**7. Methanogenic archaeal population in pseudo ruminants like camelids**

Gut methanogens remains largely uncharacterized in camel with no published studies on methanogenic archaeal populations from 16S rRNA gene clone libraries whereas much interest has been paid to domestic ruminants. The community diversity and structure of archaeal methanogens in fecal samples of Bactrian camel (*Camelus bactrianus*) maintained at two zoos from United States of America revealed the genus *Methanobrevibacter* to be the abundant ruminal methanogen however the diversity and structure of methanogens varied significantly between the two libraries with only 2 OTU's in common to both the libraries. Two and seven OTU's were found unique to first and second library, respectively [55]. The methanogenic archaeal population inside rumen of Alpaca (*Vicugna pacos*) from America resulted in a 947 non chimeric gene clone library representing 51 distinct OTU's. Thirty seven OTU's displayed ≥95% genus-level sequence affiliation with the species belonging to *Methanobrevibacter*. Six out of 37 OTU's showed ≥98% species-level sequence identity to *Mbb. millerae*; 2 OTU's showed species-level identity to *Mbb. ruminantium*; 2 OTU's showed >98% identity to *Mbb. smithii*; 27 OTU's showed 95–97.9% sequence similarity to well detected and reported *Methanobrevibacter* species. Of the remaining 14 OTU's, 3 distinct phylogenetic group were made that consisted of 4 OTU's that had 95–97.9% similarity to the species of *Methanobacterium*; other 3 OTU's showed genus level similarity with the species *of Methanosphaera*; 7 OTU's were found to be isolated phylogenetically from order *Methanobacteriales*. Overall, *Methanobrevibacter* was found to be dominant in alpaca rumen like other ruminants but in contrast as described in other ruminants *Mbb. millerae* was found to be in most number of clones showing species level identity [56]. The fecal microbiome of camels maintained at intensive and extensive system of management in Jaisalmer (Rajasthan) was evaluated through non-cultural approach. The both group's fecal metagenomes were compared with available fecal or rumen metagenomes on MG-RAST and *Mbb. smithii* was detected as a predominant archaeal methanogen [57]. A 16S rRNA gene clone library from the content of the C1 compartment (foregut) of Indian camels was constructed by cloning pooled

**121**

environment.

*Methanogenic Diversity and Taxonomy in the Gastro Intestinal Tract of Ruminants*

polymerase chain reaction (PCR)—amplified products. The sequences (n = 151) were clustered into 15 OTU's (operational taxonomic units) based on sequencing of unique RFLP pattern and divided into five species groups: *Methanobrevibacter* (*Mbb.*) *millerae* strain SM9, "*Candidatus"* Methanoplasma termitum, *Mbb. smithii*, *Mbb. ruminantium*, *Methanocorpusculum* (*M.*) *bavaricum* strain DSM 4179. The genus *Methanobrevibacter* (order *Methanobacteriales*) was the most prevalent (76.82%), followed by *Archaea* from the orders *Methanomassiliicoccales* (17.21%) and

The microbial diversity of extremophiles is of interest particularly for microbiologists and biotechnologists to decipher the enzymes and their functions, their biochemical and metabolic pathways that enable them to survive in harshest conditions. The in depth knowledge will pave the path for creating technologies that can function under extreme conditions. It will improve our current knowledge and perception about the interrelationships between various species and will continue

For researchers working to explore the microbial ecology of volcanic systems, deep under the earth, oceans, thermal vents, rice fields, waste treatments, bioremediation of soils, the rumen forms a stable and basic source of knowledge concerning anaerobic microorganisms. The knowledge of anaerobic microorganism's reaction going inside rumen flora is of invaluable importance as methanogens are also found in omnivores and humans alike and can be implicated in understanding human and animal diseases. An extensive understanding of methanogens in gastrointestinal tract will contribute to the sustainable farming of animals well into the future. The enteric fermentation in ruminants is a significant cause of methane emission in environment. Since, methane is a potent greenhouse gas, to reduce the activity and number of methane producing *Archaea*, it is desirable to have knowledge about the community structure of methanogens and their feed conversion energy mechanism. In order to control various ruminal disorders the insight into microbial ecology will help to develop nutrition and feed management strategies and also to develop better prospects of altering rumen function to mitigate methane generation while still optimizing digestibility and microbial function. This can be particularly useful for the farmer community who can benefit environment in methane mitigation from livestock at the same time increasing animal efficiency. Reductive acetogenesis is performed by acetogenic bacteria that thrive in non-ruminants and can sometimes replace methanogenesis. A comparative account of dominant methano-

to lead to the classification and assessment of ruminal archaeal species.

gens in the ruminants all over the world is depicted in **Figure 2**.

The significance of exploring the archaeal diversity lies in its great potential to identify the genes encoding plant degrading enzymes, thus contributing to an increase in understanding of the mechanisms mediating digestion in ruminants. Moreover, the functional analysis of these genes might uncover strategies for improving feed and fiber digestion in the rumen that could further be applied to manipulate pathways associated with bioreactor processes for biofuels production and to formulate feed with dietary additives that help in reducing methane emissions. A taxonomic frame of methanogens should be developed that would help elucidate the diversity, identification and classification of major rumen archaeal population. Data from antibiotic resistance genes and RATC (resistance to antibiotics and toxic compounds) can be also used to produce antibiotic resistance gene profiles to help in understanding of the microbial community ecology in every

*DOI: http://dx.doi.org/10.5772/intechopen.82829*

*Methanomicrobiales* (5.96%) [58] (**Figure 1**).

**8. Biotechnological applications of extremophiles**

*Methanogenic Diversity and Taxonomy in the Gastro Intestinal Tract of Ruminants DOI: http://dx.doi.org/10.5772/intechopen.82829*

polymerase chain reaction (PCR)—amplified products. The sequences (n = 151) were clustered into 15 OTU's (operational taxonomic units) based on sequencing of unique RFLP pattern and divided into five species groups: *Methanobrevibacter* (*Mbb.*) *millerae* strain SM9, "*Candidatus"* Methanoplasma termitum, *Mbb. smithii*, *Mbb. ruminantium*, *Methanocorpusculum* (*M.*) *bavaricum* strain DSM 4179. The genus *Methanobrevibacter* (order *Methanobacteriales*) was the most prevalent (76.82%), followed by *Archaea* from the orders *Methanomassiliicoccales* (17.21%) and *Methanomicrobiales* (5.96%) [58] (**Figure 1**).

## **8. Biotechnological applications of extremophiles**

The microbial diversity of extremophiles is of interest particularly for microbiologists and biotechnologists to decipher the enzymes and their functions, their biochemical and metabolic pathways that enable them to survive in harshest conditions. The in depth knowledge will pave the path for creating technologies that can function under extreme conditions. It will improve our current knowledge and perception about the interrelationships between various species and will continue to lead to the classification and assessment of ruminal archaeal species.

For researchers working to explore the microbial ecology of volcanic systems, deep under the earth, oceans, thermal vents, rice fields, waste treatments, bioremediation of soils, the rumen forms a stable and basic source of knowledge concerning anaerobic microorganisms. The knowledge of anaerobic microorganism's reaction going inside rumen flora is of invaluable importance as methanogens are also found in omnivores and humans alike and can be implicated in understanding human and animal diseases. An extensive understanding of methanogens in gastrointestinal tract will contribute to the sustainable farming of animals well into the future. The enteric fermentation in ruminants is a significant cause of methane emission in environment. Since, methane is a potent greenhouse gas, to reduce the activity and number of methane producing *Archaea*, it is desirable to have knowledge about the community structure of methanogens and their feed conversion energy mechanism. In order to control various ruminal disorders the insight into microbial ecology will help to develop nutrition and feed management strategies and also to develop better prospects of altering rumen function to mitigate methane generation while still optimizing digestibility and microbial function. This can be particularly useful for the farmer community who can benefit environment in methane mitigation from livestock at the same time increasing animal efficiency. Reductive acetogenesis is performed by acetogenic bacteria that thrive in non-ruminants and can sometimes replace methanogenesis. A comparative account of dominant methanogens in the ruminants all over the world is depicted in **Figure 2**.

The significance of exploring the archaeal diversity lies in its great potential to identify the genes encoding plant degrading enzymes, thus contributing to an increase in understanding of the mechanisms mediating digestion in ruminants. Moreover, the functional analysis of these genes might uncover strategies for improving feed and fiber digestion in the rumen that could further be applied to manipulate pathways associated with bioreactor processes for biofuels production and to formulate feed with dietary additives that help in reducing methane emissions. A taxonomic frame of methanogens should be developed that would help elucidate the diversity, identification and classification of major rumen archaeal population. Data from antibiotic resistance genes and RATC (resistance to antibiotics and toxic compounds) can be also used to produce antibiotic resistance gene profiles to help in understanding of the microbial community ecology in every environment.

*Extremophilic Microbes and Metabolites - Diversity, Bioprospecting and Biotechnological...*

a sequence similarity to *Mbb. ruminantium* [51].

and found *Methanomicrobiales* in lower number [54] (**Figure 1**).

**7. Methanogenic archaeal population in pseudo ruminants like** 

Gut methanogens remains largely uncharacterized in camel with no published studies on methanogenic archaeal populations from 16S rRNA gene clone libraries whereas much interest has been paid to domestic ruminants. The community diversity and structure of archaeal methanogens in fecal samples of Bactrian camel (*Camelus bactrianus*) maintained at two zoos from United States of America revealed the genus *Methanobrevibacter* to be the abundant ruminal methanogen however the diversity and structure of methanogens varied significantly between the two libraries with only 2 OTU's in common to both the libraries. Two and seven OTU's were found unique to first and second library, respectively [55]. The methanogenic archaeal population inside rumen of Alpaca (*Vicugna pacos*) from America resulted in a 947 non chimeric gene clone library representing 51 distinct OTU's. Thirty seven OTU's displayed ≥95% genus-level sequence affiliation with the species belonging to *Methanobrevibacter*. Six out of 37 OTU's showed ≥98% species-level sequence identity to *Mbb. millerae*; 2 OTU's showed species-level identity to *Mbb. ruminantium*; 2 OTU's showed >98% identity to *Mbb. smithii*; 27 OTU's showed 95–97.9% sequence similarity to well detected and reported *Methanobrevibacter* species. Of the remaining 14 OTU's, 3 distinct phylogenetic group were made that consisted of 4 OTU's that had 95–97.9% similarity to the species of *Methanobacterium*; other 3 OTU's showed genus level similarity with the species *of Methanosphaera*; 7 OTU's were found to be isolated phylogenetically from order *Methanobacteriales*. Overall, *Methanobrevibacter* was found to be dominant in alpaca rumen like other ruminants but in contrast as described in other ruminants *Mbb. millerae* was found to be in most number of clones showing species level identity [56]. The fecal microbiome of camels maintained at intensive and extensive system of management in Jaisalmer (Rajasthan) was evaluated through non-cultural approach. The both group's fecal metagenomes were compared with available fecal or rumen metagenomes on MG-RAST and *Mbb. smithii* was detected as a predominant archaeal methanogen [57]. A 16S rRNA gene clone library from the content of the C1 compartment (foregut) of Indian camels was constructed by cloning pooled

the first time in rumen. The fourth group was a single phylotype that showed 97% sequence identity with *Mbb. gottschalkii*. The last group of single phylotype showed

Likewise, the comparative diversity analysis of methanogens using 16S rRNA and *mcr*A in cattle rumen fed on a high fiber diet reported 13 OTU's consisting of 102 clones from 16S rRNA gene based library. All OTU's were clustered with order *Methanobacteriales* and were further splitted into Cluster I that had 12 OTU's related to *Methanobrevibacter* spp. and Cluster II comprised of one OTU related to *M. stadtmanae* [52]. The Surti buffaloes that were fed wheat straw and compound concentrate mixture diet generated a total of 76 clones representing 21 sequences based on PCR-RFLP patterns. BLAST analysis revealed 13 OTU's (55 clones) that showed sequence identity with *Methanomicrobium* sp., 3 OTU's (15 clones) that showed sequence similarity with *Methanobrevibacter* sp. The remaining 5 OTU's (6 clones) were associated with uncultured *Archaea*. Overall, the methanogenic population inside rumen of buffaloes was from the order of *Methanomicrobiales* (18 OTUs) and *Methanobacteriales* (3 OTUs) [53]. The rumen metagenome of buffalo using q-PCR were compared with MG-RAST based annotation of the metagenomes sequences of 16S rDNA amplicons and high throughput shotgun sequencing

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**camelids**

One can exploit enzymes from extremophile *Archaea* that can endure high temperatures and organic solvents. Acidophiles are used in coal mining to recover metallic minerals and to reduce sulfur levels. Alkaliphiles are used in paper making and spilled oil recovery, besides being used as a common ingredient in dish washing detergent and laundry soap. *Thermus aquaticus* an extremophile that endures high temperature produces an enzyme called *Taq* polymerase that has transformed molecular biology all over the world by aiding in quick DNA replication during polymerase chain reaction (PCR). The extremophiles are immensely used in medical and food microbiology, industrial fermentations to produce acetone, butanol, etc. The understanding of microbial diversity in extreme habitats like wetlands can propose research strategies and priorities to integrate understanding of plant-microbial interactions. Further, studies should provide the break through to link distribution and distinctiveness of various gastrointestinal microbes in their natural environment and to discover their genetic potential for livestock wellbeing and industrial progress by making a significant contribution in understanding ruminant nutrition. Research in microbial genomics will provide the opportunity to make sure that this knowledge is used to enhance ruminant production through an improved understanding of microbial function and ecology.

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**Author details**

Farah Naz Faridi1

Tonk, Rajasthan, India

provided the original work is properly cited.

\* and Saba Khan2

Education and Research, Jaipur, Rajasthan, India

\*Address all correspondence to: farah.faridi@gmail.com

1 Department of Bioscience and Biotechnology, Banasthali Vidyapith,

2 Department of Veterinary Pathology, Post Graduate Institute of Veterinary

© 2019 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,

*Methanogenic Diversity and Taxonomy in the Gastro Intestinal Tract of Ruminants*

*DOI: http://dx.doi.org/10.5772/intechopen.82829*

*Methanogenic Diversity and Taxonomy in the Gastro Intestinal Tract of Ruminants DOI: http://dx.doi.org/10.5772/intechopen.82829*
