Comparative characteristics of rations for feeding cattle from different regions of the Republic of Kazakhstan and the impact of animal feeding types on the faecal microbiota
Due to the huge differences in the natural and climatic conditions of Kazakhstan, animals from different regions of Kazakhstan were enrolled for this study. The difference in soil and climatic conditions of different zones has a significant impact on the type of feeding (Table 1) and the composition of diets, which has a certain effect on the microbiota of intestinal contents and methanogenic archaea in particular.
In the course of the research work, regions and specific agricultural formations were identified in the context of these regions.
In North Kazakhstan, the fodder base is represented by such fodders as alfalfa hay, herb hay, alfalfa haylage, wheat straw, fodder wheat and sunflower cake. The feed is mainly of 2 quality classes. The live weight of cattle ranged from 375 to 480 kg. Feeding type: hay-concentrate and haylage-hay-concentrate.
In the Western region, the animals were on the pasture, represented by the green mass of feather grass, hair, sage and tansy. Beef cattle are represented by the following breeds: Kazakh white-headed, Aberdeen-Angus and Hereford. Average live weight is 350–550 kg.
In the Southeast region, the fodder base consists of wheat hay, sainfoin + alfalfa hay, mountain hay, herb haylage, corn silage and crushed corn. The feed is mainly of 2 and 3 classes. Hay-concentrate type of feeding is used, as well as pastures. Livestock of Angus, Kazakh white-headed breeds and animals of the local population are kept. Live weight of young animals is in the range of 360–380 kg.
The diets of the Southern Region include natural grass hay, alfalfa hay, wheat straw, alfalfa haylage and concentrates. Hay-concentrate type of livestock feeding is widespread in the region. The average live weight of bulls for fattening of the Kazakh white-headed and Angus breeds—360–420 kg with a daily increase in live weight of 870–920 g.
The composition of the fecal microbiota depending on the type of feeding is presented in Table 2.
From the data of Table 2 it follows that the largest amount of Bacteria was found in the faeces of animals with silage-concentrated feeding (98.59 ± 13.0%), and the smallest—with pasture-concentrated (93.24 ± 3.73%) and haylage—concentrated (93.8 ± 12.41%) types of feeding. The differences amounted to 5.35 and 4.79 absolute percent, respectively. However, the differences were not significant at P < 0.95. For other types of feeding, the content was almost the same and ranged from 96.05 ± 27.16%—97.03 ± 3.88% and is also not reliable (P < 0.95).
The content of methanogenic microbes in faeces also largely depends on the type of animal feeding. Thus, the smallest number of them was found when keeping animals on pasture (1.32 ± 0.24%) and silage-concentrated type of feeding (1.54 ± 0.5%), and the largest—with haylage-concentrated type of feeding (6.01 ± 2.29%). Differences were significant at the level of P > 0.95.
With hay-concentrate and haylage-hay-concentrate types of feeding, the content of methanogenic microbes in comparison with pasture content was higher by 2.05 and 2.31 absolute percent, respectively, or more by 2.55 and 2.75 times. However, the differences were not significant (P < 0.95).
Certain differences are observed between hay-concentrate and silo-concentrate types of feeding. The difference between them in terms of the content of methanogenic microbes was 1.83 absolute percent in favor of the latter. Similar data were obtained in studies by Uprety D.C., Subash Dhar, Dong Hongmin et al.12. The authors argue that the formation of methane in the silo-concentrate type of feeding was 1.25 times lower compared to the hay-concentrated diet (283 L versus 353 L per head per day).
A similar pattern is observed with pasture-concentrated and concentrated types of feeding. Thus, in the feces of these animals, the content of methanogenic microbes was 4.87 ± 1.29% and 2.78 ± 0.22% or higher by 3.55 (P > 0.95) and 1.46 (P < 0.95) absolute percent compared to the pasture type of feeding.
Thus, the highest content of Bacteria in the faeces of animals was found with the silo-concentrate type of feeding, and the smallest amount of Arhaea was noted with the pasture type of feeding.
Fecal bacterial communities from different regions of Kazakhstan in beef and dual-purpose cattle
Microbial composition of the feces collected from the rectum of cattle was examined based on the OTU table generated by the CLC Genomics Workbench software using the SILVA database as a reference. Samples were grouped according to the geographical origin (i.e. Western, Southern, Northern and Southeast regions of Kazakhstan) for analysis. In total, 22 microbial phyla were identified. Figure 1 shows phyla distribution by Kazakh regions.
Relative abundance of fecal bacterial communities at the phylum level. The legend reports the 10 most abundant phyla.
The most abundant phylum was Firmicutes, ranging from 55.5% to 61.3% of relative abundance percentages, followed by Bacteroidetes (15.3–20.4%), Verrucomicrobia (4.4–11.7%) and Euryarchaeota (5.0–9.6%).
Firmicutes resulted to be widespread in cattle microbiota from all regions of Kazakhstan with non significant fluctuations. So, in the Northern region, their relative amount was 61.3%, in the Western 60.5%, in the Southern and Southeast 55.5%. The phylum of Bacteroidetes was next in terms of prevalence: Northern region (18.7%), Western (20.4%), Southern (15.3%), and Southeast (15.7%). The minimum amount of Euryarchaeota methanogens was found in animals of the Western region (2.4%), and the maximum in animals of the Southeast region (9.6%).
Fecal methanogens from different regions of Kazakhstan in beef and dual-purpose cattle
The relative number of fecal bacterial communities at the order level is shown in Fig. 2.
Relative abundance of fecal bacteria communities at an order level. Methanobacteriales are highlighted in pink-red. The legend reports the 10 most abundant orders.
Methane-forming archaea were mainly represented by the order Methanobacteriales (Fig. 2). Most of Methanobacteriales were detected in samples from Southeast Kazakhstan, while they were less present in Western Kazakhstan. The prevalence of other methanogenic groups was negligible.
Relative abundance of methanogens at the genus level as distributed for each Kazakh region is shown in Fig. 3.
Relative abundance of methanogens at the genus level in animal samples from different regions of Kazakhstan.
Methanobrevibacter was the most abundant genus among methanogens. The highest amount was found in the Southeast region (8.6%) and the lowest in the Western region (1.8%). This was followed by the genus Methanosphaera with a prevalence falling in the range 0.13–0.65%. Other methanogens genera were detected in trace amounts.
Heat-map of microbial community composition
To visualize the differences in the bacterial community structures of the samples, a heat-map with cluster analysis was constructed at the phylum level (Fig. 4).
Heat-map of microbial community composition with cluster analysis. The color intensity in each panel shows the relative abundance in a sample, referring to color key at the bottom.
When developing a heat map, twenty-two phyla from four regions of Kazakhstan were taken into account. Figure 4 shows that the most numerous in all samples were Firmicutes (57.3%). The dominant phyla were Bacteroidetes (17.0%), Verrucomicrobia (6.88%), Euryarchaeota (6.49%), Actinobacteria (4.77%) and Patescibacteria (3.38%).
Further, diversity indices of fecal bacterial communities in different regions were determined.
Rarefaction curves showing the magnitude of the detected OTUs depending on the selective effort did not reach a plateau in all samples of the study (Supplementary figure S1), probably also for the type of samples analyzed: optimal amplification with fecal samples was not always possible. Nevertheless, to allow a comparison among all the samples, a sequencing depth of 13,000 reads was selected for the comparisons, in order to obtain a complete overview.
To assess alpha diversity, the species richness index and the Shannon index were calculated (Figs. 5,6). Shannon diversity accounts for both abundance and evenness of taxa present. Figures 5 and 6 showed the diversity of samples across the Kazakhstan regions.
Box plots of alpha diversity by Kazakh region calculated from the set of OTU abundances.
Alpha diversity of Kazakhstan regions using the Shannon index calculated from the set of OTU abundances.
Alpha diversity indices, including the species richness index and the Shannon index, were calculated and analyzed using the Wilcoxon rank sum test between the two groups to determine the p-value for group comparisons. It was found that there is a significant difference between the variability of microbiota of cattle from North and South Kazakhstan (p-value: 0.04) and between South and West Kazakhstan (p-values: 0.001 and 0.01).
Beta diversity examines the change in species diversity between microbiotas. Principal coordinate analysis (PCoA) was performed to examine the beta diversity based on Bray–Curtis index (Fig. 7).
The effect of the regions on beta diversity of fecal bacterial community as shown by principal coordinate analysis (PCoA) based on Bray–Curtis index (green dot = South Kazakhstan; purple dot = Southeast Kazakhstan; red dot = North Kazakhstan; light blue dot = Western Kazakhstan). PCoA was carried out starting from the set of OTU abundances. Regional clusters which resulted significantly different by PERMANOVA analysis are highlighted by ovals.
The group separation observed on PCoA was further tested for significance by Permutational multivariate analysis of variance (PERMANOVA).
Table 3 shows the metadata variable used, its groups and the results of the test (pseudo-f-statistic and p-value), which resulted in a significant difference between groups.
Table 4 shows the PERMANOVA analysis for each pair of groups and the results of the test (pseudo-f-statistic and p-value). Bonferroni-corrected p-values are also shown.
Table 4 shows that two Bonferroni p-values maintain significance after Bonferroni-correction, that is when comparing samples from Western Kazakhstan with Southern (p-value 0.00599), and samples from Southeast Kazakhstan with Western Kazakhstan (p-value 0.00084). Thus, Western Kazakhstan differs from other areas of the countries in terms of beta diversity.
Source: Ecology - nature.com
