Lac bacteria are microorganisms that are necessary for the proper progress of the fermentation. They are facultative anaerobic microorganisms that can produce Lac and Acet. Lac is included in the basic acids used for ensuring the success of the conservation process [
16]. These bacteria get into the ensiled biomass while it is still on the field. They were also found in the alfalfa and clover fodder as well. Although, no significant differences were found between the species, it was obvious that
Medicago sativa, especially the Tereza variety, contained more Lac bacteria, compared with
Trifolium pratense. An aerobic environment resulted from the low content of green matter, and a higher content of Lac bacteria was associated with anaerobic environment during ensiling. Also in silage, a higher level of Lac bacteria was evident in the Tereza variety. Similarly, enterococci are Lac bacteria, but their determination relates to their ability to produce BA. These bacteria occur in biological silage additives [
17]. The use of biological additive is reflected in an increase (
p < 0.05) of their counts, compared with the control variant and the variant treated with the mixtures of organic acids and their salts. This increase is not reflected in the content of BA. The use of biological additive was not shown to affect the content of BA. This finding contrasted with the results of Nishino et al. [
5], who stated that biological additives containing
Lactobacillus casei can reduce the content of BA in silage. However, these results were obtained in silage of festulolia and maize. Simultaneously, Van Os et al. [
18] confirmed the fact that unless the acidification of silage was set in the first 10 days of fermentation, the production of BA would be significantly increased. Mainly the content of cadaverine in silages treated with chemical additive was decreased. Although, this reduction was not significant, the observed tendency confirmed the fact that the chemical additives were more suitable for preservation of biomass with low dry matter content in comparison to biological additives, with regard not only to the quality of the ensiling process, but also the content of toxic products. Moreover, the use of chemical additive resulted in a decrease (
p < 0.05) in pH of the silage to a value of 4.22. The pH value influenced the activity of the decarboxylases [
4] and also inhibited the growth of microorganisms [
19]. Low (
p < 0.05) pH value was also observed in silage produced from biomass of
Trifiolium pratense L. The species was detected with lower counts of TNM, Lac bacteria, Enterobacteriaceae, and especially enterococci. In the evaluated silages, tyramine, putrescine, and spermine were mainly detected. Putrescine is considered to be one of the factors causing ketosis [
20]. Tyramine increases blood pressure very effectively. Spermine affects the growth and division of cells. Tyramine, putrescine, and cadaverine reduce the palatability of silage for cattle. Histamine is among the most harmful amines. It induces a reduction in blood pressure and worsens blood circulation in the extremities of cattle [
7]. Our results indicated low histamine content in the evaluated silages. The highest content was found out in
Medicago sativa, especially in the Tereza variety (16.5 mg·kg
−1). Steidlova and Kalac [
21] detected histamine only in grass silage not treated with additives (7.4 mg·kg
−1). Silages treated with chemical and biological additives were devoid of histamine. In contrast, our results showed the occurrence of histamine in alfalfa and red clover silage not only in untreated samples, but also in silages treated with chemical and biological additive. This could be the result of a low content of dry matter of ensiling biomass. Nishino et al. [
5] listed the content of histamine up to 195 mg·kg
−1 in untreated grass silage. On the other hand, they mentioned that silage treated with biological additives reduced its content only by 10.3 to 18.9 mg·kg
−1. Higher effectiveness of microorganisms stimulates amine degradation and thus prevents amine accumulation in the rumen. In practice, content of amines may be relevant, especially in short term during the change of feed, since amines are rapidly degraded in adapted animals. Histamine was degraded to the greatest extent followed by tyramine, putrescine, and cadaverine [
3]. Feeding silage spiked with histamine in increments up to 1 g·day
−1 to sheep over a period of seven days [
22] and 5 g·day
−1 to heifers had no impact on dry matter intake [
23]. Holzer et al. [
24] stated that undesirable microflora consisting of bacteria (including enterobacteria and clostridia), yeasts, and fungi involved in the impairment of feed could consequently cause health complications to animals or changes in animal products. Bacteria of the Enterobacteriaceae family are microorganisms capable of producing the undesirable But. High counts of Enterobacteriaceae were detected in green biomass of
Medicago sativa, especially in the Tereza variety. The occurrence of these microorganisms in green fodder can greatly affect the success of the silage process. This fact corresponded with high (
p < 0.05) levels of BA in
Medicago sativa silages. The Enterobacteriaceae counts in silages treated with organic acids and their salts were apparently lower, although with no significant difference. The effect of chemical additives was confirmed by Selwet et al. [
6] reporting that the use of a chemical additive called KemiSile 2000 (Mikrop Čebín a.s., Čebín, Czech Republic) can reduce the occurrence of Enterobacteriaceae, in particular in silage wilted to 20% of dry matter. Herrmann et al. [
25] confirmed the inhibition of undesirable but alcohol and ammonia formation after the application of chemical additives. Fungi were particularly present in
Medicago sativa. A significant difference in the contents of DON and ZEA was not detected between the evaluated species. Fungi are aerobic microorganisms that are present during harvesting [
26] and the ensilage process in the anaerobic environment reduces their counts. Particularly, it can be evident in the use of chemical additives. Currently, no acceptable limits exist for counts of fungi and yeasts in the Czech Republic. Fungi in alfalfa and red clover silage were detected in the order of magnitude 10
2–10
3 CFU·g
−1. Scudamore and Livesey [
27] reported that the occurrence of fungi in counts higher than 10
4 CFU·g
−1 can induce animal health problems. Alonso et al. [
28] stated that the occurrence of fungi is related to the lack of hygienic quality of silage leading to loss of nutrients and dry matter. Mycotoxins entered silage directly in the field. A difference in the content of mycotoxins between green fodder and silage was not observed. In the case of DON, a reduction of mycotoxin was apparent.