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Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting

Davide Albanese, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati, Rachel Brem
2015 PLoS Computational Biology  
Applying the method to public datasets, we show that the data-driven definition of relevant phylogenetic clades accomplished by our ranking strategy identifies features in the samples that are lost if  ...  Here we present PhyloRelief, a novel feature-ranking algorithm that fills this gap by integrating the phylogenetic relationships amongst the taxa into a statistical feature weighting procedure.  ...  Given the availability of phylogenetic data, β -diversity measures incorporating phylogenetic information, such as weighted and unweighted UniFrac [19, 20] have become popular in the context of metagenomic  ... 
doi:10.1371/journal.pcbi.1004186 pmid:25815895 pmcid:PMC4376673 fatcat:fgambesv5jdtpms47sqxkswmce

Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature

Monika Yadav, Rajesh Pandey, Nar Singh Chauhan
2020 Frontiers in Microbiology  
Metagenomic dataset comparison identified the omnipresence of vanillin catabolic features across diverse populations.  ...  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  ...  Despite of a slightly higher diversity of the encoded protein features, a good correlation was observed among phylogenetic affiliation of encoded protein features and SSU rRNA gene-based diversity analysis  ... 
doi:10.3389/fmicb.2020.588545 pmid:33193247 pmcid:PMC7605359 fatcat:z54o2kaoajcobdcwcimytjxoau

Phylogeny-based classification of microbial communities

Olga Tanaseichuk, James Borneman, Tao Jiang
2013 Computer applications in the biosciences : CABIOS  
For example, similarity between species encoded by a phylogenetic tree captures the relationship between OTUs and may be useful for the analysis of complex microbial datasets where the diversity patterns  ...  microbial community data encoded by a phylogenetic tree.  ...  Funding: National Science Foundation (grant DBI-1262107) (in part) and a UCR Seed grant. Conflict of interest: none declared.  ... 
doi:10.1093/bioinformatics/btt700 pmid:24369151 fatcat:lcvht6or3jgz7pvrutekehzjum

PhyloSift: phylogenetic analysis of genomes and metagenomes

Aaron E. Darling, Guillaume Jospin, Eric Lowe, Frederick A. Matsen, Holly M. Bik, Jonathan A. Eisen
2014 PeerJ  
As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by  ...  In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis.  ...  Balance-weighted phylogenetic diversity adjusts these values by the abundance of each lineage in the sample.  ... 
doi:10.7717/peerj.243 pmid:24482762 pmcid:PMC3897386 fatcat:ems5mje33fbybis5rfopdp5m4u

Analyzing Large Microbiome Datasets Using Machine Learning and Big Data

Thomas Krause, Jyotsna Talreja Wassan, Paul Mc Kevitt, Haiying Wang, Huiru Zheng, Matthias Hemmje
2021 BioMedInformatics  
However, in contrast to classical machine learning algorithms, the use of deep learning in metagenomics is still an exception.  ...  Due to the decreasing costs for sequencing, public and private repositories for human metagenomic datasets are growing fast.  ...  Feature Selection and Extraction "Feature Selection and Extraction" is usually applied for removing irrelevant and redundant features from the high-dimensional metagenomic datasets.  ... 
doi:10.3390/biomedinformatics1030010 fatcat:yctuneamu5blfbi4243xu2d6ci

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures [article]

Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D Sepich-Poore, Austin D Swafford (+14 others)
2021 bioRxiv   pre-print
Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing  ...  biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project dataset, and more accurate prediction of human age by the gut microbiomes  ...  command (50) with unweighted UniFrac and weighted UniFrac metrics, based on 391 the WoL reference phylogeny.  ... 
doi:10.1101/2021.04.04.438427 fatcat:jq62gnxir5dmhguha7phmumfw4

SIMCOMP: A Hybrid Soft Clustering of Metagenome Reads [chapter]

Shruthi Prabhakara, Raj Acharya
2010 Lecture Notes in Computer Science  
In the second pass, the remaining fraction of reads are characterized by their species-specific composition based characteristics.  ...  The resulting cluster leaders can be used as an accurate estimate of the phylogenetic composition of the metagenomic dataset.  ...  We would like to thank Mavrommatis Konstantinos for providing datasets in [6] and Elena Marchiori and Fabio Gori for providing useful information about their paper [7] .  ... 
doi:10.1007/978-3-642-16001-1_10 fatcat:tzci2pmeonabzee2ykeinsifrm

Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia

Jacob T. Nearing, Jessica Connors, Scott Whitehouse, Johan Van Limbergen, Tamara Macdonald, Ketan Kulkarni, Morgan G. I. Langille
2019 Frontiers in Cellular and Infection Microbiology  
In this study we found distinctive differences in alpha diversity and beta diversity in samples from patients with infectious complications in the first 6 months of therapy.  ...  Finally, machine learning models based on patient metadata and bacterial species were able to classify samples with high accuracy (84.09%), with bacterial species being the most important classifying features  ...  KK also participated in data analysis and is the principal investigator for the study. SW cataloged, stored, and extracted DNA for all samples.  ... 
doi:10.3389/fcimb.2019.00028 pmid:30838178 pmcid:PMC6389711 fatcat:v4gpstgcibdhjhtpwnqs5lgahu

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.)

Julian Taffner, Tomislav Cernava, Armin Erlacher, Gabriele Berg
2019 Journal of Advanced Research  
Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere.  ...  In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of  ...  Acknowledgements This project was funded by the European Funds for Regional Development (EFRE) and co-supported by the regional government of Styria (Das Land Steiermark, Austria), project code A3-11.P  ... 
doi:10.1016/j.jare.2019.04.008 pmid:31341668 pmcid:PMC6629838 fatcat:b5ujx3t4yfhhnetkiggl2q4ggy

Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels

Naseer Sangwan, Pushp Lata, Vatsala Dwivedi, Amit Singh, Neha Niharika, Jasvinder Kaur, Shailly Anand, Jaya Malhotra, Swati Jindal, Aeshna Nigam, Devi Lal, Ankita Dua (+12 others)
2012 PLoS ONE  
Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples.  ...  This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH).  ...  Faizan Haider from University of Lucknow for helping in sample collection and Dr. Rakesh Sharma and Dr. V.  ... 
doi:10.1371/journal.pone.0046219 pmid:23029440 pmcid:PMC3460827 fatcat:eb6sbyivxnapbep5ez4tiaenwm

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

Kjersti Aagaard, Kevin Riehle, Jun Ma, Nicola Segata, Toni-Ann Mistretta, Cristian Coarfa, Sabeen Raza, Sean Rosenbaum, Ignatia Van den Veyver, Aleksandar Milosavljevic, Dirk Gevers, Curtis Huttenhower (+3 others)
2012 PLoS ONE  
Because microbial abundance and diversity might differ in pregnancy, we sought to generate comparative metagenomic signatures across gestational age strata.  ...  ., the NIH Human Microbiome Project) will enable comprehensive metagenomic characterization of the adult human microbiota, how and when these diverse microbial communities take up residence in the host  ...  In addition to detecting significant features, it also ranks features by effect size, which put features explain most of the biological difference at top.  ... 
doi:10.1371/journal.pone.0036466 pmid:22719832 pmcid:PMC3374618 fatcat:qckggebv7fhrfgdqejoakfcsna

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

Ameen Eetemadi, Navneet Rai, Beatriz Merchel Piovesan Pereira, Minseung Kim, Harold Schmitz, Ilias Tagkopoulos
2020 Frontiers in Microbiology  
We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge  ...  As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients.  ...  Datasets in which items are characterized by a high number of features while the number of items is limited are called high dimensional.  ... 
doi:10.3389/fmicb.2020.00393 pmid:32318028 pmcid:PMC7146706 fatcat:k7v3bgsqgvgtfdkgoaecjsr57e

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria

Matthew R. Olm, Nicholas Bhattacharya, Alexander Crits-Christoph, Brian A. Firek, Robyn Baker, Yun S. Song, Michael J. Morowitz, Jillian F. Banfield
2019 Science Advances  
We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC.  ...  Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants.  ...  Machine learning Preparation of metagenomic data for ML Many individual features were summarized before inclusion in the ML training dataset (table S5) .  ... 
doi:10.1126/sciadv.aax5727 pmid:31844663 pmcid:PMC6905865 fatcat:qwlrx6jgnrhgxhc5n2ot64arzm

Metagenomic Analysis using Phylogenetic Placement – A Review of the First Decade [article]

Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera
2022 arXiv   pre-print
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing.  ...  A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations  ...  This work was financially supported by the Carnegie Institution for Science at Stanford, California, USA, the Klaus Tschira Stiftung gGmbH Foundation in Heidelberg, Germany, and the Deutsche Forschungsgemeinschaft  ... 
arXiv:2202.03534v2 fatcat:vo5uowvjyjd47icuv6z63owzte

Comparative analysis of environmental sequences: potential and challenges

K. U. Foerstner, C. v. Mering, P. Bork
2006 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Environmental sequencing, also dubbed metagenomics, is increasingly being used to obtain insights into organismal communities in diverse habitats, and has a variety of potential applications foreseeable  ...  diversity, how to avoid biases from incomplete data, and how to deal with differences in species dominance or genome sizes?  ...  PHYLOGENETIC VERSUS FUNCTIONAL DIFFERENCES BETWEEN METAGENOMES While several metagenome properties are obvious, or easy to obtain (e.g. table 1), other features such as the phylogenetic spectrum or the  ... 
doi:10.1098/rstb.2005.1809 pmid:16524840 pmcid:PMC1609345 fatcat:pk2cwcpo6fh63bt22wpmzvnaza
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