McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Hentschel U. Animals in a bacterial world, a new imperative for the life sciences. Proc Nat Acad Sci USA. 2013;110:3229–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9:313–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heijtz RD, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, Pettersson S. Normal gut microbiota modulates brain development and behavior. Proc Nat Acad Sci USA. 2011;108:3047–52.
Article
CAS
PubMed Central
Google Scholar
Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF. Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe. 2012;12:277–88.
Article
CAS
PubMed
Google Scholar
Zarrinpar A, Chaix A, Yooseph S, Panda S. Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metab. 2014;20:1006–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bestion E, Jacob S, Zinger L, Di Gesu L, Richard M, White J, Cote J. Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Nat Ecol Evol. 2017;8:161.
Article
Google Scholar
Reese AT, Dunn RR. Drivers of microbiome biodiversity: A review of general rules, feces, and ignorance. MBio. 2018;9:e01294–18.
Article
PubMed
PubMed Central
Google Scholar
Sinervo B, Méndez-de-la-Cruz F, Miles DB, Heulin B, Bastiaans E, Villagrán-Santa Cruz M, Lara-Resendiz R, Martínez-Méndez N, Calderón-Espinosa ML, Meza-Lázaro RN, et al. Erosion of lizard diversity by climate change and altered thermal niches. Science. 2010;328:894–9.
Article
CAS
PubMed
Google Scholar
Hertz PE, Huey RB, Garland JT. Time budgets, thermoregulation, and maximal locomotor performance: are reptiles olympians or boy scouts? Am Zool. 1988;28:927–38.
Article
Google Scholar
Gillooly JF, Brown JH, West GB, Savage VM, Charnov EL. Effects of size and temperature on metabolic rate. Science. 2001;293:2248–51.
Article
CAS
PubMed
Google Scholar
Ladyman M, Bonnet X, Lourdais O, Bradshaw D, Naulleau G. Gestation, thermoregulation, and metabolism in a viviparous snake, Vipera aspis: evidence for fecundity-independent costs. Physiol Biochem Zool. 2003;76:497–510.
Article
PubMed
Google Scholar
Leyte-Manrique A, Ramírez-Bautista A. Diet of two populations of Sceloporus grammicus (Squamata: Phrynosomatidae) from Hidalgo. Mexico. Southwest Nat. 2010;55:98–103.
Article
Google Scholar
Lemos-Espinal JA, Ballinger RE. Comparative thermal ecology of the high-altitude lizard Sceloporus grammicus on the eastern slope of the Iztaccihuatl volcano, Puebla. Mexico. Can J Zool. 1995;73:2184–91.
Article
Google Scholar
de la Cruz FR M, de la Vega-Pérez AH D, Centenero-Alcalá H, Jiménez-Arcos VH. Anfibios y Reptiles del Parque Nacional La Malinche. Universidad Autónoma de Tlaxcala; 2018. p. 138.
Google Scholar
de la Vega-Pérez AH D, Barrios-Montiel R, Jiménez-Arcos VH, Bautista A, Bastiaans E. High-mountain altitudinal gradient influences thermal ecology of the Mesquite lizard Sceloporus grammicus. Can J Zool. 2019;97:659–68.
Article
Google Scholar
Kohl KD, Yahn J. Effects of environmental temperature on the gut microbial communities of tadpoles. Environ Microbiol. 2016;18:1561–5.
Article
PubMed
Google Scholar
Han J, Guo R, Li J, Chen Y, Guan C, Zhao W. Organ mass variation in a toad headed lizard Phrynocephalus vlangalii in response to hypoxia and low temperature in the Qinghai-Tibet Plateau, China. PloS ONE. 2016;11:e0162572.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang W, Li N, Tang X, Liu N, Zhao W. Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii. Ecol Evol. 2018;8:4695–703.
Article
PubMed
PubMed Central
Google Scholar
Navarro-Noya YE, Suárez-Arriaga MC, Rojas-Valdes A, Montoya-Ciriaco NM, Gómez-Acata S, Fernández-Luqueno F, Dendooven L. Pyrosequencing analysis of the bacterial community in drinking water wells. Microb Ecol. 2013;66:19–29.
Article
PubMed
Google Scholar
Sambrook J, Russell DW. Molecular cloning: A laboratory manual. 2nd ed. New York: Cold Spring Harb Laboratory Press; 1989.
Google Scholar
Hoffman CS, Winston F. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene. 1987;57:267–72.
Article
CAS
PubMed
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Article
CAS
PubMed
Google Scholar
Vargas Márquez F. Parques Nacionales de México. Aspectos físicos, sociales, legales, administrativos, recreativos, biológicos, culturales, situación actual y propuestas en torno a los Parques Nacionales de México. SEMARNAT. Instituto Nacional de Ecología, Mexico. 1997.
Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010;4:1340–51.
Article
PubMed
Google Scholar
Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rust. Mol Ecol. 1993;2:113–8.
Article
CAS
PubMed
Google Scholar
White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications. San Diego: Academic Press; 1990. p. 315–22.
Google Scholar
Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Machida RJ. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool. 2013;10:34.
Article
PubMed
PubMed Central
CAS
Google Scholar
Geller J, Meyer C, Parker M, Hawk H. Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Mol Ecol Resour. 2013;13:851–61.
Article
CAS
PubMed
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
CAS
PubMed
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Douglas B. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 2013;22:5271–7.
Article
PubMed
CAS
Google Scholar
Ma Z, Li L. Measuring metagenome diversity and similarity with Hill numbers. Mol Ecol Res. 2018;18:1339–55.
Article
CAS
Google Scholar
R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; R Foundation for Statiscal Computing; 2018.
Google Scholar
Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010;4:17–27.
Article
CAS
PubMed
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, et al. Vegan: community ecology package. R package version. 2017;2:4–3.
Google Scholar
Kolde KR. Maintainer Raivo. Package ‘pheatmap’. Version. 2015;1:0.8. Date: 2015-07-02.
Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.
CAS
PubMed
Google Scholar
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2015;44:D457–62.
Article
PubMed
PubMed Central
CAS
Google Scholar
Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: Statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Godon JJ, Arulazhagan P, Steyer JP, Hamelin J. Vertebrate bacterial gut diversity: size also matters. BMC Ecol. 2016;16:12.
Article
PubMed
PubMed Central
Google Scholar
Hong PY, Wheeler E, Cann IK, Mackie RI. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galapagos Islands using 16S rRNA-based pyrosequencing. ISME J. 2011;5:1461–70.
Article
PubMed
PubMed Central
Google Scholar
Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol. 2015;24:2521–36.
Article
PubMed
Google Scholar
Costello EK, Gordon JI, Secor SM, Knight R. Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J. 2010;4:1375–85.
Article
CAS
PubMed
Google Scholar
Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, Caviedes-Vidal E, Bordenstein SR. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Mol Ecol. 2017;26:1175–89.
Article
PubMed
Google Scholar
Colston TJ, Jackson CR. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol Ecol. 2016;25:3776–800.
Article
PubMed
Google Scholar
Keenan SW, Engel AS, Elsey RM. The alligator gut microbiome and implications for archosaur symbioses. Sci Rep. 2013;3:2877.
Article
PubMed
PubMed Central
Google Scholar
Jiang HY, Ma JE, Li J, Zhang XJ, Li LM, He N, Chen JP. Diets alter the gut microbiome of crocodile lizards. Front Microbiol. 2017;8:2073.
Article
PubMed
PubMed Central
Google Scholar
Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI. Molecular analysis of commensal host-microbial relationships in the intestine. Science. 2001;291:881–4.
Article
CAS
PubMed
Google Scholar
Arnesen JA, Małagocka J, Gryganskyi A, Grigoriev IV, Voigt K, Stajich JE, Henrik H. Early diverging insect-pathogenic fungi of the order entomophthorales possess diverse and unique subtilisin-like serine proteases. G3 (Bethesda). 2018;8:3311–9.
Article
CAS
Google Scholar
Mendoza L, Vilela R, Voelz K, Ibrahim AS, Voigt K, Lee SC. Human fungal pathogens of Mucorales and Entomophthorales. Cold Spring Harb Perspect Med. 2015;5:a019562.
Article
PubMed Central
CAS
Google Scholar
Okafor JI, Testrake D, Mushinsky HR, Yangco BG. A Basidiobolus sp. and its association with reptiles and amphibians in southern Florida. Sabouraudia. 1984;22:47–51.
Article
CAS
PubMed
Google Scholar
Henk DA, Fisher MC. The gut fungus Basidiobolus ranarum has a large genome and different copy numbers of putatively functionally redundant elongation factor genes. PloS ONE. 2012;7:e31268.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mishra P, Singh SK, Nilegaonkar SS. Extracellular chitinase production by some members of the saprophytic Entomophthorales group. Mycoscience. 2011;52:271–7.
Article
CAS
Google Scholar
Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. Archaea and fungi of the human gut microbiome: Correlations with diet and bacterial residents. PloS ONE. 2013;8:e66019.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolfe KH, Armisen D, Proux-Wera E, OhEigeartaigh SS, Azam H, Gordon JL, Byrne KP. Clade-and species-specific features of genome evolution in the Saccharomycetaceae. FEMS Yeast Res. 2015;15.
Article
PubMed
PubMed Central
CAS
Google Scholar
Osimani A, Garofalo C, Milanović V, Taccari M, Cardinali F, Aquilanti L, Riolo P. Insight into the proximate composition and microbial diversity of edible insects marketed in the European Union. Eur Food Res Technol. 2017;243:1157–71.
Article
CAS
Google Scholar
Comitini F, Mannazzu I, Ciani M. Tetrapisispora phaffii killer toxin is a highly specific β-glucanase that disrupts the integrity of the yeast cell wall. Microb Cell Fact. 2009;8:55.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chabé M, Lokmer A, Ségurel L. Gut protozoa: friends or foes of the human gut microbiota? Trends Parasitol. 2017;33:925–34.
Article
PubMed
Google Scholar
Olson DM. The distribution of leaf litter invertebrates along a Neotropical altitudinal gradient. J Trop Ecol. 1994;10:129–50.
Article
Google Scholar
Sam K, Koane B, Jeppy S, Sykorova J, Novotny V. Diet of land birds along an elevational gradient in Papua New Guinea. Sci Rep. 2017;7:44018.
Article
PubMed
PubMed Central
Google Scholar
Sears MW. Resting metabolic expenditure as a potential source of variation in growth rates of the sagebrush lizard. Comp Biochem Physiol A Mol Integr Physiol. 2005;140:171–7.
Article
PubMed
CAS
Google Scholar
Belzer C, De Vos WM. Microbes inside—from diversity to function: the case of Akkermansia. ISME J. 2012;6:1449–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suzuki TA, Martins FM, Nachman MW. Altitudinal variation of the gut microbiota in wild house mice. Mol Ecol. 2018;28:2378–90.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bai X, Lu S, Yang J, Jin D, Pu J, Moyá SD, Xu J. Precise fecal microbiome of the herbivorous tibetan antelope inhabiting high-altitude alpine plateau. Front Microbiol. 2018;28:2321.
Article
Google Scholar
Derrien M, Vaughan EE, Plugge CM, de Vos WM. Akkermansia muciniphila gen. nov. sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol. 2004;54:1469–76.
Article
CAS
PubMed
Google Scholar
Sonoyama K, Fujiwara R, Takemura N, Ogasawara T, Watanabe J, Ito H, Morita T. Response of gut microbiota to fasting and hibernation in Syrian hamsters. Appl Environ Microbiol. 2009;75:6451–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Konikoff T, Gophna U. Oscillospira: a central, enigmatic component of the human gut microbiota. Trends Microbiol. 2016;24:523–4.
Article
CAS
PubMed
Google Scholar
Kohl KD, Amaya J, Passement CA, Dearing MD, McCue MD. Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts. FEMS Microbiol Ecol. 2014;90:883–94.
Article
CAS
PubMed
Google Scholar
Mackie RI, Aminov RI, Hu W, Klieve AV, Ouwerkerk D, Sundset MA, Kamagata Y. Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches. Appl Environ Microbiol. 2003;69:6808–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kong Y, Teather R, Forster R. Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages. FEMS Microbiol Ecol. 2010;74:612–22.
Article
CAS
PubMed
Google Scholar
Campos P, Guivernau M, Prenafeta-Boldú FX, Cardona L. Fast acquisition of a polysaccharide fermenting gut microbiome by juvenile green turtles Chelonia mydas after settlement in coastal habitats. Microbiome. 2018;6:69.
Article
PubMed
PubMed Central
Google Scholar
Serrano-Cardozo VH, Lemos-Espinal JA, Smith GR. Comparative diet of three sympatric Sceloporus in the semiarid Zapotitlán Valley, Mexico. Rev Mex Biodivers. 2008;79:427–34.
Google Scholar
Drechsler C. An odorous Basidiobolus often producing conidia plurally and forming some diclinous sexual apparatus. Am J Bot. 1964;51:770–7.
Article
Google Scholar
Fuentefria AM, Suh SO, Landell MF, Faganello J, Schrank A, Vainstein MH, Valente P. Trichosporon insectorum sp. nov., a new anamorphic basidiomycetous killer yeast. Mycol Res. 2008;112:93–9.
Article
CAS
PubMed
Google Scholar
Criado-Fornelio A, Verdú-Expósito C, Martin-Pérez T, Heredero-Bermejo I, Pérez-Serrano J, Guàrdia-Valle L, Panisello-Panisello M. A survey for gregarines (Protozoa: Apicomplexa) in arthropods in Spain. Parasitol Res. 2017;116:99–110.
Article
CAS
PubMed
Google Scholar
Karasov W, Douglas AE. Comparative digestive physiology. Compr Physiol. 2013;3:741–83.
PubMed
PubMed Central
Google Scholar
Gouba N, Drancourt M. Digestive tract mycobiota: a source of infection. Med Mal Infect. 2015;45:9–16.
Article
CAS
PubMed
Google Scholar
Hallen-Adams HE, Suhr MJ. Fungi in the healthy human gastrointestinal tract. Virulence. 2017;8:352–8.
Article
CAS
PubMed
Google Scholar
Schweizer E, Hofmann J. Microbial type I fatty acid synthases (FAS): major players in a network of cellular FAS systems. Microbiol Mol Biol Rev. 2004;68:501–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Park MS, Lee S, Oh SY, Cho GY, Lim YW. Diversity and enzyme activity of Penicillium species associated with macroalgae in Jeju Island. J Microbiol. 2016;54:646–54.
Article
CAS
PubMed
Google Scholar
Vishniac HS. Cryptococcus friedmannii, a new species of yeast from the Antarctic. Mycologia. 1985;77:149–53.
Article
CAS
PubMed
Google Scholar
Białkowska AM, Szulczewska KM, Krysiak J, Florczak T, Gromek E, Kassassir H, Kur J, Turkiewicz M. Genetic and biochemical characterization of yeasts isolated from Antarctic soil samples. Polar Biol. 2017;40:1787–803.
Article
Google Scholar
Kohl KD, Dearing MD. Wild-caught rodents retain a majority of their natural gut microbiota upon entrance into captivity. Environ Microbiol Rep. 2014;6:191–5.
Article
PubMed
Google Scholar
Wang W, Zheng S, Sharshov K, Sun H, Yang F, Wang X, Xiao Z. Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus). Microbiol Open. 2017;6:e00429.
Article
CAS
Google Scholar
Jackson J, Tinsley R. Effects of environmental temperature on the susceptibility of Xenopus laevis and X. wittei (Anura) to Protopolystoma xenopodis (Monogenea). Parasitol Res. 2002;88:632–8.
Article
CAS
PubMed
Google Scholar
Pérez-Brocal V, Shahar-Golan R, Clark CG. A linear molecule with two large inverted repeats: the mitochondrial genome of the stramenopile Proteromonas lacerate. Genome Biol Evol. 2010;2:257–66.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hoevers JD, Snowden KF. Analysis of the ITS region and partial ssu and lsu rRNA genes of Blastocystis and Proteromonas lacertae. Parasitology. 2005;131:187–96.
Article
CAS
PubMed
Google Scholar
Bursey CR, Goldberg SR. Description of a new species of Parapharyngodon (Nematoda: Pharyngodonidae) from Mexico with a list of current species and key to species from the Panamanian region. J Parasitol. 2015;101:374–81.
Article
PubMed
Google Scholar
Pereira FB, Campião KM, Luque JL, Tavares LE. Parapharyngodon hugoi n. sp., a new nematode (Oxyuroidea: Pharyngodonidae) of the tree frog Trachycephalus typhonius (Linnaeus) from the Brazilian Pantanal, including a key to the congeners from amphibians of the American continent. Syst Parasitol. 2017;94:599–607.
Article
PubMed
Google Scholar
Bursey CR, Goldberg SR, Kraus F. New genus of Pharyngodonidae (Nematoda: oxyuridea) and other helminths in Platymantis nexipus (Anura: Ranidae) from Papua New Guinea. J Parasitol. 2009;95:669–72.
Article
PubMed
Google Scholar
Wolinska J, King KC. Environment can alter selection in host–parasite interactions. Trends Parasitol. 2009;25:236–44.
Article
PubMed
Google Scholar