Childhood malnutrition is a multifactorial disease, responsible for nearly half of all deaths in children under five. Lately, the probable association of a dysbiotic gut to malnutrition is also being eagerly investigated. The current study is an attempt to investigate this purported association through assessing the abundance of major gut bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), probionts (Bifidobacteria and Lactobacillus), butyrogens (Faecalibacterium and Roseburia) and pathogens (Escherichia and Klebsiella). The study was conducted in the suburbs of Chandigarh, India in the year 2017. The children enrolled in the study were part of Anganwadis (Rural Child Care Centres) set up under Integrated Child Development Scheme (ICDS) of Government of India where community-based management approach is being widely used for treatment of malnutrition. We used qPCR based absolute quantification as well as the 16S rRNA amplicon sequencing approach for our study. The study population included 30 children in the age group of 2-5 years who were categorized into three groups Healthy, Moderate Acute Malnutrition (MAM) and Severe Acute Malnutrition (SAM), with 10 children in each group. The selection of participants was made based on Z scores. Further, statistical tools like the One-way ANOVA, PCA and PLSDA were employed to analyze and compare the gut bacterial profile. Our investigation through the qPCR (Absolute quantification) approach revealed a significantly higher abundance of Actinobacteria in healthy, in comparison to children suffering from Severe Acute Malnutrition (SAM). Consequently, the same trend was also reflected with respect to Bifidobacterium, a prominent member of the Actinobacteria phylum. Conversely, a significant higher abundance of Lactobacillus with the diminishing nutritional status was recorded. Escherichia showed a significant higher abundance in healthy subjects compared to the malnourished; however, no such difference in abundance of Klebsiella was observed. The other target phyla [Bacteroidetes, Firmicutes and Proteobacteria] and genera (Faecalibacterium and Roseburia) showed differences in abundance; however, these were non-significant. Similarly, the bacterial taxonomy analysis of 16S rRNA gene amplicon sequencing data revealed the higher abundance of phylum Actinobacteria and its member Bifidobacterium with lower prevalence of Lactobacillus in healthy children. The pattern of gut microbiota profile in malnourished subjects suggests a dysbiotic gut depleted in Bifidobacteria, a core member of the consortia of beneficial anaerobes of the healthy child gut. © 2021. Springer-Verlag GmbH Germany, part of Springer Nature.