mSphere · 2019 · 44 citations · 47 references
Life SciencesMicrobiologyPoultry ScienceMetagenomicsMicrobial EcologyPoultry MicrobiologyAnimal Microbial EcologyGut MicrobiomeGut MicrobiotaMetagenomic AnalysisMicrobial Community ProfilingBroiler ChickensGut Microbiota CompositionIntestinal Microbial Diversity
The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.
47
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
Diet rapidly and reproducibly alters the human gut microbiome
Lawrence A. David, Corinne F. Maurice, Rachel N. Carmody et al. · Nature · 2013 · 10.2K citations · Full text
STAMP: statistical analysis of taxonomic and functional profiles
Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz et al. · Bioinformatics · 2014 · 4.3K citations · Full text