Table 7.
Correlation of operational taxonomic units from ileal digesta in hen from CC and CF systems for ileal morphology.
| Intestinal parameter | Housing | Group1 | Correlation | Taxonomy2 | Taxonomy based on NCBI BLASTn search3 |
|---|---|---|---|---|---|
| Villus Height | Conventional Cage | Otu00043 | −0.41 | Peptostreptococcaceae | Romboutsia timonensis strain Marseille-P326 |
| Otu00111 | −0.41 | Enterococcus | Enterococcus lactis; villorum, canis, cinnamoneus, canintestini; faecium | ||
| Otu00041 | −0.41 | Campylobacter | Campylobacter insulaenigrae, C. armoricus, C. helveticus | ||
| Otu00013 | −0.38 | Fusobacterium | Fusobacterium necrogenes, mortiferum, mvarium, ulcerans | ||
| Otu00008 | −0.38 | Gallibacterium | Gallibacterium anatis | ||
| Otu00175 | −0.37 | Lactobacillus | Lactobacillus aviarius | ||
| Otu00021 | −0.36 | Lactobacillus | Lactobacillus collinoides; L. siliginis; L. paracollinoides | ||
| Otu00016 | −0.36 | Clostridium_sensu_stricto_1 | Clostridium cuniculi; saudiense | ||
| Otu00150 | −0.35 | Lactobacillus | Lactobacillus aviarius; L. acidioiscis | ||
| Otu00131 | 0.36 | Lactobacillus | Lactobacillus kitasatonis | ||
| Otu00009 | 0.38 | Lactobacillus | Lactobacillus acidophilus; Lactobacillus crispatus | ||
| Otu00091 | 0.39 | Lactobacillus | L. aviarius | ||
| Otu00122 | 0.40 | Atopobium | - | ||
| Otu00018 | 0.41 | Lactobacillus | Lactobacillus gigerionum; amylolytics | ||
| Otu00118 | 0.42 | Bifidobacteriaceae | Bifidobacterium commune | ||
| Otu00156 | 0.46 | Lactobacillus | Lactobacillus kitasatonis; L. acidophilus | ||
| Cage-free | Otu00141 | −0.41 | Romboutsia | Romboutsia timonensis | |
| Otu00175 | −0.35 | Lactobacillus | L. aviaries | ||
| Crypt Depth | Conventional Cage | Otu00110 | −0.40 | Staphylococcus | Staphylococcus lentus; sciuri |
| Otu00150 | −0.38 | Lactobacillus | Lactobacillus aviarius; L. acidioiscis | ||
| Otu00166 | −0.38 | Helicobacter | Helicobacter winghamenss; pametensis, macacae, brantae | ||
| Otu00106 | −0.37 | Campylobacter | Campylobacter upsaliensis; coli, jejuni sp jejuni | ||
| Otu00146 | −0.36 | Phascolarctobacterium | Chryseobacterium oncorhynchi | ||
| Otu00179 | −0.36 | Parasutterella | - | ||
| Otu00157 | −0.36 | Yaniella | Yaniella halotolerans | ||
| Otu00148 | −0.35 | Peptostreptococcaceae | Clostridioides difficile | ||
| Otu00180 | 0.43 | Candidatus_Arthromitus | - | ||
| Cage-free | Otu00141 | −0.48 | Romboutsia | Romboutsia timonensis | |
| Otu00048 | −0.41 | Clostridium_sensu_stricto_1 | Clostridium disporicum | ||
| Otu00012 | −0.41 | Lactobacillus | L. taiwanensis; L.hominis; L. Paragasseri; L. gasseri; L. johnsonii | ||
| Otu00047 | −0.41 | Lactobacillus | Lactobacillus isolate MGYG-HGUT-01336 | ||
| Otu00069 | −0.41 | Romboutsia | Romboutsia timonensis | ||
| Otu00016 | −0.39 | Clostridium_sensu_stricto_1 | Clostridium cuniculi; saudiense | ||
| Otu00025 | −0.38 | Romboutsia | Romboutsia weinsteinii | ||
| Otu00038 | −0.36 | Romboutsia | Romboutsia timonensis | ||
| Otu00014 | −0.35 | Lactobacillus | L. delbrueckii bulgaricus | ||
| Villus Height to Crypt Depth Ratio | Conventional Cage | Otu00168 | 0.35 | Lactobacillus | L. kitasatonis |
| Otu00176 | 0.39 | Lactobacillus | L. aviarius | ||
| Otu00156 | 0.39 | Lactobacillus | Lactobacillus aviarius; L. acidioiscis | ||
| Cage-free | Otu00163 | −0.43 | Lactobacillus | L. aviaries | |
| Otu00154 | −0.37 | Clostridiaceae_1_unclassified | Clostridium nigeriense | ||
| Otu00059 | 0.35 | Lactobacillus | Lactobacillus mucosae |
Abbreviations: CC, Conventional cage; CF, cage-free.
1
Group denotes the taxonomic group assigned to each unique sequence. This table only includes those significantly different from the top 200 taxonomic groups.
2
Taxonomic assignments are based on sequence similarity to the SILVA SSU NR reference database (v 132).
3
BLASTn search results were reported if the similarity was higher than 97%—indicates sequence alignments of less than 97%.