• Title/Summary/Keyword: functional metagenomics

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Functional Metagenomics using Stable Isotope Probing: a Review

  • Vo, Nguyen Xuan Que;Kang, Ho-Jeong;Park, Joon-Hong
    • Environmental Engineering Research
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    • v.12 no.5
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    • pp.231-237
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    • 2007
  • The microbial eco-physiology has been the vital key of microbial ecological research. Unfortunately, available methods for direct identity of microorganisms and for the investigation of their activity in complicated community dynamics are limited. In this study, metagenomics was considered as a promising functional genomics tool for improving our understanding of microbial eco-physiology. Its potential applications and challenges were also reviewed. Because of tremendous diversity in microbial populations in environment, sequence analysis for whole metagenomic libraries from environmental samples seems to be unrealistic to most of environmental engineering researchers. When a target function is of interest, however, sequence analysis for whole metagenomic libraries would not be necessary. For this case, nucleic acids of active populations of interest can be selectively gained using another cutting-edge functional genomic tool, SIP (stable isotope probing) technique. If functional genomes isolated by SIP can be transferred into metagenomic library, sequence analysis for such selected functional genomes would be feasible because the reduced size of clone library may become adequate for sequencing analysis. Herein, integration of metagenomics with SIP was suggested as a novel functional genomics approach to study microbial eco-physiology in environment.

Bacillus subtilis as a Tool for Screening Soil Metagenomic Libraries for Antimicrobial Activities

  • Biver, Sophie;Steels, Sebastien;Portetelle, Daniel;Vandenbol, Micheline
    • Journal of Microbiology and Biotechnology
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    • v.23 no.6
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    • pp.850-855
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    • 2013
  • Finding new antimicrobial activities by functional metagenomics has been shown to depend on the heterologous host used to express the foreign DNA. Therefore, efforts are devoted to developing new tools for constructing metagenomic libraries in shuttle vectors replicatable in phylogenetically distinct hosts. Here we evaluated the use of the Escherichia coli-Bacillus subtilis shuttle vector pHT01 to construct a forest-soil metagenomic library. This library was screened in both hosts for antimicrobial activities against four opportunistic bacteria: Proteus vulgaris, Bacillus cereus, Staphylococcus epidermidis, and Micrococcus luteus. A new antibacterial activity against B. cereus was found upon screening in B. subtilis. The new antimicrobial agent, sensitive to proteinase K, was not active when the corresponding DNA fragment was expressed in E. coli. Our results validate the use of pHT01 as a shuttle vector and B. subtilis as a host to isolate new activities by functional metagenomics.

Oral Metagenomic Analysis Techniques

  • Chung, Sung-Kyun
    • Journal of dental hygiene science
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    • v.19 no.2
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    • pp.86-95
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    • 2019
  • The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.

Decoding the intestinal microbiota repertoire of sow and weaned pigs using culturomic and metagenomic approaches

  • Mun, Daye;Kim, Hayoung;Shin, Minhye;Ryu, Sangdon;Song, Minho;Oh, Sangnam;Kim, Younghoon
    • Journal of Animal Science and Technology
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    • v.63 no.6
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    • pp.1423-1432
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    • 2021
  • To elucidate the role and mechanism of microbes, we combined culture-dependent and culture-independent approaches to investigate differences in gut bacterial composition between sows and weaned pigs. Under anaerobic conditions, several nonselective and selective media were used for isolation from fecal samples. All isolated bacteria were identified and classified through 16S rRNA sequencing, and the microbiota composition of the fecal samples was analyzed by metagenomics using next generation sequencing (NGS) technology. A total of 278 and 149 colonies were acquired from the sow and weaned pig fecal samples, respectively. Culturomics analysis revealed that diverse bacterial genus and species belonged to Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were isolated from sow and weaned pigs. When comparing culture-dependent and culture-independent analyses, 191 bacterial species and 2 archaeal bacterial species were detected through culture-independent analysis, and a total of 23 bacteria were isolated through a culture-dependent approach, of which 65% were not detected by metagenomics. In conclusion, culturomics and metagenomics should be properly combined to fully understand the intestinal microbiota, and livestock-derived microbial resources should be informed by culturomic approaches to understand and utilize the mechanism of host-microbe interactions.

Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review

  • Choi, Ki Young;Lee, Tae Kwon;Sul, Woo Jun
    • Asian-Australasian Journal of Animal Sciences
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    • v.28 no.9
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    • pp.1217-1225
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    • 2015
  • Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

Deciphering Functions of Uncultured Microorganisms (난배양성 미생물의 기능 분석 방법)

  • Kim, Jeong-Myeong;Song, Sae-Mi;Jeon, Che-Ok
    • Korean Journal of Microbiology
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    • v.45 no.1
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    • pp.1-9
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    • 2009
  • Microbes within complex communities show quite different physiology from pure cultured microbes. However, historically the study of microbes has focused on single species in pure culture and most of microbes are unculturable in our labs, so understanding of complex communities lags behind understanding of pure cultured cells. Methodologies including stable isotope probing (SIP), a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR), isotope micrarray, and metagenomics have given insights into the uncultivated majority to link phylogenetic and functional information. Here, we review some of the most recent literatures, with an emphasis on methodological improvements to the sensitivity and utilities of these methods to link phylogeny and function in complex microbial communities.

Bacillus amyloliquefaciens and Saccharomyces cerevisiae feed supplements improve growth performance and gut mucosal architecture with modulations on cecal microbiota in red-feathered native chickens

  • Lee, Tzu-Tai;Chou, Chung-Hsi;Wang, Chinling;Lu, Hsuan-Ying;Yang, Wen-Yuan
    • Animal Bioscience
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    • v.35 no.6
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    • pp.869-883
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    • 2022
  • Objective: The aim of study was to investigate the effects of in-feed supplementation of Bacillus amyloliquefaciens (BA) and Saccharomyces cerevisiae (SC) on growth performance, gut integrity, and microbiota modulations in red-feathered native chickens (RFCs). Methods: A total of 18,000 RFCs in a commercial farm were evenly assigned into two dietary treatments (control diet; 0.05% BA and 0.05% SC) by randomization and raised for 11 weeks in two separate houses. Fifty RFCs in each group were randomly selected and raised in the original house with the partition for performance evaluations at the age of 9 and 11 weeks. Six non-partitioned RFCs per group were randomly selected for analyses of intestinal architecture and 16S rRNA metagenomics. Results: Feeding BA and SC increased the body weight and body weight gain, significantly at the age of 11 weeks (p<0.05). The villus height/crypt ratio in the small intestines and Firmicutes to Bacteroidetes ratio were also notably increased (p<0.05). The supplementation did not disturb the microbial community structure but promote the featured microbial shifts characterized by the significant increments of Bernesiella, Prevotellaceae_NK3B31_group, and Butyrucimonas, following remarkable decrements of Bacteroides, Rikenellaceae_RC9_gut_group, and Succinatimonas in RFCs with growth benefits. Besides, functional pathways of peptidoglycan biosynthesis, nucleotide excision repair, glycolysis/gluconeogenesis, and aminoacyl transfer ribonucleic acid (tRNA) biosynthesis were significantly promoted (p<0.05). Conclusion: In-feed supplementation of BA and SC enhanced the growth performance, improved mucosal architectures in small intestines, and modulated the cecal microbiota and metabolic pathways in RFCs.

Metagenomics analysis of methane metabolisms in manure fertilized paddy soil (메타게놈 분석을 이용한 돈분뇨 처리에 의한 논토양에서 메탄대사에 미치는 영향 조사)

  • Nguyen, Son G.;Ho, Cuong Tu;Lee, Ji-Hoon;Unno, Tatsuya
    • Korean Journal of Microbiology
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    • v.52 no.2
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    • pp.157-165
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    • 2016
  • Under flooded rice fields, methanogens produce methane which comes out through rice stalks, thus rice fields are known as one of the anthropogenic sources of atmospheric methane. Studies have shown that use of manure increases amount of methane emission from rice. To investigate mechanisms by which manure boosts methane emission, comparative soil metagenomics between inorganically (NPK) and pig manure fertilized paddy soils (PIG) were conducted. Results from taxonomy analysis showed that more abundant methanogens, methanotrophs, methylotrophs, and acetogens were found in PIG than in NPK. In addition, BLAST results indicated more abundant carbohydrate mabolisetm functional genes in PIG. Among the methane metabolism related genes, PIG sample showed higher abundance of methyl-coenzyme M reductase (mcrB/mcrD/mcrG) and trimethylamine-corrinoid protein Co-methyltransferase (mttB) genes. In contrast, genes that down regulate methane emission, such as trimethylamine monooxygenase (tmm) and phosphoserine/homoserine phosphotransferase (thrH), were observed more in NPK sample. In addition, more methanotrophic genes (pmoB/amoB/mxaJ), were found more abundant in PIG sample. Identifying key genes related to methane emission and methane oxidation may provide fundamental information regarding to mechanisms by which use of manure boosts methane emission from rice. The study presented here characterized molecular variation in rice paddy, introduced by the use of pig manure.

Metagenome, the Untapped Microbial Genome, toward Discovery of Novel Microbial Resources and Application into the Plant Pathology

  • Lee, Seon-Woo
    • The Plant Pathology Journal
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    • v.21 no.2
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    • pp.93-98
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    • 2005
  • Molecular ecological studies of microbial communities revealed that only tiny fraction of total microorganisms in nature have been identified and characterized, because the majority of them have not been cultivated. A concept, metagenome, represents the total microbial genome in natural ecosystem consisting of genomes from both culturable microorganisms and viable but non-culturable bacteria. The construction and screening of metagenomic libraries in culturable bacteria constitute a valuable resource for obtaining novel microbial genes and products. Several novel enzymes and antibiotics have been identified from the metagenomic approaches in many different microbial communities. Phenotypic analysis of the introduced unknown genes in culturable bacteria could be an important way for functional genomics of unculturable bacteria. However, estimation of the number of clones required to uncover the microbial diversity from various environments has been almost impossible due to the enormous microbial diversity and various microbial population structure. Massive construction of metagenomic libraries and development of high throughput screening technology should be necessary to obtain valuable microbial resources. This paper presents the recent progress in metagenomic studies including our results and potential of metagenomics in plant pathology and agriculture.