Han, X., Ding, S., Lu, J. & Li, Y. Global, regional, and national burdens of common micronutrient deficiencies from 1990 to 2019: a secondary trend analysis based on the Global Burden of Disease 2019 study. eClinicalMedicine 44, 101299 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Bailey, R. L., West, K. P. & Black, R. E. The epidemiology of global micronutrient deficiencies. Ann. Nutr. Metab. 66, 22–33 (2015).

Article  CAS  PubMed  Google Scholar 

Black, R. Micronutrient deficiency–an underlying cause of morbidity and mortality. Bull. World Health Organ. 81, 79 (2003).

PubMed  PubMed Central  Google Scholar 

Robertson, R. C., Manges, A. R., Finlay, B. B. & Prendergast, A. J. The human microbiome and child growth – first 1000 days and beyond. Trends Microbiol. 27, 131–147 (2019).

Article  CAS  PubMed  Google Scholar 

Derrien, M., Alvarez, A. S. & de Vos, W. M. The gut microbiota in the first decade of life. Trends Microbiol. 27, 997–1010 (2019).

Article  CAS  PubMed  Google Scholar 

Brown, E. M. et al. Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model. Nat. Commun. 6, 7806 (2015).

Article  CAS  PubMed  Google Scholar 

Reinert, P. Infections in malnourished infants and children. Dev. Sante 1993, 4–6 (1993).

Subramanian, S. et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510, 417–421 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Blanton, L. V. et al. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351, aad3311 (2016).

Article  PubMed  Google Scholar 

Vonaesch, P. et al. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. Proc. Natl Acad. Sci. USA 115, E8489–E8498 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Knight, L. C., Wang, M., Donovan, S. M. & Dilger, R. N. Early-life iron deficiency and subsequent repletion alters development of the colonic microbiota in the pig. Front. Nutr. 6, 120 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Reed, S. et al. Chronic zinc deficiency alters chick gut microbiota composition and function. Nutrients 7, 9768–9784 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, B. et al. Vitamin A deficiency in the early-life periods alters a diversity of the colonic mucosal microbiota in rats. Front. Nutr. 7, 580780 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Hibberd, M. C. et al. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci. Transl. Med. 9, eaal4069 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Liu, J. et al. Vitamin D deficiency in early life regulates gut microbiome composition and leads to impaired glucose tolerance in adult and offspring rats. Food Funct. 14, 5768–5786 (2023).

Article  CAS  PubMed  Google Scholar 

Pham, V. T., Dold, S., Rehman, A., Bird, J. K. & Steinert, R. E. Vitamins, the gut microbiome and gastrointestinal health in humans. Nutr. Res. 95, 35–53 (2021).

Article  CAS  PubMed  Google Scholar 

Belvoncikova, P., Splichalova, P., Videnska, P. & Gardlik, R. The human mycobiome: colonization, composition and the role in health and disease. J. Fungi 8, 1046 (2022).

Article  Google Scholar 

Gutierrez, M. W. et al. Maturational patterns of the infant gut mycobiome are associated with early-life body mass index. Cell Rep. Med. 4, 100928 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lei, J. et al. Antifungal activity of vitamin D3 against Candida albicans in vitro and in vivo. Microbiol. Res. 265, 127200 (2022).

Article  CAS  PubMed  Google Scholar 

Klassert, T. E. et al. Differential effects of vitamins A and D on the transcriptional landscape of human monocytes during infection. Sci. Rep. 7, 40599 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wurtele, H. et al. Modulation of histone H3 lysine 56 acetylation as an antifungal therapeutic strategy. Nat. Med. 16, 774–780 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kennedy, E. A. & Holtz, L. R. Gut virome in early life: origins and implications. Curr. Opin. Virol. 55, 101233 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Lim, E. S. et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat. Med. 21, 1228–1234 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Walters, W. A. et al. Longitudinal comparison of the developing gut virome in infants and their mothers. Cell Host Microbe 31, 187–198 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Singh, S., Verma, N. & Taneja, N. The human gut resistome: current concepts and future prospects. Indian J. Med. Res. 150, 345–358 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

von Wintersdorff, C. J. H. et al. The gut resistome is highly dynamic during the first months of life. Future Microbiol. 11, 501–510 (2016).

Article  Google Scholar 

van Schaik, W. The human gut resistome. Phil. Trans. R. Soc. Lond. B 370, 20140087 (2015).

Article  Google Scholar 

Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).

Article  CAS  Google Scholar 

Holowka, T., van Duin, D. & Bartelt, L. A. Impact of childhood malnutrition and intestinal microbiota on MDR infections. JAC Antimicrob. Resist. 5, dlad051 (2023).

Article  PubMed  PubMed Central  Google Scholar 

McDonnell, A. & Klemperer, K. Drug-Resistant Infections Are One of the World’s Biggest Killers, Especially for Children in Poorer Countries. We Need to Act Now https://www.cgdev.org/blog/drug-resistant-infections-are-one-worlds-biggest-killers-especially-children-poorer-countries (Center for Global Development, 2022).

Littlejohn, P. T. et al. Multiple micronutrient deficiencies alter energy metabolism in host and gut microbiome in an early-life murine model. Front. Nutr. https://www.frontiersin.org/articles/10.3389/fnut.2023.1151670 (2023).

Micronutrients 101 https://micronutrientforum.org/micronutrients101/ (Micronutrient Forum, 2022).

Forgie, A. J. et al. The impact of maternal and early life malnutrition on health: a diet-microbe perspective. BMC Med. 18, 135 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Huus, K. E. et al. Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study. Microbiome 8, 113 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wagner, V. E. et al. Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition. Sci. Transl. Med. 8, 366ra164 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Robertson, R. C. The gut microbiome in child malnutrition. Nestle Nutr. Inst. Workshop Ser. 93, 133–144 (2020).

Article  PubMed  Google Scholar 

Jochum, L. & Stecher, B. Label or concept – what is a pathobiont? Trends Microbiol. 28, 789–792 (2020).

Article  CAS  PubMed  Google Scholar 

Sunoto, S., Suharyono, S. & Gracey, M. Gastrointestinal candidiasis in malnourished children with diarrhoea. Paediatr. Indones. 20, 117–129 (1980).

Article  CAS  PubMed  Google Scholar 

Popovic, A. et al. Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut. Nat. Commun. 12, 6729 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beaber, J. W., Hochhut, B. & Waldor, M. K. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427, 72–74 (2004).

Article  CAS  PubMed  Google Scholar 

Dam, S., Pagès, J. M. & Masi, M. Stress responses, outer membrane permeability control and antimicrobial resistance in Enterobacteriaceae. Microbiology 164, 260–267 (2018).

Article  CAS  PubMed