Qiaamp stool kit

In total, 70 human faecal samples originating from healthy individuals, 68 caecal samples of chickens older than 1 month, hereafter called hens, 24 caecal samples of chickens younger than 1 month, 21 caecal samples from turkey and 20 faecal samples from pigs were collected (Table S3). The chicken’s age was taken into consideration due to the delayed appearance of Bacteroides in the caeca of commercially raised chickens [4 (link)]. DNA from all samples was purified using QIAamp Stool kit according to the manufacturer’s instructions (Qiagen) and was used as a template in SybrGreen real-time PCR (Qiagen) as described above.

The contents of paired caeca were collected and frozen at −20 °C for DNA extraction and Salmonella and Lactobacillus quantification by real-time PCR. DNA from caecal samples was extracted using a QIAamp Stool kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). Based on known genomic sequences, strain-specific real-time PCRs were designed to determine colonisation of the caecum by S. Enteritidis and each of the lactobacilli isolates (Table 1). Real-time PCR in SybrGreen format was performed exactly as described previously [26 (link)].

As part of the PanAf, 5397 chimpanzee faecal samples were non-invasively collected at 55 temporary or long-term research sites across the species range (Fig. 1, Supplementary Table 1.3 and Supplementary Fig. 3c), preserved according to the two-step ethanol–silica method^{76 (link)} and stored in the field for up to 2 years. Upon arrival to the lab, samples were stored at −20 °C. DNA extracts were isolated either manually, using the QIAamp Stool Kit (Qiagen), or using an automated process employing the QIAamp 96 PowerFecal QIAcube HT robot (Qiagen), per manufacturer instructions, modified by incorporating a pre-treatment step to improve the DNA quality and yield (Supplementary Note 1: ‘Laboratory methods’). Fourteen unlinked microsatellite loci and one sex-determining locus (amelogenin) were amplified using a two-step multiplex process^{77 (link)} with slight modifications (Supplementary Note 1: ‘Laboratory methods’ and Supplementary Fig. 1). PCR products were analyzed using an ABI Prism 3730 genetic analyzer (Thermo Fisher Scientific) and allele sizes were measured relative to ROX labeled HD400 internal size standard using Genemapper version 5.0 (Thermo Fisher Scientific). Homozygotes were identified by three identical PCR replicates and heterozygotes were confirmed by at least two unambiguous PCR replicates of each allele^{77 (link)} (Supplementary Note 1: ‘Genotype reconstruction’).