Haematol. 2023 Sep;10(9):e713–34.
Quezada-Pinedo HG, Cassel F, Duijts L, Muckenthaler MU, Gassmann M, Jaddoe VW V., et al. Maternal Iron Status in Pregnancy and Child Health Outcomes after Birth: A Systematic Review and Meta-Analysis. Nutrients. 2021 Jun 28;13(7):2221.
Li Z, Zhang Y, Wang L, Deng TK, Chiu WH, Ming W kit, et al. Microbiota of pregnancy, placenta and newborns in the third trimester: A randomized controlled study. Heliyon. 2024;10(3):e24698.
Ferro LE, Crowley LN, Bittinger K, Friedman ES, Decker JE, Russel K, et al. Effects of prebiotics, probiotics, and synbiotics on the infant gut microbiota and other health outcomes: A systematic review. Vol. 63, Critical Reviews in Food Science and Nutrition. 2023. 5620–5642 p.
Shi Y, Yin R, Pang J, Chen Y, Li Z, Su S, et al. Impact of complementary feeding on infant gut microbiome, metabolites and early development. Food Funct. 2024;15(21):10663–78.
Geniselli da Silva V, Tonkie JN, Roy NC, Smith NW, Wall C, Kruger MC, et al. The effect of complementary foods on the colonic microbiota of weaning infants: a systematic review. Crit Rev Food Sci Nutr. 2024;0(0):1–16.
Tang M, Ma C, Weinheimer-Haus EM, Robertson CE, Kofonow JM, Berman LM, et al. Different gut microbiota in U.S. formula-fed infants consuming a meat vs. dairy-based complementary foods: A randomized controlled trial. Front Nutr. 2023;9(January):1–12.
