Literature DB >> 22447586

Community structure analysis of methanogens associated with rumen protozoa reveals bias in universal archaeal primers.

Lisa D Tymensen1, Tim A McAllister.   

Abstract

The diversity of protozoan-associated methanogens in cattle was investigated using five universal archaeal small-subunit (SSU) rRNA gene primer sets. Methanobrevibacter spp. and rumen cluster C (distantly related to Thermoplasma spp.) were predominant. Significant differences in species composition among libraries indicate that some primers used previously to characterize rumen methanogens exhibit biased amplification.

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Year:  2012        PMID： 22447586      PMCID： PMC3346394          DOI： 10.1128/AEM.07994-11

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  25 in total

1.  Phylogenetic diversity of methanogenic archaea in swine waste storage pits.

Authors:  T R Whitehead; M A Cotta
Journal:  FEMS Microbiol Lett       Date:  1999-10-15       Impact factor: 2.742

2.  A greedy algorithm for aligning DNA sequences.

Authors:  Z Zhang; S Schwartz; L Wagner; W Miller
Journal:  J Comput Biol       Date:  2000 Feb-Apr       Impact factor: 1.479

3.  Integration of microbial ecology and statistics: a test to compare gene libraries.

Authors:  Patrick D Schloss; Bret R Larget; Jo Handelsman
Journal:  Appl Environ Microbiol       Date:  2004-09       Impact factor: 4.792

4.  Analysis of methanogenic archaeal communities of rumen fluid and rumen particles from Korean black goats.

Authors:  Min-Jung Gu; Md Jahangir Alam; Seon-Ho Kim; Che-Ok Jeon; Moon-Baek Chang; Young-Kyoon Oh; Sang-Cheol Lee; Sang-Suk Lee
Journal:  Anim Sci J       Date:  2011-06-15       Impact factor: 1.749

5.  Archaea in coastal marine environments.

Authors:  E F DeLong
Journal:  Proc Natl Acad Sci U S A       Date:  1992-06-15       Impact factor: 11.205

6.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Authors:  Koichiro Tamura; Daniel Peterson; Nicholas Peterson; Glen Stecher; Masatoshi Nei; Sudhir Kumar
Journal:  Mol Biol Evol       Date:  2011-05-04       Impact factor: 16.240

7.  Some rumen ciliates have endosymbiotic methanogens.

Authors:  B J Finlay; G Esteban; K J Clarke; A G Williams; T M Embley; R P Hirt
Journal:  FEMS Microbiol Lett       Date:  1994-04-01       Impact factor: 2.742

8.  Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence.

Authors:  Eun Chule Shin; Byoung Rock Choi; Woo Jin Lim; Su Young Hong; Chang Long An; Kye Man Cho; Young Kyun Kim; Jin Mee An; Jung Mi Kang; Sung Sill Lee; Hoon Kim; Han Dae Yun
Journal:  Anaerobe       Date:  2004-12       Impact factor: 3.331

9.  Phylogenetic analysis of methanogens from the bovine rumen.

Authors:  M F Whitford; R M Teather; R J Forster
Journal:  BMC Microbiol       Date:  2001-05-16       Impact factor: 3.605

10.  16S rDNA directed PCR primers and detection of methanogens in the bovine rumen.

Authors:  L C Skillman; P N Evans; C Strömpl; K N Joblin
Journal:  Lett Appl Microbiol       Date:  2006-03       Impact factor: 2.858
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  19 in total

1.  Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle.

Authors:  Henning Seedorf; Sandra Kittelmann; Peter H Janssen
Journal:  Appl Environ Microbiol       Date:  2014-11-21       Impact factor: 4.792

2.  Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen.

Authors:  Morten Poulsen; Clarissa Schwab; Bent Borg Jensen; Ricarda M Engberg; Anja Spang; Nuria Canibe; Ole Højberg; Gabriel Milinovich; Lena Fragner; Christa Schleper; Wolfram Weckwerth; Peter Lund; Andreas Schramm; Tim Urich
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

3.  Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.

Authors:  Timothy J Snelling; Buğra Genç; Nest McKain; Mick Watson; Sinéad M Waters; Christopher J Creevey; R John Wallace
Journal:  PLoS One       Date:  2014-09-24       Impact factor: 3.240

4.  Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs.

Authors:  Martin A Fischer; Simon Güllert; Sven C Neulinger; Wolfgang R Streit; Ruth A Schmitz
Journal:  Front Microbiol       Date:  2016-08-23       Impact factor: 5.640

5.  Rumen microbial communities influence metabolic phenotypes in lambs.

Authors:  Diego P Morgavi; Estelle Rathahao-Paris; Milka Popova; Julien Boccard; Kristian F Nielsen; Hamid Boudra
Journal:  Front Microbiol       Date:  2015-10-12       Impact factor: 5.640

Review 6.  Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock.

Authors:  Chengjian Yang; John A Rooke; Irene Cabeza; Robert J Wallace
Journal:  Front Microbiol       Date:  2016-02-12       Impact factor: 5.640

Review 7.  Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances.

Authors:  Amlan Patra; Tansol Park; Minseok Kim; Zhongtang Yu
Journal:  J Anim Sci Biotechnol       Date:  2017-01-26

8.  Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range.

Authors:  Gemma Henderson; Faith Cox; Siva Ganesh; Arjan Jonker; Wayne Young; Peter H Janssen
Journal:  Sci Rep       Date:  2015-10-09       Impact factor: 4.379

9.  Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers.

Authors:  Yuhong Niu; Qingxiang Meng; Shengli Li; Liping Ren; Bo Zhou; Thomas Schonewille; Zhenming Zhou
Journal:  PLoS One       Date:  2016-06-03       Impact factor: 3.240

10.  The rumen microbial metagenome associated with high methane production in cattle.

Authors:  R John Wallace; John A Rooke; Nest McKain; Carol-Anne Duthie; Jimmy J Hyslop; David W Ross; Anthony Waterhouse; Mick Watson; Rainer Roehe
Journal:  BMC Genomics       Date:  2015-10-23       Impact factor: 3.969
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