References
- Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977;31:1–9.
- Muegge BD , Kuczynski J , Knights D , et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332(6032):970–974.
- Fraher MH , O’Toole PW , Quigley EMM . Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol. 2012;9:312–322.
- Kelly CD . IV. Bacteria. Bot Rev. 1954;20:417–424.
- Levin M . Les microbes dans les regions arctiques. Ann Inst Pasteur. 1899;13:558–567.
- Sieburth JM . Gastrointestinal microflora of Antarctic Birds. J. Bacteriol. 1959;77(5):521–531.
- Džunková M , D’Auria G , Pérez-Villarroya D , et al. Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications. PLoS One. 2012;7(10):e47654.
- Leser TD , Amenuvor JZ , Jensen TK , et al. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol. 2002;68(2):673–690.
- Ryu H , Grond K , Verheijen B , et al. Intestinal microbiota and species diversity of Campylobacter and Helicobacter spp. in migrating shorebirds in Delaware Bay. Appl Environ Microbiol. 2014;80(6):1838–1847.
- Arnal M-E , Zhang J , Messori S , et al. Early changes in microbial colonization selectively modulate intestinal enzymes, but not inducible heat shock proteins in young adult Swine. PLoS One. 2014;9(2):e87967.
- Burbach K , Seifert J , Pieper DH , et al. Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions. Microbiologyopen. 2016;5(1):70–82.
- Costa E , Puhl NJ , Selinger LB , et al. Characterization of mucosa-associated bacterial communities of the mouse intestine by terminal restriction fragment length polymorphism: utility of sampling strategies and methods to reduce single-stranded DNA artifacts. J Microbiol Methods. 2009;78(2):175–180.
- Sakamoto M , Hayashi H , Benno Y . Terminal restriction fragment length polymorphism analysis for human fecal microbiota and its application for analysis of complex bifidobacterial communities. Microbiol Immunol. 2003;47(2):133–142.
- Lone AG , Selinger LB , Uwiera RR , et al. Campylobacter jejuni colonization is associated with a dysbiosis in the cecal microbiota of mice in the absence of prominent inflammation. PLoS One. 2013;8(9):e75325.
- Le Chatelier E , Nielsen T , Qin J , et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013;500(7464):541–546.
- Qin J , Li R , Raes J , et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
- Amend AS , Seifert KA , Bruns TD . Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol. 2010;19(24):5555–5565.
- Waldenström J , Axelsson-Olsson D , Olsen B , et al. Campylobacter jejuni colonization in wild birds: results from an infection experiment. PLoS One. 2010;5(2):e9082.
- Dick LK , Bernhard AE , Brodeur TJ , et al. Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl Environ Microbiol. 2005;71(6):3184–3191.
- Jedlicka A , Vo ATE . Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples. Mol Ecol Res. 2014;14:1183–1197.
- Ariefdjohan MW , Savaiano DA , Nakatsu CH . Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutr J. 2010;9:23.
- Claassen S , du Toit E , Kaba M , et al. A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J Microbiol Methods. 2013;94(2):103–110.
- Kawase J , Kurosaki M , Kawakami Y , et al. Comparison of two methods of bacterial DNA extraction from human fecal samples contaminated with Clostridium perfringens, Staphylococcus aureus, Salmonella Typhimurium, and Campylobacter jejuni. Jpn J Infect Dis. 2014;67(6):441–446.
- Maukonen J , Simões C , Saarela M . The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples. FEMS Microbiol Ecol. 2012;79(3):697–708.
- McOrist AL , Jackson M , Bird AR . A comparison of five methods for extraction of bacterial DNA from human faecal samples. J Microbiol Methods. 2002;50(2):131–139.
- Persson S , de Boer RF , Kooistra-Smid AM , et al. Five commercial DNA extraction systems tested and compared on a stool sample collection. Diagn Microbiol Infect Dis. 2011;69(3):240–244.
- Li M , Gong J , Cottrill M , et al. Evaluation of QIAamp DNA Stool Mini Kit for ecological studies of gut microbiota. J Microbiol Methods. 2003;54(1):13–20.
- Ferrand J , Patron K , Legrand-Frossi C , et al. Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice. J Microbiol Methods. 2014;105:180–185.
- Hart ML , Meyer A , Johnson PJ , et al. Comparative evaluation of DNA extraction methods from feces of multiple host species for downstream next-generation sequencing. PLoS One. 2015;10(11):e0143334.
- Josefsen MH , Andersen SC , Christensen J , et al. Microbial food safety: potential of DNA extraction methods for use in diagnostic metagenomics. J Microbiol Methods. 2015;114:30–34.
- Henderson G , Cox F , Kittelmann S , et al. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One. 2013;8(9):e74787.
- Gill FB . Ornithology. 3rd ed. New York City (NY): W.H. Freeman and Company; 2007; 1–12.
- Waite DW , Taylor MW . Characterizing the avian gut microbiota: membership, driving influences, and potential function. Front Microbiol. 2014;5:223.
- Banks JC , Cary SC , Hogg ID . The phylogeography of Adelie penguin faecal flora. Environ Microbiol. 2009;11(3):577–588.
- Lu J , Santo Domingo JW , Lamendella R , et al. Phylogenetic diversity and molecular detection of bacteria in gull feces. Appl Environ Microbiol. 2008;74(13):3969–3976.
- Berensmeier S . Magnetic particles for the separation and purification of nucleic acids. Appl Microbiol Biotechnol. 2006;73(3):495–504.
- Miller DN , Bryant JE , Madsen EL , et al. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol. 1999;65(11):4715–4724.
- Regnaut S , Lucas FS , Fumagalli L . DNA degradation in avian faecal samples and feasibility of non-invasive genetic studies of threatened capercaillie populations. Conserv Genet. 2006;7(3):449–453.
- Barbosa A , Palacios MJ . Health of Antarctic birds: a review of their parasites, pathogens and diseases. Polar Biology. 2009;32(8):1095–1115.
- Dewar ML , Arnould JP , Dann P , et al. Interspecific variations in the gastrointestinal microbiota in penguins. Microbiologyopen. 2013;2(1):195–204.
- Monteiro L , Bonnemaison D , Vekris A , et al. Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J Clin Microbiol. 1997;35(4):995–998.
- Salonen A , Nikkilä J , Jalanka-Tuovinen J , et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Meth. 2010;81(2):127–134.
- Ringvold A , Anderssen E , Kjønniksen I . UV absorption by uric acid in diurnal bird aqueous humor. Invest Ophthalmol Vis Sci. 2000;41(8):2067–2069.
- Jones MA , Marston KL , Woodall CA , et al. Adaptation of Campylobacter jejuni NCTC11168 to high-level colonization of the avian gastrointestinal tract. Infect Immun. 2004;72(7):3769–3776.
- Bahrndorff S , Garcia AB , Vigre H , et al. Intestinal colonization of broiler chickens by Campylobacter spp. in an experimental infection study. Epidemiol Infect. 2015;143(11):2381–2389.
- Cawthraw SA , Wassenaar TM , Ayling R , et al. Increased colonization potential of Campylobacter jejuni strain 81116 after passage through chickens and its implication on the rate of transmission within flocks. Epidemiol Infect. 1996;117(1):213–215.
- Gripp E , Hlahla D , Didelot X , et al. Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle. BMC Genomics. 2011;12:584.
- Nagamine CM , Shen Z , Luong RH , et al. Co-infection of the Siberian hamster (Phodopus sungorus) with a novel Helicobacter sp. and Campylobacter sp. J Med Microbiol. 2015;64(Pt 5):575–581.