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1. Full Text EMPeror: A tool for visualizing high-throughput microbial community data
by Vázquez-Baeza, Yoshiki and Pirrung, Meg and Gonzalez, Antonio and Knight, Rob
GigaScience, ISSN 2047-217X, 2013, Volume 2, Issue 1, pp. 16 - 16
Background: As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers... 
Microbial ecology | Data visualization | QIIME | MULTIDISCIPLINARY SCIENCES
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2. Full Text Longitudinal analysis of microbial interaction between humans and the indoor environment
by Lax, Simon and Smith, Daniel P and Hampton-Marcell, Jarrad and Owens, Sarah M and Handley, Kim M and Scott, Nicole M and Gibbons, Sean M and Larsen, Peter and Shogan, Benjamin D and Weiss, Sophie and Metcalf, Jessica L and Ursell, Luke K and Vázquez-Baeza, Yoshiki and Van Treuren, Will and Hasan, Nur A and Gibson, Molly K and Colwell, Rita and Dantas, Gautam and Knight, Rob and Gilbert, Jack A and Argonne National Lab. (ANL), Argonne, IL (United States)
Science, ISSN 0036-8075, 08/2014, Volume 345, Issue 6200, pp. 1048 - 1052
The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families... 
BACTERIA | FUNGI | HUMAN SKIN MICROBIOTA | MULTIDISCIPLINARY SCIENCES | DIVERSITY | TIME | HOUSE | SPREAD | SURFACES | Floors and Floorcoverings | Microbiota - physiology | Beds - microbiology | Humans | Bacteria - genetics | Foot - microbiology | Host-Pathogen Interactions | Pets - microbiology | Animals | Microbiota - genetics | Surface Properties | Bacteria - classification | Family | Bacteria - pathogenicity | Hand - microbiology | Nose - microbiology | Metagenome | Household Articles | Host-bacteria relationships | Household ecology | Microbiological research | Research | Families & family life | Microorganisms | Residences | Communities | Households | Health | Indoor environments | Signatures | Contamination | Inhabitants | Indoor Microbiology | Bacteria | Human Microbiome
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3. Full Text Normalization and microbial differential abundance strategies depend upon data characteristics
by Weiss, Sophie and Xu, Zhenjiang Zech and Peddada, Shyamal and Amir, Amnon and Bittinger, Kyle and Gonzalez, Antonio and Lozupone, Catherine and Zaneveld, Jesse R and Vázquez-Baeza, Yoshiki and Birmingham, Amanda and Hyde, Embriette R and Knight, Rob
Microbiome, ISSN 2049-2618, 2017, Volume 5, Issue 1, p. 27
Background: Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library... 
Differential abundance | Normalization | Statistics | Microbiome | EXPRESSION ANALYSIS | DISPERSION | MICROBIOLOGY | BIOCONDUCTOR | UNIFRAC | MODELS | RNA-SEQ | PACKAGE | DIVERSITY | DNA, Bacterial - genetics | Gene Library | Base Sequence | Ecosystem | Humans | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Microbial Consortia - genetics | Bacterial Load - statistics & numerical data | Bacteria - genetics | Sequence Analysis, DNA | Microorganisms | Research | Comparative analysis | Ribosomal RNA
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4. Full Text A communal catalogue reveals Earth's multiscale microbial diversity
by Thompson, Luke R and Sanders, Jon G and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J and Prill, Robert J and Tripathi, Anupriya and Gibbons, Sean M and Ackermann, Gail and Navas-Molina, Jose A and Janssen, Stefan and Kopylova, Evguenia and Vázquez-Baeza, Yoshiki and González, Antonio and Morton, James T and Mirarab, Siavash and Xu, Zhenjiang Zech and Jiang, Lingjing and Haroon, Mohamed F and Kanbar, Jad and Zhu, Qiyun and Song, Se Jin and Kosciolek, Tomasz and Bokulich, Nicholas A and Lefler, Joshua and Brislawn, Colin J and Humphrey, Gregory and Owens, Sarah M and Hampton-Marcell, Jarrad and Berg-Lyons, Donna and McKenzie, Valerie and Fierer, Noah and Fuhrman, Jed A and Clauset, Aaron and Stevens, Rick L and Shade, Ashley and Pollard, Katherine S and Goodwin, Kelly D and Jansson, Janet K and Gilbert, Jack A and Knight, Rob and Agosto Rivera, Jose L and Al-Moosawi, Lisa and Alverdy, John and Amato, Katherine R and Andras, Jason and Angenent, Largus T and Antonopoulos, Dionysios A and Apprill, Amy and Armitage, David and Ballantine, Kate and Bárta, Jiří and Baum, Julia K and Berry, Allison and Bhatnagar, Ashish and Bhatnagar, Monica and Biddle, Jennifer F and Bittner, Lucie and Boldgiv, Bazartseren and Bottos, Eric and Boyer, Donal M and Braun, Josephine and Brazelton, William and Brearley, Francis Q and Campbell, Alexandra H and Caporaso, J. Gregory and Cardona, Cesar and Carroll, JoLynn and Cary, S. Craig and Casper, Brenda B and Charles, Trevor C and Chu, Haiyan and Claar, Danielle C and Clark, Robert G and Clayton, Jonathan B and Clemente, Jose C and Cochran, Alyssa and Coleman, Maureen L and Collins, Gavin and Colwell, Rita R and Contreras, Mónica and Crary, Benjamin B and Creer, Simon and Cristol, Daniel A and Crump, Byron C and Cui, Duoying and Daly, Sarah E and Davalos, Liliana and Dawson, Russell D and Defazio, Jennifer and Delsuc, Frédéric and Dionisi, Hebe M and Dominguez-Bello, Maria Gloria and Dowell, Robin and Dubinsky, Eric A and Dunn, Peter O and Ercolini, Danilo and Espinoza, Robert E and Ezenwa, Vanessa and ... and Earth Microbiome Project Consortiu and Earth Microbiome Project Consortium and Naturvetenskapliga fakulteten and Faculty of Sciences and Göteborgs universitet and Gothenburg University and Institutionen för marina vetenskaper and Department of marine sciences
Nature, ISSN 0028-0836, 11/2017, Volume 551, Issue 7681, pp. 457 - 463
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite... 
CONSISTENT | ARCHAEAL | EVOLUTION | MARINE BACTERIAL | GLOBAL PATTERNS | BACTERIAL DIVERSITY | MULTIDISCIPLINARY SCIENCES | OPERON COPY NUMBER | ONTOLOGY | COMMUNITIES | NESTEDNESS | Humans | RNA, Ribosomal, 16S - analysis | Geographic Mapping | Plants - microbiology | Gene Dosage | Archaea - isolation & purification | Biodiversity | Bacteria - genetics | Bacteria - isolation & purification | Ecology - methods | Animals | Microbiota - genetics | RNA, Ribosomal, 16S - genetics | Archaea - genetics | Earth (Planet) | Environmental aspects | Observations | Microbial colonies | Biological diversity | Analytical methods | Nucleotide sequence | Microbiology | Taxonomy | rRNA | Ecology | Genomes | Gene sequencing | Meta-analysis | Earth | Studies | Microorganisms | Ribonucleic acids | Phylogenetics | Bacteria | Deoxyribonucleic acid--DNA | DNA sequencing | Geosciences, Multidisciplinary | Climate Research | Klimatforskning | Oceanografi, hydrologi, vattenresurser | Oceanography, Hydrology, Water Resources | Annan geovetenskap och miljövetenskap | Multidisciplinär geovetenskap | Ekologi | Other Earth and Related Environmental Sciences | CVI Infection Biology | CVI Infectiebiologie | Food Quality and Design | VLAG | Infectiebiologie | Infection Biology
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5. Full Text Meta-analyses of studies of the human microbiota
by Lozupone, Catherine A and Stombaugh, Jesse and Gonzalez, Antonio and Ackermann, Gail and Wendel, Doug and Vázquez-Baeza, Yoshiki and Jansson, Janet K and Gordon, Jeffrey I and Knight, Rob
Genome Research, ISSN 1088-9051, 10/2013, Volume 23, Issue 10, pp. 1704 - 1714
Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the... 
BACTERIA | TWINS | ENTEROTYPES | INTESTINAL MICROBIOTA | BIOCHEMISTRY & MOLECULAR BIOLOGY | PATTERNS | BODY HABITATS | DELIVERY | HUMAN GUT MICROBIOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DISEASE | GENETICS & HEREDITY | DIVERSITY | Crohn Disease - epidemiology | Crohn Disease - genetics | Humans | Metagenomics - methods | Infant | Biodiversity | Bacteria - genetics | Pregnancy Trimester, First | Sequence Analysis, DNA | Pregnancy | Feces - microbiology | Microbiota | DNA, Bacterial - genetics | Aging | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Adult | Crohn Disease - microbiology | Female | Metagenome | Intestines | Genetic aspects | Research | Microbiology | Genetic variation
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6. Full Text Qiita: rapid, web-enabled microbiome meta-analysis
by Gonzalez, Antonio and Navas-Molina, Jose A and Kosciolek, Tomasz and McDonald, Daniel and Vázquez-Baeza, Yoshiki and Ackermann, Gail and DeReus, Jeff and Janssen, Stefan and Swafford, Austin D and Orchanian, Stephanie B and Sanders, Jon G and Shorenstein, Joshua and Holste, Hannes and Petrus, Semar and Robbins-Pianka, Adam and Brislawn, Colin J and Wang, Mingxun and Rideout, Jai Ram and Bolyen, Evan and Dillon, Matthew and Caporaso, J. Gregory and Dorrestein, Pieter C and Knight, Rob and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Nature Methods, ISSN 1548-7091, 10/2018, Volume 15, Issue 10, pp. 796 - 798
Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be... 
DIVERSITY | QIIME | BIOCHEMICAL RESEARCH METHODS | Usage | Public software | Research | Microbiota (Symbiotic organisms) | Analysis | Meta-analysis | Webs | Microbiomes | microbiome, bioinformatics software, open source software
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7. Full Text Temporal variability is a personalized feature of the human microbiome
by Flores, Gilberto E and Caporaso, J Gregory and Henley, Jessica B and Rideout, Jai R.am and Domogala, Daniel and Chase, John and Leff, Jonathan W and Vázquez-Baeza, Yoshiki and Gonzalez, Antonio and Knight, Rob and Dunn, Robert R and Fierer, Noah
Genome biology, ISSN 1474-760X, 2014, Volume 15, Issue 12, pp. 531 - 531
Background: It is now apparent that the complex microbial communities found on and in the human body vary across individuals. What has largely been missing... 
SEARCH | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | PATTERNS | ECOLOGY | DIVERSITY | GUT MICROBIOTA | BACTERIAL | COMMUNITIES | CHILDREN | Genome, Bacterial | Humans | Middle Aged | Tongue - microbiology | Male | Phylogeny | Forehead - microbiology | Healthy Volunteers | Young Adult | Feces - microbiology | Bacteria - isolation & purification | Microbiota | Bacteria - classification | Adult | Female | Hand - microbiology | Genomics - methods | Longitudinal Studies | Research
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8. Full Text Suppression of the gut microbiome ameliorates age‐related arterial dysfunction and oxidative stress in mice
by Brunt, Vienna E and Gioscia‐Ryan, Rachel A and Richey, James J and Zigler, Melanie C and Cuevas, Lauren M and Gonzalez, Antonio and Vázquez‐Baeza, Yoshiki and Battson, Micah L and Smithson, Andrew T and Gilley, Andrew D and Ackermann, Gail and Neilson, Andrew P and Weir, Tiffany and Davy, Kevin P and Knight, Rob and Seals, Douglas R
The Journal of Physiology, ISSN 0022-3751, 05/2019, Volume 597, Issue 9, pp. 2361 - 2378
Age‐related arterial dysfunction, characterized by oxidative stress‐ and inflammation‐mediated endothelial dysfunction and arterial stiffening, is the primary... 
arterial stiffness | endothelial function | inflammation | gut dysbiosis | Ageing | TRIMETHYLAMINE-N-OXIDE | ANTIBIOTICS | PHYSIOLOGY | INTESTINAL MICROBIOTA | ATHEROSCLEROSIS | NEUROSCIENCES | IMPACT | MAJOR SHAREHOLDERS | NITRIC-OXIDE | VASCULAR ENDOTHELIAL DYSFUNCTION | CARDIOVASCULAR-DISEASE ENTERPRISES | Oxidative stress | Medical research | Metabolites | Microbiota (Symbiotic organisms) | Physiological aspects | Medicine, Experimental | Risk factors | Endothelium | Dysbacteriosis | Microbiomes | Antioxidants | Microbiota | Trimethylamine | Antibiotics | Aging | Aorta | Plasma levels | Acetylcholine | Carotid artery | Cardiovascular diseases | Age
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9. Full Text Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection
by Weingarden, Alexa and González, Antonio and Vázquez-Baeza, Yoshiki and Weiss, Sophie and Humphry, Gregory and Berg-Lyons, Donna and Knights, Dan and Unno, Tatsuya and Bobr, Aleh and Kang, Johnthomas and Khoruts, Alexander and Knight, Rob and Sadowsky, Michael J
Microbiome, ISSN 2049-2618, 03/2015, Volume 3, Issue 1, p. 10
Background: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard... 
Short- and long-term changes in microbiota following FMT | MICROBIOLOGY | GUT MICROBIOTA | Infection | Care and treatment | Relapse | Antibiotics | Microbiota (Symbiotic organisms) | RNA | Analysis | Diseases
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10. Full Text SnapShot: The Human Microbiome
by González, Antonio and Vázquez-Baeza, Yoshiki and Knight, Rob
Cell, ISSN 0092-8674, 07/2014, Volume 158, Issue 3, pp. 690 - 690.e1
Trilions of bacteria populate the human body, with research efforts focusing on documenting the complexity of these communities and their contributions to... 
GUT MICROBIOME | BIOCHEMISTRY & MOLECULAR BIOLOGY | CELL BIOLOGY | Pregnancy | Microbiota | Humans | Child, Preschool | Female | Infant | Inflammatory Bowel Diseases - microbiology | Organ Specificity | Obesity - microbiology | Infant, Newborn
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11. Full Text Striped UniFrac: enabling microbiome analysis at unprecedented scale
by McDonald, Daniel and Vázquez-Baeza, Yoshiki and Koslicki, David and McClelland, Jason and Reeve, Nicolai and Xu, Zhenjiang and Gonzalez, Antonio and Knight, Rob
Nature Methods, ISSN 1548-7091, 11/2018, Volume 15, Issue 11, pp. 847 - 848
BIOCHEMICAL RESEARCH METHODS
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12. Full Text Guiding longitudinal sampling in IBD cohorts
by Vázquez-Baeza, Yoshiki and Gonzalez, Antonio and Xu, Zhenjiang Zech and Washburne, Alex and Herfarth, Hans H and Sartor, R Balfour and Knight, Rob
Gut, ISSN 0017-5749, 09/2018, Volume 67, Issue 9, pp. 1743 - 1744
A critical experimental design question for clinical studies is whether a finite budget should best be spent collecting samples from more patients or... 
intestinal microbiology | Crohn's disease | GASTROENTEROLOGY & HEPATOLOGY | Colitis, Ulcerative | Crohn Disease | Humans | Inflammatory bowel disease | Design | Studies | Liver | Microbiomes | Phylogenetics | Phylogeny | Gene expression | Sampling | Patients | 2312 | 1506 | crohn’s disease | PostScript
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13. Full Text Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians
by Allaband, Celeste and McDonald, Daniel and Vázquez-Baeza, Yoshiki and Minich, Jeremiah J and Tripathi, Anupriya and Brenner, David A and Loomba, Rohit and Smarr, Larry and Sandborn, William J and Schnabl, Bernd and Dorrestein, Pieter and Zarrinpar, Amir and Knight, Rob
Clinical Gastroenterology and Hepatology, ISSN 1542-3565, 01/2019, Volume 17, Issue 2, pp. 218 - 230
Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense... 
Prognosis | Gut Microbiome | Diagnosis | Study Design | Clinician | RNA | FECAL SAMPLES | PATTERNS | CLASSIFICATION | IDENTIFICATION | MASS-SPECTROMETRY | METAGENOMICS | COLLECTION METHODS | ECOLOGY | WIDE ASSOCIATION | GASTROENTEROLOGY & HEPATOLOGY | Metabolites | Ribosomal RNA | Analysis | Gastrointestinal diseases
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