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Journal articles on the topic 'QIIME 2'

Author: Grafiati

Published: 8 June 2021

Last updated: 29 July 2025

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1

Keefe, Christopher R., Matthew R. Dillon, Elizabeth Gehret, et al. "Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay." PLOS Computational Biology 19, no. 11 (2023): e1011676. http://dx.doi.org/10.1371/journal.pcbi.1011676.

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Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving many different tools. Additionally, many biologists are not trained in how to effectively record their bioinformatics analysis steps to ensure reproducibility, so critical information is often missing. Software tools used in bioinformatics can automate provenance tracking of the results they generate, removing most barriers to bioinformatics reproducibility.

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2

Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, et al. "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature Biotechnology 37, no. 8 (2019): 852–57. http://dx.doi.org/10.1038/s41587-019-0209-9.

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Raspet, Isaiah, Elizabeth Gehret, Chloe Herman, et al. "Facilitating bootstrapped and rarefaction-based microbiome diversity analysis with q2-boots." F1000Research 14 (January 15, 2025): 87. https://doi.org/10.12688/f1000research.156295.1.

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Background We present q2-boots, a QIIME 2 plugin that facilitates bootstrapped and rarefaction-based microbiome diversity analysis. This plugin provides eight new actions that allow users to apply any of thirty different alpha diversity metrics and twenty-two beta diversity metrics to bootstrapped or rarefied feature tables, using a single QIIME 2 Pipeline command, or more granular QIIME 2 Action commands. Results Given a feature table, an even sampling depth, and the number of iterations to perform (n), the command qiime boots core-metrics will resample the feature table n times and compute a

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Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, et al. "Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature Biotechnology 37, no. 9 (2019): 1091. http://dx.doi.org/10.1038/s41587-019-0252-6.

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Bolyen, Evan, Matthew R. Dillon, Nicholas A. Bokulich, et al. "Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity." F1000Research 9 (June 29, 2020): 657. http://dx.doi.org/10.12688/f1000research.24751.1.

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The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined

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Bolyen, Evan, Matthew R. Dillon, Nicholas A. Bokulich, et al. "Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity." F1000Research 9 (October 28, 2020): 657. http://dx.doi.org/10.12688/f1000research.24751.2.

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The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined

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7

Shah, Manasi S., Todd Z. DeSantis, Thomas Weinmaier, et al. "Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer." Gut 67, no. 5 (2017): 882–91. http://dx.doi.org/10.1136/gutjnl-2016-313189.

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ObjectiveColorectal cancer (CRC) is the second leading cause of cancer-associated mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC and indicate transition in the adenoma–carcinoma sequence. Re-analysing raw sequence and metadata from several studies uniformly, we sought to identify a composite and generalisable microbial marker for CRC.DesignRaw 16S rRNA gene sequence data sets from nine studies were processed with two pipelines, (1) QIIME closed reference (QIIME-CR) or (2) a strain-specific method herein termed SS-UP (Strain Select, UPARSE bioinformatics

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Zhao, Jingcheng, Yunhui Qi, Peng Liu, et al. "Prebiotic Effects of a Cranberry Beverage in a Randomized, Placebo-Controlled, Crossover Clinical Trial." Current Developments in Nutrition 5, Supplement_2 (2021): 1190. http://dx.doi.org/10.1093/cdn/nzab054_045.

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Abstract Objectives The objective was to evaluate the prebiotic effects of a milled whole cranberry beverage on modulating the gut microbiota in young adults. Methods Adults (n = 17; ages 18–42 y; BMI 30.5 ± 3.1 kg/m2) were enrolled in a 60-d, two-period, randomized, placebo-controlled, crossover clinical study. Throughout the study, participants were fed a standardized 10-d cycle menu on site. During each 20-d treatment period, participants consumed twice daily a whole cranberry or placebo beverage (240 mL per serving). Treatment periods were separated by an 11-wk washout period and preceded

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Heidrich, Vitor, Petr Karlovsky, and Lukas Beule. "‘SRS’ R Package and ‘q2-srs’ QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)." Applied Sciences 11, no. 23 (2021): 11473. http://dx.doi.org/10.3390/app112311473.

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Several ecological data types, especially microbiome count data, are commonly sample-wise normalized before analysis to correct for sampling bias and other technical artifacts. Recently, we developed an algorithm for the normalization of ecological count data called ‘scaling with ranked subsampling (SRS)’, which surpasses the widely adopted ‘rarefying’ (random subsampling without replacement) in reproducibility and in safeguarding the original community structure. Here, we describe an implementation of the SRS algorithm in the ‘SRS’ R package and the ‘q2-srs’ QIIME 2 plugin. We also provide ac

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10

Rivers, Adam R., Kyle C. Weber, Terrence G. Gardner, Shuang Liu, and Shalamar D. Armstrong. "ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis." F1000Research 7 (September 6, 2018): 1418. http://dx.doi.org/10.12688/f1000research.15704.1.

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The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of t

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11

Liu, Xiang, Jing Tao, Jing Li, et al. "Dysbiosis of Fecal Microbiota in Allergic Rhinitis Patients." American Journal of Rhinology & Allergy 34, no. 5 (2020): 650–60. http://dx.doi.org/10.1177/1945892420920477.

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Background The gut microbiota plays an important role in shaping the immune system and may be closely connected to the development of allergic diseases. Objective This study aimed to determine the gut microbiota composition in Chinese allergic rhinitis (AR) patients as compared with healthy controls (HCs). Methods We collected stool samples from 93 AR patients and 72 age- and sex-matched HCs. Gut microbiota composition was analyzed using QIIME targeting the 16S rRNA gene. Functional pathways were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.

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12

Ramiro-Garcia, Javier, Gerben D. A. Hermes, Christos Giatsis, et al. "NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes." F1000Research 5 (November 23, 2018): 1791. http://dx.doi.org/10.12688/f1000research.9227.2.

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Background: Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises meta-analyses, although this fact is often disregarded. Results: To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence anal

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13

Jayasudha, Rajagopalaboopathi, Taraprasad Das, Sama Kalyana Chakravarthy, et al. "Gut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy." PLOS ONE 15, no. 12 (2020): e0243077. http://dx.doi.org/10.1371/journal.pone.0243077.

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Studies have documented dysbiosis in the gut mycobiome in people with Type 2 diabetes mellitus (T2DM). However, it is not known whether dysbiosis in the gut mycobiome of T2DM patients would be reflected in people with diabetic retinopathy (DR) and if so, is the observed mycobiome dysbiosis similar in people with T2DM and DR. Gut mycobiomes were generated from healthy controls (HC), people with T2DM and people with DR through Illumina sequencing of ITS2 region. Data were analysed using QIIME and R software. Dysbiotic changes were observed in people with T2DM and DR compared to HC at the phyla a

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Bradley, Patrick H., and Katherine S. Pollard. "phylogenize: correcting for phylogeny reveals genes associated with microbial distributions." Bioinformatics 36, no. 4 (2019): 1289–90. http://dx.doi.org/10.1093/bioinformatics/btz722.

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Abstract Summary Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME 2 and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and env

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15

Ramiro-Garcia, Javier, Gerben D. A. Hermes, Christos Giatsis, et al. "NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes." F1000Research 5 (July 22, 2016): 1791. http://dx.doi.org/10.12688/f1000research.9227.1.

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Background Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises true meta-analyses, although this fact is often disregarded. Results To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence a

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16

Dillon, Matthew R., Evan Bolyen, Anja Adamov, et al. "Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops." PLOS Computational Biology 17, no. 6 (2021): e1009056. http://dx.doi.org/10.1371/journal.pcbi.1009056.

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In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had 75 enrolled participants who joined from at least 25 different countries on 6 continents, and we had 22 instructors on 4 continents. In the 5-day workshop, participants worked hands-on with a cloud-based shared compute cluster that we deployed for this course. The event was well received, and participants provided feedback and suggestions in a postworkshop questionnaire. In January of 2021, we follow

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Letunic, Ivica, and Peer Bork. "Interactive Tree Of Life (iTOL) v4: recent updates and new developments." Nucleic Acids Research 47, W1 (2019): W256—W259. http://dx.doi.org/10.1093/nar/gkz239.

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Abstract The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding t

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18

Çebi Kılıçoğlu, Melike. "Ağır Metal ile Kontamine Toprakta Fungal Mikrobiyomun Metagenomik Analizi." Turkish Journal of Agriculture - Food Science and Technology 11, no. 9 (2023): 1671–77. http://dx.doi.org/10.24925/turjaf.v11i9.1671-1677.6261.

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Gelişen sanayi faaliyetleri ile birlikte günümüzün en önemli sorunlarından biri haline gelen ağır metal kontaminasyonu tüm canlı organizmalar için ciddi bir tehdittir. Bazı funguslar ağır metallere karşı direnç mekanizmalarına sahiptir ve bu durum iyileştirme süreçleri için sürdürülebilir bir yaklaşım olarak kabul edilmektedir. Bu çalışmanın amacı ağır metal kontaminasyonunun yüksek oranlarda olduğu alanlardaki dirençli fungal mikrobiyotayı belirleyerek ağır metallerin biyolojik ıslah yaklaşımlarına ışık tutmaktır. Araştırmada yüksek oranda ağır metal kirliliğine sahip Samsun Organize Sanayi B

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19

Derdak, Reda, Javier Quinteiro, Souraya Sakoui, et al. "Isolation and Identification of Dominant Bacteria from Raw Donkey Milk Produced in a Region of Morocco by QIIME 2 and Evaluation of Their Antibacterial Activity." Scientific World Journal 2021 (August 9, 2021): 1–7. http://dx.doi.org/10.1155/2021/6664636.

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Recently, the interest in donkey milk has increased considerably because it proved high nutritive and functional values of their ingredients. Its chemical composition is widely studied, but its microbiota, especially lactic acid bacteria, remains less studied. This study focuses on analyzing, isolating, and identifying lactic acid bacteria and evaluating their capacity to produce biomolecules with antibacterial activity. Among 44 strains identified, 43 are Gram-positive, and most are catalase-negative and cocci-shaped. Five strains were selected to evaluate their antibacterial activity against

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Clemmons, Brooke A., Sung B. Shin, Timothy P. L. Smith, et al. "Ruminal Protozoal Populations of Angus Steers Differing in Feed Efficiency." Animals 11, no. 6 (2021): 1561. http://dx.doi.org/10.3390/ani11061561.

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Feed accounts for as much as 70% of beef production costs, and improvement of the efficiency with which animals convert feed to product has the potential to have substantial financial impact on the beef industry. The rumen microbiome plays a key role in determining feed efficiency; however, previous studies of rumen microbiota have not focused on protozoal communities despite the estimation that these organisms represent approximately 50% of rumen content biomass. Protozoal communities participate in the regulation of bacterial populations and nitrogen cycling—key aspects of microbiome dynamic

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Ryu, Hyewon. "Analysis of gut and mucosal microbiomes in patients with extrahepatic cholangiocarcinoma." Journal of Clinical Oncology 43, no. 4_suppl (2025): 620. https://doi.org/10.1200/jco.2025.43.4_suppl.620.

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620 Background: Cholangiocarcinoma is an aggressive malignancy with a poor prognosis. While gut microbial dysbiosis is linked to various diseases, including biliary disorders and cancer, its association with cholangiocarcinoma remains unclear. Methods: This study compared the mucosal and gut microbiomes of patients with extrahepatic cholangiocarcinoma (n = 21) to those with cholecystitis (n = 21) and healthy individuals (n = 28). Mucosal microbiomes were collected from cancer lesions and gallbladders, with fecal samples obtained from 31 participants. The 16S rRNA gene (V3 and V4 region) was se

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Telmadarrehei, Telmah, Juliet D. Tang, Olanrewaju Raji, et al. "A Study of the Gut Bacterial Community of Reticulitermes virginicus Exposed to Chitosan Treatment." Insects 11, no. 10 (2020): 681. http://dx.doi.org/10.3390/insects11100681.

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A thorough understanding of microbial communities in the gut of lower termites is needed to develop target-specific and environmentally benign wood protection systems. In this study, the bacterial community from Reticulitermes virginicus was examined by Illumina sequencing of 16S ribosomal RNA (rRNA) spanning the V3 and V4 regions. Prior to library preparation, the termites were subjected to five treatments over an 18-day period: three groups were fed on wood treated with 0.5% chitosan, 25% acetic acid, or water, the fourth group was taken directly from the original collection log, and the fif

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Scarsella, Elisa, J. Skyla Fay, Guillaume Jospin, Jessica K. Jarett, Zhandra Entrolezo, and Holly H. Ganz. "Characterization and Description of the Fecal Microbiomes of Domestic Pet Ferrets (Mustela putorius furo) Living in Homes." Animals 13, no. 21 (2023): 3354. http://dx.doi.org/10.3390/ani13213354.

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The domestic ferret (Mustela putorius furo) is a popular companion pet in the United States, with an estimated population of 500,000. Despite being obligate carnivores with a fast digestive system, little is known about their gut microbiomes. This study aims to compare the fecal microbiomes of healthy domestic ferrets and cats, which are both obligate carnivores. We collected and analyzed stool samples from 36 healthy ferrets and 36 healthy cats, sequencing the V4 region of the 16S rRNA gene. Using QIIME 2, we assessed the alpha and beta diversities and identified the taxa differences. Compare

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Barrett, Helen, Luisa Gomez-Arango, Shelley Wilkinson, et al. "A Vegetarian Diet Is a Major Determinant of Gut Microbiota Composition in Early Pregnancy." Nutrients 10, no. 7 (2018): 890. http://dx.doi.org/10.3390/nu10070890.

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The composition of the gut microbiota can be influenced by dietary composition. In pregnancy, the maternal gut microbiome has associations with maternal and infant metabolic status. There is little known regarding the impact of a vegetarian diet in pregnancy on maternal gut microbiota. This study explored the gut microbiota profile in women who were vegetarian or omnivorous in early gestation. Women were selected from participants in the Study of PRobiotics IN Gestational diabetes (SPRING) randomised controlled trial. Nine women identified as vegetarians were matched to omnivorous women in a 1

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Chan, Lok Chun, Yuqi Zhang, Xiaoqing Kuang, et al. "Captopril Alleviates Chondrocyte Senescence in DOCA-Salt Hypertensive Rats Associated with Gut Microbiome Alteration." Cells 11, no. 19 (2022): 3173. http://dx.doi.org/10.3390/cells11193173.

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Gut microbiota is the key controller of healthy aging. Hypertension and osteoarthritis (OA) are two frequently co-existing age-related pathologies in older adults. Both are associated with gut microbiota dysbiosis. Hereby, we explore gut microbiome alteration in the Deoxycorticosterone acetate (DOCA)-induced hypertensive rat model. Captopril, an anti-hypertensive medicine, was chosen to attenuate joint damage. Knee joints were harvested for radiological and histological examination; meanwhile, fecal samples were collected for 16S rRNA and shotgun sequencing. The 16S rRNA data was annotated usi

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Roquigny, Roxane, Amy Novinscak, Geneviève Léger, Nathan Marcoux, David L. Joly, and Martin Filion. "Deciphering the Rhizosphere and Geocaulosphere Microbiomes of Potato Following Inoculation with the Biocontrol Agent Pseudomonas fluorescens Strain LBUM223." Phytobiomes Journal 2, no. 2 (2018): 92–99. http://dx.doi.org/10.1094/pbiomes-03-18-0013-r.

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The phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 shows biocontrol potential against Streptomyces scabies, which causes common scab of potato. To better characterize the impact of inoculating this specific biocontrol agent under field conditions, the microbiomes of the rhizosphere and the geocaulosphere of potato plants were characterized using next-generation sequencing. A single initial application or biweekly applications of LBUM223 were performed up to 11 weeks after planting. Rhizosphere and geocaulosphere soils (when potato tubers were produced) were

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Grosu, Iulian A., Gina C. Pistol, Ionelia Taranu, and Daniela E. Marin. "The Impact of Dietary Grape Seed Meal on Healthy and Aflatoxin B1 Afflicted Microbiota of Pigs after Weaning." Toxins 11, no. 1 (2019): 25. http://dx.doi.org/10.3390/toxins11010025.

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The study investigated the effect of grape seed (GS) meal, aflatoxin (AFB1), or their combination on the large intestine microbiota of weanling piglets. Twenty-four piglets were allocated into four groups based on diet composition: (1) Control group; (2) AFB1 (320 g/kg feed) group; (3) GS group (8% inclusion in the diet); (4) AFB1 + GS group. After 30 days of experiment, the colon content was used for microbiota analyses; after isolation of total bacterial genomic DNA, V3/V4 regions of the 16S rRNA amplicons were sequenced using the Illumina MiSeq platform. The raw sequences were analyzed usin

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Akita, Hironaga, Yoshiki Shinto, and Zen-ichiro Kimura. "Analysis of the Bacterial Community of Metal Scrap Using an Enrichment Culture Approach." Applied Biosciences 2, no. 1 (2023): 23–30. http://dx.doi.org/10.3390/applbiosci2010004.

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Microbiologically influenced corrosion (MIC) of metal alloys is promoted by biofilms formed on metal surfaces. In the marine environment, MIC causes serious metal infrastructure problems, which lead to significant economic losses. In this study, we used an enrichment culture approach to examine the bacterial community that grows on metal surface at levels below the detection limit as a preliminary study for developing guidelines to prevent biofilm formation. An enrichment culture approach was employed to analyze the bacterial community on metal surface without biofilms and corrosion. Genomic D

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May-Mutul, Carla G., Miguel A. López-Garrido, Aileen O’Connor-Sánchez, et al. "Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens." Plants 11, no. 22 (2022): 3098. http://dx.doi.org/10.3390/plants11223098.

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During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota’s alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden)

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Thatrimontrichai, Anucha, Manapat Praditaukrit, Gunlawadee Maneenil, Supaporn Dissaneevate, Kamonnut Singkhamanan, and Komwit Surachat. "Butyrate Producers in Very Low Birth Weight Infants with Neither Culture-Proven Sepsis nor Necrotizing Enterocolitis." Nutrients 17, no. 8 (2025): 1329. https://doi.org/10.3390/nu17081329.

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Background/Objectives: Severe infection (sInfection; either late-onset culture-proven sepsis or necrotizing enterocolitis) in very low birth weight (VLBW) infants increases mortality rates and may show long-term progression. The fecal microbiome composition in VLBW infants with and without sInfection was classified in the sInfection and non-sInfection groups. Methods: Gut microbiomes, secondary information from a previous randomized trial, were analyzed using QIIME 2 software. The biodiversity and abundance of the gut microbiota between the sInfection and non-sInfection groups were compared. R

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Knudsen, Kristel S., Sverre Lehmann, Rune Nielsen, et al. "The lower airways microbiome and antimicrobial peptides in idiopathic pulmonary fibrosis differ from chronic obstructive pulmonary disease." PLOS ONE 17, no. 1 (2022): e0262082. http://dx.doi.org/10.1371/journal.pone.0262082.

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Background The lower airways microbiome and host immune response in chronic pulmonary diseases are incompletely understood. We aimed to investigate possible microbiome characteristics and key antimicrobial peptides and proteins in idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). Methods 12 IPF patients, 12 COPD patients and 12 healthy controls were sampled with oral wash (OW), protected bronchoalveolar lavage (PBAL) and right lung protected sterile brushings (rPSB). The antimicrobial peptides and proteins (AMPs), secretory leucocyte protease inhibitor (SLPI

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Chaiyasut, Chaiyavat, Sasithorn Sirilun, Nucharee Juntarachot, et al. "Effect of Dextranase and Dextranase-and-Nisin-Containing Mouthwashes on Oral Microbial Community of Healthy Adults—A Pilot Study." Applied Sciences 12, no. 3 (2022): 1650. http://dx.doi.org/10.3390/app12031650.

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This study analyzed the alteration of oral microbial composition in healthy subjects after using dextranase-containing mouthwash (DMW; Mouthwash formulation I) and dextranase-and-nisin-containing mouthwash (DNMW; Mouthwash formulation II). Eighteen participants were recruited and were randomly allocated to two groups: G1 (DMW user; n = 8) and G2 (DNMW user; n = 10). The subjects were instructed to use the provided mouthwash regularly twice a day for 30 days. The bleeding on probing (BOP), plaque index (PI), probing depth (PBD), and gingival index (GI) were analyzed, and saliva samples were col

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Taylor, Morag, Henry M. Wood, Stephen P. Halloran, and Philip Quirke. "Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing." Journal of Clinical Pathology 70, no. 7 (2016): 600–606. http://dx.doi.org/10.1136/jclinpath-2016-204165.

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AimsWith a growing interest in the influence the gut microbiome has on the development of colorectal cancer (CRC), we investigated the feasibility and stability of isolating and typing microbial DNA from guaiac faecal occult blood test (gFOBt) cards. This has the future potential to screen the microbial populations present in confirmed colorectal neoplasia cases with aims to predict the presence and development of CRC.MethodsFresh stool samples from three healthy volunteers were applied to gFOBt cards. DNA was extracted from both the cards and fresh stool samples. A series of additional cards

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James, Carrie, Sandra L. Rodriguez-Zas, and Maria R. C. de Godoy. "PSXI-32 Effects of algae DHA on fatty acid profile of plasma red blood cell membrane and fecal microbiota of adult cats." Journal of Animal Science 98, Supplement_4 (2020): 319. http://dx.doi.org/10.1093/jas/skaa278.569.

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Abstract There is evidence that algae can be a sustainable alternative of omega-3 polyunsaturated fatty acids (w-3 PUFA; DHA and EPA) in the diets of felines, but more information is needed to determine bioavailability of algal w-3 PUFAs in felines. Therefore, the objective of this study was to determine the effects of dietary supplementation of algae DHA on plasma and red blood cell (RBC) membrane fatty acid profiles and fecal microbiota of adult cats. A complete randomized design was utilized with thirty female and male adult cats (mean age: 1.8 ± 0.03 yr, mean BW: 4.5 ± 0.8 kg) which were f

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Hussain, Shehnaz K., Tien S. Dong, Vatche Agopian, et al. "Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis." Nutrients 12, no. 5 (2020): 1395. http://dx.doi.org/10.3390/nu12051395.

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The gut microbiome is a key factor in chronic liver disease progression. In prior research, we found that the duodenal microbiome was associated with sex, ethnicity, and cirrhosis complications. Here, we examined the association between diet and the duodenal microbiome in patients with liver cirrhosis. This study included 51 participants who completed a detailed food frequency questionnaire and donated duodenal biopsies for microbiome characterization by 16S ribosomal RNA gene sequencing. Data were analyzed for alpha diversity, beta diversity, and association of taxa abundance with diet qualit

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Savalia, Harshitkumar J., Nimisha Patel, Krishna Mohan Singh, et al. "Dominance of Prevotella Species in Tobacco Consumers: A Metagenomic Preliminary Study." Biosciences Biotechnology Research Asia 21, no. 2 (2024): 671–87. http://dx.doi.org/10.13005/bbra/3255.

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ABSTRACT: The human mouth cavity provides valuable clinical information about both oral and overall well-being. Tobacco has an impact on the oral microbiome, which is connected to a range of systemic disorders. Global studies are examining tobacco usage and other factors, including bacteria's role in oral cancer. Although there have been studies examining the connection between tobacco and the oral microbiota using 16S rRNA amplicon sequencing, there is a lack of investigations application of metagenomic sequences. we investigate, a total of 64 samples were obtained from each of the three cate

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Matsumura, Mitsuki, Hisako Fujihara, Kanna Maita, et al. "Combinatorial Effects of Cisplatin and PARP Inhibitor Olaparib on Survival, Intestinal Integrity, and Microbiome Modulation in Murine Model." International Journal of Molecular Sciences 26, no. 3 (2025): 1191. https://doi.org/10.3390/ijms26031191.

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This study investigated the effects of the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib, alone and in combination with cisplatin, on intestinal integrity, survival, and microbiome composition using a murine model. Statistical analyses were conducted using one-way analysis of variance with Bonferroni correction for multiple comparisons, considering p-values of <0.05 as statistically significant. Microbiome profiling was performed using Qiime 2 software. Histopathological and microbiome analyses revealed Olaparib’s protective effects on intestinal integrity, mitigating cisplatin-ind

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Bronzato, Juliana D., Brenda P. F. A. Gomes, and Tsute Chen. "Taxonomic Diversity and Clinical Correlations in Periapical Lesions by Next-Generation Sequencing Analysis." Genes 16, no. 7 (2025): 775. https://doi.org/10.3390/genes16070775.

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Objectives: The aim of this study was to assess the taxonomic diversity of the microbiota associated with periapical lesions of endodontic origin and to determine whether microbial profiles vary across different populations and clinical characteristics using a unified in silico analysis of next-generation sequencing (NGS) data. Methods: Raw 16S rRNA sequencing data from three published studies were retrieved from the NCBI Sequence Read Archive and reprocessed using a standardized bioinformatics pipeline. Amplicon sequence variants were inferred using DADA2, and taxonomic assignments were perfo

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Dekker Nitert, Marloes, Luisa F. Gomez-Arango, Helen L. Barrett, et al. "Iron supplementation has minor effects on gut microbiota composition in overweight and obese women in early pregnancy." British Journal of Nutrition 120, no. 3 (2018): 283–89. http://dx.doi.org/10.1017/s0007114518001149.

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AbstractFe is an essential nutrient for many bacteria, and Fe supplementation has been reported to affect the composition of the gut microbiota in both Fe-deficient and Fe-replete individuals outside pregnancy. This study examined whether the dose of Fe in pregnancy multivitamin supplements affects the overall composition of the gut microbiota in overweight and obese pregnant women in early pregnancy. Women participating in the SPRING study with a faecal sample obtained at 16 weeks’ gestation were included in this substudy. For each subject, the brand of multivitamin used was recorded. Faecal

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Hernandez, Shane R., Alexander M. Stelzleni, Wil Sims, Dylan B. Davis, Jeferson M. Lourenco, and R. Lawton Stewart. "2 Measuring the Impact of Heat Stress Abatement Strategies on Fecal Microbiome in Finishing Steers During the Summer Months in the Southeast United States." Journal of Animal Science 99, Supplement_3 (2021): 4–5. http://dx.doi.org/10.1093/jas/skab235.007.

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Abstract This study evaluated the effect of heat stress abatement strategies on the faecal microbiome of finishing beef steers in the Southeastern United States. The study was designed as a completely randomized block using 32 steers (BW 453k 4 kg) stratified by weight and randomly assigned to one of four treatment groups: covered with fans (CWF), covered no fans (CNF), outside with shade (SHADE), and outside without shade (OUT). All steers were housed outside from June to July and were brought up on a common feedlot ration. After-which steers were placed into treatments on d -10 and covered s

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Murugesan, S., M. Kumar, M. Saadaoui, et al. "P322 Mycobiome signature in pediatric patients with Inflammatory Bowel Disease." Journal of Crohn's and Colitis 17, Supplement_1 (2023): i462. http://dx.doi.org/10.1093/ecco-jcc/jjac190.0452.

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Abstract Background Inflammatory bowel disease (IBD) encompasses dysregulation of mucosal immunity involving multiple factors including diet, medication, family history, and the gut microbiome. The symptoms of Pediatric IBD are different from an adult-onset disease. Based on the clinical conditions, IBD can be classified into three categories: Crohn’s disease (CD), Ulcerative colitis (UC), and IBD-unclassified (IBDU). The gut bacteriome alteration is widely reported in IBD. But the gut mycobiome link to the disease remains sparse. This study compared mycobiome profile changes in pediatric pati

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Anggoro, Naufal Sebastian, Hermin Pancasakti Kusumaningrum, Anto Budiharjo, Wijanarka Wijanarka, Muhammad Zainuri, and Tony Hadibarata. "Profiling of Seawater Bacterial Diversity in Tanjung Mas Port Using 16S rRNA eDNA Metabarcoding and Next-Generation Sequencing (NGS)." ILMU KELAUTAN: Indonesian Journal of Marine Sciences 29, no. 1 (2024): 61–70. http://dx.doi.org/10.14710/ik.ijms.29.1.61-70.

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Tanjung Emas Port is the entry and exit point for trade commodities, both regional and international filled with many ships. This condition makes biofouling a very massive process in that place by various types of marine bacteria. The initial formation of a biofilm is relevant to bacterial diversity, colonization and adhesion. The objective of the study was assessing bacterial diversity in relation to with biofouling within Tanjung Mas Port Semarang, by using 16S rRNA eDNA metabarcoding Next-Generation Sequencing (NGS). Seawater samples from aquatic sites of Tanjung Mas harbor was used for DNA

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Weinert, Jennifer R., Amy S. Biddle, and Carey A. Williams. "PSIV-14 Fecal Microbiome of Horses Grazing Integrated Warm- and Cool-Season Grass Rotational Pasture Systems." Journal of Animal Science 98, Supplement_4 (2020): 276–77. http://dx.doi.org/10.1093/jas/skaa278.499.

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Abstract The objective of this study was to characterize shifts in the fecal microbiota of horses grazing different forage types within integrated cool- and warm-season grass (CSG; WSG) pasture systems and to explore relationships between forage nutrients and microbial composition. Eight mares grazed integrated rotational systems containing mixed CSG and one of two WSG: bermudagrass or crabgrass. Fecal samples were collected after 2–3 weeks grazing WSG, CSG, and following an orchardgrass hay diet (HAY). Forage nutrients were determined by near-infrared spectroscopy and analyzed by two-way ANOV

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Walsh, Mary L., Courtney Meason-Smith, Carolyn Arnold, Jan S. Suchodolski, and Erin M. Scott. "Evaluation of the ocular surface mycobiota in clinically normal horses." PLOS ONE 16, no. 2 (2021): e0246537. http://dx.doi.org/10.1371/journal.pone.0246537.

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The eye is host to myriad bacterial, fungal, and viral organisms that likely influence ocular surface physiology in normal and diseased states. The ocular surface mycobiota of horses has not yet been described using NGS techniques. This study aimed to characterize the ocular surface fungal microbiota (mycobiota) in healthy horses in 2 environmental conditions (stalled versus pasture). Conjunctival swabs of both eyes were obtained from 7 adult stallions stabled in an open-air pavilion and 5 adult mares living on pasture. Genomic DNA was extracted from ocular surface swabs and sequenced using pr

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Oba, Patrícia M., Hannah D. Holscher, Rose Ann Mathai, Juhee Kim, and Kelly S. Swanson. "Diet Influences the Oral Microbiota of Infants during the First Six Months of Life." Nutrients 12, no. 11 (2020): 3400. http://dx.doi.org/10.3390/nu12113400.

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Background: Oral microorganisms contribute to oral health and disease, but few have studied how infant feeding methods affect their establishment. Methods: Infant (n = 12) feeding records and tongue and cheek swabs were collected within 48 h of birth, and after 2, 4, and 6 mo. DNA was extracted from samples, bacterial and fungal amplicons were generated and sequenced using Illumina MiSeq, and sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analysis System (SAS) to evaluate differences over time and among breast-fed, formula-fed, mixed-fed, and

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Kinstler, Sydney, Yanshao Li, Phillip Miller, et al. "151 Effects of carbohydrate source on performance and gastrointestinal microbiota in nursery pigs." Journal of Animal Science 97, Supplement_2 (2019): 86. http://dx.doi.org/10.1093/jas/skz122.156.

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Abstract An experiment was conducted to determine the effects of carbohydrate source on growth performance and gastrointestinal microbiota in nursery pigs. Ninety-six pigs weaned at 21 d were randomly allotted to 16 pens (6 pigs/pen; 4 pens/treatment) with sex being represented evenly in each pen. Pigs had ad libitum access to feed and water for the 2-phase nursery period (28 d). Dietary treatments included: 1) NutrisureTM(a food-grade cooked cereal grain product), 2) oatmeal (food-grade oatmeal grain), 3) steam-rolled oats (SRO), or 4) dried-distillers grains as a negative control (DDGS). Ile

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Ali Ahmad, Manal, Koen Venema, Carole Ayoub Moubareck, Gabi Wazz, Tarek Mahdy, and Mirey Karavetian. "Changes in energy homeostasis, gut peptides, and gut microbiota in Emiratis with obesity after bariatric surgery." PLOS ONE 20, no. 2 (2025): e0318699. https://doi.org/10.1371/journal.pone.0318699.

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Background Obesity is a growing health concern worldwide, including United Arab Emirates. Bariatric surgery is an effective treatment option, with to date unclear weight loss mechanisms. In this prospective study, we explored post-bariatric surgery changes in energy homeostasis, gut peptides, hormones, and gut microbiota. Method We recruited 19 Emirati adults who were planning to undergo sleeve gastrectomy (SG). We assessed the energy requirements using 24-hour diet recalls, indirect calorimetry for resting energy expenditure (REE), and a questionnaire for appetite. Anthropometrics included bo

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Bycura, Dierdra, Anthony C. Santos, Arron Shiffer, et al. "Impact of Different Exercise Modalities on the Human Gut Microbiome." Sports 9, no. 2 (2021): 14. http://dx.doi.org/10.3390/sports9020014.

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In this study we examined changes to the human gut microbiome resulting from an eight-week intervention of either cardiorespiratory exercise (CRE) or resistance training exercise (RTE). Twenty-eight subjects (21 F; aged 18–26) were recruited for our CRE study and 28 subjects (17 F; aged 18–33) were recruited for our RTE study. Fecal samples for gut microbiome profiling were collected twice weekly during the pre-intervention phase (three weeks), intervention phase (eight weeks), and post-intervention phase (three weeks). Pre/post VO2max, three repetition maximum (3RM), and body composition meas

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Robeson, Michael S., Devon R. O’Rourke, Benjamin D. Kaehler, et al. "RESCRIPt: Reproducible sequence taxonomy reference database management." PLOS Computational Biology 17, no. 11 (2021): e1009581. http://dx.doi.org/10.1371/journal.pcbi.1009581.

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Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardization limits cross-study comparisons. To address these challenges, we de

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Thomas, Minu S., Marissa DiBella, Christopher N. Blesso, et al. "Comparison between Egg Intake versus Choline Supplementation on Gut Microbiota and Plasma Carotenoids in Subjects with Metabolic Syndrome." Nutrients 14, no. 6 (2022): 1179. http://dx.doi.org/10.3390/nu14061179.

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We previously demonstrated that intake of three eggs/d for 4 weeks increased plasma choline and decreased inflammation in subjects with metabolic syndrome (MetS). The purpose of the current study was to further explore the effects of phosphatidylcholine (PC) provided by eggs versus a choline bitartrate (CB) supplement on the gut microbiota, trimethylamine N-oxide (TMAO) formation, and plasma carotenoids lutein and zeaxanthin in MetS. This randomized, controlled crossover clinical trial included 23 subjects with MetS. Following a washout period of 2 weeks without consuming any choline-containin

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