Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet
by
, , , , , and
Tiziana Maria Mahayri
1,2
,
Kateřina Olša Fliegerová
1,*
,
Silvana Mattiello
3,
Stefania Celozzi
3,
Jakub Mrázek
1,
Chahrazed Mekadim
1,
Hana Sechovcová
1,4,
Simona Kvasnová
1,
Elie Atallah
2 and
Giuseppe Moniello
2 1
Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
2
Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
3
Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
4
Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences in Prague, 16500 Prague, Czech Republic
*
Author to whom correspondence should be addressed.
Animals 2022, 12(16), 2011; https://doi.org/10.3390/ani12162011
Submission received: 10 May 2022
/
Revised: 29 July 2022
/
Accepted: 5 August 2022
/
Published: 9 August 2022
(This article belongs to the Section Animal Reproduction)
Simple Summary
Comparison of bacterial diversity and composition of feces from cows and goats offered the same pasture-based diet revealed that the animal species had no effect on bacterial species richness and diversity, but significantly affected species evenness. Both diet and host species influence the gut microbiome.
Abstract
The aim of this study was to compare the diversity and composition of fecal bacteria in goats and cows offered the same diet and to evaluate the influence of animal species on the gut microbiome. A total of 17 female goats (Blond Adamellan) and 16 female cows (Brown Swiss) kept on an organic farm were fed pasture and hay. Bacterial structure in feces was examined by high-throughput sequencing using the V4–V5 region of the 16S rRNA gene. The Alpha diversity measurements of the bacterial community showed no statistical differences in species richness and diversity between the two groups of ruminants. However, the Pielou evenness index revealed a significant difference and showed higher species evenness in cows compared to goats. Beta diversity measurements showed statistical dissimilarities and significant clustering of bacterial composition between goats and cows. Firmicutes were the dominant phylum in both goats and cows, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. Linear discriminant analysis with effect size (LEfSe) showed a total of 36 significantly different taxa between goats and cows. Notably, the relative abundance of Ruminococcaceae UCG-005, Christensenellaceae R-7 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Ruminococcus 1, Ruminococcaceae UCG-002, Lachnospiraceae NK4A136 group, Treponema 2, Lachnospiraceae AC2044 group, and Bacillus was higher in goats compared to cows. In contrast, the relative abundance of Turicibacter, Solibacillus, Alloprevotella, Prevotellaceae UCG-001, Negativibacillus, Lachnospiraceae UCG-006, and Eubacterium hallii group was higher in cows compared with goats. Our results suggest that diet shapes the bacterial community in feces, but the host species has a significant impact on community structure, as reflected primarily in the relative abundance of certain taxa.
