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Integrating pan-genome with metagenome for microbial community profiling
2021
Computational and Structural Biotechnology Journal
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Advances in sequencing technology have led to the increased availability of genomes and metagenomes, which has greatly facilitated microbial pan-genome and metagenome analysis in the community. ...
, and function in communities. ...
Metagenomics can be used for taxonomic analysis and functional analysis to track community dynamics [21] . ...
doi:10.1016/j.csbj.2021.02.021
pmid:33841754
pmcid:PMC8010324
fatcat:cy6ub5uvwrcx3j3bor7uy4wovu
GPU-Meta-Storms: Computing the similarities among massive microbial communities using GPU
2013
2013 7th International Conference on Systems Biology (ISB)
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Therefore, the high-performance of GPU-Meta-Storms in comparison with massive metagenomic samples could thus enable in-depth data mining from massive metagenomic data, and make the real-time analysis and ...
In this work, we have developed an optimized GPU-based metagenomic comparison algorithm, GPU-Meta-Storms, to evaluate the quantitative phylogenetic similarity among massive metagenomic samples, and implemented ...
Fig. 1 . 1 An example for common binary phylogenetic tree with leaf node abundance and branch length of two metagenomic samples. P1 and P2 values are the abundance of two samples in each species. ...
doi:10.1109/isb.2013.6623796
fatcat:czgh6l3h4reqzk55znycsbvhaa
Tapping Soil Microbiota: Overlooked Underground Players in Agricultural Production
2019
World Journal of Agriculture and Soil Science
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Despite the abundance and diversity, soil microorganisms have been largely overlooked until recent a few years, due to the untapped functions caused by the difficulties in microbe isolation and culture ...
Soil microbiota, by definition, is the microbial communities that reside in specific soil niches. ...
It should be noted that although shotgun metagenomics can analyze the presence or absence of the microbial functional genes in the soil microbiota, this is merely an analysis at DNA level and can only ...
doi:10.33552/wjass.2019.03.000557
fatcat:vbla44qt5req3dsop3y6khzv5y
Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature
2020
Frontiers in Microbiology
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A combination of SSU rRNA gene diversity, metagenomic RNA features diversity, phylogenetic affiliation of metagenome encoded proteins, uniformly (R = 0.99) indicates the abundance of Bacteroidetes followed ...
These results highlight the human gut microbial features and metabolic bioprocess involved in vanillin catabolism to overcome its antimicrobial activity. ...
Despite it, variability in microbial taxonomic distribution and abundance profile was observed across various populations. ...
doi:10.3389/fmicb.2020.588545
pmid:33193247
pmcid:PMC7605359
fatcat:z54o2kaoajcobdcwcimytjxoau
Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation
2015
BMC Genomics
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Results: In this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional ...
Conclusions: Metagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation ...
Acknowledgements This work was supported by the National Natural Science Foundation of China (31360268 and 31160229). We thank Dr. ...
doi:10.1186/s12864-015-1378-7
pmid:25887697
pmcid:PMC4369366
fatcat:qnkwng52qjagra53wrpsuv7mdu
Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data
2012
Bioinformatics
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However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure ...
It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar ...
ACKNOWLEDGEMENTS We thank Professor Tao Jiang and Xingping Cui from University of California, Riverside (UCR) for insightful comments and discussions. Conflict of interest: None declared. ...
doi:10.1093/bioinformatics/bts470
pmid:22843983
fatcat:ao4vkc3lgnem7mbq4vzaryc2be
Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis
2017
BMC Genomics
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Integrative analysis of metagenomic samples from multiple periodontitis studies is a powerful way to examine microbiota diversity and interactions within host oral cavity. ...
Methods: A total of 43 subjects were recruited to participate in two previous studies profiling the microbial community of human subgingival plaque samples using shotgun metagenomic sequencing. ...
Acknowledgements We thank David Martin for editorial assistance in English language. ...
doi:10.1186/s12864-016-3254-5
pmid:28198672
pmcid:PMC5310281
fatcat:5odkh33rjbbthb36vdvbym5bci
Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing
2012
Journal of Microbiological Methods
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However, data correlating total microbial composition and their functions are lacking. ...
Archaea, fungi and viruses made up the minor communities in the overall microbial diversity. ...
Kelly S Swanson for providing canine metagenomics data. ...
doi:10.1016/j.mimet.2012.01.001
pmid:22265636
pmcid:PMC7114314
fatcat:orm44w67cffh3c7cgv446qx6uy
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
2021
eLife
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Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously ...
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. ...
PhyloPhlAn 3 PhyloPhlAn 3 is an easy-to-use method to perform taxonomic contextualization and phylogenetic analysis of microbial genomes and of metagenome-assembled genomes (MAGs). ...
doi:10.7554/elife.65088
pmid:33944776
pmcid:PMC8096432
fatcat:cuk4wnr3vvhjxekdjtuybmjnpq
Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community
2017
Biotechnology for Biofuels
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Functional analysis and carbohydrate-active enzyme profiles confirmed that APACMC had been successfully enriched for the targeted functions. ...
Phylogenetic analysis showed that APACMC harbored a broad range of pectinolytic bacteria and many of them were previously unrecognized. ...
A more accurate microbial taxonomic analysis and function characterization were conducted. ...
doi:10.1186/s13068-017-0885-y
pmid:28852421
pmcid:PMC5568718
fatcat:imco52sfg5e3hfclckz2tfzg5a
Metagenomic Analysis of the Pygmy Loris Fecal Microbiome Reveals Unique Functional Capacity Related to Metabolism of Aromatic Compounds
2013
PLoS ONE
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The comparative analysis of function classification revealed that the metagenome of the pygmy loris was characterized by an overrepresentation of those sequences involved in aromatic compound metabolism ...
An analysis of 78,619 pyrosequencing reads generated from pygmy loris fecal DNA extracts was performed to help better understand the microbial diversity and functional capacity of the pygmy loris gut microbiome ...
host and the diet adopted by the host [1] . ...
doi:10.1371/journal.pone.0056565
pmid:23457582
pmcid:PMC3574064
fatcat:3bfijzeorzfh5m672bd2qirxva
Computational meta'omics for microbial community studies
2014
Molecular Systems Biology
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This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. ...
Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. ...
of metagenome assembly in the human microbiome. ...
doi:10.1038/msb.2013.22
pmid:23670539
pmcid:PMC4039370
fatcat:dkg3vcg4pzakrhxyjtnxecerrq
Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics
2021
Frontiers in Microbiology
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The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. ...
Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders. ...
We adopted a metagenomic approach to establish whether gut microbial communities differ between two closely related Pardosa species in the Pardosa laura group, namely, P. agraria and P. laura, and further ...
doi:10.3389/fmicb.2021.758794
pmid:34975785
pmcid:PMC8718803
fatcat:yt3bsfkvnff3nff6r4uq7efpty
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
2020
BMC Bioinformatics
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Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to ...
Abundance estimates at genome resolution are provided for each sample in a dataset. ...
genomes; C) a phylogenetic tree of MAGs with average abundance in feces and cecum on a centered log 2 scale; D) a heatmap of abundance on a centered log 2 scale in which MAGs were clustered by phylogenetic ...
doi:10.1186/s12859-020-03585-4
pmid:32571209
fatcat:j25xtujnz5dnjhvtw2cvwdgliu
Shotgun metagenomics, from sampling to analysis
2017
Nature Biotechnology
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Understanding the functions and characterizing specific strains of these communities offer biotechnological promise in therapeutic discovery, or innovative ways to synthesize products using microbial factories ...
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and human health. ...
Assembly-free metagenomic profiling Taxonomic profiling of metagenomes identifies which microbial species are present in a metagenome, and estimates their abundance. ...
doi:10.1038/nbt.3935
pmid:28898207
fatcat:r4sddqxi7vfh3iautypgdvlxmu
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