3.2. Performance Parameters
A summary of performance parameters is provided in Table 3
. As it was conceived, the effect of experimental phase was significant (p
< 0.01) on all the studied parameters related with performance. No changes were found in ADFI of animals of two producing types (Duroc vs F2) or those that consumed different experimental diets (NP vs. LP) throughout the course of study (p
> 0.05). In each phase, animals of two producing types were, on average, fed same amount of feed on the daily basis (p
> 0.05); however, during the last phase, LP diet was consumed more than NP (3.2 vs 2.9 kg/day; p
At the entry of animals to the fattening facilities (9 weeks old) the piglets were distributed based on minimum BW variation to yield iso-weighed pens considering producing type (Duroc and F2) and diet (LP or NP). The data provided for the initial BW (Table 3
) show the least variation between genotypes (23.3 vs. 24.5 SEM 1.17; Duroc and F2, respectively) and diets (23.9 vs 23.9 SEM 1.14; LP and NP, respectively), which did not differ statistically (p
= 1.0 for genotype and diet at the initial BW). However, at the end of each experimental phase, the average BW of F2 animals (52.9, 80.5, and 103.8; at the end of P1, P2 and P3, respectively) were higher (p
< 0.05) compared to Duroc pigs (49.9, 73.6, and 96.5; at the end of P1, P2, and P3, respectively).
Composition of diet (LP or NP) did not influence the BW throughout the feeding phases (p > 0.05). Thus, no variations in BW were found between animals fed different diets.
F2 animals showed numerically higher ADG with respect to Duroc ones in all the feeding phases, although differences did only reach statistical significance during the second (weeks 15 to 18 of age) phase (0.99 vs. 0.84 p < 0.01; F2 vs. Duroc, respectively). Variations in performance led to a higher overall ADG in animals of F2 with respect to Duroc (0.85 vs. 0.76 for F2 and Duroc pigs, respectively, p < 0.01). Protein level in the diet did not influence the ADG of the animals throughout the experiment (p > 0.05). Neither producing type of the animals (Duroc and F2) nor CP content of the diet (LP and NP) influenced the efficiency of animals to convert feed into body mass expressed as gain:feed ratio (p > 0.05). No interactions were found between producing type of the animal and diet composition (PT × Di) in performance parameters measured during the experiment (p > 0.05).
3.3. Coefficient of Total Tract Apparent Digestibility (CTTAD) of the Nutrients
Results from CTTAD determination are showed in Table 4
. Dry matter digestibility during the third phase of the study (week 22 to 25 of age) was lower, compared with the other two phases (0.934 vs 0.945 and 0.948 p
< 0.01; P3 vs P2 and P1, respectively). No differences were found in total tract digestibility of DM between Duroc and F2 or between animals fed NP or LP diets (p
> 0.05). As the CP content recommended for each feeding phase reduced gradually in diets from first to third phase, the coefficient of total tract digestibility of CP decreased accordingly (0.736, 0.701, and 0.683 for P1, P2, and P3, respectively, p
< 0.01). Besides, in overall, animals of F2 genotype apparently digested more CP than Duroc (0.724 vs 0.689 for F2 vs Duroc, respectively, p
< 0.05), where no effect of diet was observed for the total tract digestibility of CP. The apparent digestibility of NDF was similar to that of CP and decreased (p
< 0.01) along the phases of the experiment up to 21.6% at the third phase (0.304 and 0.286 for P1 and P2, respectively). No effects of producing type or CP content of the diet were observed in digestibility of NDF content (p
> 0.05). Moreover, no interactions between main factors were found in CTTADs (DM, CP, and NDF) measured during the experiment (p
3.5. Fecal Microbial Characterization
A total number of 7,155,810 reads were obtained, with an average of 119,263 reads per sample. Good’s coverage index resulted in an average of 99.86%, indicating that most of the microbial population present in the samples was covered by the analysis.
All four groups (F2 and Duroc with two level of protein in the diet) shared the 64.13% of the OTUs present in the analysis (see Figure 1
) and only an average of 0.54% of the OTUs was specific in each group. Duroc animals showed numerically less specific OTUs than F2 (2.79 vs 3.88%), as well as the animals fed LP diets compared to NP diets (2.59 vs 3.47%). In general, the shared proportion of OTUs was high (96.12, 97.21, 97.41, and 96.53% in Duroc, F2, NP, and LP diets, respectively), indicating a very stable core population in the feces from finishing pigs.
Richness index of diversity showed significant differences between genotypes and diets, with diversity being higher in NP diets and F2 animals (Table 6
< 0.05 in both cases).
Reads belonging to the kingdom Archaea accounted for an average of 0.15% of the total number of sequenced reads and no differences were found in the relative abundance of archaea between either producing types or diets (p > 0.05).
Nineteen different phyla were identified within the kingdom Bacteria, although only nine phyla (Actinobacteria, Bacteroidetes, Fibrobacteres, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, Tenericutes, and Verrucomicrobia) presented mean abundances above 0.1%. Firmicutes was the most abundant phyla in both genotypes (72.4 ± 6.13% in Duroc and 73.5 ± 4.81% in F2), followed by Bacteroidetes and Proteobacteria. Among main phyla, a genotype effect was found on Bacteroidetes, Proteobacteria, and Verrucomicrobia phyla (Figure 2
), with Duroc having higher abundances in the former phylum and lower in rest.
Diet did not affect the microbial composition of the animals at phyla level (p
> 0.05), but in NP diets, Duroc animals presented a lower proportion of Firmicutes than F2 (interaction effect, p
< 0.05). Hence, the Bacteroidetes:Firmicutes ratio tended to be lower in Duroc animals (p
= 0.08, Supplementary Materials Figure S1
A description of the main families identified within the four most abundant phyla is shown in Figures S2 and S3
. Duroc animals showed higher abundances in families Atopobiaceae
= 0.007) and Coriobacteriaceae
= 0.004) from phylum Actinobacteria, family Prevotellaceae
= 0.049) from phylum Bacteroidetes, and family Lachnospiraceae
= 0.003) from phylum Firmicutes. On the other hand, F2 animals showed higher abundances in family Eggerthellaceae
< 0.001) from phylum Actinobacteria; families Paludibacteraceae
= 0.006), Porphyromonadaceae
< 0.001), and Tannerellaceae
< 0.001) from phylum Bacteroidetes; families Clostridiaceae
= 0.003) and Peptococcaceae
= 0.001) from phylum Firmicutes; and family Succinivibrionaceae
= 0.036) from phylum Proteobacteria (Figure S2
Diet only affected family Geobacteraceae
= 0.001) from phylum Proteobacteria, having higher abundances in animals fed NP diets than those fed LP diets. Interaction effects were present in families Clostridiales Family XIII, Incertae Sedis
= 0.038, NP > LP in Duroc animals), and Eubacteriaceae
= 0.036, F2 > Duroc in LP diets) from phylum Firmicutes and family Geobacteraceae
= 0.019, Duroc animals fed NP diets were higher than the rest of animals) from phylum Proteobacteria (Figure S3
SPLS-DA analysis enabled the selection of the most predictive or discriminative taxons in the data that helped to classify the samples according to either diet or genotype effect (see Figure S4
); from the 10 most predictive taxons, only those with relative abundances higher than 0.01% were considered. In this scenario, five taxons were found to be the most responsible of the differences between genotypes (two varieties of Holdemanella biformis
, uncultured Coriobacteriales bacterium, uncultured Bacteroidetes bacterium, and uncultured Prevotellaceae
bacterium) and two related with differences between diets (Blautia sp.
canine oral taxon 143 and Selenomonas bovis
We compared all the detected phyla and the most abundant bacterial genera (>0.1%, N = 34), with those producing and digestive efficiency parameters studied in the trial (Table 7
) using Spearman correlation rank between performance parameters and abundant genera. Only significant correlation values (p
< 0.05, r > |0.58|) were considered. In Duroc animals, up to nine different genera and two phyla either positively or negatively were correlated with performance (BW, ADG, or digestibility), meanwhile in F2 animals, this correlation was only found in two genera and one phylum. LP diets also presented more correlations between microbiota and performance (five genera and two phyla) than in NP diets (three genera and one phylum).