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Pakistan being one of the Lower \u2013Middle income countries (LMIC) is facing this challenge tremendously. The objective of this study is to determine the impact of IDA on gut microbial diversity as well as its relationship with microbial metabolites.16\u00a0S rRNA gene profiling of healthy and IDA affected meconium samples was performed with additional meta-data collected through questionnaire. The anemia was linked to different dietary parameters through chi-square test of independence and Generalized Linear Latent Variable Model (GLLVM). Anaerobic bacterial genera such as <jats:italic>Coprococcus<\/jats:italic>,<jats:italic> Anaerovoracaceae<\/jats:italic>, strongly associated with anemia and negatively correlated with red meat and fish consumption. Moreover, these microbes positively correlated with branched short chain fatty acids (BSCFAs) production. BSCFAs have strong implications in metabolic disorders. 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