Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks

[1]  Yue Li,et al.  Age-Related Variations in Intestinal Microflora of Free-Range and Caged Hens , 2017, Front. Microbiol..

[2]  A. Best,et al.  Characterization of Gut Microbiome Dynamics in Developing Pekin Ducks and Impact of Management System , 2017, Front. Microbiol..

[3]  Lusheng Huang,et al.  Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness , 2016, Scientific Reports.

[4]  Ondřej Polanský,et al.  Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota , 2015, Applied and Environmental Microbiology.

[5]  Weiyun Zhu,et al.  Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function , 2015, Scientific Reports.

[6]  H. Gan,et al.  Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses , 2015, Gut Pathogens.

[7]  Hassan Razvi,et al.  The microbiome of the urinary tract—a role beyond infection , 2015, Nature Reviews Urology.

[8]  Jana Seifert,et al.  News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals , 2014, Computational and structural biotechnology journal.

[9]  F. Bushman,et al.  Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. , 2014, Gastroenterology.

[10]  W. D. de Vos,et al.  Impact of diet on human intestinal microbiota and health. , 2014, Annual review of food science and technology.

[11]  Heather K. Allen,et al.  Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations , 2014, The ISME Journal.

[12]  V. Shcherbakova,et al.  Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces. , 2013, International journal of systematic and evolutionary microbiology.

[13]  Jesse R. Zaneveld,et al.  Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences , 2013, Nature Biotechnology.

[14]  Robert C. Edgar,et al.  UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.

[15]  W. Wanek,et al.  Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing , 2013, Proceedings of the National Academy of Sciences.

[16]  Nicholas A. Bokulich,et al.  Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing , 2012, Nature Methods.

[17]  Timothy L. Tickle,et al.  Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment , 2012, Genome Biology.

[18]  A. Rebolé,et al.  Wheat- and barley-based diets with or without additives influence broiler chicken performance, nutrient digestibility and intestinal microflora. , 2012, Journal of the science of food and agriculture.

[19]  S. Salzberg,et al.  FLASH: fast length adjustment of short reads to improve genome assemblies , 2011, Bioinform..

[20]  R. Ley,et al.  The Antibacterial Lectin RegIIIγ Promotes the Spatial Segregation of Microbiota and Host in the Intestine , 2011, Science.

[21]  C. Huttenhower,et al.  Metagenomic biomarker discovery and explanation , 2011, Genome Biology.

[22]  Yongxiang Zhang,et al.  Saccharofermentans acetigenes gen. nov., sp. nov., an anaerobic bacterium isolated from sludge treating brewery wastewater. , 2010, International journal of systematic and evolutionary microbiology.

[23]  Xiuzhu Dong,et al.  Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen. , 2010, International journal of systematic and evolutionary microbiology.

[24]  I. Martínez,et al.  A small variation in diet influences the Lactobacillus strain composition in the crop of broiler chickens. , 2010, Systematic and applied microbiology.

[25]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[26]  Lu Wang,et al.  The NIH Human Microbiome Project. , 2009, Genome research.

[27]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[28]  Bin Zhang,et al.  Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R , 2008, Bioinform..

[29]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[30]  K. Finster,et al.  Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques. , 2006, Poultry science.

[31]  T. Dumonceaux,et al.  Characterization of Intestinal Microbiota and Response to Dietary Virginiamycin Supplementation in the Broiler Chicken , 2006, Applied and Environmental Microbiology.

[32]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[33]  M. M. Boiago,et al.  Intestinal mucosa development in broiler chickens fed natural growth promoters , 2005 .

[34]  G. Macfarlane,et al.  Effect of pH and Antibiotics on Microbial Overgrowth in the Stomachs and Duodena of Patients Undergoing Percutaneous Endoscopic Gastrostomy Feeding , 2005, Journal of Clinical Microbiology.

[35]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[36]  J. Maurer,et al.  Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken , 2003, Applied and Environmental Microbiology.

[37]  K. Yamauchi Review on Chicken Intestinal Villus Histological Alterations Related with Intestinal Function , 2002 .

[38]  A. Bird,et al.  A comparison of five methods for extraction of bacterial DNA from human faecal samples. , 2002, Journal of microbiological methods.

[39]  J. Madara,et al.  Molecular physiology and pathophysiology of tight junctions. IV. Regulation of tight junctions by extracellular stimuli: nutrients, cytokines, and immune cells. , 2000, American journal of physiology. Gastrointestinal and liver physiology.

[40]  H. Kamisoyama,et al.  Effects of fasting and refeeding on structures of the intestinal villi and epithelial cells in White Leghorn hens. , 1996, British poultry science.

[41]  U. Hopfer,et al.  Regional specificity of iron uptake by small intestinal brush-border membranes from normal and iron-deficient mice. , 1985, The American journal of physiology.

[42]  S. Hurwitz,et al.  Glucose homeostasis in the chicken. , 1982, The Journal of nutrition.

[43]  O. Bouchez,et al.  Overfeeding and genetics affect the composition of intestinal microbiota in Anas platyrhynchos (Pekin) and Cairina moschata (Muscovy) ducks. , 2014, FEMS microbiology ecology.

[44]  I. Zulkifli,et al.  Gut microflora and intestinal morphology of commercial broiler chickens and red jungle fowl fed diets containing palm kernel meal. , 2009 .

[45]  B. Slominski,et al.  Effects of diet type and enzyme addition on growth performance and gut health of broiler chickens during subclinical Clostridium perfringens challenge. , 2009, Poultry science.

[46]  Jessica J Hellmann,et al.  The application of rarefaction techniques to molecular inventories of microbial diversity. , 2005, Methods in enzymology.

[47]  M. Vinardell,et al.  Jejunal and cecal 3-oxy-methyl-D-glucose absorption in chicken using a perfusion system in vivo. , 1987, Comparative biochemistry and physiology. A, Comparative physiology.

[48]  G. S. Heard,et al.  Gastrointestinal absorption of vitamin B-6 in the chicken (Gallus domesticus). , 1986, The Journal of nutrition.