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]