Pernthaler J. Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol. 2005;3:537–46.
Google Scholar
Gast RJ, Sanders RW, Caron DA. Ecological strategies of protists and their symbiotic relationships with prokaryotic microbes. Trends Microbiol. 2009;17:563–9.
Google Scholar
Wein T, Romero Picazo D, Blow F, Woehle C, Jami E, Reusch TBH, et al. Currency, exchange, and inheritance in the evolution of symbiosis. Trends Microbiol. 2019;27:836–49.
Google Scholar
Ushida K, Newbold CJ, Jouany J-P. Interspecies hydrogen transfer between the rumen ciliate Polyplastron multivesiculatum and Methanosarcina barkeri. J Gen Appl Microbiol. 1997;43:129–31.
Google Scholar
D’Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat Prod Rep. 2018;35:455–88.
Google Scholar
Graf JS, Schorn S, Kitzinger K, Ahmerkamp S, Woehle C, Huettel B, et al. Anaerobic endosymbiont generates energy for ciliate host by denitrification. Nature. 2021;591:445–50.
Google Scholar
Bell T, Bonsall MB, Buckling A, Whiteley AS, Goodall T, Griffiths RI. Protists have divergent effects on bacterial diversity along a productivity gradient. Biol Lett. 2010;6:639–42.
Google Scholar
Johnke J, Baron M, de Leeuw M, Kushmaro A, Jurkevitch E, Harms H, et al. A generalist protist predator enables coexistence in multitrophic predator-prey systems containing a phage and the bacterial predator bdellovibriot. Front Ecol Evol. 2017;5:536.
Leibold MA. A graphical model of keystone predators in food webs: trophic regulation of abundance, incidence, and diversity patterns in communities. Am Nat. 1996;147:784–812.
Glücksman E, Bell T, Griffiths RI, Bass D. Closely related protist strains have different grazing impacts on natural bacterial communities. Environ Microbiol. 2010;12:3105–13.
Google Scholar
Espinoza-Vergara G, Hoque MM, McDougald D, Noorian P. The impact of protozoan predation on the pathogenicity of Vibrio cholerae. Front Microbiol. 2020;11:17.
Google Scholar
Gao Z, Karlsson I, Geisen S, Kowalchuk G, Jousset A. Protists: puppet masters of the rhizosphere microbiome. Trends Plant Sci. 2019;24:165–76.
Google Scholar
Rosenberg K, Bertaux J, Krome K, Hartmann A, Scheu S, Bonkowski M. Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana. ISME J. 2009;3:675–84.
Google Scholar
Chudnovskiy A, Mortha A, Kana V, Kennard A, Ramirez JD, Rahman A, et al. Host-protozoan interactions protect from mucosal infections through activation of the inflammasome. Cell. 2016;167:444–.e14.
Google Scholar
Nieves-Ramírez ME, Partida-Rodríguez O, Laforest-Lapointe I, Reynolds LA, Brown EM, Valdez-Salazar A, et al. Asymptomatic intestinal colonization with protist blastocystis is strongly associated with distinct microbiome ecological patterns. mSystems. 2018;3:e00007–18.
Google Scholar
Mizrahi I. Rumen symbioses. In: Eugene Rosenberg, Edward F. DeLong, Stephen Lory, Erko Stackebrandt, Thompson F, editors. The Prokaryotes. Springer Berlin Heidelberg; 2013. p. 533–44.
Sylvester JT, Karnati SKR, Yu Z, Morrison M, Firkins JL. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J Nutr. 2004;134:3378–84.
Google Scholar
Newbold CJ, de la Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The role of ciliate protozoa in the rumen. Front Microbiol. 2015;6:1313.
Google Scholar
Firkins JL, Yu Z, Park T, Plank JE. Extending Burk Dehority’s perspectives on the role of ciliate protozoa in the rumen. Front Microbiol. 2020;11:123.
Google Scholar
Williams AG, Coleman GS. The rumen protozoa. New York, NY: Springer Science & Business Media; 2012.
Solomon R, Jami E. Rumen protozoa: from background actors to featured role in microbiome research. Environ Microbiol Rep. 2021;13:45–49.
Google Scholar
Shabat SKB, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Berg Miller ME, et al. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J. 2016;10:2958.
Google Scholar
Lima J, Auffret MD, Stewart RD, Dewhurst RJ, Duthie C-A, Snelling TJ, et al. Identification of rumen microbial genes involved in pathways linked to appetite, growth, and feed conversion efficiency in cattle. Front Genet. 2019;10:701.
Google Scholar
Jami E, White BA, Mizrahi I. Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency. PLoS ONE. 2014;9:e85423.
Google Scholar
Delgado B, Bach A, Guasch I, González C, Elcoso G, Pryce JE, et al. Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle. Sci Rep. 2019;9:11.
Google Scholar
Wallace RJ, Sasson G, Garnsworthy PC, Tapio I, Gregson E, Bani P, et al. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci Adv. 2019;5:eaav8391.
Google Scholar
Belanche A, de la Fuente G, Pinloche E, Newbold CJ, Balcells J. Effect of diet and absence of protozoa on the rumen microbial community and on the representativeness of bacterial fractions used in the determination of microbial protein synthesis. J Anim Sci. 2012;90:3924–36.
Google Scholar
Belanche A, de la Fuente G, Moorby JM, Newbold CJ. Bacterial protein degradation by different rumen protozoal groups. J Anim Sci. 2012;90:4495–504.
Google Scholar
Belanche A, de la Fuente G, Newbold CJ. Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions. FEMS Microbiol Ecol. 2015;91:fiu026.
Google Scholar
Hackmann TJ, Firkins JL. Maximizing efficiency of rumen microbial protein production. Front Microbiol. 2015;6:465.
Google Scholar
Popova M, Martin C, Rochette Y, Graviou D, Morgavi DP. Methanogenesis kinetics and fermentation patterns in the rumen of sheep with or without protozoa. In: Ruminant physiology: digestion, metabolism and effects of nutrition on reproduction and welfare. Netherlands: Wageningen Academic publishers; 2009. 320.
Levy B, Jami E. Exploring the prokaryotic community associated within the rumen ciliate protozoa population. Front Microbiol. 2018;9:2526.
Google Scholar
Borrel G, Brugère J-F, Gribaldo S, Schmitz RA, Moissl-Eichinger C. The host-associated archaeome. Nat Rev Microbiol. 2020;18:622–36.
Google Scholar
Lloyd D, Williams AG, Amann R, Hayes AJ, Durrant L, Ralphs JR. Intracellular prokaryotes in rumen ciliate protozoa: Detection by confocal laser scanning microscopy after in situ hybridization with fluorescent 16S rRNA probes. Eur J Protistol. 1996;32:523–31.
Jouany JP. Effect of rumen protozoa on nitrogen utilization by ruminants. J Nutr. 1996;126:1335S–46S.
Google Scholar
Coleman GS, Sandford DC. The engulfment and digestion of mixed rumen bacteria and individual bacterial species by single and mixed species of rumen ciliate protozoa grown in-vivo. J Agric Sci. 1979;92:729–42.
Zachut M, Honig H, Striem S, Zick Y, Boura-Halfon S, Moallem U. Periparturient dairy cows do not exhibit hepatic insulin resistance, yet adipose-specific insulin resistance occurs in cows prone to high weight loss. J Dairy Sci. 2013;96:5656–69.
Google Scholar
National Research Council. 2001. Nutrient Requirements of Dairy Cattle: Seventh Revised Edition. Washington, DC: The National Academies Press; 2001.
Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976;72:248–54.
Google Scholar
Stevenson DM, Weimer PJ. Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol. 2007;75:165–74.
Google Scholar
NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. The NIH human microbiome project. Genome Res. 2009;19:2317–23.
Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, et al. Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community. PLoS ONE. 2016;11:e0151220.
Google Scholar
Wobbrock JO, Findlater L, Gergle D, Higgins JJ. The aligned rank transform for nonparametric factorial analyses using only ANOVA procedures. Proceedings of the SIGCHI Conference on Human Factors in Computing Systems. New York, NY, USA: Association for Computing Machinery; 2011. p. 143–6.
Elkin LA, Kay M, Higgins JJ, Wobbrock JO. An aligned rank transform procedure for multifactor contrast tests. https://arxiv.org/abs/2102.11824.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Google Scholar
Hammer Ø, Harper DAT, Ryan PD. PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron. 2001;4:9.
Oksanen J. vegan: community ecology package. R package version 2.5-7. 2011. http://cran.r-project.org/package=vegan.
van den Boogaart KG, Tolosana-Delgado R. ‘compositions’: a unified R package to analyze compositional data. Comput Geosci. 2008;34:320–38.
Krzywinski M, Altman N, Blainey P. Points of significance: nested designs. For studies with hierarchical noise sources, use a nested analysis of variance approach. Nat Methods. 2014;11:977–8.
Google Scholar
R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2019.
Chernomor O, von Haeseler A, Minh BQ. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 2016;65:997–1008.
Google Scholar
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:256–9.
Belanche A, de la Fuente G, Newbold CJ. Study of methanogen communities associated with different rumen protozoal populations. FEMS Microbiol Ecol. 2014;90:663–77.
Google Scholar
Ungerfeld EM. Metabolic hydrogen flows in rumen fermentation: principles and possibilities of interventions. Front Microbiol. 2020;11:589.
Google Scholar
Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, et al. The effect of host genetics on the gut microbiome. Nat Genet. 2016;48:1407–12.
Google Scholar
Henderson G, Cox F, Ganesh S, Jonker A, Young W, Global Rumen Census Collaborators, et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep.2015;5:1–15.
Fukami T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu Rev Ecol Evol Syst. 2015;46:1–23.
Shaani Y, Zehavi T, Eyal S, Miron J, Mizrahi I. Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects. ISME J. 2018;12:2446–57.
Google Scholar
Paul RG, Williams AG, Butler RD. Hydrogenosomes in the rumen entodiniomorphid ciliate Polyplastron multivesiculatum. J Gen Microbiol. 1990;136:1981–9.
Google Scholar
Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, et al. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J. 2019;13:2617–32.
Google Scholar
Gong J, Qing Y, Zou S, Fu R, Su L, Zhang X, et al. Protist-bacteria associations: gammaproteobacteria and alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa. Front Microbiol. 2016;7:498.
Google Scholar
Park T, Yu Z. Do ruminal ciliates select their preys and prokaryotic symbionts? Front Microbiol. 2018;9:1710.
Google Scholar
Matz C, Nouri B, McCarter L, Martinez-Urtaza J. Acquired type III secretion system determines environmental fitness of epidemic Vibrio parahaemolyticus in the interaction with bacterivorous protists. PLoS ONE. 2011;6:e20275.
Google Scholar
Kamke J, Soni P, Li Y, Ganesh S, Kelly WJ, Leahy SC, et al. Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep. BMC Res Notes. 2017;10:367.
Google Scholar
Jami E, Mizrahi I. Composition and similarity of bovine rumen microbiota across individual animals. PLoS ONE. 2012;7:e33306.
Google Scholar
Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA. 2009;106:1948–53.
Google Scholar
Indugu N, Vecchiarelli B, Baker LD, Ferguson JD, Vanamala JKP, Pitta DW. Comparison of rumen bacterial communities in dairy herds of different production. BMC Microbiol. 2017;17:190.
Google Scholar
Pope PB, Smith W, Denman SE, Tringe SG, Barry K, Hugenholtz P, et al. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science. 2011;333:646–8.
Google Scholar
Saleem M, Fetzer I, Dormann CF, Harms H, Chatzinotas A. Predator richness increases the effect of prey diversity on prey yield. Nat Commun. 2012;3:1305.
Google Scholar
Simek K, Vrba J, Pernthaler J, Posch T, Hartman P, Nedoma J, et al. Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. Appl Environ Microbiol. 1997;63:587–95.
Google Scholar
Socolar J, Washburne A. Prey carrying capacity modulates the effect of predation on prey diversity. Am Nat. 2015;186:333–47.
Google Scholar
Gutierrez J. Observations on bacterial feeding by the rumen ciliate Isotricha prostoma. J Protozool. 1958;5:122–6.
Coleman GS. The metabolism of Escherichia coli and other bacteria by Entodinium caudatum. J Gen Microbiol. 1964;37:209–23.
Google Scholar
Canter EJ, Cuellar-Gempeler C, Pastore AI, Miller TE, Mason OU. Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves. Ecology. 2018;99:652–60.
Google Scholar
Paine RT. Food web complexity and species diversity. Am Nat. 1966;100:65–75.
Audebert C, Even G, Cian A, Loywick A, Merlin S, Blastocystis Investigation Group,et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Sci Rep. 2016;6:25255.
Google Scholar
Chabé M, Lokmer A, Ségurel L. Gut protozoa: friends or foes of the human gut microbiota? Trends Parasitol. 2017;33:925–34.
Google Scholar
Asgari M, Steiner CF. Interactive effects of productivity and predation on zooplankton diversity. Oikos. 2017;126:1617–24.
Google Scholar
Tokura M, Ushida K, Miyazaki K, Kojima Y. Methanogens associated with rumen ciliates. FEMS Microbiol Ecol. 1997;22:137–43.
Google Scholar
Irbis C, Ushida K. Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa. J Gen Appl Microbiol. 2004;50:203–12.
Google Scholar
Karakoç C, Radchuk V, Harms H, Chatzinotas A. Interactions between predation and disturbances shape prey communities. Sci Rep. 2018;8:2968.
Google Scholar
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