Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens

Tajima, Kiyoshi; Nagamine, Takafumi; Matsui, Hiroki; Nakamura, Mako; Aminov, Rustam

doi:10.1111/j.1574-6968.2001.tb10694.x

Cited by 161 publications

(116 citation statements)

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“…Many studies have been conducted to investigate the methanogenic diversity in the -E-mail: zhuweiyun@njau.edu.cn rumen. Tajima et al (2001) found that the predominant species were affiliated with Methanomicrobium mobile in the rumen of Holstein dry cows in Japan. From the rumen of Hereford-Cross cattle in Ontario, almost half of the clones of archaea were related to Methanobrevibacter ruminantium (Wright et al, 2007).…”

Section: Introductionmentioning

confidence: 95%

Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle

Pei

Mao

Cheng

et al. 2010

Animal

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Three methanogen 16S rRNA gene clone libraries were constructed from liquid (LM), solid (SM) and epithelium (EM) fractions taken from the rumen of Jinnan cattle in China. After the amplification by PCR using methanogen-specific primers Met86F and Met1340R, equal quantities of PCR products from the same fractions from each of the four cattle were mixed together and used to construct the three libraries. Sequence analysis showed that the 268 LM clones were divided into 35 phylotypes with 18 sequences of phylotypes affiliated with the genus Methanobrevibacter (84.3% of clones). The 135 SM clones were divided into 19 phylotypes with 11 phylotypes affiliated with the genus Methanobrevibacter (77.8%). The 267 EM clones were divided into 33 phylotypes with 15 phylotypes affiliated with the genus Methanobrevibacter (77.2%). Clones closely related to Methanomicrobium mobile and Methanobrevibacter wolinii were only found in the LM library, and those to Methanobrevibacter ruminantium and Methanobrevibacter gottschalkii only in the SM library. LM library comprised 12.4% unidentified euryarchaeal clones, SM library 23.7% and EM library 25.5%, respectively. Five phylotypes (accession number: EF055528 and EF055531-EF055534) did not belong to the Euryarchaeota sequences we had known. One possible new genus (represented by phylotype E17, accession number EF055528) belonging to Methanobacteriaceae was identified from EM library. Quantitative real-time PCR for the first time revealed that epithelium fraction had significantly higher density of methanogens, with methanogenic mcrA gene copies (9.95 log 10 (copies per gram of wet weight)) than solid (9.26, P , 0.01) and the liquid (8.44, P , 0.001). The three clone libraries also appeared different in Shannon index (EM library 2.12, LM library 2.05 and SM library 1.73). Our results showed that there were apparent differences in the methanogenic diversity and abundance in the three different fractions within the rumen of Jinnan cattle, with Methanobrevibacter species predominant in all the three libraries and with epithelium fraction having more unknown species and higher density of methanogens.Keywords: rumen methanogen, molecular diversity, different fractions ImplicationsInterest in methanogens from ruminants has resulted from the role of methane in global warming and from the fact that cattle typically lose 2% to 12% of ingested energy as methane (Johnson and Johnson, 1995). However, little is known about their distribution in the rumen of Chinese ruminants. To understand their diversity distribution and their abundance, three methanogenic 16S rRNA gene libraries were constructed from different fractions of rumen of Jinnan cattle and their density determined by quantitative real-time PCR. Our results showed that Methanobrevibacter species were predominant in all three libraries, and that there were differences in the methanogenic diversity and abundance in the three different fractions within the rumen. The study for the first time demonstrated that many unidentified sequences wer...

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Section: Introductionmentioning

confidence: 95%

Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle

Pei

Mao

Cheng

et al. 2010

Animal

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“…are members of the order Methanomicrobiales that appear to be abundant in certain rumens (Yanagita et al, 2000;Tajima et al, 2001;Shin et al, 2004;Chaudhary et al, 2012), although the basis of their apparent dominance over Methanobrevibacter spp. in those cases is not known.…”

Section: Overview Of Rumen Ecology/methanogensmentioning

confidence: 99%

Progress in the development of vaccines against rumen methanogens

Wedlock

Janssen

Leahy

et al. 2013

Animal

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Vaccination against rumen methanogens offers a practical approach to reduce methane emissions in livestock, particularly ruminants grazing on pasture. Although successful vaccination strategies have been reported for reducing the activity of the rumen-dwelling organism Streptococcus bovis in sheep and S. bovis and Lactobacillus spp. in cattle, earlier approaches using vaccines based on whole methanogen cells to reduce methane production in sheep have produced less promising results. An anti-methanogen vaccine will need to have broad specificity against methanogens commonly found in the rumen and induce antibody in saliva resulting in delivery of sufficiently high levels of antibodies to the rumen to reduce methanogen activity. Our approach has focussed on identifying surface and membrane-associated proteins that are conserved across a range of rumen methanogens. The identification of potential vaccine antigens has been assisted by recent advances in the knowledge of rumen methanogen genomes. Methanogen surface proteins have been shown to be immunogenic in ruminants and vaccination of sheep with these proteins induced specific antibody responses in saliva and rumen contents. Current studies are directed towards identifying key candidate antigens and investigating the level and types of salivary antibodies produced in sheep and cattle vaccinated with methanogen proteins, stability of antibodies in the rumen and their impact on rumen microbial populations. In addition, there is a need to identify adjuvants that stimulate high levels of salivary antibody and are suitable for formulating with protein antigens to produce a low-cost and effective vaccine.Keywords: vaccine, antigen, antibody, methane, methanogens, Methanobrevibacter ruminantium Implications A number of different mitigation strategies are being investigated for reducing methane emissions from livestock, including the development of vaccines that specifically target the methane-producing methanogens in the rumen. Previous studies on vaccinating ruminants against the rumen-dwelling organisms Streptococcus bovis and Lactobacillus spp. have demonstrated the feasibility of vaccinating animals to produce salivary antibodies that neutralise the activity of these microbes in the rumen (Shu et al., 1999(Shu et al., , 2000a(Shu et al., , 2000b(Shu et al., and 2001Gill et al., 2000). Owing to the complexity of the rumen microbiota and diversity of methanogens in the rumen, an effective vaccine for reducing methane emissions from ruminants will need to target a wide range of methanogens in the rumen among an even more diverse assemblage of bacteria, fungi and protozoa. This paper reviews the progress towards developing an anti-methanogen vaccine. IntroductionA range of different strategies are being investigated to reduce methane emissions from farmed ruminants (reviewed by Martin et al., 2010;Buddle et al., 2011;Clark, 2013). Vaccination of ruminants against rumen methanogens has the potential to reduce methane emissions by decreasing the number or activity of meth...

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“…In foregut fermenters, bacterial cells are degraded later in the acidic stomach, where gastric lysozyme acts as a digestive enzyme (Ruiz et al, 1994) and bacterial biomass is the animal's main source of protein (Stevens and Hume, 1995). The rumen harbors all three domains of life: bacteria (mostly Firmicutes and the PrevotellaBacteroides (Tajima et al, 2001a;Eckburg et al, 2005)); archaea (such as Methanobrevibacter and Thermoplasma (Tajima et al, 2001b)); and eukarya, both protozoa (ciliates and flagellates; (Orpin, 1976;Vogels et al, 1980) and fungi (anaerobic phycomycetes (Mackie, 1997)). …”

Section: Introductionmentioning

confidence: 99%

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

et al. 2011

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Foregut fermentation occurs in mammalian ruminants and in one bird, the South American folivorous hoatzin. This bird has an enlarged crop with a function analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant matter, providing energy to the host from foregut fermentation, in addition to the fermentation that occurs in their hindguts (cecum/colon). As foregut fermentation represents an evolutionary convergence between hoatzins and ruminants, our aim was to compare the community structure of foregut and hindgut bacterial communities in the cow and hoatzin to evaluate the influences of host phylogeny and organ function in shaping the gut microbiome. The approach used was to hybridize amplified bacterial ribosomal RNA genes onto a high-density microarray (PhyloChip). The results show that the microbial communities cluster primarily by functional environment (foreguts cluster separately from hindguts) and then by host. Bacterial community diversity was higher in the cow than in the hoatzin. Overall, compared with hindguts, foreguts have higher proportions of Bacteroidetes and Spirochaetes, and lower proportions of Firmicutes and Proteobacteria. The main host differences in gut bacterial composition include a higher representation of Spirochaetes, Synergistes and Verrucomicrobia in the cow. Despite the significant differences in host phylogeny, body size, physiology and diet, the function seems to shape the microbial communities involved in fermentation. Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts.

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Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens

Cited by 161 publications

References 35 publications

Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle

Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle

Progress in the development of vaccines against rumen methanogens

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

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