TABLE 1

Details of studies included in the meta-analysis

ReferenceNo. of samplesHypervariable region(s)Sequencing platformAvg % assigned sequences per sampleDNA extraction methodSample type(s)Study observation(s)Age of pigs at samplingCountry(ies) of originData availability (accession no.)
J. Trachsel, B. E. Bass, and H. K. Allen, unpublished52V1 to V3Illumina MiSeq76.2%PowerSoil-htp 96-well soil DNA isolation kitIleum digesta, fecalSubset of samples taken before heat stress treatment7 wksUnited States PRJNA335425
17 24V1 to V2Illumina MiSeq88.9%NAbIleum digestaPigs challenged with E. coli F4+ and fed IgG had a lower relative abundance of Enterococcaceae and Streptococcaceae and increased ileal diversity6 wksDenmark PRJNA302730
15 a 18V4Illumina MiSeq75.4%QIAamp DNA stool minikitColon digestaPigs fed DDGSc had a different microbial community structure9 wksUnited States PRJEB11368
45 a 40V3 to V4454 FLX74.1%QIAamp DNA stool minikitColon digesta, fecalNo differences in the gut microbiota between conventionally and organically raised pigs24 wksDenmark, France, Italy, Sweden PRJNA266576
66 39V4Illumina MiSeq85.2%PowerFecal DNA isolation kit (MoBio)FecalDifference between the fecal microbiota of black and white breed pigs3–12 wksSouth Korea PRJNA252973
67 53V1 to V3454 FLX83.3%QIAamp DNA stool minikitColon, ileal digestaSow-reared and formula-fed piglets had a different gut microbiota3 wksUnited States PRJNA266806
13 20V4Illumina MiSeq75.8%CustomIleum, cecum digestaNo effect of high or low amylose/amylopectin ratio diets on the gut microbiota21 wksChina PRJNA281781
68 19V4Illumina MiSeq81.3%PowerFecal DNA isolation kit (MoBio)FecalDifferences in fecal microbiota by production phasePiglets, growers, finishers, sowsSouth Korea PRJNA267233
16 14V3 to V5Illumina MiSeq73.2%PowerSoil DNA isolation kit (MoBio)Cecum digestaMinor differences in the cecal microbiota of pigs fed 70% enzymatically modified cornstarch or control starch14 wksAustria PRJEB8696
11 62V4Illumina MiSeq80.6%PowerFecal DNA isolation kit (MoBio)FecalNo effect of diet with 0.2% chlortetracycline, sulfathiazole, and penicillin on the fecal microbiota3–12 wksSouth Korea PRJNA257009
10 94V4Illumina MiSeq51.9%ZR fecal DNA MiniPrep (Zymo Research)FecalSubtherapeutic tylosin, but not chlortetracycline, altered the fecal microbiota3–19 wksCanada PRJNA244928
12 44V1 to V3454 FLX87.6%PowerSoil DNA isolation kit (MoBio)Ileal mucosaNo effect of in-feed chlortetracycline or high-complexity diets on the ileal mucosa microbiota6–11 wksCanada PRJNA257705
7 80V1 to V3454 FLX62.8%Ultra-Clean soil DNA isolation kit (MoBio)Gastric mucosa, duodenum, jejunum, ileum cecum, colon digesta and mucosa, fecalReduced diversity in the ileum versus colon, ASP250-altered gut microbiota15 wksUnited States PRJNA72355
8 101V1 to V3454 FLX54.1%PowerSoil DNA isolation kitFecalCarbadox resulted in early but not late alterations of the fecal microbiota6–15 wksUnited States PRJNA237795 ; SAMN02645017 to SAMN02645066
69 23V1 to V3454 FLX47.3%Ultra-Clean Fecal DNA isolation kit (MoBio)FecalThe fecal microbiota of Landrace pigs differed that of from pigs of the Duroc breed15 wksSouth Korea PRJNA263439
14 92V1 to V2454 FLX83.2%PowerSoil DNA isolation kit (MoBio)Gastric, ileum, colon mucosaGut microbiota affected by Ca-P content and diet type7 wksAustria PRJEB1576
70 10V3Illumina HiSeq 200088.8%QIAamp DNA stool minikit (Qiagen)Cecum digestaFostering of piglets changes cecal microbiota3 wksChina PRJNA214736
18 59V1 to V3454 FLX80.7%PowerSoil DNA isolation kit (MoBio)FecalFecal microbiota differed between high- and low-Salmonella-shedder pigs8–11 wksUnited States PRJNA169497
9 12V3454 FLX67.5%Powermax soil DNA isolation kit (MoBio)FecalIn-feed ASP250 altered fecal microbiota18–20 wksUnited States PRJNA72355 ; SRP004660
6 83V1 to V3454 FLX44.4%CustomFecalIn-feed ASP250 altered fecal microbiota3–13 wksUnited States PRJNA72355 ; SRP008126
  • a Data are from studies that describe using commercial pigs.

  • b NA, not available.

  • c DDGS, distillers’ dried grains with solubles.