Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

Weber, M.; Teeling, Hanno; Huang, Sixing; Waldmann, Jost; Kassabgy, Mariette; Fuchs, Bernhard M.; Klindworth, Anna; Klockow, Christine; Wichels, Antje; Gerdts, Gunnar; Amann, Rudolf; Glöckner, Frank Oliver

doi:10.1038/ismej.2010.180

Cited by 51 publications

(43 citation statements)

References 60 publications

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“…The rumen microbiome is rich in microbial interactions between members, such as metabolic cooperation, synergism, predation, cell-cell signalling and structural organisation such as biofilms (McAllister et al, 1994;Hobson and Stewart, 1997;Erickson et al, 2002). Genomic information, bioinformatic tools for the phylogenetic assignment of sequences (Weber et al, 2011) and the application of techniques that can provide information on direct interactions between microbes in the environment, such as fluorescence in situ hybridization and single-cell sequencing, will provide invaluable insights of the ecosystem.…”

Section: Linking Genomics and Metagenomics Data To Nutrition And Othementioning

confidence: 99%

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

Morgavi

Kelly

Janssen

et al. 2013

Animal

203

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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Section: Linking Genomics and Metagenomics Data To Nutrition And Othementioning

confidence: 99%

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

Morgavi

Kelly

Janssen

et al. 2013

Animal

203

163

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“…그러나 최근 DNA pyrosequencing 기술의 등장으로 표층해수는 물론, 심해의 극한환경에 서식하는 해양미생물의 다양성 분석이 가능 하게 되었다 (Huber et al, 2007;Weber et al, 2010). et al, 2010;Imhoff et al, 2011;McGenity et al, 2012).…”

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“…그러나 최근 DNA pyrosequencing 기술의 등장으로 표층해수는 물론, 심해의 극한환경에 서식하는 해양미생물의 다양성 분석이 가능 하게 되었다 (Huber et al, 2007;Weber et al, 2010). et al, 2010;Imhoff et al, 2011;McGenity et al, 2012). 대서양과 태평양 지역에 걸쳐 적도 부근의 표층해수에 서식 하는 미생물의 분포가 조사되었으며 (Rusch et al, 2007), 북극, 남극, 아메리카, 아프리카, 하와이 등에서 수심 5500 m에 이르는 해양심층수, 해저토양, 해저열수구 등에 서식하는 해양미생물의 분포도 보고되었다 (Zinger et al, 2011).…”

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Comparison of Bacterial Diversity in the Water Columns of Goseong Deep Seawaters

Khang

2013

The Korean Journal of Microbiology

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Microbial diversities in the 300 m and 500 m deep seawaters near Goseong, Gangwon Province (South Korea), were investigated. Pyrosequencing of 16S rRNA genes of marine microbes resulted in 19,474 reads from the 300 m deep seawaters, which consisted of Alphaproteobacteria (57.41%) and Gammaproteobacteria (38.85%), and 82,806 reads from the 500 m deep seawaters, which consisted of Gammaproteobacteria (99.64%) mostly. Rhodobacterales (57.31%) were dominant in the 300 m deep seawaters, but Alteromonadales (45.65%) and Oceanospirillales (34.61%) were dominant in the 500 m deep seawaters. On the bases of operational taxonomic units and diversity indexes (Shannon and Simpson), biodiversity of marine bacteria in the 500 m deep seawaters was shown to be higher than that in the 300 m deep seawaters.

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“…바다에는 육지보다 훨씬 더 많은 종류의 미생물이 서식하고 있지만 배양기술의 한계로 그 동안 해양미생물에 대한 연구가 활발하게 진행되지 못하였으나, 최근 next-generation sequencing (NGS) 기술의 등장으로 다양한 해양미생물의 생태를 파악하는 것이 가능하게 되었다 (Weber et al, 2010). 일반적으로 해양 표 층수에는 alphaproteobacteria와 gammaproteobacteria에 속한 광합성세균들이나 bacterioplankton 등이 주로 서식하고 있으며 (Pontarpet al, 2012;Ritchieand Johnson, 2012), 수심 500 m 이 상의 해저에 있는 침적토에는 용존산소의 부족으로 황환원균 (Desulfobacteraceae)이나 메탄균(Methanobacteriale)과 같은 혐기성 미생물 등이 주로 서식하고 있다 (Anderson et al, 2011;Edgcomb et al, 2011).…”

unclassified

“…심 해에 분포하는 해양미생물 군집의 생태를 파악하면 해양환경관리 나 저온성 효소나 생리활성물질 등을 개발하기 위한 연구에 도움 이 될 수 있다 (Heidelberg et al, 2010;Imhoff et al, 2011;McGenity et al, 2012). 본 연구는 울릉도 연안의 해양심층수에 서식하는 미생물군집의 분포를 이해하기 위하여 16S rRNA gene 을 기준으로 각 균주에 해당하는 염기서열을 pyrosequencing 방 법으로 분석하여 1500 m 심해에 존재하는 해양미생물의 생태분 포를 조사하였다 (Weber et al, 2010;Hong et al, 2011).…”

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Marine Prokaryotic Diversity of the Deep Sea Waters at the Depth of 1500 m Off the Coast of the Ulleung Island in the East Sea (Korea)

Kim¹,

Khang²

2012

The Korean Journal of Microbiology

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Microbial diversity in the 1500 m depth sea waters off the coast of Ulleung island of the East Sea, Korea, was investigated. Genomic DNAs were extracted directly from the marine microbes filtered through ultramembrane filters. Pyrosequencing of 16S rDNAs of these microbes resulted in 13,029 reads, of which uncultured bacteria consisted of 54.1%, alphaproteobacteria 23.4%, and gammaproteobacteria 22.3%. Other classes such as flavobacteria, actinobacteria, and epsilonproteobacteria were distributed within 0.2% of total reads. Among the cultivable bacteria, it was found that Rhodobacteraceae family of alphaproteobacteria, Alteromonadaceae, Halomonadaceae, and Piscirickettsiaceae families of gammaproteobacteria were mostly distributed in the deep-sea waters.

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Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

Cited by 51 publications

References 60 publications

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

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

Comparison of Bacterial Diversity in the Water Columns of Goseong Deep Seawaters

Marine Prokaryotic Diversity of the Deep Sea Waters at the Depth of 1500 m Off the Coast of the Ulleung Island in the East Sea (Korea)

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