Similarly, Proteobacteria were more expressed in corn stalks than oak leaves diets. The Chao1
(114.2 vs 143.5) and Shannon-Wiener (3.5 vs 3.7) indices of domesticated Sika deer consuming oak leaves were decreased compared to those feeding on corn stalks (Table 1). Moreover, the Libshuff analysis also showed that the bacterial communities between two diets were significantly differed (P<0.0001). Rarefaction curves at 3% distance levels revealed 74% and 66% coverage for the OL and CS groups, respectively (Figure 2). Figure 1 Composition of 16S check details rRNA gene libraries at the phylum level. Clones obtained from the OL and CS groups representing by black and grey bars, respectively. Table 1 Number of OTUs, diversity and coverage at 3% distance level using the MOTHUR platform Groups Clones OTUs Chao 1a Shannon-Wienerb Coverage OL 139 57 114.2 (81.1,192.8) 3.5 (3.3,3.7) 0.74 CS 100 50 143.5 (85.8,294.1) 3.7 (3.4,3.8) 0.66 a Chao1 is a nonparametric estimator of the richness in a sample. It is based on the number of rare ribotypes (singletons and doublets) and used to predict the species richness. click here b The Shannon-Wiener index is a nonparametric diversity index that combines estimates of richness (total numbers of ribotypes) and evenness (relative abundance of each ribotype) suggesting diversity. It takes into account the
abundance of individual taxa and can be used as an overall indicator of the level of diversity in a sample. Figure 2 Rarefaction curves for bacterial 16S rRNA gene libraries. Dark and gray represent Sika deer feeding on oak leaves-based (OL group) and corn stalks-based (CS group) diets, respectively. Rarefaction curves were generated from the platform MOTHUR using the furthest neighbor method. Using the software program MOTHUR and a sequence identity criterion cut off of 97%, the 139 OL clone sequences were assigned to 57 OTUs and the 100 CS clone sequences were assigned to 50 OTUs (Table 1).To determine the Oxalosuccinic acid nearest valid
related species, the 16S rRNA gene sequences were compared using GenBank’s Basic Local Alignment Search Tool (BLAST). Within the OL library, 53 of the 57 OTUs (i.e. 97.2% of clones) had 85% or greater sequence Defactinib cell line identities to genus Prevotella (Table 2). Within these OTUs, 23 OTUs (38.1% of clones) showed 87-92% sequence identities to P. brevis, 11 OTUs (16.5% of clones) had 86-90% sequence identities to P. shahii, 3 OTUs (23.8% of clones) had 91-92% sequence identities to P. veroralis, 6 OTUs (12.3% of clones) had distant sequence identities to P. salivae, and the remaining 9 OTUs (6.5% of clones) showed sequence identities to several Prevotella species including P. albensis, P. dentalis, P. ruminicola, P. multiformis, P. stercorea, P. bryantii and P. copri (Table 2). Of the remaining 4 OTUs (of the 57 total OTUs), 2 OTUs (1.4% of clones) were distantly related (85%) to Alistipes shahii, 1 OTU (0.7% of clones) had 84% identity to Barnesiella intestinihominis, and 1 OTU (0.