Intestinal parasitic infections can change gut microbiota and short-chain fatty acids (SCFAs). We aimed to study the interaction among Strongyloides stercoralis, human gut microbiota, and serum SCFAs in a community. Fifty-two subjects in Donchang sub-district, Khon Kaen Province, northeastern Thailand, were included based on specific inclusion and exclusion criteria. Characteristics of the participants were matched between those positive for S. stercoralis infection alone (no other intestinal parasites; Ss+, n = 26) and uninfected controls (infection status confirmed by PCR; Ss, n = 26). Serum short-chain fatty acids were evaluated by gas chromatography-mass spectrometry. DNA was extracted from individual faecal samples and then pooled into two groups (Ss+ and Ss) for amplification and sequencing of the V3-V4 region of the 16S gene with next-generation technology. We explored the impact of infection with S. stercoralis on the faecal microbiota: individuals infected with this parasite exhibited increased alpha diversity of bacteria. At the genus level, gut microbiota in Ss+ patients showed high abundances of Escherichia-Shigella and Bacteroides but low abundances of the genera Bifidobacterium, Lactobacillus, and Blautia. PCR of individual samples to identify certain species of interest gave results consistent with those from next-generation sequencing of pooled samples and showed that significantly more Ss+ samples contained Bacteroides fragilis. Intriguingly, a major SCFA, acetic acid, was 3 significantly decreased in S. stercoralis infection. In conclusion, S. stercoralis infection caused an imbalance of gut microbiota and decreased acetic acid in serum. This information adds to the knowledge concerning the effect of intestinal nematode-related chronic diseases.