Effects of Ampicillin on the Gut Microbiome of an Adult Male as Determined by 16S rRNA V4 Metagenomics Sequencing and Greengenes Bioinformatics Suite

Abstract

Aims: To determine the effects of ampicillin on the relative abundance of the gut microbiota using Next Generation Sequencing (NGS) metagenomics platform and to predict metabolic functions with bioinformatics suite. Methods: The subject who has taken no antibiotics for the past six months provided fecal sample on day 0 (pre-antibiotics), day 10 (antibiotics) to treat sour throat infection and after 90 days (post-antibiotics). DNA was extracted, metagenomics library prepared and 16S rRNA V4 region was amplified using custom bar-coded primers before sequencing with IlluminaMiseq program. Sequence reads were analyzed with IlluminaBasespace algorithm and greengenes bioinformatics suites. Metabolic functional prediction was accomplished using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm. Results: Pre-antibiotics sequence reads were classified into 20 phyla, 35 Class, 71 Order, 147 Family, 275 Genera, and 401 Species-level categories. Ampicillin significantly influenced the gut microbiota as the sequence reads were reduced to 8 phyla, 15 Class, 24 Order, 41 Family, 72 Genera, and 98 Species-level categories. Post-antibiotics sample (90 days after antibiotic treatment) generated sequence reads classified into 17 phyla, 28 Class, 60 Order, 120 Family, 221 Genera, and 313 Species-level categories. Conclusion: Ampicillin reduced the diversity of the core bacterial phylogenetic taxa with a corresponding increase in Firmicutes-Bacteroidetes ratio from 2.4:1 (pre-antibiotics) to 6.5:1 (antibiotics). A high proportion of Veillonella species were observed during ampicillin intake. Some bacterial metabolic functions such as carbohydrate (Ascorbate and aldarate), amino acid (D-Arginine and D-ornithine) and vitamin (pantothenate and CoA biosynthesis) metabolisms were stimulated by ampicillin in the subject.