Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs

Maltecca, Christian; Dunn, Rob; He, Yuqing; McNulty, Nathan P.; Schillebeeckx, Constantino; Schwab, Clint; Shull, Caleb; Fix, Justin; Tiezzi, Francesco

doi:10.1186/s42523-021-00118-z

Animal Microbiome

Table 2 Summary of OTUs significantly associated with growth traits in two systems

From: Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs

Trait	Time	OTU	Genus	b TE	SE TE	Var% TE	adj-p TE	b NU	SE_NU	Varr%_NU	adj-p NU
ADG	TP2	m263	Collinsella	− 1.550	0.350	1.638	0.001	− 1.656	0.505	1.364	0.024
ADG	TP2	m560	Peptococcus	2.191	0.260	5.885	0.000	1.498	0.427	2.164	0.016
ADG	TP2	m1178	Selenomonas	− 1.657	0.258	3.300	0.000	− 1.603	0.419	2.011	0.008
ADG	TP3	m147	Peptococcus	1.676	0.353	2.095	0.000	1.834	0.285	5.494	0.000
ADG	TP3	m40684	Prevotella	− 1.075	0.345	0.832	0.041	− 1.644	0.559	2.894	0.045
ADG	TP3	m68	Prevotella	− 1.558	0.471	0.913	0.028	− 1.631	0.515	1.819	0.030
BF	TP2	m1090	Clostridium sensu stricto	− 1.017	0.365	0.523	0.048	− 1.244	0.347	1.609	0.007
BF	TP2	m370	Clostridium sensu stricto	− 0.838	0.274	0.648	0.029	− 0.974	0.344	1.346	0.039
BF	TP2	m1641	Lactobacillus	1.177	0.292	1.039	0.002	1.107	0.384	1.192	0.035
BF	TP2	m17	Lactobacillus	1.032	0.246	1.335	0.002	2.325	0.470	3.508	0.000
BF	TP2	m28987	Lactobacillus	1.048	0.244	1.416	0.001	2.171	0.461	3.298	0.000
BF	TP2	m33615	Lactobacillus	0.956	0.201	1.657	0.000	0.934	0.329	1.297	0.038
BF	TP2	m35073	Lactobacillus	0.498	0.170	0.689	0.038	1.105	0.357	1.363	0.023
BF	TP2	m52033	Lactobacillus	0.967	0.248	1.155	0.004	2.166	0.472	3.120	0.000
BF	TP2	m9	Lactobacillus	0.930	0.202	1.542	0.001	0.933	0.321	1.301	0.034
BF	TP2	m560	Peptococcus	1.337	0.236	2.201	0.000	1.686	0.410	2.738	0.002
BF	TP3	m470	Bacteroides	− 1.468	0.395	0.979	0.006	− 2.512	0.878	0.959	0.037
BF	TP3	m638	Bacteroides	− 1.322	0.462	0.530	0.042	− 4.532	1.469	1.234	0.023
BF	TP3	m16	Blautia	0.538	0.186	0.635	0.039	1.069	0.274	2.120	0.003
BF	TP3	m472	Blautia	1.286	0.308	1.170	0.002	1.661	0.367	3.266	0.000
BF	TP3	m564	Blautia	1.199	0.273	1.265	0.001	1.867	0.358	4.103	0.000
BF	TP3	m595	Blautia	1.874	0.464	1.148	0.002	2.080	0.320	5.407	0.000
BF	TP3	m649	Blautia	1.003	0.322	0.625	0.026	1.040	0.351	1.282	0.030
BF	TP3	m2023	Butyricicoccus	1.511	0.296	1.783	0.000	1.877	0.406	6.652	0.000
BF	TP3	m80	Butyricicoccus	− 1.547	0.248	2.627	0.000	− 1.277	0.332	2.651	0.004
BF	TP3	m1540	Clostridium sensu stricto	− 0.805	0.266	0.612	0.031	− 2.958	0.744	2.058	0.002
BF	TP3	m40	Clostridium sensu stricto	− 1.908	0.602	0.887	0.023	− 2.175	0.615	3.745	0.008
BF	TP3	m57	Clostridium sensu stricto	− 0.687	0.179	1.013	0.004	− 1.616	0.558	0.960	0.034
BF	TP3	m518	Clostridium XlVa	1.599	0.540	0.599	0.035	1.336	0.473	1.224	0.039
BF	TP3	m88	Coprococcus	0.868	0.203	1.369	0.001	1.712	0.387	6.359	0.001
BF	TP3	m69	Dorea	− 2.756	0.866	0.693	0.023	− 3.235	0.827	2.053	0.003
BF	TP3	m23	Faecalibacterium	0.735	0.201	0.998	0.007	1.237	0.290	3.830	0.001
BF	TP3	m27249	Faecalibacterium	0.917	0.237	1.078	0.004	0.886	0.309	1.707	0.036
BF	TP3	m37847	Faecalibacterium	0.754	0.237	0.746	0.023	1.121	0.321	2.759	0.009
BF	TP3	m2495	Helicobacter	− 1.142	0.287	1.017	0.003	− 2.405	0.679	1.484	0.008
BF	TP3	m561	Helicobacter	− 1.099	0.334	0.692	0.017	− 3.036	0.795	1.683	0.004
BF	TP3	m1834	Lachnospiracea_incertae_sedis	0.881	0.315	0.494	0.047	− 1.766	0.517	1.285	0.011
BF	TP3	m17	Lactobacillus	0.584	0.197	0.613	0.035	2.130	0.381	4.050	0.000
BF	TP3	m28987	Lactobacillus	0.531	0.187	0.567	0.043	1.933	0.346	3.953	0.000
BF	TP3	m327	Methanobrevibacter	− 0.931	0.277	0.786	0.015	− 1.226	0.330	2.232	0.005
BF	TP3	m478	Murdochiella	− 0.579	0.198	0.594	0.037	− 1.397	0.406	1.590	0.010
BF	TP3	m10347	Oligosphaera	− 1.089	0.251	1.210	0.001	− 2.363	0.560	2.216	0.001
BF	TP3	m851	Oligosphaera	− 1.514	0.313	1.499	0.000	− 3.752	1.084	1.384	0.009
BF	TP3	m796	Oscillibacter	1.466	0.389	0.939	0.005	1.888	0.656	1.339	0.035
BF	TP3	m147	Peptococcus	2.935	0.304	6.434	0.000	1.840	0.274	5.505	0.000
BF	TP3	m477	Peptococcus	− 0.608	0.212	0.560	0.041	− 0.932	0.344	1.043	0.049
BF	TP3	m272	Peptoniphilus	− 0.639	0.193	0.734	0.016	− 1.199	0.317	2.257	0.004
BF	TP3	m68	Prevotella	− 1.315	0.419	0.651	0.025	− 1.947	0.492	2.574	0.003
BF	TP3	m326	Pseudobutyrivibrio	0.866	0.300	0.557	0.040	1.964	0.369	5.067	0.000
BF	TP3	m19	Roseburia	0.981	0.204	1.656	0.000	1.134	0.311	4.060	0.006
BF	TP3	m255	Roseburia	1.249	0.241	1.846	0.000	1.833	0.389	8.778	0.000
BF	TP3	m294	Roseburia	1.257	0.213	2.373	0.000	1.859	0.354	5.378	0.000
BF	TP3	m325	Roseburia	1.451	0.279	1.838	0.000	1.792	0.395	6.258	0.000
BF	TP3	m628	Roseburia	1.423	0.331	1.200	0.001	1.327	0.387	2.404	0.010
BF	TP3	m955	Roseburia	1.409	0.479	0.552	0.037	1.757	0.501	1.610	0.009
BF	TP3	m688	Ruminococcus	− 1.568	0.261	2.470	0.000	− 2.876	0.519	3.558	0.000
BF	TP3	m122	Streptococcus	− 0.739	0.253	0.577	0.038	− 2.169	0.459	2.474	0.000
BF	TP3	m910	Streptococcus	1.082	0.285	0.993	0.005	1.374	0.363	2.188	0.004
BF	TP3	m1571	Subdivision5_genera_incertae_sedis	− 0.885	0.311	0.523	0.043	− 1.549	0.543	0.938	0.037
BF	TP3	m557	Subdivision5_genera_incertae_sedis	− 1.537	0.466	0.712	0.017	− 1.203	0.378	1.348	0.019
BF	TP3	m878	Subdivision5_genera_incertae_sedis	− 1.070	0.327	0.712	0.018	− 1.233	0.402	1.784	0.024
BF	TP3	m53	Succinivibrio	− 0.687	0.228	0.632	0.032	− 2.642	0.439	16.999	0.000
BF	TP3	m801	Succinivibrio	− 1.139	0.333	0.832	0.013	− 2.035	0.582	1.883	0.009
BF	TP3	m224	Treponema	− 1.218	0.236	1.878	0.000	− 3.836	0.591	4.715	0.000
IMF	TP3	m147	Peptococcus	2.070	0.345	3.205	0.000	0.901	0.215	1.318	0.022

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