Publications

Systematic Analyses Uncover Robust Salivary Microbial Signatures and Host-Microbiome Perturbations in Oral Squamous Cell Carcinoma
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DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis
Microbial data analysis poses significant challenges due to its high dimensionality, sparsity, and compositionality. Recent advances …
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A Conserved Interdomain Microbial Network Underpins Cadaver Decomposition despite Environmental Variables
Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly …
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Alterations in Gut Microbiota and Metabolites Associated with Altitude-Induced Cardiac Hypertrophy in Rats during Hypobaric Hypoxia Challenge
The gut microbiota is involved in host responses to high altitude. However, the dynamics of intestinal microecology and their …
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Phytochemicals Delivery Systems in Muscle Food Preservation: An Updated Review of Micro/Nano Encapsulation, Active Edible Packaging and Their Combinations
The quality assurance of muscle foods poses a significant challenge, as they serve as crucial dietary sources for human health. …
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Screening of Lactic Acid Bacteria from Freshwater Fish Intestines and Their Effects on Growth, Immunity, and Disease Resistance in Zebrafish
This study aims to isolate the freshwater fish–derived potential probiotics and evaluate their beneficial effects on the growth, …
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Impacts of Food Additives on Gut Microbiota and Host Health
The rapidly expanding food industry necessitates the use of food additives to achieve specific purposes. However, this raises new …
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Epimedium Polysaccharides Mitigates Porphyromonas Gingivalis-Exacerbated Intestinal Inflammation by Suppressing the Th17 Pathway and Modulating the Gut Microbiota
This study aimed to investigate the potential alleviating effect of Epimedium polysaccharide (EP) on intestinal inflammation aggravated …
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Green Tea Polyphenols Reduced Porphyromonas Gingivalis Virulence and Ameliorated Aggravated Gut Inflammation by Improving Immunity and Gut Microbiota Dysbiosis
Porphyromonas gingivalis (PG), a key periodontal pathogen, has been implicated in various systemic diseases, including colorectal …
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Partial Order Relation--Based Gene Ontology Embedding Improves Protein Function Prediction
Protein annotation has long been a challenging task in computational biology. Gene Ontology (GO) has become one of the most popular …
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Effects of Vaginal Microbiota Transfer on the Neurodevelopment and Microbiome of Cesarean-Born Infants: A Blinded Randomized Controlled Trial
$<$h2$>$Summary$<$/h2$><$p$>$The microbiomes of cesarean-born infants differ from vaginally delivered infants and are …
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Paired Microbiome and Metabolome Analyses Associate Bile Acid Changes with Colorectal Cancer Progression
Colorectal cancer (CRC) is driven by genomic alterations in concert with dietary influences, with the gut microbiome implicated as an …
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Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/-- Bacteria
PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact …
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Meta-Analysis Reveals Helicobacter Pylori Mutual Exclusivity and Reproducible Gastric Microbiome Alterations during Gastric Carcinoma Progression
Accumulating evidence shows that the gastric bacterial community may contribute to the development of gastric cancer (GC). However, the …
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StrainPanDA: Linked Reconstruction of Strain Composition and Gene Content Profiles via Pangenome-Based Decomposition of Metagenomic Data
Microbial strains of variable functional capacities coexist in microbiomes. Current bioinformatics methods of strain analysis cannot …
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Systematic Evaluation of Antimicrobial Food Preservatives on Glucose Metabolism and Gut Microbiota in Healthy Mice
Certain antimicrobial preservatives (APs) have been shown to perturb gut microbiota. So far, it is not yet fully known that whether …
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Cancer Type Classification Using Plasma Cell-Free RNAs Derived from Human and Microbes
The utility of cell-free nucleic acids in monitoring cancer has been recognized by both scientists and clinicians. In addition to human …
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Diurnal and Eating-Associated Microbial Patterns Revealed via High-Frequency Saliva Sampling
The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, …
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Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation
Understanding the microbial and chemical diversities, as well as what affects these diversities, is important for modern manufacturing …
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An Examination of Data from the American Gut Project Reveals That the Dominance of the Genus Bifidobacterium Is Associated with the Diversity and Robustness of the Gut Microbiota
Bifidobacterium and Lactobacillus are beneficial for human health, and many strains of these two genera are widely used as probiotics. …
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Gut Microbiome-Targeted Modulations Regulate Metabolic Profiles and Alleviate Altitude-Related Cardiac Hypertrophy in Rats
Evidence suggests that gut microbiome changes upon hypobaric hypoxia exposure; however, it remains elusive whether this microbiome …
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Zebrafish Model for Human Gut Microbiome-Related Studies: Advantages and Limitations
Germ-free models and bacterial transplantation technology facilitate the mechanism study of the host-gut microbe interaction. Among …
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Gut Microbiota from Green Tea Polyphenol-Dosed Mice Improves Intestinal Epithelial Homeostasis and Ameliorates Experimental Colitis
Alteration of the gut microbiota may contribute to the development of inflammatory bowel disease (IBD). Epigallocatechin-3-gallate …
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A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition
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Toxicant Substitutes in Immunological Assays for Mycotoxins Detection: A Mini Review
Recurring mycotoxins contamination has posedaseriousthreatto food safety worldwide. Competitive immunoassays are widely used techniques …
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PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community
The dysbiosis of gut microbiota is associated with the pathogenesis of human disease. However, observing shifts in the microbe …
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Vitamin D Metabolites and the Gut Microbiome in Older Men
The vitamin D receptor is highly expressed in the gastrointestinal tract where it transacts gene expression. With current limited …
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Alteration in Gut Microbiota Is Associated with Dysregulation of Cytokines and Glucocorticoid Therapy in Systemic Lupus Erythematosus
A growing corpus of evidence implicates the involvement of the commensal microbiota and immune cytokines in the initiation and …
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Multiple-Disease Detection and Classification across Cohorts via Microbiome Search
Microbiome-based disease classification depends on well-validated disease-specific models or a priori organismal markers. These are …
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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age
Human gut microbiomes are known to change with age, yet the relative value of human microbiomes across the body as predictors of age, …
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Phylogenomics of 10,575 Genomes Reveals Evolutionary Proximity between Domains Bacteria and Archaea
The authors build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on 381 markers. The results …
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Optimizing Sequencing Protocols for Leaderboard Metagenomics by Combining Long and Short Reads
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of …
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Best Practices for Analysing Microbiomes
Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best …
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Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue
Abstract Microbes can be used effectively as trace evidence, at least in research settings. However, it is unknown whether skin …
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Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2
Correspondence,
Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andr\'es Mauricio Caraballo-Rodr\'iguez, John Chase, Emily K. Cope, Ricardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G. I. Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey v. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J. J. Van Der Hooft, Fernando Vargas, Yoshiki V\'azquez-Baeza, Emily Vogtmann, Max Von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H. D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J. Gregory Caporaso
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Identification of New High Affinity Targets for Roquin Based on Structural Conservation
Abstract. Post-transcriptional gene regulation controls the amount of protein produced from a specific mRNA by altering both its decay …
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Chlorogenic Acid Attenuates Cadmium-Induced Intestinal Injury in Sprague--Dawley Rats
Chronic exposure to cadmium (Cd) causes remarkable damage to the liver and gastrointestinal tract. Previous studies have revealed that …
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Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems
Studying perturbations in the gut ecosystem using animal models of disease continues to provide valuable insights into the role of the …
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A Gut Microbiome Signature for Cirrhosis Due to Nonalcoholic Fatty Liver Disease
Development of cirrhosis in individuals with non-alcoholic fatty liver disease can predict mortality. Here the authors used a unique …
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Calour: An Interactive, Microbe-Centric Analysis Tool
Microbiome analyses can be challenging because microbial strains are numerous, and often, confounding factors in the data set are also …
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Striped UniFrac: Enabling Microbiome Analysis at Unprecedented Scale
Correspondence
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Microbiome Tools for Forensic Science
Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and …
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Microbial Effects of Livestock Manure Fertilization on Freshwater Aquaculture Ponds Rearing Tilapia (Oreochromis Shiranus) and North African Catfish (Clarias Gariepinus)
The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial …
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Antibiotic-Induced Microbiome Depletion Alters Metabolic Homeostasis by Affecting Gut Signaling and Colonic Metabolism
Antibiotic-induced microbiome depletion is one of the most common approaches to modulate the gut microbiome. Here the authors …
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Taxon-Specific Aerosolization of Bacteria and Viruses in an Experimental Ocean-Atmosphere Mesocosm
Factors controlling the transfer of microbes from the ocean to the atmosphere are unclear. Here, Michaud et al. study this process in …
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American Gut: An Open Platform for Citizen Science Microbiome Research
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have …
Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip v. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey v. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki V\'azquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, The American Gut Consortium, Rob Knight
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Exposure to Toxic Metals Triggers Unique Responses from the Rat Gut Microbiota
Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the …
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Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new …
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Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction
$<$h3$>$ABSTRACT$<$/h3$>$ $<$p$>$Gut microbiota dysbiosis contributes to the onset and perpetuation of inflammatory …
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Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models
Death investigations often include an effort to establish the postmortem interval (PMI) in cases in which the time of death is …
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Guiding Longitudinal Sampling in IBD Cohorts
We read with interest the work by Pascal et al published recently in Gut .1 Here, they report the volatile microbial signatures of …
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A Communal Catalogue Reveals Earth's Multiscale Microbial Diversity
$<$p$>$As phase 1 of the Earth Microbiome Project, analysis of 16S ribosomal RNA sequences from more than 27,000 environmental …
Luke R. Thompson, Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann, Jose A. Navas-Molina, Stefan Janssen, Evguenia Kopylova, Yoshiki V\'azquez-Baeza, Antonio Gonz\'alez, James T. Morton, Siavash Mirarab, Zhenjiang Zech Xu, Lingjing Jiang, Mohamed F. Haroon, Jad Kanbar, Qiyun Zhu, Se Jin Song, Tomasz Kosciolek, Nicholas A. Bokulich, Joshua Lefler, Colin J. Brislawn, Gregory Humphrey, Sarah M. Owens, Jarrad Hampton-Marcell, Donna Berg-Lyons, Valerie McKenzie, Noah Fierer, Jed A. Fuhrman, Aaron Clauset, Rick L. Stevens, Ashley Shade, Katherine S. Pollard, Kelly D. Goodwin, Janet K. Jansson, Jack A. Gilbert, Rob Knight, The Earth Microbiome Project Consortium, Jose L. Agosto Rivera, Lisa Al-Moosawi, John Alverdy, Katherine R. Amato, Jason Andras, Largus T. Angenent, Dionysios A. Antonopoulos, Amy Apprill, David Armitage, Kate Ballantine, Jir\textasciicaron\'i B\'arta, Julia K. Baum, Allison Berry, Ashish Bhatnagar, Monica Bhatnagar, Jennifer F. Biddle, Lucie Bittner, Bazartseren Boldgiv, Eric Bottos, Donal M. Boyer, Josephine Braun, William Brazelton, Francis Q. Brearley, Alexandra H. Campbell, J. Gregory Caporaso, Cesar Cardona, JoLynn Carroll, S. Craig Cary, Brenda B. Casper, Trevor C. Charles, Haiyan Chu, Danielle C. Claar, Robert G. Clark, Jonathan B. Clayton, Jose C. Clemente, Alyssa Cochran, Maureen L. Coleman, Gavin Collins, Rita R. Colwell, M\'onica Contreras, Benjamin B. Crary, Simon Creer, Daniel A. Cristol, Byron C. Crump, Duoying Cui, Sarah E. Daly, Liliana Davalos, Russell D. Dawson, Jennifer Defazio, Fr\'ed\'eric Delsuc, Hebe M. Dionisi, Maria Gloria Dominguez-Bello, Robin Dowell, Eric A. Dubinsky, Peter O. Dunn, Danilo Ercolini, Robert E. Espinoza, Vanessa Ezenwa, Nathalie Fenner, Helen S. Findlay, Irma D. Fleming, Vincenzo Fogliano, Anna Forsman, Chris Freeman, Elliot S. Friedman, Giancarlo Galindo, Liza Garcia, Maria Alexandra Garcia-Amado, David Garshelis, Robin B. Gasser, Gunnar Gerdts, Molly K. Gibson, Isaac Gifford, Ryan T. Gill, Tugrul Giray, Antje Gittel, Peter Golyshin, Donglai Gong, Hans-Peter Grossart, Kristina Guyton, Sarah-Jane Haig, Vanessa Hale, Ross Stephen Hall, Steven J. Hallam, Kim M. Handley, Nur A. Hasan, Shane R. Haydon, Jonathan E. Hickman, Glida Hidalgo, Kirsten S. Hofmockel, Jeff Hooker, Stefan Hulth, Jenni Hultman, Embriette Hyde, Juan Diego Ib\'a\~nez-\'Alamo, Julie D. Jastrow, Aaron R. Jex, L. Scott Johnson, Eric R. Johnston, Stephen Joseph, Stephanie D. Jurburg, Diogo Jurelevicius, Anders Karlsson, Roger Karlsson, Seth Kauppinen, Colleen T. E. Kellogg, Suzanne J. Kennedy, Lee J. Kerkhof, Gary M. King, George W. Kling, Anson v. Koehler, Monika Krezalek, Jordan Kueneman, Regina Lamendella, Emily M. Landon, Kelly Lane-DeGraaf, Julie LaRoche, Peter Larsen, Bonnie Laverock, Simon Lax, Miguel Lentino, Iris I. Levin, Pierre Liancourt, Wenju Liang, Alexandra M. Linz, David A. Lipson, Yongqin Liu, Manuel E. Lladser, Mariana Lozada, Catherine M. Spirito, Walter P. MacCormack, Aurora MacRae-Crerar, Magda Magris, Antonio M. Mart\'in-Platero, Manuel Mart\'in-Vivaldi, L. Margarita Mart\'inez, Manuel Mart\'inez-Bueno, Ezequiel M. Marzinelli, Olivia U. Mason, Gregory D. Mayer, Jamie M. McDevitt-Irwin, James E. McDonald, Krista L. McGuire, Katherine D. McMahon, Ryan McMinds, M\'onica Medina, Joseph R. Mendelson, Jessica L. Metcalf, Folker Meyer, Fabian Michelangeli, Kim Miller, David A. Mills, Jeremiah Minich, Stefano Mocali, Lucas Moitinho-Silva, Anni Moore, Rachael M. Morgan-Kiss, Paul Munroe, David Myrold, Josh D. Neufeld, Yingying Ni, Graeme W. Nicol, Shaun Nielsen, Jozef I. Nissimov, Kefeng Niu, Matthew J. Nolan, Karen Noyce, Sarah L. O'Brien, Noriko Okamoto, Ludovic Orlando, Yadira Ortiz Castellano, Olayinka Osuolale, Wyatt Oswald, Jacob Parnell, Juan M. Peralta-S\'anchez, Peter Petraitis, Catherine Pfister, Elizabeth Pilon-Smits, Paola Piombino, Stephen B. Pointing, F. Joseph Pollock, Caitlin Potter, Bharath Prithiviraj, Christopher Quince, Asha Rani, Ravi Ranjan, Subramanya Rao, Andrew P. Rees, Miles Richardson, Ulf Riebesell, Carol Robinson, Karl J. Rockne, Selena Marie Rodriguezl, Forest Rohwer, Wayne Roundstone, Rebecca J. Safran, Naseer Sangwan, Virginia Sanz, Matthew Schrenk, Mark D. Schrenzel, Nicole M. Scott, Rita L. Seger, Andaine Seguin-Orlando, Lucy Seldin, Lauren M. Seyler, Baddr Shakhsheer, Gabriela M. Sheets, Congcong Shen, Yu Shi, Hakdong Shin, Benjamin D. Shogan, Dave Shutler, Jeffrey Siegel, Steve Simmons, Sara Sj\"oling, Daniel P. Smith, Juan J. Soler, Martin Sperling, Peter D. Steinberg, Brent Stephens, Melita A. Stevens, Safiyh Taghavi, Vera Tai, Karen Tait, Chia L. Tan, Neslihan Tas\c, D. Lee Taylor, Torsten Thomas, Ina Timling, Benjamin L. Turner, Tim Urich, Luke K. Ursell, Daniel Van Der Lelie, William Van Treuren, Lukas Van Zwieten, Daniela Vargas-Robles, Rebecca Vega Thurber, Paola Vitaglione, Donald A. Walker, William A. Walters, Shi Wang, Tao Wang, Tom Weaver, Nicole S. Webster, Beck Wehrle, Pamela Weisenhorn, Sophie Weiss, Jeffrey J. Werner, Kristin West, Andrew Whitehead, Susan R. Whitehead, Linda A. Whittingham, Eske Willerslev, Allison E. Williams, Stephen A. Wood, Douglas C. Woodhams, Yeqin Yang, Jesse Zaneveld, Iratxe Zarraonaindia, Qikun Zhang, Hongxia Zhao
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Evidence for Fungal and Chemodenitrification Based N extsubscript2O Flux from Nitrogen Impacted Coastal Sediments
$<$p$>$Predicting nitrous oxide emissions (N\textsubscript2O) remains difficult due to the numerous N\textsubscript2O production …
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Normalization and Microbial Differential Abundance Strategies Depend upon Data Characteristics
Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, …
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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the …
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Lifestyle Chemistries from Phones for Individual Profiling
Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often …
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Tiny Microbes, Enormous Impacts: What Matters in Gut Microbiome Studies?
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Secondary Structure Prediction of Single Sequences Using RNAstructure
RNA secondary structure is often predicted using folding thermodynamics. RNAstructure is a software package that includes structure …
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Prediction of Secondary Structures Conserved in Multiple RNA Sequences
RNA structure is conserved by evolution to a greater extent than sequence. Predicting the conserved structure for multiple homologous …
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Experiment-Assisted Secondary Structure Prediction with RNAstructure
Experimental probing data can be used to improve the accuracy of RNA secondary structure prediction. The software package RNAstructure …
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Microbiome-Wide Association Studies Link Dynamic Microbial Consortia to Disease
Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are dramatically increasing access to the microbiome …
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Correlation Detection Strategies in Microbial Data Sets Vary Widely in Sensitivity and Precision
Disruption of healthy microbial communities has been linked to numerous diseases, yet microbial interactions are little understood. …
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Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies
Immediate freezing at -20$^\circ$C or below has been considered the gold standard for microbiome preservation, yet this approach is not …
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Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project
The role of the human microbiome is the subject of continued investigation resulting in increased understanding. However, current …
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Open-Source Sequence Clustering Methods Improve the State Of the Art
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into …
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Microbial Community Assembly and Metabolic Function during Mammalian Corpse Decomposition
Decomposition spawns a microbial zoo The death of a large animal represents a food bonanza for microorganisms. Metcalf et al. monitored …
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Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota
Microbiota-based prediction of chronic infections is promising yet not well established. Early childhood caries (ECC) is the most …
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Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures
Recently, non-coding RNAs (ncRNAs) have been discovered with novel functions, and it has been appreciated that there is pervasive …
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Subsistence Strategies in Traditional Societies Distinguish Gut Microbiomes
Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we …
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Ribosomal RNA, the Lens into Life
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
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Dietary Effects on Human Gut Microbiome Diversity
The human gut harbours diverse and abundant microbes, forming a complex ecological system that interacts with host and environmental …
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Which Is More Important for Classifying Microbial Communities: Who's There or What They Can Do?
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial …
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Meta-Analyses of Human Gut Microbes Associated with Obesity and IBD
Recent studies have linked human gut microbes to obesity and inflammatory bowel disease, but consistent signals have been difficult to …
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Structural Basis for Diversity in the SAM Clan of Riboswitches
In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). …
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Advancing Our Understanding of the Human Microbiome Using QIIME
Abstract High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in …
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Air Proteins Control Differential TRAMP Substrate Specificity for Nuclear RNA Surveillance
RNA surveillance systems function at critical steps during the formation and function of RNA molecules in all organisms. The RNA …
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Statistical Evaluation of Improvement in RNA Secondary Structure Prediction
With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms …
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Deep Sequencing-Based Identification of Small Non-Coding RNAs in Streptomyces Coelicolor
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Multilign: An Algorithm to Predict Secondary Structures Conserved in Multiple RNA Sequences
Motivation: With recent advances in sequencing, structural and functional studies of RNA lag behind the discovery of sequences. …
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Intestinal Microbiota and Immune Related Genes in Sea Cucumber (Apostichopus Japonicus) Response to Dietary $eta$-Glucan Supplementation
$\beta$-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal …
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