References
- Aakko J, Pietilä S, Toivonen R, Rokka A, Mokkala K, Laitinen K, Elo L, Hänninen A. A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota. Sci Rep. 2020;10(1):12411. https://doi.org/10.1038/s41598-020-69241-2
- Abeli T, Dalrymple S, Godefroid S, Mondoni A, Müller JV, Rossi G, Orsenigo S. Ex situ collections and their potential for the restoration of extinct plants. Conserv Biol. 2020;34(2):303–313. https://doi.org/10.1111/cobi.13391
- Accetto T, Avguštin G. The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity? Syst Appl Microbiol. 2019;42(2):107–116. https://doi.org/10.1016/j.syapm.2018.10.001
- Altschul DM, Wallace EK, Sonnweber R, Tomonaga M, Weiss A. Chimpanzee intellect: Personality, performance and motivation with touchscreen tasks. R Soc Open Sci. 2017;4(5):170169. https://doi.org/10.1098/rsos.170169
- Amato KR, Lake BR, Ozminkowski S, Jiang H, Moy M, Sardaro MLS, Fultz A, Hopper LM. Exploring the utility of the gut microbiome as a longitudinal health monitoring tool in sanctuary chimpanzees (Pan troglodytes). Am J Primatol. 2025;87(3):e70004. https://doi.org/10.1002/ajp.70004
- Aragón-Vela J, Solis-Urra P, Ruiz-Ojeda FJ, Álvarez-Mercado AI, Olivares-Arancibia J, Plaza-Diaz J. Impact of exercise on gut microbiota in obesity. Nutrients. 2021;13(11):3999. https://doi.org/10.3390/nu13113999
- AZA Ape TAG. Chimpanzee (Pan troglodytes) care manual. Silver Spring (USA): Association of Zoos and Aquariums; 2010.
- Bakour S, Rathored J, Lo CI, Mediannikov O, Beye M, Ehounoud CB, Biagini P, Raoult D, Fournier PE, Fenollar F. Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov. New Microbes New Infect. 2016;11:93–102. https://doi.org/10.1016/j.nmni.2016.03.004
- Baniel A, Petrullo L, Mercer A, Reitsema L, Sams S, Beehner JC, Bergman TJ, Snyder-Mackler N, Lu A. Maternal effects on early-life gut microbiota maturation in a wild nonhuman primate. Curr Biol. 2022;32(20):4508–4520.e6. https://doi.org/10.1016/j.cub.2022.08.037
- Cabana F, Jasmi R, Maguire R. Great ape nutrition: low-sugar and high-fibre diets can lead to increased natural behaviours, decreased regurgitation and reingestion, and reversal of prediabetes. Int. Zoo Yb. 2018;52:48–61. https://doi.org/10.1111/izy.12172
- Campbell TP, Sun X, Patel VH, Sanz C, Morgan D, Dantas G. The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography. ISME J. 2020;14(6):1584– 1599. https://doi.org/10.1038/s41396-020-0634-2
- Cantwell A, Buckholtz JW, Atencia R, Rosati AG. The origins of cognitive flexibility in chimpanzees. Dev Sci. 2022 Sep;25(5):e13266. https://doi.org/10.1111/desc.1326
- Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May;7(5):335–336. https://doi.org/10.1038/nmeth.f.303
- Carlsen F, de Jongh T, Pluháčková J. EAZA best practice guidelines for chimpanzees (Pan troglodytes) – 1st edition. Amsterdam (The Netherlands): European Association of Zoos and Aquariums; 2022. https://doi.org/10.61024/BPG2022ChimpanzeesEN
- Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, Travis DA, Long HT, Tuan BV, Minh VV, et al. Captivity humanizes the primate microbiome. Proc Natl Acad Sci USA. 2016;113(37):10376–10381. https://doi.org/10.1073/pnas.1521835113
- Costantini D, Masi S, Rachid L, Beltrame M, Rohmer M, Krief S. Mind the food: rapid changes in antioxidant content of diet affect oxidative status of chimpanzees. Am J Physiol Regul Integr Comp Physiol. 2021;320(5):R728–R734. https://doi.org/10.1152/ajpregu.00003.2021
- Degnan PH, Pusey AE, Lonsdorf EV, Goodall J, Wroblewski EE, Wilson ML, Rudicell RS, Hahn BH, Ochman H. Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park. Proc Natl Acad Sci USA. 2012;109(32):13034–13039. https://doi.org/10.1073/pnas.1110994109
- Dias BDC, Lamarca AP, Machado DT, Kloh VP, de Carvalho FM, Vasconcelos ATR. Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans. Anim Microbiome. 2025;7(1):20. https://doi.org/10.1186/s42523-025-00379-y
- Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013 Oct;10(10):996–998. https://doi.org/10.1038/nmeth.2604
- El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 2013;11(7):497–504. https://doi.org/10.1038/nrmicro3050
- Fu L, Lou Y, Guo Y, Zhou F, Ma J, Wang S, Gu Y, Fu B, Lu W. Seminal plasma microbiomes, sperm parameters, and cryopreservation in a healthy fertile population. Front Microbiol. 2024;15:1401326. https://doi.org/10.3389/fmicb.2024.1401326
- Goodall J. The chimpanzees of Gombe: patterns of behavior. Cambridge (USA): Harvard University Press; 1986.
- Koliada A, Syzenko G, Moseiko V, Budovska L, Puchkov K, Perederiy V, Gavalko Y, Dorofeyev A, Romanenko M, Tkach S, et al. Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population. BMC Microbiol. 2017;17(1):120. https://doi.org/10.1186/s12866-017-1027-1
- Komodromou I, Andreou E, Vlahoyiannis A, Christofidou M, Felekkis K, Pieri M, Giannaki CD. Exploring the dynamic relationship between the gut microbiome and body composition across the human lifespan: A systematic review. Nutrients. 2024;16(5):660. https://doi.org/10.3390/nu16050660
- Kovatcheva-Datchary P, Nilsson A, Akrami R, Lee YS, De Vadder F, Arora T, Hallen A, Martens E, Björck I, Bäckhed F. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab. 2015;22(6):971–982. https://doi.org/10.1016/j.cmet.2015.10.001
- Le HH, Lee MT, Besler KR, Comrie JMC, Johnson EL. Characterization of interactions of dietary cholesterol with the murine and human gut microbiome. Nat Microbiol. 2022;7(9):1390–1403. https://doi.org/10.1038/s41564-022-01195-9
- Li Y, Xu X, Guo Z, Li Q, Wang Y, Jian D, Zhang G, Tian X, Chen S, Luo Z. Neonatal Streptococcus pneumoniae infection induces long-lasting dysbiosis of the gut microbiota in a mouse model. Front Microbiol. 2022;13:961684. https://doi.org/10.3389/fmicb.2022.961684
- Litty D, Müller V. Butyrate production in the acetogen Eubacterium limosum is dependent on the carbon and energy source. Microb Biotechnol. 2021;14(6):2686–2692. https://doi.org/10.1111/1751-7915.13779
- Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett. 2009;294(1):1–8. https://doi.org/10.1111/j.1574-6968.2009.01514.x
- Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011 Nov;27(21):2957–2963. https://doi.org/10.1093/bioinformatics/btr507
- Moeller AH, Ochman H. Factors that drive variation among gut microbial communities. Gut Microbes. 2013 Sep-Oct;4(5):403-8. https://doi.org/10.4161/gmic.26039
- Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H. Social behavior shapes the chimpanzee pan-microbiome. Sci Adv. 2016;2(1):e1500997. https://doi.org/10.1126/sciadv.1500997
- Mohamed Qadir R, Assafi MS. The association between body mass index and the oral Firmicutes and Bacteroidetes profiles of healthy individuals. Malays Fam Physician. 2021;16(3):36–43. https://doi.org/10.51866/oa1129
- Narat V, Amato KR, Ranger N, Salmona M, Mercier-Delarue S, Rupp S, Ambata P, Njouom R, Simon F, Giles-Vernick T, et al. A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo. Sci Rep. 2020;10(1):19107. https://doi.org/10.1038/s41598-020-75847-3
- Nishida AH, Ochman H. A great-ape view of the gut microbiome. Nat Rev Genet. 2019;20(4):195–206. https://doi.org/10.1038/s41576-018-0085-z
- Pan X, Liu F, Song Y, Wang H, Wang L, Qiu H, Price M, Li J. Motor stereotypic behavior was associated with immune response in macaques: Insight from transcriptome and gut microbiota analysis. Front Microbiol. 2021;12:644540. https://doi.org/10.3389/fmicb.2021.644540
- Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol. 2023;31(9):959–971. https://doi.org/10.1016/j.tim.2023.03.018
- Pascual A, Kalcher-Sommersguter E, Riba D, Crailsheim D. Long-term assessment of captive chimpanzees: Influence of social group composition, seasonality and biographic background. Animals. 2023;13(3):424. https://doi.org/10.3390/ani13030424
- Pusey AE, Oehlert GW, Williams JM, Goodall J. Influence of ecological and social factors on body mass of wild chimpanzees. Int J Primatol. 2005;26(1):3–31. https://doi.org/10.1007/s10764-005-0721-2
- Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590–D596. https://doi.org/10.1093/nar/gks1219
- Reese AT, Phillips SR, Owens LA, Venable EM, Langergraber KE, Machanda ZP, Mitani JC, Muller MN, Watts DP, Wrangham RWet al. Age patterning in wild chimpanzee gut microbiota diversity reveals differences from humans in early life. Curr Biol. 2021;31(3):613–620.e3. https://doi.org/10.1016/j.cub.2020.10.075
- Ren D, Li L, Schwabacher AW, Young JW, Beitz DC. Mechanism of cholesterol reduction to coprostanol by Eubacterium coprostanoligenes ATCC 51222. Steroids. 1996;61(1):33–40. https://doi.org/10.1016/0039-128x(95)00173-n
- Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and butyrate-producing colon bacteria: Importance and strategies for their stimulation in the human gut. Front Microbiol. 2016;7:979. https://doi.org/10.3389/fmicb.2016.00979
- Roth G. Convergent evolution of complex brains and high intelligence. Philos Trans R Soc Lond B Biol Sci. 2015;370(1684):20150049. https://doi.org/10.1098/rstb.2015.0049
- Rouskas K, Guela M, Pantoura M, Pagkalos I, Hassapidou M, Lalama E, Pfeiffer AFH, Decorte E, Cornelissen V, Wilson-Barnes S, et al. The influence of an AI-driven personalized nutrition program on the human gut microbiome and its health implications. Nutrients. 2025;17(7):1260. https://doi.org/10.3390/nu17071260
- Staerk J, Colchero F, Kenney MA, Wilson KA, Foden WB, Carr JA, Pereboom Z, Bland L, Flesness N, Martin T, et al. A decision framework to integrate in-situ and ex-situ management for species in the European Union. Front Conserv Sci. 2024;4:1298850. https://doi.org/10.3389/fcosc.2023.1298850
- Sun Y, Zhang S, Nie Q, He H, Tan H, Geng F, Ji H, Hu J, Nie S. Gut firmicutes: Relationship with dietary fiber and role in host homeostasis. Crit Rev Food Sci Nutr. 2023;63(33):12073–12088. https://doi.org/10.1080/10408398.2022.2098249
- Szekely BA, Singh J, Marsh TL, Hagedorn C, Werre SR, Kaur T. Fecal bacterial diversity of human-habituated wild chimpanzees (Pan troglodytes schweinfurthii) at Mahale Mountains National Park, Western Tanzania. Am J Primatol. 2010;72(7):566–574. https://doi.org/10.1002/ajp.20809
- Tutin CEG, Fernandez M. Composition of the diet of chimpanzees and comparisons with that of sympatric lowland gorillas in the lopé reserve, gabon. Am J Primatol. 1993;30(3):195–211. https://doi.org/10.1002/ajp.1350300305
- van den Heuvel MP, Ardesch DJ, Scholtens LH, de Lange SC, van Haren NEM, Sommer IEC, Dannlowski U, Repple J, Preuss TM, Hopkins WD, et al. Human and chimpanzee shared and divergent neurobiological systems for general and specific cognitive brain functions. Proc Natl Acad Sci USA. 2023;120(22):e2218565120. https://doi.org/10.1073/pnas.2218565120
- Visser F, Drouilly M, Moodley Y, Michaux JR, Somers MJ. Mismatch between conservation needs and actual representation of