Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 7, e7910

Effects of Particle Size of Ground Alfalfa Hay on Caecal Bacteria and Archaea Populations of Rabbits


Effects of Particle Size of Ground Alfalfa Hay on Caecal Bacteria and Archaea Populations of Rabbits

Mei Yuan et al. PeerJ.


This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance of Methanosphaera was reduced from 35.47% to 8.62% (P < 0.001). In conclusion, as the particle size of alfalfa meal decreased, both the bacterial and archaeal population in the caecum of rabbit experienced alterations, however archaea response earlier than bacteria to the decrease of alfalfa meal particle size.

Keywords: Archaea; Bacteria; Caecum; Fiber particle size; Rabbits.

Conflict of interest statement

The authors declare there are no competing interests.


Figure 1
Figure 1. Venn diagram representation of the shared and exclusive bacterial (A) and archaeal (B) OTUs at 97% similarity level of the four treatment groups.
The percentage data in parentheses is the sequence abundance of the corresponding OTUs out of the total OTU.
Figure 2
Figure 2. Hierarchical clustering of bacterial (A) and archaeal (B) communities assessed using weighted UniFrac metric analysis of OTUs at 97% similarity.
The scale bar shows approximate weighted UniFrac metric similarity coefficient of 0.25 in bacteria, the archae group 2,500 µm = tag number 2,500-1, 2,500-2, 2,500-3, 2,500-4, 2,500-4, 2,500-5 and 2,500-6; group 1,000 µm = tag number 1,000-1, 1,000-2, 1,000-3, 1,000-4, 1,000-5 and 1,000-6; group 100 µm = tag number 100-1, 100-2, 100-3, 100-4, 100-5 and 100-6; group 10 µm = tag number 10-1, 10-2, 10-3, 10-4, 10-5 and 10-6.
Figure 3
Figure 3. Principal co-ordinate analysis (PCoA) scores plot generated from rabbits caecum sample by a weighted UniFrac analysis at the 97% similarity level.
Bacteria (A) and archaea (B).
Figure 4
Figure 4. Phylum level composition of bacteria.
A color-coded bar plot shows the average relative abundance of bacterial phyla (>0.1%) distribution in different treatment groups.
Figure 5
Figure 5. Genus level composition.
Bar plots show average relative abundance (%) of bacterial (A) and archaeal (B) in different particle sizes. Only bacterial genera with relative abundance more than 1% are shown.

Similar articles

See all similar articles


    1. Arrazuria R, Elguezabal N, Juste RA, Derakhshani H, Khafipour E. Mycobacterium avium subspecie sparatuberculosis infection modifies gut microbiota under different dietary conditions in a rabbit model. Frontiers in Microbiology. 2016;7:446–460. doi: 10.3389/fmicb.2016.00446. - DOI - PMC - PubMed
    1. Bao Z, Li Y, Zhang J, Li L, Zhang P, Huang FR. Effect of particle size of wheat on nutrient digestibility, growth performance, and gut microbiota in growing pigs. Livestock Science. 2016;183:33–39. doi: 10.1016/j.livsci.2015.11.013. - DOI
    1. Bäuerl C, Collado MC, Zúñiga M, Blas E, Pérez Martínez G. Changes in cecal microbiota and mucosal gene expression revealed new aspects of epizootic rabbit enteropathy. PLOS ONE. 2014;9(8):e105707 doi: 10.1371/journal.pone.0105707. - DOI - PMC - PubMed
    1. Bennegadi N, Fonty G, Millet L, Gidenne T, Licois D. Effects of age and dietary fibre level on caecal microbial communities of conventional and specific pathogen-free rabbits. Microbial Ecology in Health and Disease. 2003;15:23–32. doi: 10.1080/08910600310015574. - DOI
    1. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. - DOI - PMC - PubMed

Grant support

This work was supported by the National Natural Science Foundation of China (31402104). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

LinkOut - more resources