**4. Microbial diversity and abundance in rumen**

As explained above, microorganisms present in gastrointestinal tracts (GIT) of ruminants and their relationship yield several benefits to the host. The composition of microbiome in GIT varies according to several conditions. Microbial populations can be affected by factors such as type and race of animal, age of the host, diets, feeds, farming practicing and geographical regions [40].

The microbial diversity presents in ruminant's changes across different points of the GIT. Mao et al. [41] studied the microbial population of 10 distinct sites of the GIT in dairy cattle and observed that the microbial diversity differed for the analyzed points. They reported 21 different phyla belonged to Firmicutes (64.81%), Bacteroidetes (15.06%) and Proteobacteria (13.29%). At genus level, the most abundant genera in cattle GIT included *Prevotella*, *Treponema*, *Succiniclasticum*, *Ruminococcus*, *Acetitomaculum*, *Mogibacterium*, *Butyrivibrio* and *Acinetobacter* as well as many different unclassified genera, among which Prevotella, unclassified Ruminococcaceae, unclassified Rikenellaceae, unclassified Christensenellaceae and unclassified Bacteriodales were predominant.

A study carried out by Henderson et al. [42] determined the rumen microbiology of 32 species or subspecies of animals from 35 different countries of seven world regions and evaluated the differences among them. Seven bacterial groups comprised around 67.1% of the total bacterial sequenced, they corresponded to *Prevotella*, *Butyrivibrio* and *Ruminococcus*, as well as unclassified *Lachnospiraceae*, *Ruminococcaceae*, *Bacteroidales* and *Clostridiales*, but were not present in the same proportions in all animal species tested. The abundance of archaea worldwide was similar in all the sampled analyzed, and all belonged to methanogens and corresponded to *Methanobrevibacter gottschalkii* and *M. ruminantium*. *Methanosphaera* sp. and two *Methanomassiliicoccaceae*-affiliated groups, contributing to 89.2% of total archaeal community in rumen. Even in the same region, the age of the animal is other important factor that contributed to considerable differences in microbial diversity. It has been demonstrated that the ruminal microbiota of young dairy cattle is more heterogeneous than microbial community of those cows reaching maturity (2 years). In general, microbial communities in the rumen of dairy cows have been dominated by bacteria (>90%), followed by eukarya (2–8%) and a small abundance of archaea (1.0%). Similarly, a metagenomic study of the rumen microbiome in Holstein dairy cows reported 26 bacterial phyla belonging to Bacteroidetes (61–80%), followed by Firmicutes (12–23%), Proteobacteria (3–10%), Spirochaeta, Fibrobacteres and Actinobacteria (up to 2%). Again, they reported that *Prevotella* from Bacteroidetes was the most abundant genus (>50%), followed by *Bacteroides* (10.91%) and *Parabacteroides* (1.73%). In the case of Firmicutes, the predominant genera were *Abiotrophia*, *Acetivibrio* and *Acetohalobium*. In the archaeal community, the genera *Methanobrevibacter*, being the predominant genera, and accounted 0.5% of the total microbial abundance [43].

CH<sup>4</sup>

56 Livestock Science

regions [40].

quently, global warming [39].

**4. Microbial diversity and abundance in rumen**

unclassified Bacteriodales were predominant.

 production can be accomplished by the reduction of acetate and methyl-containing C1 compounds, nonetheless these pathways are not common in the rumen [38]. About 2–12% of gross energy intake (GEI) produced in the rumen by fermentation is converted to methane, which apart from leading to the loss of the feed energy, results in the emission and conse-

As explained above, microorganisms present in gastrointestinal tracts (GIT) of ruminants and their relationship yield several benefits to the host. The composition of microbiome in GIT varies according to several conditions. Microbial populations can be affected by factors such as type and race of animal, age of the host, diets, feeds, farming practicing and geographical

The microbial diversity presents in ruminant's changes across different points of the GIT. Mao et al. [41] studied the microbial population of 10 distinct sites of the GIT in dairy cattle and observed that the microbial diversity differed for the analyzed points. They reported 21 different phyla belonged to Firmicutes (64.81%), Bacteroidetes (15.06%) and Proteobacteria (13.29%). At genus level, the most abundant genera in cattle GIT included *Prevotella*, *Treponema*, *Succiniclasticum*, *Ruminococcus*, *Acetitomaculum*, *Mogibacterium*, *Butyrivibrio* and *Acinetobacter* as well as many different unclassified genera, among which Prevotella, unclassified Ruminococcaceae, unclassified Rikenellaceae, unclassified Christensenellaceae and

A study carried out by Henderson et al. [42] determined the rumen microbiology of 32 species or subspecies of animals from 35 different countries of seven world regions and evaluated the differences among them. Seven bacterial groups comprised around 67.1% of the total bacterial sequenced, they corresponded to *Prevotella*, *Butyrivibrio* and *Ruminococcus*, as well as unclassified *Lachnospiraceae*, *Ruminococcaceae*, *Bacteroidales* and *Clostridiales*, but were not present in the same proportions in all animal species tested. The abundance of archaea worldwide was similar in all the sampled analyzed, and all belonged to methanogens and corresponded to *Methanobrevibacter gottschalkii* and *M. ruminantium*. *Methanosphaera* sp. and two *Methanomassiliicoccaceae*-affiliated groups, contributing to 89.2% of total archaeal community in rumen. Even in the same region, the age of the animal is other important factor that contributed to considerable differences in microbial diversity. It has been demonstrated that the ruminal microbiota of young dairy cattle is more heterogeneous than microbial community of those cows reaching maturity (2 years). In general, microbial communities in the rumen of dairy cows have been dominated by bacteria (>90%), followed by eukarya (2–8%) and a small abundance of archaea (1.0%). Similarly, a metagenomic study of the rumen microbiome in Holstein dairy cows reported 26 bacterial phyla belonging to Bacteroidetes (61–80%), followed by Firmicutes (12–23%), Proteobacteria (3–10%), Spirochaeta, Fibrobacteres and Actinobacteria (up to 2%). Again, they reported that *Prevotella* from Bacteroidetes was the most abundant genus (>50%), followed by *Bacteroides* (10.91%) and *Parabacteroides* (1.73%). In the case of Firmicutes, the predominant genera were *Abiotrophia*, *Acetivibrio* and *Acetohalobium*. Earlier, Kim et al. [44] analyzed the diversity of bacteria and archaea based on 16S ribosomal RNA (rRNA) and reported 13,478 bacterial and 3516 archaeal sequences, which correspond to 7000 and 1500 species of bacteria and archaea, respectively. Among nineteen phyla of bacterial domain, the most abundant were *Firmicutes* (57.9%), *Bacteroidetes* (26.7%) and *Proteobacteria* (6.9%). Within *Firmicutes*, the most abundant class was *Clostridia* (>90%), and the rest belonged to *Bacilli*, *Erysipelotrichi* and unclassified *Firmicutes*. In the *Clostridia* class, the predominant genera were *Buryrivibrio*, *Acetivibrio*, *Ruminococcus*, *Succiniclasticum*, *Pseudobutyrivibrio* and *Mogibacterium*. In the *Bacteroidetes* phylum, the predominant class was *Bacteroidia*, and *Prevotella* represented the most abundant genera. All the five classes of *Proteobacteria* were represented in the rumen bacterial sequences. More than 99% of the archaeal sequences correspond to the phylum *Euryarchaeota*, followed by 11 sequences of the phylum *Crenarchaeota*. About 94% of all archaeal sequences were assigned to the classes *Methanobacteria*, *Methanomicrobia*, *Thermoplasmata* and *Methanopyri*, all of them within phylum *Euryarchaeota*. However, this microbial abundance in rumen can be considerably different between the extremely high and low methane emitters. While archaea are 2.49 times more, bacteria are less (0.98×) in high emitters. In addition, *Euryarcheota* and *Crenarcheota* recorded an increase in high emitters (2.48× and 3.00×, respectively), and at genus level, *Methanobrevibacter* and *Methanosphaera* have been found more abundant (2.44× and 2.54×, respectively). In case of bacterial domain, there were no significant differences between *Firmicutes* and *Bacteroides* between high and low emitters, but *Proteobacteria* was 0.24 times less in high emitters. At genus level, *Desulfovibrio* was two times more in high emitters than low emitters. However, a higher abundance of *Succinovibrionaceae* was recorded in low emitters along with a change in acetate and hydrogen concentration profile, resulting in a low methanogenesis [45]. These microbial dynamics in animals of different types and from different regions clearly demonstrate that it is possible to develop strategies to mitigate livestock methane emission through microbial manipulation strategies. Various studies [46, 47] have suggested that it is possible to adapt the rumen microorganisms by manipulating the feeding management in the young animal, which have been found to persist in their later life. These results suggested that the methane emissions can be decreased considerably by manipulation of rumen microbiome through feed alterations.

As mentioned earlier, the composition of population in rumen is affected by the age and diet of the animal. Li et al. [47] evaluated the rumen microbiota of pre-ruminant calves of 14- and 42-day-old calves fed milk replacers based on 454-pyrosequencing of 16S rDNA and reported a total of 170 bacterial genera in the developing rumen of 14-day-old calves. They, further demonstrated that microbiota changed according to their dietary modifications and physiological changes in the host. Moreover, the transition from 14 to 42 days had a significant impact on the ruminal microbial composition. The most abundant phylum, *Bacteroidetes*, increased significantly his abundance from 45.7 (14 days) to 74.8% (42 days), the phylum *Synergistetes* also increased, while the abundance of *Firmicutes*, *Proteobacteria* and *Fusobacteria* decreased during this time. The results of these two age groups are different from those based on the rumen of 12-month-old animal, where the most abundant phyla were *Bacteroidetes* (52%), *Firmicutes* (42.7%), *Spirochaetes* (2.3%) and *Fibrobacteres* (1.9%). This study clearly demonstrated that the changes in feed affect and change the dynamics of ruminal microbiome. Petri et al. [48] studied the impact of diet and its impact of an acidotic challenge on the composition of six different bacterial targets from heifers fed forage, mixed forage, high grain, post-acidic challenge (4 and 12 h) and recovery. They observed that all of the bacterial target groups were affected by dietary treatment, with exception of *S. bovis*, *Raminococcus* spp. and *Fibrobacter succinogenes* represented a large percentage of the bacterial population present in the mixed forage diet. *Prevotella* corresponds to the most abundant genera in the acidotic challenge, but the lowest in the animal fed forage. *Megasphaera elsdenii* was present in abundance in the sample of 12 h after acidotic challenge, but its abundance decreased during recovery, while at the same time *S. ruminantium* increased in proportion. Both *S. ruminantium* and *M. elsdenii* accounted the smallest proportion of the bacterial population in heifers fed forages.
