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Integrating pan-genome with metagenome for microbial community profiling

Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning
2021 Computational and Structural Biotechnology Journal  
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

Xiaoquan Su, Xuetao Wang, Jian Xu, Kang Ning
2013 2013 7th International Conference on Systems Biology (ISB)  
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

Yuan Wang
2019 World Journal of Agriculture and Soil Science  
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

Monika Yadav, Rajesh Pandey, Nar Singh Chauhan
2020 Frontiers in Microbiology  
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

Bo Xu, Weijiang Xu, Junjun Li, Liming Dai, Caiyun Xiong, Xianghua Tang, Yunjuan Yang, Yuelin Mu, Junpei Zhou, Junmei Ding, Qian Wu, Zunxi Huang
2015 BMC Genomics  
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

X. Su, J. Xu, K. Ning
2012 Bioinformatics  
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

Dongmei Ai, Ruocheng Huang, Jin Wen, Chao Li, Jiangping Zhu, Li Charlie Xia
2017 BMC Genomics  
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

Hein Min Tun, Manreetpal Singh Brar, Nina Khin, Li Jun, Raymond Kin-Hi Hui, Scot E. Dowd, Frederick Chi-Ching Leung
2012 Journal of Microbiological Methods  
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

Francesco Beghini, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart (+5 others)
2021 eLife  
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

Man Zhou, Peng Guo, Tao Wang, Lina Gao, Huijun Yin, Cheng Cai, Jie Gu, Xin Lü
2017 Biotechnology for Biofuels  
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

Bo Xu, Weijiang Xu, Fuya Yang, Junjun Li, Yunjuan Yang, Xianghua Tang, Yuelin Mu, Junpei Zhou, Zunxi Huang, Paul D. Cotter
2013 PLoS ONE  
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

N. Segata, D. Boernigen, T. L. Tickle, X. C. Morgan, W. S. Garrett, C. Huttenhower
2014 Molecular Systems Biology  
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

Runbiao Wu, Luyu Wang, Jianping Xie, Zhisheng Zhang
2021 Frontiers in Microbiology  
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

Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski, Lee Ann McCue
2020 BMC Bioinformatics  
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

Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman, Nicola Segata
2017 Nature Biotechnology  
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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