Sequence analysis, phylum and OTU classification Sequencing of 130 samples yielded 51,825,306 quality-controlled sequences, clustering into 8285 operational taxonomic units (OTUs; 0.03 distance level). Throughout all gut sites 24 phyla were identified with Firmicutes, Proteobacteria, and Tenericutes being the most abundant ones. In Figure S1A, Tables S1A–D, relative abundances of all phyla are delineated with respect to age and groups. The results showed that in the jejunum and cecum, Firmicutes and Proteobacteria were the dominating luminal and mucosal-associated phyla in all birds investigated (Tables S2, S3). At the first day of life Proteobacteria were significantly higher in the jejunal (P = 0.0000, q = 0.0000) and cecal (P = 0.016; q = 0.059) mucosa of the birds and decreased thereafter, as no significant differences were found between samples from day 14 to day 28 of age (P = 0.140; q = 0.438 and P = 0.519; q = 0.955). On the contrary, Firmicutes were significantly lower at day 1 and increased thereafter (P = 0.001; q = 0.016 and P = 0.006; q = 0.055 in the jejunal and cecal mucosa, respectively). For infected birds, relative abundances of bacterial phyla at the two sampling time points carried out post infection are represented in Figure S1B, Tables S4A–D. Figure 1 shows that the phylum Proteobacteria decreased while Firmicutes increased at either 21 (7 dpi) or 28 days of age (14 dpi). There was a significant decrease in Actinobacteria and Proteobacteria in the jejunal mucosa at 14 dpi (P = 0.006; q = 0.100 and P = 0.005; q = 0.100), while Firmicutes and Bacteroidetes were more abundant in the infected birds compared to the controls (P = 0.005; q = 0.100 and P = 0.023; q = 0.217, Table S4A). However, in the cecal content and cecal mucosa, Bacteroidetes (P = 0.001; q = 0.019) increased at 7 dpi, but decreased (P = 0.002; q = 0.026 and P = 0.005; q = 0.048) at 14 dpi in the infected birds compared with the controls, indicating that the Campylobacter infection modulates the jejunal and cecal phylum abundances in different ways. Figure 1 Relative abundances (%) of the most abundant phyla in the infected birds compared with the controls at the two sampling points post infection of (A) jejunum and (B) cecum. Data are presented as the mean values and standard deviation (SD). JM, jejunal mucosa; JC, jejunal content; CM, cecum mucosa; CC, cecum content; control (c); infected (i). In Table 1, the 50 most abundant OTUs from all birds are listed including the internal OTU number, relative abundance together with the reference strain and similarity (compared with strains of the Greengenes database). Relative OTUs abundances at different ages in all birds are shown in Tables S5A–D, S6A–D. The OTUs and species abundances sorted by age at the four gut sites of the birds are shown in the heatmaps of Figure S2. In total, the 50 most abundant OTUs accounted for 73.9% of all sequences and of those 42 OTUs differed significantly in their relative abundances over all gut sites independent of the age (Tables 2, 3). At the first day of age, a notable high relative abundance of OTU 1, 25, 27, and 35 (best type strain hits: Escherichia coli, Enterococcus faecalis, Clostridium paraputrificum, and Clostridium sartagoforme) were found in both jejunal and cecal mucosa (Tables S5A,C), whereas OTU 38 (best type strain hit: Acinetobacter johnsonii) was only abundant in the jejunal mucosa and OTU 42 (best type strain hit: C. paraputrificum) was only abundant in the cecal mucosa. All these abundant OTUs decreased by age. In the jejunal mucosa, OTU 1 was the most abundant (57.9%), followed by the other four OTUs which ranged between 2.6 and 7.9%. Similarly, in the mucosa of the cecum, OTU 1 was highly abundant (65.9%), followed by OTUs 27, 25, 35, and 42 which ranged between 7.8 and 3.3%. Table 1 The 50 most abundant OTUs retrieved from different gut sites from all birds independent of the infection status. OTUs No. of sequences Relative abundance (%) Best type strain hita Similarity (%) OTU 1 642068 10.64 Escherichia coli (GU968184.1) 100 OTU 2 341923 5.66 Lactobacillus johnsonii (HM772969.1) 100 OTU 3 339288 5.62 Lactobacillus salivarius (NZ_AEBA01000145.1) 100 OTU 4 310060 5.14 Clostridium spp. (FJ808599.1) 87 OTU 5 273783 4.54 Enterococcus durans (FJ917726.1) 100 OTU 6 209121 3.46 Anaerotruncus colihominis (NR_027558.1) 100 OTU 7 208070 3.45 Eubacterium desmolans (L34618.1) 98 OTU 8 161864 2.68 Clostridium cellulolyticum (X71847.1) 87 OTU 9 157466 2.61 Spiroplasma lampyridicola (AY189134.1) 82 OTU 10 151864 2.52 Clostridium leptum (AJ305238.1) 97 OTU 11 130587 2.16 Eubacterium desmolans (L34618.1) 99 OTU 12 127446 2.11 Eubacterium desmolans (L34618.1) 98 OTU 13 120732 2.00 Clostridium papyrosolvens (NR_026102.1) 87 OTU 14 113436 1.88 Eubacterium coprostanoligenes (HM037995.1) 92 OTU 15 98491 1.63 Clostridium straminisolvens (NR_024829.1); Clostridium thermocellum (AB558166.1) 87 OTU 16 87863 1.46 Clostridium cellulolyticum (NC_011898.1) 87 OTU 17 70842 1.17 Bacillus subtilis (FJ608705.1) 94 OTU 18 67038 1.11 Lactobacillus reuteri (EU547311.1) 99 OTU 19 66212 1.10 Ruminococcus bromii (NR_025930.1) 94 OTU 20 65592 1.09 Eubacterium desmolans (L34618.1) 95 OTU 21 53133 0.88 Clostridium cellulolyticum (NC_011898.1); Clostridium papyrosolvens (NR_026102.1) 87 OTU 22 49736 0.82 Clostridium thermocellum (AB558166.1) 85 OTU 23 47570 0.79 Clostridium thermosuccinogenes (Y18180.1); Clostridium thermocellum (AB558166.1) 86 OTU 24 40373 0.67 Clostridium leptum (AJ305238.1) 95 OTU 25 36925 0.61 Enterococcus faecalis (FJ607291.1) 100 OTU 26 35311 0.58 Proteus mirabilis (GU477712.1) 100 OTU 27 31154 0.52 Clostridium paraputrificum (AY442815.1) 100 OTU 28 29186 0.48 Variovorax paradoxus (HQ005421.1) 100 OTU 29 28876 0.48 Campylobacter subsp. jejuni (NC_008787.1) 100 OTU 30 27988 0.46 Clostridium leptum (AJ305238.1) 93 OTU 31 23587 0.39 Anaerotruncus colihominis (NR_027558.1) 93 OTU 32 23559 0.39 Lactobacillus crispatus (FN692037.1) 100 OTU 33 22863 0.38 Phyllobacterium myrsinacearum (AY785330.1) 100 OTU 34 21547 0.36 Catabacter hongkongensis (AY574991.1); Clostridium thermosuccinogenes (Y18180.1) 86 OTU 35 20378 0.34 Clostridium sartagoforme (FJ384380.1) 100 OTU 36 18849 0.31 Acetivibrio cellulolyticus (L35515.1) 95 OTU 37 18055 0.30 Clostridium papyrosolvens (NR_026102.1) 86 OTU 38 17890 0.30 Acinetobacter johnsonii (EU977694.1) 100 OTU 39 15658 0.26 Clostridium papyrosolvens (NR_026102.1) 87 OTU 40 15361 0.25 Lactobacillus johnsonii (EU381128.1) 96 OTU 41 15143 0.25 Clostridium thermosuccinogenes (Y18180.1) 87 OTU 42 14985 0.25 Clostridium paraputrificum (AY442815.1) 100 OTU 43 14682 0.24 Marinobacter sp. (FJ889664.1) 99 OTU 44 14652 0.24 Clostridium papyrosolvens (NR_026102.1) 87 OTU 45 14304 0.24 Shigella flexneri (CP000266.1) 99 OTU 46 13619 0.23 Clostridium cellulolyticum (NC_011898.1) 86 OTU 47 13307 0.22 Clostridium papyrosolvens (NR_026102.1) 86 OTU 48 13152 0.22 Clostridium papyrosolvens (NR_026102.1) 87 OTU 49 12978 0.21 Clostridium papyrosolvens (NR_026102.1) 87 OTU 50 12418 0.21 Lactobacillus salivarius (NZ_AEBA01000145.1) 98 a Greengenes best type strain hit accession numbers are listed in parenthesis. Table 2 Relative abundances (%) of the most abundant OTUs in different gut sites of control birds (day 1–28). OTUs ID Jejunum mucosa Jejunum content Cecum mucosa Cecum content JM-JC CM-CC JM-CM JC-CC Mean SD Mean SD Mean SD Mean SD P-values q-valuesa P-values q-valuesa P-values q-valuesa P-values q-valuesa OTU 49 0 0.02 0.05 0.11 0.01 0.02 0.01 0.02 0.056 0.164 0.655 0.858 0.366 0.623 0.133 0.326 OTU 25 1.89 4.01 0.06 0.07 1.05 2.95 0.01 0.02 0.001 0.011 0.015 0.067 0.365 0.623 0.001 0.011 OTU 5 12.41 25.84 13.09 21.85 0.28 0.56 0.07 0.09 0.920 0.990 0.039 0.134 0.002 0.017 0.001 0.011 OTU 30 0.45 1.45 0.40 0.72 0.74 1.11 1.25 2.09 0.913 0.990 0.385 0.643 0.808 0.946 0.059 0.170 OTU 9 0.90 2.72 1.03 3.05 3.56 9.78 5.82 15.04 0.938 0.990 0.514 0.765 0.196 0.401 0.091 0.244 OTU 13 1.34 5.22 0.75 1.84 1.36 4.51 1.41 4.43 0.714 0.890 0.831 0.946 0.940 0.990 0.549 0.770 OTU 15 0.07 0.20 0.13 0.32 1.17 1.98 4.21 9.38 0.792 0.942 0.095 0.250 0.005 0.030 0.001 0.011 OTU 18 2.36 8.46 2.34 6.03 0.08 0.23 0.03 0.09 0.961 0.994 0.409 0.665 0.081 0.220 0.013 0.059 OTU 21 0.65 2.01 0.32 0.87 0.53 1.11 1.08 3.21 0.588 0.787 0.599 0.796 0.812 0.946 0.294 0.526 OTU 33 0.96 1.38 2.57 5.92 0 0 0 0 0.341 0.603 0.001 0.011 OTU 12 0.95 2.20 1.25 4.71 2.42 5.21 5.41 11.82 0.776 0.929 0.285 0.519 0.491 0.739 0.131 0.326 OTU 28 3.21 7.19 2.99 7.77 0 0 0 0 0.941 0.990 0.006 0.034 0.001 0.011 0.001 0.011 OTU 37 0.12 0.56 0 0.01 0.39 1.93 0.07 0.28 0.140 0.326 0.939 0.990 0.947 0.991 0.177 0.379 OTU 40 0.05 0.11 1.08 1.53 0 0 0.10 0.44 0.001 0.011 0.464 0.722 0.001 0.011 0.008 0.043 OTU 3 10.36 20.66 18.43 23.28 0.39 0.63 1.52 5.30 0.252 0.475 0.517 0.765 0.001 0.011 0.002 0.017 OTU 26 0.03 0.07 0.03 0.06 1.34 2.35 1.75 3.25 0.483 0.737 0.691 0.875 0.001 0.011 0.003 0.020 OTU 19 0.80 1.99 0.22 0.57 1.09 2.22 1.01 2.17 0.189 0.395 0.979 0.997 0.961 0.994 0.134 0.326 OTU 44 0.04 0.15 0.02 0.04 0.06 0.12 0.07 0.14 0.748 0.908 0.660 0.858 0.452 0.715 0.052 0.155 OTU 39 0.02 0.07 0.01 0.02 0.07 0.20 0.08 0.19 0.769 0.927 0.726 0.893 0.253 0.475 0.046 0.147 OTU 29 0 0 0 0 0 0 0 0 0.002 0.017 OTU 2 10.86 14.76 24.38 24.19 0.13 0.26 0.31 1.13 0.046 0.147 0.817 0.946 0.001 0.011 0.001 0.011 OTU 38 1.51 5.31 0.17 0.67 0 0 0 0 0.145 0.326 0.002 0.017 OTU 42 0.51 1.20 0.01 0.03 0.67 1.71 0.01 0.03 0.012 0.057 0.041 0.136 0.717 0.890 0.669 0.864 OTU 17 0.46 1.30 0.02 0.05 2.79 7.57 0.05 0.15 0.041 0.136 0.063 0.176 0.243 0.466 0.571 0.770 OTU 1 14.87 24.08 5.33 7.93 22.17 26.59 13.03 17.69 0.069 0.190 0.231 0.452 0.295 0.526 0.062 0.176 OTU 11 0.69 1.32 0.51 0.97 2.63 7.62 3.10 5.11 0.362 0.623 0.692 0.875 0.458 0.719 0.003 0.020 OTU 4 0.51 2.00 0.17 0.56 1.34 4.60 2.14 7.58 0.571 0.770 0.611 0.806 0.525 0.770 0.147 0.326 OTU 48 0 0 0 0 0 0 0 0 0.036 0.131 OTU 14 0.24 0.69 0.22 0.43 3.77 8.30 4.66 10.97 0.542 0.770 0.747 0.908 0.023 0.091 0.004 0.025 OTU 46 0 0.02 0.01 0.02 0.26 0.65 0.25 0.50 0.348 0.609 0.991 1.000 0.028 0.106 0.039 0.134 OTU 31 0.23 0.55 0.05 0.12 0.87 1.67 0.33 0.51 0.137 0.326 0.170 0.368 0.166 0.364 0.016 0.068 OTU 45 0.05 0.09 0.01 0.01 0.35 0.56 1.02 1.62 0.023 0.091 0.096 0.250 0.016 0.068 0.004 0.025 OTU 10 0.37 1.03 0.20 0.46 4.39 11.22 4.97 10.40 0.477 0.736 0.824 0.946 0.013 0.059 0.003 0.020 OTU 32 0.12 0.43 0.23 0.79 0 0 0 0 0.540 0.770 0.868 0.975 0.012 0.057 0.006 0.034 OTU 8 0.28 1.29 0.03 0.10 1.43 5.01 2.34 7.10 0.537 0.770 0.551 0.770 0.370 0.624 0.138 0.326 OTU 6 1.17 3.54 0.13 0.28 9.20 15.81 1.39 1.56 0.238 0.461 0.007 0.039 0.021 0.087 0.001 0.011 OTU 36 0.03 0.11 0.11 0.22 0.68 1.66 0.25 0.49 0.144 0.326 0.263 0.488 0.003 0.020 0.220 0.445 OTU 35 0.57 1.28 0.02 0.04 0.90 2.13 0.02 0.08 0.012 0.057 0.034 0.126 0.542 0.770 0.867 0.975 OTU 7 1.07 2.73 1.41 2.66 3.52 7.28 6.47 12.19 0.832 0.946 0.282 0.518 0.125 0.320 0.037 0.132 OTU 16 0.73 3.50 0.27 1.01 1.41 3.77 1.96 4.92 0.905 0.990 0.562 0.770 0.400 0.656 0.146 0.326 OTU 27 0.98 2.31 0.02 0.07 1.56 4.02 0.01 0.05 0.012 0.057 0.048 0.151 0.563 0.770 0.719 0.890 OTU 20 1.68 4.52 0.05 0.18 0.86 4.28 0.91 4.07 0.049 0.151 0.981 0.997 0.448 0.715 0.997 1.000 OTU 50 0.09 0.15 0.84 0.95 0 0.01 0.06 0.23 0.001 0.011 0.486 0.737 0.001 0.011 0.002 0.017 OTU 22 0 0 0 0.02 0 0 0 0.01 0.231 0.452 0.882 0.985 OTU 47 0.12 0.53 0 0.02 0.32 1.55 0.06 0.22 0.191 0.395 0.917 0.990 0.933 0.990 0.180 0.381 OTU 41 0 0.01 0 0 0 0 0 0 0.228 0.452 1.000 1.000 OTU 23 0.12 0.50 0.01 0.02 0.07 0.20 0.09 0.23 0.136 0.326 0.682 0.874 0.819 0.946 0.024 0.093 OTU 43 0.01 0.03 0 0 0 0 0 0 OTU 34 0.03 0.14 0 0 0.06 0.16 0.14 0.38 0.903 0.990 0.417 0.672 0.390 0.645 0.051 0.155 OTU 24 0.11 0.52 0.18 0.39 1.18 1.89 1.10 1.90 0.567 0.770 0.973 0.997 0.001 0.011 0.003 0.020 a q-value: The False Discovery Rate (FDR) adjusted p-value using Benjamini and Hochberg method and the q < 0.25 after FDR correction considered significant. Statistically significant values are formatted in bold. Table 3 Relative abundances (%) of the most abundant OTUs in different gut sites of infected birds (days 21 and 28). OTUs ID Jejunum mucosa Jejunum content Cecum mucosa Cecum content JM-JC CM-CC JM-CM JC-CC Mean SD Mean SD Mean SD Mean SD P-values q-valuesa P-values q-valuesa P-values q-valuesa P-values q-valuesa OTU 49 0.18 0.28 0.43 0.98 0.61 1.44 0.52 0.91 0.689 0.880 0.936 0.989 0.550 0.791 0.516 0.776 OTU 25 0.02 0.04 0.08 0.09 0.00 0.00 0 0 0.077 0.178 0.063 0.168 OTU 5 1.65 2.21 8.89 6.18 0.01 0.01 0 0 0.009 0.043 0.761 0.927 0.001 0.007 0.001 0.007 OTU 30 0.31 0.94 0.06 0.08 0.30 0.38 0.16 0.12 0.957 0.989 0.355 0.596 1.000 1.000 0.013 0.056 OTU 9 0.17 0.39 0.14 0.14 1.47 4.29 2.06 5.88 0.903 0.987 0.575 0.791 0.530 0.785 0.217 0.408 OTU 13 0.64 1.06 0.72 1.35 2.87 3.77 2.65 2.58 0.955 0.989 0.950 0.989 0.056 0.159 0.020 0.071 OTU 15 0.08 0.13 0.01 0.02 1.24 0.89 2.13 1.23 0.049 0.146 0.040 0.126 0.001 0.007 0.001 0.007 OTU 18 4.67 9.39 6.34 11.77 0.19 0.44 0.14 0.36 0.572 0.791 0.857 0.986 0.102 0.218 0.011 0.051 OTU 21 0.28 0.58 0.16 0.19 1.63 2.60 1.93 2.41 0.565 0.791 0.611 0.611 0.085 0.191 0.009 0.043 OTU 33 1.11 1.14 0.13 0.13 0.00 0.00 0.00 0.00 0.008 0.041 1.000 1.000 0.001 0.007 0.001 0.007 OTU 12 0.51 0.74 0.06 0.08 0.06 0.09 0.05 0.05 0.056 0.159 0.929 0.989 0.062 0.168 0.796 0.949 OTU 28 1.19 1.20 0.20 0.21 0.00 0.00 0.00 0.00 0.015 0.060 0.016 0.060 0.001 0.007 0.001 0.007 OTU 37 0.14 0.27 0.01 0.02 0.35 0.18 0.51 0.27 0.074 0.178 0.077 0.178 0.207 0.394 0.001 0.007 OTU 40 0.07 0.08 1.35 0.83 0.01 0.01 0.00 0.01 0.001 0.007 0.881 0.987 0.008 0.041 0.001 0.007 OTU 3 11.02 13.33 29.61 19.69 0.52 0.56 0.41 0.45 0.067 0.173 0.865 0.986 0.004 0.023 0.001 0.007 OTU 26 0 0 0.01 0.05 0.01 0.01 0.01 0.01 0.542 0.791 0.801 0.949 0.070 0.176 0.990 1.000 OTU 19 0.14 0.29 0.31 0.24 3.24 7.48 2.09 5.77 0.372 0.613 0.614 0.823 0.107 0.223 0.441 0.700 OTU 44 0.43 1.20 0.07 0.12 0.49 0.94 1.06 2.17 0.594 0.809 0.574 0.791 0.552 0.791 0.014 0.059 OTU 39 0.02 0.05 0.13 0.20 0.59 0.79 1.02 1.34 0.072 0.178 0.318 0.539 0.001 0.007 0.016 0.060 OTU 29 0.30 0.66 0.01 0.03 3.92 6.25 0.38 0.51 0.052 0.152 0.049 0.146 0.036 0.115 0.005 0.028 OTU 2 19.98 22.32 23.46 10.10 0.85 1.46 0.19 0.30 0.834 0.975 0.285 0.493 0.002 0.012 0.001 0.007 OTU 38 0 0.01 0 0 0 0 0 0 0.690 0.012 OTU 42 0 0 0 0 0 0 0 0 OTU 17 0.62 1.33 0.25 0.31 4.45 6.58 0.12 0.18 0.451 0.703 0.002 0.012 0.091 0.201 0.531 0.785 OTU 1 0.11 0.18 0.81 1.36 0.28 0.40 0.19 0.36 0.145 0.292 0.760 0.927 0.280 0.491 0.255 0.455 OTU 11 1.09 1.39 0.10 0.10 2.01 2.44 2.31 3.56 0.026 0.086 0.761 0.927 0.907 0.987 0.007 0.038 OTU 4 3.43 6.60 0.13 0.11 12.51 8.03 16.82 10.92 0.154 0.303 0.162 0.315 0.016 0.060 0.001 0.007 OTU 48 0.41 1.14 0.01 0.02 2.29 7.23 0.38 1.17 0.225 0.414 0.747 0.927 0.817 0.962 0.222 0.413 OTU 14 0.24 0.65 0.07 0.07 0.45 0.84 1.41 2.08 0.364 0.606 0.122 0.251 0.619 0.824 0.076 0.178 OTU 46 0.21 0.60 0.01 0.02 0.49 0.81 0.52 0.87 0.306 0.524 0.757 0.927 0.396 0.646 0.016 0.060 OTU 31 0.03 0.06 0.03 0.04 0.37 0.52 0.08 0.07 0.955 0.989 0.057 0.159 0.012 0.055 0.019 0.068 OTU 45 0 0 0 0 0 0 0 0 1.000 1.000 0.281 0.491 OTU 10 0.26 0.82 0.09 0.12 0.29 0.57 0.22 0.30 0.960 0.989 0.896 0.987 0.891 0.987 0.175 0.336 OTU 32 2.90 3.72 3.80 3.98 0.18 0.46 0.05 0.11 0.872 0.986 0.567 0.791 0.004 0.023 0.001 0.007 OTU 8 1.21 2.88 0.05 0.09 7.75 7.99 6.25 8.70 0.036 0.115 0.917 0.989 0.021 0.073 0.001 0.007 OTU 6 0.82 1.99 0.10 0.13 4.11 2.46 1.24 1.97 0.455 0.703 0.026 0.086 0.019 0.068 0.001 0.007 OTU 36 0.21 0.40 0.23 0.21 0.34 0.37 0.19 0.22 0.893 0.987 0.441 0.700 0.473 0.724 0.871 0.986 OTU 35 0 0 0 0 0 0 0 0 OTU 7 0.24 0.40 0.08 0.17 4.65 13.62 6.23 18.65 0.095 0.205 0.692 0.880 0.501 0.760 0.062 0.168 OTU 16 0.19 0.27 0.29 0.47 1.37 1.80 1.55 1.94 0.776 0.932 0.653 0.862 0.074 0.178 0.048 0.146 OTU 27 0 0 0 0 0 0 0 0 OTU 20 0.22 0.67 0.03 0.05 4.32 13.62 0.62 1.88 0.849 0.986 0.770 0.932 0.576 0.791 0.424 0.686 OTU 50 0.10 0.17 1.20 0.73 0.01 0.01 0.01 0.01 0.001 0.007 0.979 1.000 0.013 0.056 0.001 0.007 OTU 22 0.14 0.42 0 0 2.08 5.32 3.60 9.82 0.107 0.223 0.671 0.877 0.236 0.430 0.001 0.007 OTU 47 0.03 0.06 0.01 0.01 0.20 0.10 0.31 0.23 0.244 0.440 0.092 0.201 0.001 0.007 0.001 0.007 OTU 41 0.99 2.99 0 0 0.50 0.87 1.28 3.32 0.723 0.913 0.923 0.989 OTU 23 0.63 1.18 0.02 0.02 2.39 2.31 2.88 2.65 0.124 0.252 0.448 0.703 0.064 0.168 0.001 0.007 OTU 43 8.90 28.14 0 0 0 0 0 0 OTU 34 0.02 0.05 0 0 0.85 0.79 1.54 1.09 0.148 0.294 0.068 0.173 0.001 0.007 0.001 0.007 OTU 24 0 0 0.05 0.07 0.15 0.13 0.12 0.11 0.674 0.877 0.082 0.187 a q-value: The False Discovery Rate (FDR) adjusted p-value using Benjamini and Hochberg method and the q < 0.25 after FDR correction considered significant. Statistically significant values are formatted in bold. The OTUs and species abundances sorted by gut sites of the infected birds compared with the control birds are shown in the heatmaps (Figure 2). Interestingly, in the infected birds, the abundance of E. coli and Eubacterium desmolans (best type strain hits) were lower at different gut sites (Figure 3A). On the contrary, Clostridium spp. abundance was higher in the infected birds compared with the negative controls (Figure 3B). Figure 2 Heatmap showing the relative abundances (%) of the 50 most-abundant OTUs sorted by gut sites of the infected birds compared with the controls at the two sampling points post infection. The heat map integrates relative abundance of a given phylotype. Colour scaling is ranged from 0 to ≥ 25%. n.d, not detected. Figure 3 Relative abundances (%) of the most relevant OTUs in the infected birds compared with the controls at the two sampling points post infection (A) OTUs 1 and 12, (B) OTUs 4 and 29. JM, jejunal mucosa; JC, jejunal content; CM, cecum mucosa; CC, cecum content.