A ‘universal’ type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities

Chaban, Bonnie; Hill, Janet E.

doi:10.1038/ismej.2011.96

Cited by 29 publications

(25 citation statements)

References 44 publications

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“…Type II chaperonin sequences are considered to be more diverse than the previously used markers and thus might serve as a better marker for the diversity studies (Chaban and Hill 2012). Phylogenetic trees constructed by using chaperonin type II markers are in well agreement with 16S rRNA-based trees, but rather, they provide a more detailed resolution of the closely related groups, or it could help to discriminate different subspecies.…”

Section: Marker-based Alternatives To Study Methanogen Diversitymentioning

confidence: 88%

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Chaudhary

Gaci

Borrel

et al. 2015

Appl Microbiol Biotechnol

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Until recently, human gut microbiota was believed to be colonized by few methanogenic archaeal species. Much higher microbial diversity within the human gut was revealed by the use of molecular approaches as compared to routine microbiological techniques, but still, a lot remains unknown. Molecular techniques has the advantage of being rapid, reproducible, and can be highly discriminative as compared to conventional culturing methods. Some of them provide both qualitative and quantitative information. However, the choice of method should be taken with care to avoid biases. The advent of next-generation sequencing gives much deeper information from which functional and ecological hypotheses can be drawn. In this review, molecular techniques that are currently used together with their possible future developments to study gut methanogenic communities are indicated along with their limitations and difficulties that are encountered during their implementation. Moreover, the high amount of metagenomics data from the human gut microbiome indicate that this environment could be a paradigm for new directions in methanogen diversity studies and help to develop new approaches for other environments as well. Concerning humans, this should help us to better understand the possible association of methanogens with some of the diseased conditions and their peculiar distribution among age groups in human.

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Section: Marker-based Alternatives To Study Methanogen Diversitymentioning

confidence: 88%

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Chaudhary

Gaci

Borrel

et al. 2015

Appl Microbiol Biotechnol

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“…Thus it is reasonable to consider the use of this framework for evaluating barcoding targets for Archaea, including 16S rRNA and the Type II chaperonin (ortholog of cpn 60) [60].…”

Section: Discussionmentioning

confidence: 99%

The Chaperonin-60 Universal Target Is a Barcode for Bacteria That Enables De Novo Assembly of Metagenomic Sequence Data

et al. 2012

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Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances (“barcode gap”) was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.

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“…For methanogens, the methyl coenzyme-M reductase (mcrA) gene of the methanogenesis pathway is also a phylogenetic marker (Luton et al, 2002) that has been used in rumen studies (Denman et al, 2007). Recently, the diversity of rumen methanogens was investigated using the gene encoding type II chaperonins (Chaban and Hill, 2012). Less universally distributed genes, indicative of certain functions, have also been used to study the parts of the microbial community.…”

Section: Rumen Microbial Diversitymentioning

confidence: 99%

Rumen microbial (meta)genomics and its application to ruminant production

Morgavi

Kelly

Janssen

et al. 2013

Animal

205

163

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Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome–host models and inform strategies promoting less-polluting, more robust and efficient ruminants.

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A ‘universal’ type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities

Cited by 29 publications

References 44 publications

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

The Chaperonin-60 Universal Target Is a Barcode for Bacteria That Enables De Novo Assembly of Metagenomic Sequence Data

Rumen microbial (meta)genomics and its application to ruminant production

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