Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death
Aivelo T, Norberg A (2018) Parasite-microbiota interactions potentially affect intestinal communities in wild mammals. J Anim Ecol 87:438–447PubMed
Article
PubMed Central
Google Scholar
Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP (2016) Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol 31:689–699PubMed
Article
PubMed Central
Google Scholar
Amaral WZ, Lubach GR, Proctor A, Lyte M, Phillips GJ, Coe CL (2017) Social influences on Prevotella and the gut microbiome of young monkeys. Psychosom Med 79:888–897PubMed
PubMed Central
Article
Google Scholar
Amato KR, Sanders GJ, Song SJ, Nute M, Metcalf JL, Thompson LR et al. (2019) Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J 13:576–587CAS
PubMed
Article
PubMed Central
Google Scholar
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57:289–300
Google Scholar
Björk JR, Dasari M, Grieneisen L, Archie EA (2019) Primate microbiomes over time: longitudinal answers to standing questions in microbiome research. Am J Primatol 81:e22970PubMed
PubMed Central
Article
Google Scholar
Brooks JW (2016) Postmortem changes in animal carcasses and estimation of the postmortem interval. Vet Pathol 53:929–940CAS
PubMed
Article
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583CAS
PubMed
PubMed Central
Article
Google Scholar
Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS et al. (2019) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res 47:e103CAS
PubMed
PubMed Central
Article
Google Scholar
Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA et al. (2016) Captivity humanizes the primate microbiome. Proc Natl Acad Sci U S A 113:10376–10381CAS
PubMed
PubMed Central
Article
Google Scholar
Cryan JF, Dinan TG (2012) Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci 13:701–712CAS
PubMed
Article
PubMed Central
Google Scholar
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S et al. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107:14691–14696PubMed
PubMed Central
Article
Google Scholar
Dill-McFarland KA, Neil KL, Zeng A, Sprenger RJ, Kurtz CC, Suen G et al. (2014) Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels. Mol Ecol 23:4658–4669CAS
PubMed
Article
PubMed Central
Google Scholar
Donaldson GP, Lee SM, Mazmanian SK (2016) Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 14:20–32CAS
PubMed
Article
PubMed Central
Google Scholar
Dubois S, Fenwick N, Ryan EA, Baker L, Baker SE, Beausoleil NJ et al. (2017) International consensus principles for ethical wildlife control. Conserv Biol J Soc Conserv Biol 31:753–760Article
Google Scholar
Earl JP, Adappa ND, Krol J, Bhat AS, Balashov S, Ehrlich RL et al. (2018) Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes. Microbiome 6:190PubMed
PubMed Central
Article
Google Scholar
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200CAS
PubMed
PubMed Central
Article
Google Scholar
Ericsson AC, Johnson PJ, Lopes MA, Perry SC, Lanter HR (2016) A microbiological map of the healthy equine gastrointestinal tract. PLoS ONE 11:e0166523PubMed
PubMed Central
Article
CAS
Google Scholar
García-Amado MA, Michelangeli F, Gueneau P, Perez ME, Domínguez-Bello MG (2007) Bacterial detoxification of saponins in the crop of the avian foregut fermenter Opisthocomus hoazin. J Anim Feed Sci 16:82–85Article
Google Scholar
Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K et al. (2016) Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep 14:2142–2153CAS
PubMed
Article
PubMed Central
Google Scholar
Gomez A, Petrzelkova K, Yeoman CJ, Vlckova K, Mrázek J, Koppova I et al. (2015) Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology. Mol Ecol 24:2551–2565CAS
PubMed
Article
PubMed Central
Google Scholar
Gorvitovskaia A, Holmes SP, Huse SM (2016) Interpreting Prevotella and bacteroides as biomarkers of diet and lifestyle. Microbiome 4:15PubMed
PubMed Central
Article
Google Scholar
Gregorová S, Forejt J (2000) PWD/Ph and PWK/Ph inbred mouse strains of Mus m. musculus subspecies–a valuable resource of phenotypic variations and genomic polymorphisms. Folia Biol 46:31–41
Google Scholar
Gu S, Chen D, Zhang J-N, Lv X, Wang K, Duan L-P et al. (2013) Bacterial community mapping of the mouse gastrointestinal tract. PLoS ONE 8:e74957Heimesaat MM, Boelke S, Fischer A, Haag L-M, Loddenkemper C, Kühl AA et al. (2012) Comprehensive postmortem analyses of intestinal microbiota changes and bacterial translocation in human flora associated mice. PloS ONE 7:e40758CAS
PubMed
PubMed Central
Article
Google Scholar
Hird SM (2017) Evolutionary biology needs wild microbiomes. Front Microbiol 8:725Iljazovic A, Roy U, Gálvez EJC, Lesker TR, Zhao B, Gronow A et al. (2020) Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation. Mucosal Immunol 14:113–124PubMed
PubMed Central
Article
CAS
Google Scholar
Ingala MR, Simmons NB, Wultsch C, Krampis K, Speer KA, Perkins SL (2018) Comparing microbiome sampling methods in a wild mammal: fecal and intestinal samples record different signals of host ecology, evolution. Front Microbiol 9:803Karasov WH, Douglas AE (2013) Comparative digestive physiology. Compr Physiol 3:741–783PubMed
PubMed Central
Google Scholar
Kartzinel TR, Hsing JC, Musili PM, Brown BRP, Pringle RM (2019) Covariation of diet and gut microbiome in African megafauna. Proc Natl Acad Sci U S A 116:23588–23593CAS
PubMed
PubMed Central
Article
Google Scholar
Kohl KD, Dearing MD (2016) The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins. Front Microbiol 7:1165Kohl KD, Luong K, Dearing MD (2015) Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida). J Mammal 96:90–93Article
Google Scholar
Kohl KD, Varner J, Wilkening JL, Dearing MD (2018) Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets. J Anim Ecol 87:323–330PubMed
Article
PubMed Central
Google Scholar
Kreisinger J, Bastien G, Hauffe HC, Marchesi J, Perkins SE (2015) Interactions between multiple helminths and the gut microbiota in wild rodents. Philos Trans R Soc B Biol Sci 370:20140295Kreisinger J, Čížková D, Vohánka J, Piálek J (2014) Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing. Mol Ecol 23:5048–5060CAS
PubMed
Article
PubMed Central
Google Scholar
Kreisinger J, Kropáčková L, Petrželková A, Adámková M, Tomášek O, Martin J-F et al. (2017) Temporal stability and the effect of transgenerational transfer on fecal microbiota structure in a long distance migratory bird. Front Microbiol 8:50Laukaitis CM, Critser ES, Karn RC (1997) Salivary androgen-binding protein (ABP) mediates sexual isolation in Mus musculus. Evol Int J Org Evol 51:2000–2005CAS
Article
Google Scholar
Lawrence K, Lam K, Morgun A, Shulzhenko NLöhr C (2019) Effect of temperature and time on the thanatomicrobiome of the cecum, ileum, kidney, and lung of domestic rabbits. J Vet Diagn Invest 31. https://doi.org/10.1177/1040638719828412Legendre P, Anderson MJ (1999) Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol Monogr 69:1–24Article
Google Scholar
Li D, Chen H, Mao B, Yang Q, Zhao J, Gu Z et al. (2017) Microbial biogeography and core microbiota of the rat digestive tract. Sci Rep 7:45840PubMed Central
Article
CAS
Google Scholar
Maslanik T, Tannura K, Mahaffey L, Loughridge AB, Benninson L, Ursell L et al. (2012) Commensal bacteria and MAMPs are necessary for stress-induced increases in IL-1β and IL-18 but not IL-6, IL-10 or MCP-1. PLoS ONE 7:e50636CAS
PubMed
PubMed Central
Article
Google Scholar
Matsuo Y, Komiya S, Yasumizu Y, Yasuoka Y, Mizushima K, Takagi T et al. (2020) Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinIONTM nanopore sequencing confers species-level resolution. bioRxiv. https://doi.org/10.1101/2020.05.06.078147McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM et al. (2017) The effects of captivity on the mammalian gut microbiome. Integr Comp Biol 57:690–704PubMed
PubMed Central
Article
Google Scholar
McMurdie PJ, Holmes S (2014) Waste not, want not: why rarefying microbiome data is inadmissible. PLOS Comput Biol 10:e1003531PubMed
PubMed Central
Article
CAS
Google Scholar
Menke S, Meier M, Sommer S (2015) Shifts in the gut microbiome observed in wildlife faecal samples exposed to natural weather conditions: lessons from time-series analyses using next-generation sequencing for application in field studies. Methods Ecol Evol 6:1080–1087Article
Google Scholar
Miller AW, Oakeson KF, Dale C, Dearing MD (2016) Microbial community transplant results in increased and long-term oxalate degradation. Micro Ecol 72:470–478CAS
Article
Google Scholar
Pafčo B, Čížková D, Kreisinger J, Hasegawa H, Vallo P, Shutt K et al. (2018) Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species. Sci Rep 8:5933Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L et al. (2014) Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158:1000–1010CAS
PubMed
PubMed Central
Article
Google Scholar
Pechal JL, Schmidt CJ, Jordan HR, Benbow ME (2018) A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition. Sci Rep 8:5724PubMed
PubMed Central
Article
CAS
Google Scholar
Pollock J, Glendinning L, Wisedchanwet T, Watson M (2018) The madness of microbiome: attempting to find consensus “best practice” for 16S microbiome studies. Appl Environ Microbiol 84:e02627–17PubMed
PubMed Central
Article
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596CAS
PubMed
Article
PubMed Central
Google Scholar
R Core Team (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
Google Scholar
Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K et al. (2017) Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell 171:1015–1028.e13CAS
PubMed
PubMed Central
Article
Google Scholar
Round JL, Mazmanian SK (2009) The gut microbiome shapes intestinal immune responses during health and disease. Nat Rev Immunol 9:313–323CAS
PubMed
PubMed Central
Article
Google Scholar
Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C et al. (2013) Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2:e01202PubMed
PubMed Central
Article
CAS
Google Scholar
Sommer F, Ståhlman M, Ilkayeva O, Arnemo JM, Kindberg J, Josefsson J et al. (2016) The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos. Cell Rep 14:1655–1661CAS
PubMed
Article
PubMed Central
Google Scholar
Stalder GL, Pinior B, Zwirzitz B, Loncaric I, Jakupović D, Vetter SG et al. (2019) Gut microbiota of the European Brown Hare (Lepus europaeus). Sci Rep 9:2738CAS
PubMed
PubMed Central
Article
Google Scholar
Stanley D, Geier MS, Chen H, Hughes RJ, Moore RJ (2015) Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences. BMC Microbiol 15:51PubMed
PubMed Central
Article
Google Scholar
Stearns JC, Lynch MDJ, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG et al. (2011) Bacterial biogeography of the human digestive tract. Sci Rep 1:170CAS
PubMed
PubMed Central
Article
Google Scholar
Stothart MR, Palme R, Newman AEM (2019) It’s what’s on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal. Proc R Soc B Biol Sci 286:20192111Article
Google Scholar
Suzuki TA, Martins FM, Nachman MW (2019) Altitudinal variation of the gut microbiota in wild house mice. Mol Ecol 28:2378–2390CAS
PubMed
Article
PubMed Central
Google Scholar
Suzuki TA, Nachman MW (2016) Spatial heterogeneity of gut microbial composition along the gastrointestinal tract in natural populations of house mice (EG Zoetendal, Ed.). PLoS ONE 11:e0163720PubMed
PubMed Central
Article
CAS
Google Scholar
Tanca A, Manghina V, Fraumene C, Palomba A, Abbondio M, Deligios M et al. (2017) Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse. Front Microbiol 8:391Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B et al. (2020) Current sampling methods for gut microbiota: a call for more precise devices. Front Cell Infect Microbiol 10:151Tang W, Zhu G, Shi Q, Yang S, Ma T, Mishra SK et al. (2019) Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: dynamic changes and functional predictions. MicrobiologyOpen 8:e789Trevelline BK, Fontaine SS, Hartup BK, Kohl KD (2019) Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc R Soc B Biol Sci 286:20182448Article
Google Scholar
Tuomisto S, Karhunen PJ, Pessi T (2013) Time-dependent post mortem changes in the composition of intestinal bacteria using real-time quantitative PCR. Gut Pathog 5:35Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031PubMed
Article
PubMed Central
Google Scholar
Vasemägi A, Visse M, Kisand V (2017) Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish. mSphere 2:e00418–17PubMed
PubMed Central
Article
Google Scholar
Videvall E, Strandh M, Engelbrecht A, Cloete S, Cornwallis C (2017) Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling. Mol Ecol Resour 18:424–434PubMed
Article
CAS
PubMed Central
Google Scholar
Vlčková K, Shutt-Phillips K, Heistermann M, Pafčo B, Petrželková KJ, Todd A et al. (2018) Impact of stress on the gut microbiome of free-ranging western lowland gorillas. Microbiol Read Engl 164:40–44Article
CAS
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267CAS
PubMed
PubMed Central
Article
Google Scholar
Wang J, Linnenbrink M, Künzel S, Fernandes R, Nadeau M-J, Rosenstiel P et al. (2014) Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proc Natl Acad Sci U S A 111:E2703–2710CAS
PubMed
PubMed Central
Article
Google Scholar
Warne RW, Kirschman L, Zeglin L (2017) Manipulation of gut microbiota reveals shifting community structure shaped by host developmental windows in amphibian larvae. Integr Comp Biol 57:786–794PubMed
Article
PubMed Central
Google Scholar
Weldon L, Abolins S, Lenzi L, Bourne C, Riley EM, Viney M (2015) The gut microbiota of wild mice. PLoS ONE 10:e0134643PubMed
PubMed Central
Article
CAS
Google Scholar
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108CAS
PubMed
PubMed Central
Article
Google Scholar
Yan W, Sun C, Zheng J, Wen C, Ji C, Zhang D et al. (2019) Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota. Front Microbiol 10:2126Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM et al. (2015) Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe 17:385–391CAS
PubMed
PubMed Central
Article
Google Scholar
Zemanova MA (2019) Poor implementation of non-invasive sampling in wildlife genetics studies. Rethink Ecol 4:119–132Article
Google Scholar
Zemanova MA (2020) Towards more compassionate wildlife research through the 3Rs principles: moving from invasive to non-invasive methods. Wildl Biol 2020. https://doi.org/10.2981/wlb.00607Zhao W, Wang Y, Liu S, Huang J, Zhai Z, He C et al. (2015) The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments. PLoS ONE 10:e0117441PubMed
PubMed Central
Article
CAS
Google Scholar
Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32:723–735CAS
PubMed
Article
PubMed Central
Google Scholar More