Viral metagenomic overview between the AVL-J-infected chickens and controls
The gut virome composition was investigated at the order, family, genus, and species levels in the AVL-J-infected chickens and controls. At the order level in the two groups, the top six orders included Herpesvirales, Caudovirales, Picornavirales, Bunyavirales, Tymovirales, and Ortervirales (Fig. 1A). The predominant order was Herpesvirales, accounting for more than 96% in the two groups. The relative abundance of Caudovirales in the controls was higher than that in the AVL-J-infected chickens (P < 0.01). Viral families represented by only one or two individuals of each group were excluded from the analysis to avoid spurious associations. In both the chicken groups, the four dominant phyla were Herpesviridae, Alloherpesviridae, Genomoviridae, and Partitiviridae (Fig. 1B). The relative abundance of Herpesviridae and Myoviridae showed an obvious decrease in the AVL-J-infected chickens compared with the controls (P < 0.05). Conversely, the relative abundance of Alloherpesviridae and Genomoviridae significantly increased in the AVL-J-infected chickens compared with the controls (P < 0.01). At the genus level, there was a significant difference in the relative abundance of the top four genera between the two groups, namely, Varicellovirus, Cyprinivirus, Roseolovirus, and Simplexvirus (P < 0.05). Additionally, the relative abundance of Cyprinivirus, Roseolovirus, Mardivirus, Gemykibivirus, Percavirus, and Pahexavirus was significantly increased, but there was a decrease in the relative abundance of Varicellovirus, Simplexvirus, Limestonevirus, Rhadinovirus, Bixzunavirus, Prasinovirus, Polerovirus, Cheoctovirus, and Cyclovirus in the AVL-J-infected chickens compared with the controls (Fig. 1C). Overall, the chicken gut virome contained a diverse range of viruses. At the order, family, and genus levels, the results indicated that AVL-J infection significantly altered the chicken gut virome composition.
Host sources of these viruses included bacteria, archaea, fungi, protozoa, algae, invertebrates, vertebrates, and plants. In the AVL-J-infected chickens, the most abundant species found were Bubaline alphaherpesvirus 1, Cyprinid herpesvirus 1, Human betaherpesvirus 7, and Suid alphaherpesvirus 1. Whereas, Bubaline alphaherpesvirus 1, Cyprinid herpesvirus 1, Suid alphaherpesvirus 1, and Macacine alphaherpesvirus 1 were the most abundant species in the controls (Fig. 1D). The relative abundance in 366 species showed significant differences between the two groups (P < 0.05) (S1). Interestingly, among the 366 species, 44 species were detected only in the controls, whereas 33 species were found only in the AVL-J-infected chickens. Among the 77 species, Caudovirales species showed the most significant differences between the two groups. Figure 2 shows the phylogenetic analysis of the 77 species based on the taxonomy data from the NCBI (Fig. 2). Moreover, the predominant species detected only in the AVL-J-infected chickens or controls did not show a close phylogenetic relationship. In summary, the AVL-J-infected chickens showed a significant alteration in the diversity, evenness, and richness of species compared with the healthy control gut, suggesting that AVL-J infection significantly altered the composition of the gut virome in chickens.
Dominant taxa between the ALV-J-infected chickens and controls
Figure 3A depicts the PLS-DA scatter plots for the ALV-J-infected chickens and controls. The first PLS component is used to discriminate between the ALV-J-infected chickens and controls, whereas the second PLS component separates each sample within the two groups. These taxa showed a large variation within the groups, and they were different between the two groups. Furthermore, we used the LEfSe for the quantitative analysis of biomarkers within the two groups (Fig. 3B). The LEfSe provided two main outputs, describing the effect sizes of differences observed between the ALV-J-infected chickens and controls. The LEfSe revealed 19 viral clades showing statistically significant and biologically consistent differences in the ALV-J-infected chickens, whereas, 16 viral clades were detected in the controls. The four most abundant taxa in the ALV-J-infected chickens were Alloherpesviridae, Cyprinivirus, Roseolovirus, and Cyprinid herpesvirus 1. They were used as biomarkers at the family, genus, and species levels in the ALV-J-infected chickens. In contrast to this, in the controls, the predominant taxa were Caudovirales, Myoviridae, Eptesicus fuscus gammaherpesvirus, and Suid alphaherpesvirus 1. They were used as biomarkers at the order, family, genus, and species levels in the controls.