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Correcting for batch effects in case-control microbiome studies [article]

Sean Gibbons, Claire Duvallet, Eric J. Alm
<span title="2017-07-24">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In this paper, we compare different batch-correction methods applied to microbiome case-control studies.  ...  Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses.  ...  Therefore, model-free methods are needed for 492 correcting batch effects across microbiome datasets. Fortunately, case-control 493 studies can be internally normalized by their own control samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/165910">doi:10.1101/165910</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ejpzbkezefdtzmtfwfbkgvbdxu">fatcat:ejpzbkezefdtzmtfwfbkgvbdxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503165937/https://www.biorxiv.org/content/biorxiv/early/2018/03/17/165910.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1e/51/1e514b1d7b8c9dc5f74120df7eb9900ab2eec0ed.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/165910"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Correcting for batch effects in case-control microbiome studies

Sean M. Gibbons, Claire Duvallet, Eric J. Alm, Morgan Langille
<span title="2018-04-23">2018</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Acknowledgments We thank Sean Kearney and members of the Alm and Irizarry labs for helpful feedback, and  ...  Here, we describe a model-free data-normalization procedure for controlling batch effects in case-control microbiome studies that enables pooling data across studies.  ...  Methods developed for batch-correction in microarray data, like limma and ComBat, can partially reduce batch effects in microbiome studies (Figs 2-4) , but appear to obscure real patterns if batch effects  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006102">doi:10.1371/journal.pcbi.1006102</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29684016">pmid:29684016</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5940237/">pmcid:PMC5940237</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hnugsqcpyvd3ricodlshp7dsqe">fatcat:hnugsqcpyvd3ricodlshp7dsqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428110135/https://dspace.mit.edu/bitstream/handle/1721.1/117510/pcbi.1006102.pdf;jsessionid=A5798D5113B3B6E4A73D97DAB98046D7?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c4/98/c498802c7a385c6c9566bd07d235fda162f279e8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006102"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940237" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Population Structure Discovery in Meta-Analyzed Microbial Communities and Inflammatory Bowel Disease [article]

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier, Curtis Huttenhower
<span title="2020-08-31">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We have thus developed MMUPHin (Meta-analysis Methods with a Uniform Pipeline for Heterogeneity in microbiome studies) for joint normalization, meta-analysis, and population structure discovery using microbial  ...  Microbial community studies in general, and of the human microbiome in inflammatory bowel disease (IBD) in particular, have now achieved a scale at which it is practical to associate features of the microbiome  ...  be approached with caution, since in 373 many cases unwanted sources of technical variation between studies (i.e. batch effects) are so 374 large as to potentially mask biological signals even after correction  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.08.31.261214">doi:10.1101/2020.08.31.261214</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z32fip35orfudfvmsbrs77nd5a">fatcat:z32fip35orfudfvmsbrs77nd5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201211154511/https://www.biorxiv.org/content/biorxiv/early/2020/08/31/2020.08.31.261214.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/31/54/3154cef95f4d128581e2ae20b227e0dc31dc5a5a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.08.31.261214"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Evaluating supervised and unsupervised background noise correction in human gut microbiome data

Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin, Nandita R. Garud, Nicola Segata
<span title="2022-02-07">2022</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Supervised methods to correct for background noise, originally designed for gene expression and RNA-seq data, are commonly applied to microbiome data but may be limited because they cannot account for  ...  As new and larger metagenomic datasets become increasingly available, background noise correction will become essential for generating reproducible microbiome analyses.  ...  McLaren for helpful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1009838">doi:10.1371/journal.pcbi.1009838</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35130266">pmid:35130266</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8853548/">pmcid:PMC8853548</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3kva7busdnavvgjjsbaphvmyca">fatcat:3kva7busdnavvgjjsbaphvmyca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220210050042/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009838&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/65/b5/65b562251ac2d627ea6b33c06d7e3fffe1ff1940.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1009838"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8853548" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Assessing and removing the effect of unwanted technical variations in microbiome data [article]

Muhamad Fachrul, Guillaume Méric, Michael Inouye, Sünje Johanna Pamp, Agus Salim
<span title="2021-05-22">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Additionally, we benchmarked the performance of a novel batch correcting tool used in this study, RUV-III-NB (https://github.com/limfuxing/ruvIIInb/), to other popular batch correction methods, including  ...  Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations.  ...  variation in datasets and the effects of correcting for batch 185 effects, we performed principal component analysis (PCA) on the microbiome composition matrix 186 data and calculated the silhouette statistics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.21.445058">doi:10.1101/2021.05.21.445058</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tx6os26hhjbl7otm3dbzf6glwm">fatcat:tx6os26hhjbl7otm3dbzf6glwm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716201409/https://www.biorxiv.org/content/biorxiv/early/2021/05/25/2021.05.21.445058.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9e/b7/9eb7856cee83c8d6dde9d8084c0e0282031cc236.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.21.445058"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A multivariate method to correct for batch effects in microbiome data [article]

Yiwen Wang, Kim-Anh Lê Cao
<span title="2020-10-28">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We compare our approaches with existing batch correction methods removeBatchEffect and ComBat on simulated and three case studies.  ...  The resulting batch effect corrected data can then be input in any downstream statistical analysis.  ...  Acknowledgments We thank A/Prof Olivier Chapleur from INRAE for his help in interpreting the variable selection results from the AD data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.27.358283">doi:10.1101/2020.10.27.358283</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qxsvo55wmvc7nog4izqgm7ypla">fatcat:qxsvo55wmvc7nog4izqgm7ypla</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201212162930/https://www.biorxiv.org/content/biorxiv/early/2020/10/28/2020.10.27.358283.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0b/af/0bafd7c7fb6c2e8cc6146ecbef682e21ff9cb4c0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.27.358283"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Increasing Comparability and Utility of Gut Microbiome Studies in Parkinson's Disease: A Systematic Review

Jeffrey M. Boertien, Pedro A.B. Pereira, Velma T.E. Aho, Filip Scheperjans
<span title="2019-09-04">2019</span> <i title="IOS Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rjfvujhshbbnhe2c6qorj3du6e" style="color: black;">Journal of Parkinson&#39;s Disease</a> </i> &nbsp;
Accordingly, sixteen human case-control studies have published gut microbiome composition changes in PD and reported over 100 differentially abundant taxa covering all taxonomic levels from phylum to genus  ...  Here, differences in methodologies and the presence of possible confounders in the study populations are assessed for their potential to confound the results of gut microbiome studies in PD.  ...  Besides the method of lysis, which will be the same for case and control samples in studies, contamination of reagents can introduce batch effects that might drive artificial differences between PD and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/jpd-191711">doi:10.3233/jpd-191711</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31498131">pmid:31498131</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6839453/">pmcid:PMC6839453</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fouqna5sgzaxbhhv7gkzatccie">fatcat:fouqna5sgzaxbhhv7gkzatccie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200509161414/https://helda.helsinki.fi/bitstream/handle/10138/307426/jpd_9_jpd191711.pdf;jsessionid=99EE3864FB36F846B8B785A69FB8375C?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d1/fa/d1fa2e6b95af2c478259717d6ee96c3b69d5c55c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/jpd-191711"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839453" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota [article]

Shirin Moossavi, Kelsey Fehr, Theo J. Moraes, Ehsan Khafipour, Meghan B. Azad
<span title="2020-04-23">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Low biomass samples in microbiome research are prone to reagent contamination; yet, quality control procedures for low biomass samples in large-scale microbiome studies are not well established.ResultsIn  ...  control efforts in low biomass microbiome research.  ...  are 153 infrequently reported for microbiome studies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.20.052035">doi:10.1101/2020.04.20.052035</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2pkomsg2nbajja3v6ho7ktze7m">fatcat:2pkomsg2nbajja3v6ho7ktze7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200509125834/https://www.biorxiv.org/content/biorxiv/early/2020/04/23/2020.04.20.052035.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ea/67/ea67a52a8b70754ea25bb4f8fcaa760232dddff1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.20.052035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study

Martijn G. H. Sanders, Tamar Nijsten, Joost Verlouw, Robert Kraaij, Luba M. Pardo, Thomas L. Dawson
<span title="2021-05-24">2021</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Methods This was a cross sectional study embedded in a population-based study.  ...  Associations between the microbiome composition of cases and controls was calculated using multivariate statistics (permANOVA) and univariate statistics.  ...  We tested for differences in the microbiome composition between SD cases and controls using permANOVA.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0251136">doi:10.1371/journal.pone.0251136</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34029350">pmid:34029350</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lgbxkfo5jjhmvnujwrrgcsetzi">fatcat:lgbxkfo5jjhmvnujwrrgcsetzi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716075909/https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pone.0251136/1/pone.0251136.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&amp;X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210716%2Fauto%2Fstorage%2Fgoog4_request&amp;X-Goog-Date=20210716T062454Z&amp;X-Goog-Expires=86400&amp;X-Goog-SignedHeaders=host&amp;X-Goog-Signature=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" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/09/82/0982f05203dfacae24ce83851022daaaacd892c2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0251136"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Large-Scale Meta-Longitudinal Microbiome Data with a Known Batch Factor

Vera-Khlara S. Oh, Robert W. Li
<span title="2022-02-22">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/githwx23ynaxdoftesby3jya3y" style="color: black;">Genes</a> </i> &nbsp;
We highlight that the influence of batch factors is significant on subsequent downstream analyses, including longitudinal differential abundance tests, by performing a case study of microbiome time course  ...  data with two treatment groups and a simulation study of mimic microbiome longitudinal counts.  ...  Note that blue bars indicate samples that still show batch effect in two corrected datasets (ARSyNSeq and ComBatSeq) and uncorrected data. Figure 5 . 5 Figure 5.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/genes13030392">doi:10.3390/genes13030392</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35327945">pmid:35327945</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8953633/">pmcid:PMC8953633</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o4lypft57fgkffsj6qvv56vk6m">fatcat:o4lypft57fgkffsj6qvv56vk6m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220502123627/https://mdpi-res.com/d_attachment/genes/genes-13-00392/article_deploy/genes-13-00392-v2.pdf?version=1645611881" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f1/2f/f12f95bd6cfe6645d853f0e16ca92212200b402b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/genes13030392"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8953633" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions

Federico Baldini, on behalf of the NCER-PD Consortium, Johannes Hertel, Estelle Sandt, Cyrille C. Thinnes, Lorieza Neuberger-Castillo, Lukas Pavelka, Fay Betsou, Rejko Krüger, Ines Thiele
<span title="2020-06-09">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/sim25qtjzrbhfpgmid2b4zhpd4" style="color: black;">BMC Biology</a> </i> &nbsp;
Herein, we addressed this question by an analysis of stool samples from the Luxembourg Parkinson's Study (n = 147 typical PD cases, n = 162 controls).  ...  While alterations in the gut microbiome composition have been reported in PD, their functional consequences remain unclear.  ...  Acknowledgements We would like to give special thanks to all the participating patients in the study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12915-020-00775-7">doi:10.1186/s12915-020-00775-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32517799">pmid:32517799</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x26n4kvykbgqronbdg7wqouh5a">fatcat:x26n4kvykbgqronbdg7wqouh5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200610055900/https://bmcbiol.biomedcentral.com/track/pdf/10.1186/s12915-020-00775-7" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a8/86/a886179388a0e9b643fc3d9d77838c6710052fc0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12915-020-00775-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota

Shirin Moossavi, Kelsey Fehr, Ehsan Khafipour, Meghan B. Azad
<span title="2021-02-10">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wf7hw6dszneotfrzxhzcmknpdy" style="color: black;">Microbiome</a> </i> &nbsp;
Low biomass samples in microbiome research are prone to reagent contamination; yet, quality control procedures for low biomass samples in large-scale microbiome studies are not well established.  ...  Conclusion This study provides important insight to advance quality control efforts in low biomass microbiome research.  ...  Acknowledgements We are grateful to all the families who took part in this study, and the whole CHILD team, which includes interviewers, nurses, computer and laboratory technicians, clerical workers, research  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40168-020-00998-4">doi:10.1186/s40168-020-00998-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33568231">pmid:33568231</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5zeag2oagvhnbjejn2jpwzdf6y">fatcat:5zeag2oagvhnbjejn2jpwzdf6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716110923/https://prism.ucalgary.ca/bitstream/handle/1880/113092/40168_2020_Article_998.pdf;jsessionid=E6E188D052D5A8EFA42F1B08D29709A5?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/23/cc/23cc8aecf609be52c8d0a1469550ed032a9ba497.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40168-020-00998-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Benchmark of data processing methods and machine learning models for gut microbiome-based diagnosis of inflammatory bowel disease [article]

Ryszard Kubinski, Jean-Yves Djamen-Kepaou, Timur Zhanabaev, Alex Hernandez-Garcia, Stefan Bauer, Falk Hildebrand, Tamas Korcsmaros, Sani Karam, Prévost Jantchou, Kamran Kafi, Ryan D. Martin
<span title="2021-05-04">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
IBD diagnostic tools.ResultsWe collected fifteen 16S rRNA microbiome datasets (7707 samples) from North America to benchmark combinations of gut microbiome features, data normalization methods, batch  ...  Prior to training a non-linear machine learning model on taxonomic features, it is important to apply a compositional normalization method and remove batch effects with the naive zero-centering method.  ...  We would also like to thank Sébastien Giguère (Valence Discovery) for his guidance during our methodology development.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.03.442488">doi:10.1101/2021.05.03.442488</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yqrcwfs2ujbcvco5fxdcm2gufm">fatcat:yqrcwfs2ujbcvco5fxdcm2gufm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716204135/https://www.biorxiv.org/content/biorxiv/early/2021/05/04/2021.05.03.442488.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a4/ab/a4ab0fb0d8d56ea61bd51d1e5b1cfefa889d4f1c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.03.442488"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Meta-analysis generates and prioritizes hypotheses for translational microbiome research

Claire Duvallet
<span title="2018-01-19">2018</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hqhbgym6bfdm5jsesxfb3g5wza" style="color: black;">Microbial Biotechnology</a> </i> &nbsp;
Researchers can attempt to correct for these batch effects computationally, but such methods may be effective in only a limited number of cases (e.g. case-control studies; Gibbons et al., 2017) .  ...  In the future, methods-focused meta-analyses should be undertaken to identify ways to improve our tools, for example by developing methods to correct for batch across studies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/1751-7915.13047">doi:10.1111/1751-7915.13047</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29349912">pmid:29349912</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5812236/">pmcid:PMC5812236</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/db5gfj7w5zfwncedkaxxsntfz4">fatcat:db5gfj7w5zfwncedkaxxsntfz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191013112836/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5812236&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8a/b8/8ab878b6e1649deb687d606260e8881d78bdb128.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/1751-7915.13047"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812236" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Gut microbiome alterations in fecal samples of treatment-naïve de novo Parkinson's disease patients [article]

Jeffrey M Boertien, Kirsi Murtomäki, Pedro AB Pereira, Sygrid van der Zee, Tuomas H Mertsalmi, Reeta Levo, Tanja Nojonen, Elina Mäkinen, Elina Jaakkola, Pia Laine, Lars Paulin, Eero Pekkonen (+4 others)
<span title="2022-02-22">2022</span> <i title="Cold Spring Harbor Laboratory"> medRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Relevant variables such as technical batches, diet and constipation were assessed for their potential effects.  ...  Here, the gut microbiome composition of treatment-naïve de novo PD subjects was assessed compared to healthy controls (HC) in two large independent case-control cohorts (n=136 and 56 PD, n=85 and 87 HC  ...  We thank Kari Lindholm for the help in the data collection. We thank Velma Aho for her work on the Finnish gut microbiome PD follow-up study and her advice concerning data analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.02.18.22270887">doi:10.1101/2022.02.18.22270887</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hboodxa2rbgoncqgrb4fjqy55a">fatcat:hboodxa2rbgoncqgrb4fjqy55a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220423133733/https://www.medrxiv.org/content/medrxiv/early/2022/02/22/2022.02.18.22270887.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cf/d9/cfd997006fa820d6b022794991f3b512ec34ccb8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.02.18.22270887"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> medrxiv.org </button> </a>
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