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. 2018 Mar 15;16:131–139. doi: 10.1016/j.csbj.2018.03.002

Table 1.

Summary of the studies investigating chicken microbiome in respect to the influence of feeding impact with metagenomics and metaproteomics methodologies.

Metagenome details Study focus Diet GIT sections Number of samples Sampling time Reference
GS-FLX sequencing
Reads: 1.291.219
Av. length: 234–399 bp
Effects of subtherapeutic levels of virginia and tylosin and the coccidial monensin on bacteria composition from the chicken caecum (metagenomics and 16S) 7 d of basal diet followed by supplementation with: Monensin sodium, Monensin sodium + virginiamycin or tylosin phosphate Caeca Pooled samples per treatment 0 d, 7 d, 14 d and 35 d Ross × Ross chickens [11]
Illumina MiSeq2000
Reads: 81.772.788
Av. length: 110 bp
Elucidation of the functions of the cecal microbiota and characterization of the community profile (metagenomics and 16S) Wheat based diet with 5% maize Caeca 20 42 d of Ross broilers [5]
Illumina HiSeq2000
Reads: 52.485.882
Av. length: 100 bp
Study if variation of fatness is link to the composition of gut microbial metagenome. Lean and fat lines were employed. Commercial diet Feces 29 Fat and lean lines. Weeks 37 to 40 [54]
Illumina HiSeq2000
Reads: 37.9 million (per sample)
Av. length: 100 bp
Comparison of two lines of chickens (fat and lean). Understand the influence of the host in the gut microbiota Commercial diet Feces 6 35 wks [15]
Illumina HiSeq 2000
Av. length: 100 bp
Antibiotic resistance genes annotation from metagenome of pig, chicken and human and its co-occurrence with associated genetic elements Commercial diet Feces 8 20 d and 80 d [51]
454 sequencing
Reads: 24–30 million
Av. length: 100 bp
Phylotype and functional gene content characterization before and after inoculation with Campylobacter jejuni Commercial diet and 14 days post-hatching one group was challenged with 10^5 CFU of C. jejuni Caeca 2 28 d (14 d of challenge) [45]
GS-FLX sequencing
Reads: 94.926 (low FCR); 63.891 (high FCR)
Av. length: 227 bp
Characterization of poultry fecal microbiome of low and high feed conversion ratio (FCR) broilers Commercial diet Feces Pooled samples for high and low FCR 49 d broiler strain MY [53]
Illumina HiSeq 2000
Reads: 4.737.146
Investigate the occurrence, diversity and abundance of antibiotic resistance genes in feces of layers and broilers Commercial diet Feces Pooled samples 6 wk broilers and 52 wk laying hens [50]
Metaproteomics Microbial composition in the healthy chicken gut Attlee's nonmedicated poultry feed Feces Pooled samples 18 wk white leghorn chickens [57]
Dietary effect of mineral phosphorous and microbial phytase 3 diets with P from plant sources (BD−), 3 diets with P supplementation (BD+).
BD− and BD+ supplemented with 0, 500 and 12,500 U/kg of E. coli phytase
Crop
Caeca
Pooled samples per treatment 25 d broilers Ross 308 [58]