Supplementary information
1. DNA larvae extraction protocol
This protocole is adapted from QIAamp DNA Mini kit Tissue instructions to be applied for DNA extractions from larvae stored in Ethanol.
1- Homogenize flask and sample 10ml in a 15ml Falcon Tube.
Centrifuge 10 min at 3000T/min (14G).
Remove the supernatant.
2- Add 1.5 ml of PBS and transfer in a 1.5 ml Eppendorf.
Centrifuge10 min at 3000T/min.
Remove the supernatant.
Repeat step 2.
3- Add 100µl buffer ATL and freeze samples at -20°C.
4- Mix samples with a Pellet-Mixer.
5- Add 20 µl of Proteinase K, mix by vortexing and incubate at 56°C all the night. Do not centrifuge.
6- Add 200 µl Buffer AL, mix by vortexing, and incubate at 70°C for 30 min.
7- Add 200 µl of ethanol (96-100%), mix slowly.
8- Carefully apply the mixture from step 7 to the QIAamp Mini spin column (in a 2ml collection tube) without wetting the rim. Centrifuge 1 min at 10000 rpm. Place the QIAamp Mini-spin column in a clean 2 ml collection tube and discard the tube containing the filtrate.
9- Carefully open the QIAamp Mini spin column and add 500 µl buffer AW1 without wetting the rim. Close the cap, and centrifuge at 10 000 rpm for 1 min. Place the QIAamp Mini-spin column in a clean 2 ml collection tube and discard the collection tube containing the filtrate.
10- Carefully open the QIAamp Mini-spin column and add 500 µl buffer AW2 without wetting the rim. Close the cap, and centrifuge at 10 000 rpm for 1 min. Centrifuge again at full speed for 1 min.
11- Place the QIAamp Mini spin column in a clean 1.5 ml eppendorf and discard the old collection tube with the filtrate. Add 100 µl TE/Tween 0,05%. Incubate at room temperature for 1 min and Centrifuge at 10 000 rpm for 1 min.
12- Repeat Step 11.
2. DNA dried feces extraction protocol
Only modifications on the Stool Pathogen Detection protocol from QIAamp DNA Stool kit for DNA extraction from dried feces are indicated.
1- Weigh 100mg dried stool in a 2 ml micro-centrifuge tube and add 300 µl PBS 1x. Incubate at room temperature for 10 min.
3- Incubate at 70°C all the night.
8’- Repeat step 8 one time.
9- Pipet 25 µl proteinase K into a new 1.5 ml microcentrifugetybe.
11- Add 500 µl Buffer AL and vortex for 15 s.
12- Incubate at 70°C for 30 minutes.
13- Add 700 µl of ethanol (96-100% and mix by vortexing.
18- Transfer the QIAamp spin column into a new, labeled 1.5 ml microcentrifuge tube. Carefully open the QIAamp spin column and pipet 100 µl TE/Tween 0,05% directly onto the QIAamp membrane. Close the cap and incubate at room temperature for 1 min, then centrifuge at full speed for 1 min to elute DNA.
3. Precisions on helminths identification in bonobo samples and pathogenicity
From the egg size and shape of the helminthsobserved in bonobos, wecansuggest more precise identification. The egg size and shape of the Strongyloidessp. observedhereinis consistent with S. fuelleborni (Hasegawa et al. 1983; Dupain et al. 2009). According to egg size and host-specificity, Capillariawasprobably C. brochieri, a speciesdescribed in bonobos by Justine (1988). Enterobiuswaslikely to be E. anthropopitheci (Sandosham 1950, Hugot 1993, Hasegawa et al. 2005). One of the bonobo sampleshad a veryhigh CPL for Enterobius (2200 egg/g). Coprophagybehavior, observed in bonobos in anotherstudy area (Sakamaki, 2010) but also in bonobos of Manzano (Narat, et al. in prep), probablyincreasesre-infection and mayaccount for thissurprisingresult. The Toxocarasp. found in bonobos of Manzano (and neverdescribedbefore in thisspecies) isprobably a spurious infection according to its life cycle, caused for example by consumption of foodcontaminated by canidfeces (dogs are used by local people for traditional net hunting in the forestduring the entireday). According to theirshape and size, the Troglodytellasp. detected in bonobos is compatible withbeing T. abrassarti (described in chimpanzees). Occurringathighprevalence in Africangreat apes, thisciliateisprobably a symbiontknown to facilitatefiber fermentation (Pomajbíková et al. 2010). Among the strongylidsfound in bonobos, molecular data confirmed the presence of O. stephanostomum, Necatorsp. and a Nematodirus-likespecies in bonobos. The latter mightbe N. weinbergii, whichwasidentified by Railliet and Henry in 1909, and is the onlyspecies of thisgenusthat has been described in a primate (chimpanzee) (Neveu-Lemaire, 1917). O. stephanostomumwasfound in several primate species in Uganda (chimpanzees and severalmonkeyspecies) (Krief et al. 2008; 2010; Ghai et al. 2014).