Fresh faecal samples were collected from a patient who had not taken ABs within the previous 3 months. The patient (a 68-year-old man) was admitted to the Department for Internal Medicine at the University Hospital Kiel (Germany) due to an infected cardiac pacemaker. A clinical examination identified inflamed skin and subcutaneous tissue around the pacemaker, and laboratory findings revealed an elevated C-reactive protein level (CRP 19.7 mg/litre; normal value <8 mg/litre) and a full blood count within normal ranges. The patient did not present any intestinal disorders. The pacemaker had been placed to treat the patient's sick sinus syndrome, first diagnosed in 1994. His cardiovascular risk factors were arterial hypertension and non-insulin-dependent diabetes mellitus. The patient was regularly taking amlodipine, ramipril, hydrochlorothiazide and glimepiride on a daily basis and Marcumar according to his international normalised ratio values. AB therapy was initiated with a combined intravenous therapy of ampicillin/sulbactam and cefazolin on the day of admission as a single dose and continued with intravenous cefazolin alone for the next 14 days. The patient's CRP level returned to normal within 1 week after the beginning of AB therapy. Faecal samples were collected on the day of admission, prior to AB treatment (day 0, FS-0), on days 3, 6, 11 and 14 of AB treatment (FS-3, FS-6, FS-11 and FS-14, respectively) and 40 days after AB therapy (FS-40). Fresh faeces were collected, frozen immediately and stored at −80°C until further processing. Informed consent was obtained from the patient, and the study was approved by the Ethical Board of the Medical Faculty of the Christian-Albrecht-University, Kiel, Germany. The patient provided written informed consent. Full descriptions of the materials and methods used for the following are available in the Materials and Methods in the online supplement: nucleic acid and RNA extraction; 16S rDNA and 16S rRNA sequencing; metagenome sequencing; mRNA purification, amplification and sequencing; metagenomic and metatranscriptomic analysis; protein extraction, separation and identification and data processing; and metabolite extraction, separation and identification and data processing. All sequences have been entered in the European Bioinformatics Institute database, under accession number ERP001506.