Metagenomics as a new technological tool to gain scientific knowledge
30 Jan 2009-World Journal of Microbiology & Biotechnology (Springer Netherlands)-Vol. 25, Iss: 6, pp 945-954
TL;DR: This review addresses the following question, how to take advantage of, and how can the authors improve the, metagenomic technology for accommodating the needs of microbial biologists and enzymologists.
Abstract: Metagenomics (also Environmental Genomics, Ecogenomics or Community Genomics) is an emerging approach to studying microbial communities in the environment. This relatively new technique enables studies of organisms that are not easily cultured in a laboratory, thus differing from traditional microbiology that relies almost entirely on cultured organisms. Metagenomics technology thus holds the premise of new depths of understanding of microbes and, importantly, is a new tool for addressing biotechnological problems, without tedious cultivation efforts. DNA sequencing technology has already made a significant breakthrough, and generation of gigabase-pairs of microbial DNA sequences is not posing a challenge any longer. However, conceptual advances in microbial science will not only rely on the availability of innovative sequencing platforms, but also on sequence-independent tools for getting an insight into the functioning of microbial communities. This is an important issue, as we know that even the best annotations of genomes and metagenomes only create hypotheses of the functionality and substrate spectra of encoded proteins which require experimental testing by classical disciplines such as physiology and biochemistry. In this review, we address the following question, how to take advantage of, and how can we improve the, metagenomic technology for accommodating the needs of microbial biologists and enzymologists?
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TL;DR: A comprehensive review on microbial keratinases is presented giving an account of chronological progress of research along with the major milestones, and major focus has been on the key characteristics of keratinase, such as substrate specificity, keratin degradation mechanisms, molecular properties, and their role in prion decontamination along with other pharmaceutical applications.
Abstract: Keratinases are special proteases which attack the highly recalcitrant keratin substrates. They stand apart from the conventional proteases due to their broad substrate specificity towards a variety of insoluble keratin rich substrates like feather, wool, nail, hair. Owing to this ability, keratinases find immense applications in various environmental and biotechnological sectors. The current boost in keratinase research has come up with the discovery of the ability of keratinases to address the challenging issue of prion decontamination. Here we present a comprehensive review on microbial keratinases giving an account of chronological progress of research along with the major milestones. Major focus has been on the key characteristics of keratinases, such as substrate specificity, keratin degradation mechanisms, molecular properties, and their role in prion decontamination along with other pharmaceutical applications. We conclude by critically evaluating the present state of the keratinases discussing their commercial status along with future research directions.
117 citations
Cites background from "Metagenomics as a new technological..."
...Metagenomic techniques can also be exploited to explore the untapped keratinolytic potential of diverse microflora (Ferrer et al., 2005; Guazzaroni et al., 2009; Steele et al., 2009)....
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TL;DR: This review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.
Abstract: Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity. Thus, we have shifted from the old concept of microbes as harmful organisms to a broader panorama, in which the signal of the relationship between humans and microbes is flexible and directly dependent on our own decisions and practices. In parallel, metagenomics has also been playing a major role in the prospection of “hidden” genetic features and the development of biotechnological applications, through the discovery of novel genes, enzymes, pathways, and bioactive molecules with completely new or improved biochemical functions. Therefore, this review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.
97 citations
Cites background from "Metagenomics as a new technological..."
...In this sense, the later approach allows the overall reconstruction of the community structure, potentially revealing metabolic pathways of the whole microbiome and assigning minor or major geoecological roles to community members [4, 6, 9, 10]....
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TL;DR: The traditional molecular techniques like DGGE, RFLP and FISH are covered with respect to how they are applied to study the composition, diversity and dynamics of insect gut symbiotic microbiota.
Abstract: Insectgutsymbioticmicrobiotaplayessentialrolesinthegrowth,development, pathogenesis and environmental adaptation of host insects. The molecular and systems level analysis of insect gut symbiotic microbial community will allow us to discover novel biocatalysts for biomass deconstruction and to develop innovative strategies for pest management. We hereby review the various molecular biology techniques as applied to insect gut symbiont analysis. This review aims to serve as an informative resource for experimental design and research strategy development in the field. We first discuss various strategies for sample preparation and their pros and cons. The traditional molecular techniques like DGGE, RFLP and FISH are covered with respect to how they are applied to study the composition, diversity and dynamics of insect gut symbiotic microbiota. We then focus on the various 'omics' techniques. The metagenome analysis together with the recent advancements in next-generation sequencing will provide enormous sequencing information, allowing in-depth microbial diversity analysis and modeling of pathways for biological processes such as biomass degradation. The metagenome sequencing will also enable the study of system dynamics and gene expression with metatranscriptome and metaproteome methods. The integration of different 'omics' level data will allow us to understand how insect gut works as a system to carry out its functions. The molecular and systems-level understanding will also guide the reverse design of next-generation biorefinery.
78 citations
Cites background from "Metagenomics as a new technological..."
...The ultimate goal of metagenomics is to acquire a global view of the composition and function of the microbial community (Guazzaroni et al., 2009)....
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TL;DR: A correlation between the composition and putative metabolic functionality of the gut microbiome and host diet is demonstrated, and it is suggested that this relationship could be exploited for the discovery of symbionts and biocatalysts useful for biorefinery applications.
Abstract: Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested that this relationship could be exploited for the discovery of symbionts and biocatalysts useful for biorefinery applications.
64 citations
Cites background from "Metagenomics as a new technological..."
...Metagenome analysis requires comprehensive coverage of most multiple species in the sample [76]....
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Journal Article•
TL;DR: A metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding ‘higher’ Nasutitermes species shows the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis, the first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation.
Abstract: Publisher: NPG; Journal: Nature: Nature; Article Type: Biology letter DOI: 10.1038/nature06269 Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite Falk Warnecke 1 *, Peter Luginbuhl 2 *, Natalia Ivanova 1 , Majid Ghassemian 2 , Toby H. Richardson 2 †, Justin T. Stege 2 , Michelle Cayouette 2 †, Alice C. McHardy 3 †, Gordana Djordjevic 2 , Nahla Aboushadi 2 , Rotem Sorek 1 , Susannah G. Tringe 1 , Mircea Podar 4 , Hector Garcia Martin 1 , Victor Kunin 1 , Daniel Dalevi 1 , Julita Madejska 1 , Edward Kirton 1 , Darren Platt 1 , Ernest Szeto 1 , Asaf Salamov 1 , Kerrie Barry 1 , Natalia Mikhailova 1 , Nikos C. Kyrpides 1 , Eric G. Matson 5 , Elizabeth A. Ottesen 6 , Xinning Zhang 5 , Myriam Hernandez 7 , Catalina Murillo 7 , Luis G. Acosta 7 , Isidore Rigoutsos 3 , Giselle Tamayo 7 , Brian D. Green 2 , Cathy Chang 2 †, Edward M. Rubin 1 , Eric J. Mathur 2 †, Dan E. Robertson 2 , Philip Hugenholtz 1 & Jared R. Leadbetter 5 * DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA. 2 Verenium Corporation (formerly Diversa), 4955 Directors Place, San Diego, California 92121, USA. 3 IBM Thomas J. Watson Research Center, PO Box 218, Yorktown Heights, New York 10598, USA. 4 Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, Tennessee 37831-6026, USA. 5 Department of Environmental Science and Engineering, Division of Biology, Mailcode 138-78, California Institute of Technology, Pasadena, California 91125, USA. INBio, Instituto Nacional de Biodiversidad, Apdo. Postal 22-3100 Santo Domingo de Heredia, Costa Rica. †Present addresses: Synthetic Genomics, Inc., 11149 North Torrey Pines Road, Suite 100, La Jolla, California 92037, USA (T.H.R., E.J.M.); Max Planck Institute for Computer Science, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany (A.C.M.); Stratagene, 11011 North Torrey Pines Road, La Jolla, California 92037, USA (M.C.); E. O. Wilson Foundation, 10190 Telesis Court, San Diego, California 92121, USA (C.C.). *These authors contributed equally to this work. From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms 1 and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis 2 . Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding Nasutitermes species to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important Page 1 of 33
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References
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TL;DR: It is demonstrated through metagenomic and biochemical analyses that changes in the relative abundance of the Bacteroidetes and Firmicutes affect the metabolic potential of the mouse gut microbiota and indicates that the obese microbiome has an increased capacity to harvest energy from the diet.
Abstract: The worldwide obesity epidemic is stimulating efforts to identify host and environmental factors that affect energy balance. Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes. Here we demonstrate through metagenomic and biochemical analyses that these changes affect the metabolic potential of the mouse gut microbiota. Our results indicate that the obese microbiome has an increased capacity to harvest energy from the diet. Furthermore, this trait is transmissible: colonization of germ-free mice with an 'obese microbiota' results in a significantly greater increase in total body fat than colonization with a 'lean microbiota'. These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity.
10,126 citations
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TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Abstract: We have applied “whole-genome shotgun sequencing” to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity. Microorganisms are responsible for most of the biogeochemical cycles that shape the environment of Earth and its oceans. Yet, these organisms are the least well understood on Earth, as the ability to study and understand the metabolic potential of microorganisms has been hampered by the inability to generate pure cultures. Recent studies have begun to explore environ
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TL;DR: Using metabolic function analyses of identified genes, the human genome is compared with the average content of previously sequenced microbial genomes and humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.
Abstract: The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.
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TL;DR: It is shown that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment.
Abstract: The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.
3,535 citations
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TL;DR: MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets, is introduced and provides graphical and statistical output for comparing different data sets.
Abstract: Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random “shotgun” approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.
2,803 citations
"Metagenomics as a new technological..." refers background in this paper
...Therefore, a general strategy for sample processing could be recommended for metagenomic studies in the future, in which multiple microbial groups are processesed separately by using single micro-droplets, cell-free translation systems and cell-sorting (‘‘single-cell genomics’’) and integrate this data with those obtained using mixed microbial communities ( Huson et al. 2007; Lasken 2007; Ishoey et al. 2008)....
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...To circumvent the variability of factors affecting data processing, the overall goals of a metagenomic project have to be balanced with the diversity and structure of the community, allowing an estimation of the necessary amount of sequence to reach a desired assembly depth (Johnson and Slatkin 2006; Huson et al. 2007 )....
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