Zaiss, M. M. & Harris, N. L. Interactions between the intestinal microbiome and helminth parasites. Parasite Immunol. 38, 5–11 (2016).
Google Scholar
Cortés, A., Peachey, L. E., Jenkins, T. P., Scotti, R. & Cantacessi, C. Helminths and microbes within the vertebrate gut—not all studies are created equal. Parasitology 146, 1371–1378 (2019).
Google Scholar
Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14, e1002533 (2016).
Google Scholar
Claesson, M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178–184 (2012).
Google Scholar
Clemente, J. C., Ursell, L. K., Parfrey, L. W. & Knight, R. The impact of the gut microbiota on human health: An integrative view. Cell 148, 1258–1270 (2012).
Google Scholar
McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Nat. Acad. Sci. 110, 3229–3236 (2013).
Google Scholar
Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).
Google Scholar
Tremaroli, V. & Bäckhed, F. Functional interactions between the gut microbiota and host metabolism. Nature 489, 242–249 (2012).
Google Scholar
Brown, E. M., Sadarangani, M. & Finlay, B. B. The role of the immune system in governing host-microbe interactions in the intestine. Nat. Immunol. 14, 660–667 (2013).
Google Scholar
Kim, S., Covington, A. & Pamer, E. G. The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens. Immunol. Rev. 279, 90–105 (2017).
Google Scholar
Ducarmon, Q. R. et al. Gut microbiota and colonization resistance against bacterial enteric infection. Microbiol. Mol. Biol. Rev. 83, e00007-19 (2019).
Google Scholar
Sorbara, M. T. & Pamer, E. G. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them. Mucosal Immunol. 12, 1–9 (2019).
Google Scholar
Jourdan, P. M., Lamberton, P. H. L., Fenwick, A. & Addiss, D. G. Soil-transmitted helminth infections. Lancet 391, 252–265 (2018).
Google Scholar
Wammes, L. J., Mpairwe, H., Elliott, A. M. & Yazdanbakhsh, M. Helminth therapy or elimination: Epidemiological, immunological, and clinical considerations. Lancet Infect. Dis. 14, 1150–1162 (2014).
Google Scholar
Jenkins, T. P. et al. Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis. BMC Biol. 19, 1–17 (2021).
Google Scholar
Holm, J. B. et al. Chronic Trichuris muris infection decreases diversity of the intestinal microbiota and concomitantly increases the abundance of Lactobacilli. PLoS ONE 10, e0125495 (2015).
Google Scholar
Ducarmon, Q. R. et al. Dynamics of the bacterial gut microbiota during controlled human infection with Necator americanus larvae. Gut Microbes 12, 1840764 (2020).
Google Scholar
Broadhurst, M. J. et al. Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon. PLoS Pathog. 8, e1003000 (2012).
Google Scholar
Kreisinger, J., Bastien, G., Hauffe, H. C., Marchesi, J. & Perkins, S. E. Interactions between multiple helminths and the gut microbiota in wild rodents. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20140295 (2015).
Google Scholar
Filyk, H. A. & Osborne, L. C. The multibiome: The intestinal ecosystem’s influence on immune homeostasis, health, and disease. EBioMedicine 13, 46–54 (2016).
Google Scholar
Cantacessi, C. et al. Impact of experimental hookworm infection on the human gut microbiota. J. Infect. Dis. 210, 1431–1434 (2014).
Google Scholar
Li, R. W. et al. Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. Infect. Immun. 80, 2150–2157 (2012).
Google Scholar
Reynolds, L. A., Brett Finlay, B. & Maizels, R. M. Cohabitation in the intestine: Interactions among helminth parasites, bacterial microbiota, and host immunity. J. Immunol. 195, 4059–4066 (2015).
Google Scholar
Lee, S. C. et al. Helminth colonization is associated with increased diversity of the gut microbiota. PLoS Negl. Trop. Dis. 8, e2880 (2014).
Google Scholar
Rosa, B. A. et al. Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia. Microbiome 6, 33 (2018).
Google Scholar
Newbold, L. K. et al. Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota. ISME J. 11, 663–675 (2017).
Google Scholar
Baxter, N. T. et al. Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric Peromyscus populations. Appl. Environ. Microbiol. 81, 396–404 (2015).
Google Scholar
Cooper, P. et al. Patent human infections with the whipworm, Trichuris trichiura, are not associated with alterations in the faecal microbiota. PLoS ONE 8, e76573 (2013).
Google Scholar
Rapin, A. & Harris, N. L. Helminth-bacterial interactions: Cause and consequence. Trends Immunol. 39, 724–733 (2018).
Google Scholar
Cowlishaw, G. & Dunbar, R. I. Primate Conservation Biology (University of Chicago Press, 2000).
Google Scholar
Estrada, A. et al. Impending extinction crisis of the world’s primates: Why primates matter. Sci. Adv. 3, e1600946 (2017).
Google Scholar
Barelli, C. et al. The gut microbiota communities of wild arboreal and ground-feeding tropical primates are affected differently by habitat disturbance. mSystems 5, 3 (2020).
Google Scholar
Barelli, C. et al. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: Implications for conservation. Sci. Rep. 5, 14862 (2015).
Google Scholar
Barelli, C. et al. Altitude and human disturbance are associated with helminth diversity in an endangered primate, Procolobus gordonorum. PLoS ONE 14, e0225142 (2019).
Google Scholar
Barelli, C. et al. Loss of protozoan and metazoan intestinal symbiont biodiversity in wild primates living in unprotected forests. Sci. Rep. 10, 1–12 (2020).
Google Scholar
Aivelo, T. & Norberg, A. Parasite-microbiota interactions potentially affect intestinal communities in wild mammals. J. Anim. Ecol. 87, 438–447 (2018).
Google Scholar
Vlčková, K. et al. Relationships between gastrointestinal parasite infections and the fecal microbiome in free-ranging western lowland gorillas. Front. Microbiol. 9, 1202 (2018).
Google Scholar
Mann, A. E. et al. Biodiversity of protists and nematodes in the wild nonhuman primate gut. ISME J. 14, 609–622 (2020).
Google Scholar
de Winter, I. I. et al. Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs. Sci. Rep. 10, 16818 (2020).
Google Scholar
Ghai, R. R. et al. Hidden population structure and cross-species transmission of whipworms (Trichuris sp.) in humans and non-human primates in Uganda. PLoS Negl. Trop. Dis. 8, e3256 (2014).
Google Scholar
Nutman, T. B. Human infection with Strongyloides stercoralis and other related Strongyloides species. Parasitology 144, 263–273 (2017).
Google Scholar
Stephenson, L. S., Holland, C. V. & Cooper, E. S. The public health significance of Trichuris trichiura. Parasitology 121, S73–S95 (2000).
Google Scholar
Viney, M. E. The biology of Strongyloides spp. WormBook https://doi.org/10.1895/wormbook.1.141.2 (2015).
Google Scholar
Renelies-Hamilton, J. et al. Exploring interactions between Blastocystis sp., Strongyloides spp. and the gut microbiomes of wild chimpanzees in Senegal. Infect. Genet. Evol. 74, 104010 (2019).
Google Scholar
Afrin, T. et al. Sequential changes in the host gut microbiota during infection with the intestinal parasitic nematode. Front. Cell Infect. Microbiol. 9, 217 (2019).
Google Scholar
Rubel, M. A. et al. Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. Genome Biol. 21, 122 (2020).
Google Scholar
Jenkins, T. P. et al. Author Correction: A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area. Sci. Rep. 9, 8571 (2019).
Google Scholar
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012).
Google Scholar
van der Zande, H. J. P., Zawistowska-Deniziak, A. & Guigas, B. Immune regulation of metabolic homeostasis by helminths and their molecules. Trends Parasitol. 35, 795–808 (2019).
Google Scholar
Maeda, Y. & Takeda, K. Host–microbiota interactions in rheumatoid arthritis. Exp. Mol. Med. 51, 1–6 (2019).
Google Scholar
Biddle, A., Stewart, L., Blanchard, J. & Leschine, S. Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities. Diversity 5, 627–640 (2013).
Google Scholar
Brulc, J. M. et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc. Natl. Acad. Sci. USA 106, 1948–1953 (2009).
Google Scholar
Hale, V. L. et al. Diet versus phylogeny: A comparison of gut microbiota in captive Colobine monkey species. Microb. Ecol. 75, 515–527 (2018).
Google Scholar
Trosvik, P. et al. Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate. Microbiome 6, 84 (2018).
Google Scholar
Liu, B. et al. Western diet feeding influences gut microbiota profiles in apoE knockout mice. Lipids Health Dis. 17, 159 (2018).
Google Scholar
Bhute, S. S. et al. Gut microbial diversity assessment of Indian Type-2-diabetics reveals alterations in Eubacteria, Archaea, and Eukaryotes. Front. Microbiol. 8, 214 (2017).
Google Scholar
Wang, Y. et al. Phocea, Pseudoflavonifractor and Lactobacillus intestinalis: Three potential biomarkers of gut microbiota that affect progression and complications of obesity-induced Type 2 diabetes Mellitus. Diabetes Metab. Syndr. Obes. 13, 835–850 (2020).
Google Scholar
Yarahmadi, M. et al. The anti-giardial effectiveness of fungal and commercial chitosan against Giardia intestinalis cysts in vitro. J. Parasit. Dis. 40, 75–80 (2016).
Google Scholar
Dinleyici, E. C. et al. Clinical efficacy of Saccharomyces boulardii or metronidazole in symptomatic children with Blastocystis hominis infection. Parasitol. Res. 108, 541–545 (2011).
Google Scholar
Lepczyńska, M. & Dzika, E. The influence of probiotic bacteria and human gut microorganisms causing opportunistic infections on ST3. Gut Pathog. 11, 6 (2019).
Google Scholar
Huseyin, C. E., O’Toole, P. W., Cotter, P. D. & Scanlan, P. D. Forgotten fungi—the gut mycobiome in human health and disease. FEMS Microbiol. Rev. 41, 479–511 (2017).
Google Scholar
Mittermeier, R. A., Myers, N., Gill, P. C. & Mittermeier, C. G. Hotspots: Earth’s Richest and Most Endangered Terrestrial Ecoregions (CEMEX, 2000).
Platts, P. J. et al. Delimiting tropical mountain ecoregions for conservation. Environ. Conserv. 38, 312–324 (2011).
Google Scholar
Ruiz-Lopez, M. J. et al. A novel landscape genetic approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum). Heredity 116, 167–176 (2016).
Google Scholar
Cavada, N., Tenan, S., Barelli, C. & Rovero, F. Effects of anthropogenic disturbance on primate density at the landscape scale. Conserv. Biol. 33, 873–882 (2019).
Google Scholar
Laurance, W. F. et al. Averting biodiversity collapse in tropical forest protected areas. Nature 489, 290–294 (2012).
Google Scholar
Rovero, F. et al. Primates decline rapidly in unprotected forests: Evidence from a monitoring program with data constraints. PLoS ONE 10, e0118330 (2015).
Google Scholar
International Union for the Conservation of Nature and Natural Resources (IUCN). 2021. IUCN red list of threatened species version 2020-2. International Union for the Conservation of Nature and Natural Resources http://www.iucnredlist.org. (Accessed 21 Apr 2021).
Modrý, D., Pafčo, B., Petrželková, K. J. & Hasegawa, H. Parasites of Apes: An Atlas of Coproscopic Diagnostics (2018).
Gillespie, T. R. Noninvasive assessment of gastrointestinal parasite infections in free-ranging primates. Int. J. Primatol. 27, 1129–1143 (2006).
Google Scholar
Hasegawa, H. Methods of collection and identification of minute nematodes from the feces of primates, with special application to coevolutionary study of pinworms. In Primate Parasite Ecology: The Dynamics of Host-parasite Relationships (eds Huffman, M. A. & Chapman, C. A.) 29–46 (Cambridge University Press, 2009).
Mallott, E. K., Malhi, R. S. & Garber, P. A. High-throughput sequencing of fecal DNA to identify insects consumed by wild Weddell’s saddleback tamarins (Saguinus weddelli, Cebidae, Primates) in Bolivia. Am. J. Phys. Anthropol. 156, 474–481 (2015).
Google Scholar
Mallott, E. K., Garber, P. A. & Malhi, R. S. Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white-faced capuchins (Cebus capucinus). Am. J. Phys. Anthropol. 162, 241–254 (2017).
Google Scholar
Albanese, D., Fontana, P., De Filippo, C., Cavalieri, D. & Donati, C. MICCA: A complete and accurate software for taxonomic profiling of metagenomic data. Sci. Rep. 5, 9743 (2015).
Google Scholar
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021) https://www.R-project.org.
Lenth, R., Singmann, H., Love, J., Buerkner, P. & Herve, M. Emmeans: Estimated marginal means, aka least-squares means. R package version, Vol. 1, 3 (2018) https://CRAN.R-project.org/package=emmeans.
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