Changes in weather often trigger a myriad of negative impacts on the environment, which eventually affect human health. During the early months of 2016, Malaysia experienced El Niño, with an extremely dry season of almost zero rainfall. At the same time, an increase of more than twofold in fecal secretary immunoglobulin-A (SIgA) levels of healthy preschool children aged 2-6 years was observed, accompanied by an increase in phylum Bacteroidetes, predominantly attributed to genus Bacteroides and Odoribacter, which also positively correlated with fecal SIgA levels. Here, we present evidence to illustrate the detrimental effects of weather change on a microscopic "environment," the human gut ecosystem. We also discuss the protective effects of probiotic against dysbiosis as induced by weather change. The increase in Bacteroidetes was at an expense of decreased genus Faecalibacterium and Veillonella (phylum Firmicutes), whereas children consuming probiotic had a decrease in genus Collinsella, Atopobium, and Eggerthella (phylum Actinobacteria) instead.