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Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, et al. "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature Biotechnology 37, no. 8 (July 24, 2019): 852–57. http://dx.doi.org/10.1038/s41587-019-0209-9.
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Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, et al. "Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature Biotechnology 37, no. 9 (August 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, Jason T. Ladner, Brendan B. Larsen, Crystal M. Hepp, Darrin Lemmer, 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 (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2’s unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.
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Bolyen, Evan, Matthew R. Dillon, Nicholas A. Bokulich, Jason T. Ladner, Brendan B. Larsen, Crystal M. Hepp, Darrin Lemmer, 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 (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2’s unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.
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Shah, Manasi S., Todd Z. DeSantis, Thomas Weinmaier, Paul J. McMurdie, Julia L. Cope, Adam Altrichter, Jose-Miguel Yamal, and Emily B. Hollister. "Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer." Gut 67, no. 5 (March 24, 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 pipeline). A total of 509 samples (79 colorectal adenoma, 195 CRC and 235 controls) were analysed. Differential abundance, meta-analysis random effects regression and machine learning analyses were carried out to determine the consistency and diagnostic capabilities of potential microbial biomarkers.ResultsDefinitive taxa, including Parvimonas micra ATCC 33270, Streptococcus anginosus and yet-to-be-cultured members of Proteobacteria, were frequently and significantly increased in stools from patients with CRC compared with controls across studies and had high discriminatory capacity in diagnostic classification. Microbiome-based CRC versus control classification produced an area under receiver operator characteristic (AUROC) curve of 76.6% in QIIME-CR and 80.3% in SS-UP. Combining clinical and microbiome markers gave a diagnostic AUROC of 83.3% for QIIME-CR and 91.3% for SS-UP.ConclusionsDespite technological differences across studies and methods, key microbial markers emerged as important in classifying CRC cases and such could be used in a universal diagnostic for the disease. The choice of bioinformatics pipeline influenced accuracy of classification. Strain-resolved microbial markers might prove crucial in providing a microbial diagnostic for CRC.
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Zhao, Jingcheng, Yunhui Qi, Peng Liu, Andrew Severin, Maryam Sayadi, Inke Paetau-Robinson, and Wendy White. "Prebiotic Effects of a Cranberry Beverage in a Randomized, Placebo-Controlled, Crossover Clinical Trial." Current Developments in Nutrition 5, Supplement_2 (June 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 by 10-d run-in periods on the controlled study diet. Fecal samples were collected before and after the dietary intervention for bacterial compositional analysis and short-chain fatty acid analysis by LC-MS/MS. The V5-V6 region of the 16S rRNA gene in fecal DNA was amplified and sequenced. Taxonomy was assigned using the q2-feature-classifier in QIIME2 and matched against the Greengenes 13_8 database. Differential abundance was analyzed using ANCOM2 in R. Alpha-diversity was assessed using Faith's PD, Shannon diversity, and observed OTU richness generated by QIIME 2 and compared between treatments using Mann-Whitney U test. Beta-diversity was compared between treatments using PERMANOVA of the weighted and unweighted UniFrac distances between samples generated by QIIME 2. Results Coriobacteriaceae was significantly more abundant after participants consumed the cranberry as compared with the placebo beverage (ANCOM W > 0.7). The clinically-important pathogen Clostridium perfringens was present after consumption of the placebo beverage, but was a structural zero (not present) after consumption of the cranberry beverage. Alpha-diversity, beta-diversity, and fecal short-chain fatty acid concentrations did not differ between treatments. Conclusions Daily consumption of a whole cranberry beverage resulted in favorable change in the composition of the gut microbiota and thus showed prebiotic potential. Funding Sources Ocean Spray Cranberries, Inc.
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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 trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.
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Jayasudha, Rajagopalaboopathi, Taraprasad Das, Sama Kalyana Chakravarthy, Gumpili Sai Prashanthi, Archana Bhargava, Mudit Tyagi, Padmaja Kumari Rani, Rajeev Reddy Pappuru, and Sisinthy Shivaji. "Gut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy." PLOS ONE 15, no. 12 (December 1, 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 and genera level. Mycobiomes of HC, T2DM and DR could be discriminated by heat map analysis, Beta diversity analysis and LEfSE analysis. Spearman correlation of fungal genera indicated more negative correlation in HC compared to T2DM and DR mycobiomes. This study demonstrates dysbiosis in the gut mycobiomes in people with T2DM and DR compared to HC. These differences were significant both at the phyla and genera level between people with T2DM and DR as well. Such studies on mycobiomes may provide new insights and directions to identification of specific fungi associated with T2DM and DR and help developing novel therapies for Diabetes Mellitus and DR.
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Liu, Xiang, Jing Tao, Jing Li, Xiaolin Cao, Yong Li, Xuefeng Gao, and Yong Fu. "Dysbiosis of Fecal Microbiota in Allergic Rhinitis Patients." American Journal of Rhinology & Allergy 34, no. 5 (April 27, 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. Statistical analysis was performed using the R program, linear discriminant analysis effect size (LefSe), analysis of QIIME, and statistical analysis of metagenomic profiles, among other tests. Results Compared with HCs, AR patients had significantly lower gut-microbiota α-diversity ( P < .001). The gut microbiota composition significantly differed between the 2 study groups. At the phylum level, the relative abundance of Bacteroidetes was higher while those of Actinobacteria and Proteobacteria were lower in the AR group than in the HC group ( P < .001, q < 0.001). At the genus level, Escherichia-Shigella, Prevotella, and Parabacteroides ( P < .001, q < 0.001) had significantly higher relative abundances in the AR group than in the HC group. LefSe analysis indicated that Escherichia-Shigella, Lachnoclostridium, Parabacteroides, and Dialister were potential biomarkers for AR. In addition, predictive metagenome functional analysis showed that pyruvate, porphyrin, chlorophyll, purine metabolism, and peptidoglycan biosynthesis significantly differed between the AR and HC groups. Conclusion A comparison of the gut microbiota of AR patients and HCs suggested that dysbiosis of the fecal microbiota is involved in the development of AR. The present results may reveal key differences and identify targets for preventive or therapeutic intervention.
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Ramiro-Garcia, Javier, Gerben D. A. Hermes, Christos Giatsis, Detmer Sipkema, Erwin G. Zoetendal, Peter J. Schaap, and Hauke Smidt. "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 analysis that was validated with different mock communities and benchmarked against QIIME as a frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed for the evaluation of important causes of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 97.78%. On average 99.95% and 88.43% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.21% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not achieved with QIIME. Conclusions: Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.
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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 (October 7, 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 environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization. Availability and implementation phylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/phylogenize. Supplementary information Supplementary data are available at Bioinformatics online.
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Ramiro-Garcia, Javier, Gerben D. A. Hermes, Christos Giatsis, Detmer Sipkema, Erwin G. Zoetendal, Peter J. Schaap, and Hauke Smidt. "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 analysis that was validated with different mock communities and benchmarked against QIIME as the currently most frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed evaluating important factors of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 96%. On average 99.94% and 92.02% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.02% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not the case when samples were analysed using QIIME. Conclusions Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.
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Derdak, Reda, Javier Quinteiro, Souraya Sakoui, Boutaina Addoum, Jorge Rodríguez Castro, Manuel Rey Méndez, Abdelaziz Soukri, and Bouchra El Khalfi. "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 Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli. Different induction methods allowed to amplify the antibacterial effects against these pathogenic strains.
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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 (April 1, 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 throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.
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Dillon, Matthew R., Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W. Debelius, et al. "Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops." PLOS Computational Biology 17, no. 6 (June 24, 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 followed this workshop with a second fully online workshop, incorporating lessons from the first. Here, we present details on the technology and protocols that we used to run these workshops, focusing on the first workshop and then introducing changes made for the second workshop. We discuss what worked well, what didn’t work well, and what we plan to do differently in future workshops.
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Clemmons, Brooke A., Sung B. Shin, Timothy P. L. Smith, Mallory M. Embree, Brynn H. Voy, Liesel G. Schneider, Dallas R. Donohoe, Kyle J. McLean, and Phillip R. Myer. "Ruminal Protozoal Populations of Angus Steers Differing in Feed Efficiency." Animals 11, no. 6 (May 27, 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 dynamics. The present study focused on identifying potential associations of protozoal community profiles with feed efficiency. Weaned steers (n = 50) 7 months of age weighing approximately 260 kg were adapted to a growing ration and GrowSafe for 2 weeks prior to a 70-day feed efficiency trial. The GrowSafe system is a feeding system that monitors feed intake in real time. Body weights were collected on the first day and then every 7 days of the feed efficiency trial, and on the final day, approximately 50 mL of rumen content were collected via orogastric tubing and frozen at −80 °C. Body weight and feed intake were used to calculate residual feed intake (RFI) as a measure of feed efficiency, and steers were categorized as high (n = 14) or low (n = 10) RFI based on ±0.5 standard deviations about the mean RFI. Microbial DNA was extracted, and the eukaryotic component profiled by amplification and sequencing of 18S genes using degenerate primers that can amplify this locus across a range of protists. The taxonomy of protozoal sequences was assigned using QIIME 1.9 and analyzed using QIIME and SAS 9.4 with significance determined at α ≤ 0.05. Greater abundances of unassigned taxa were associated with high-RFI steers (p = 0.03), indicating a need for further study to identify component protozoal species. Differences were observed between low- and high-RFI steers in protozoal community phylogenetic diversity, including weighted beta-diversity (p = 0.04), Faith’s phylogenetic diversity (p = 0.03), and observed Operational taxonomic unit (OUT) (p = 0.03). The unassigned taxa and differences in phylogenetic diversity of protozoal communities may contribute to divergences observed in feed efficiency phenotypes in beef steers.
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Telmadarrehei, Telmah, Juliet D. Tang, Olanrewaju Raji, Amir Rezazadeh, Lakshmi Narayanan, Rubin Shmulsky, and Dragica Jeremic. "A Study of the Gut Bacterial Community of Reticulitermes virginicus Exposed to Chitosan Treatment." Insects 11, no. 10 (October 8, 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 fifth group was starved. Metagenomic sequences were analyzed using QIIME 2 to understand the treatments’ effects on the dynamics of the gut bacteria. Four dominant phyla were detected: Bacteroidetes (34.4% of reads), Firmicutes (20.6%), Elusimicrobia (15.7%), and Proteobacteria (12.9%). A significant effect of chitosan treatment was observed in two phyla; Firmicutes abundance was significantly lower with chitosan treatment when compared to other groups, while Actinobacteria was lower in unexposed and starved termites. The results suggest that chitosan treatment not only affects the structure of the microbial community in the gut, but other treatments such as starving also cause shifts in termite gut communities.
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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 (January 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 sampled every 2 weeks. Following soil DNA extractions, 16S rRNA gene amplification and sequencing were performed using the Illumina MiSeq technology. The QIIME pipeline was used for data analyses. Results were generated from 45 rhizosphere and 27 geocaulosphere samples, for which 63,502 and 44,469 different operational taxonomical units were observed. Diversity comparisons between both datasets were performed. To our knowledge, this is the first time that the geocaulosphere microbiome is characterized and compared with the rhizosphere microbiome following inoculation with a specific microorganism. Eleven phyla accounted for 95% of the diversity, with Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria being the most abundant ones. Overall, the results obtained suggest that P. fluorescens strain LBUM223 does not significantly alter the autochthonous rhizosphere nor geocaulosphere microbiomes.
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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 (January 8, 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 using the v.1.9.1 QIIME pipeline software. 157 numbers of OTUs were identified among all four dietary groups with 26 of them being prevalent above 0.05% in the total relative abundance. GS and AFB1 increase the relative abundance of phylum Bacteroidetes and Proteobacteria, while decreasing the Firmicutes abundance in a synergic manner as compared with the individual treatments. An additive or synergistic action of the two treatments was identified for Lactobacillus, Prevotella and Campylobacter, while rather an antagonistic effect was observed on Lachnospira. The action mechanisms of aflatoxin B1 and grape seed meal that drive the large intestine microbiota to these changes are not known and need further investigations.
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Barrett, Helen, Luisa Gomez-Arango, Shelley Wilkinson, H. McIntyre, Leonie Callaway, Mark Morrison, and Marloes Dekker Nitert. "A Vegetarian Diet Is a Major Determinant of Gut Microbiota Composition in Early Pregnancy." Nutrients 10, no. 7 (July 12, 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 1:2 ratio. Microbiota analyses were performed using 16S rRNA gene amplicon sequencing and analysed using the Quantitative Insights Into Microbial Ecology (QIIME) and Calypso software tools. There was no difference in alpha diversity, but beta diversity was slightly reduced in vegetarians. There were differences seen in the relative abundance of several genera in those on a vegetarian diet, specifically a reduction in Collinsella, Holdemania, and increases in the relative abundances of Roseburia and Lachnospiraceae. In this sub-analysis of gut microbiota from women in early pregnancy, a vegetarian as compared to omnivorous diet, was associated with a different gut microbiome, with features suggesting alterations in fermentation end products from a mixed acid fermentation towards more acetate/butyrate.
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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 (December 23, 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 were prepared from one volunteer, and extracted at time points between 2 weeks and 3 years. The V4 region of the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq at 2×250 bp read lengths. Data were analysed using QIIME software.ResultsSamples were grouped both by volunteer and by type (fresh or gFOBt), and compared a variety of ways: visual inspection of taxa, α and β diversity, intraclass correlation. In all comparisons, samples grouped by volunteer, and not by sample type. The different time points showed no appreciable differences with increased storage time.ConclusionsThis study has demonstrated that there is good concordance between microbial DNA isolated from fresh stool sample, and from the matched gFOBt card. Samples stored for up to 3 years showed no detrimental effect on measureable microbial DNA. This study has important future implications for investigating microbial influence on CRC development and other pathologies.
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Hussain, Shehnaz K., Tien S. Dong, Vatche Agopian, Joseph R. Pisegna, Francisco A. Durazo, Pedram Enayati, Vinay Sundaram, 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 (May 13, 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 quality and components using QIIME 2 pipelines. Diet quality was assessed through calculation of the Healthy Eating Index 2010. Participants with higher adherence to protein recommendations exhibited increased microbial richness and evenness (p = 0.03) and a different microbial profile compared to those with lower adherence (p = 0.03). Prevotella-9 and Agathobacter were increased in association with increased protein adherence. Fiber consumption was also associated with the duodenal microbial profile (p = 0.01), with several taxa exhibiting significantly decreased or increased abundance in association with fiber intake. Coffee drinking was associated with microbial richness and evenness (p = 0.001), and there was a dose–response association between coffee drinking and relative abundance of Veillonella (p = 0.01). We conclude that protein, fiber, and coffee are associated with diversity and composition of the duodenal microbiome in liver cirrhosis.
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Dekker Nitert, Marloes, Luisa F. Gomez-Arango, Helen L. Barrett, H. David McIntyre, Gregory J. Anderson, David M. Frazer, and Leonie K. Callaway. "Iron supplementation has minor effects on gut microbiota composition in overweight and obese women in early pregnancy." British Journal of Nutrition 120, no. 3 (May 23, 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 microbiome composition was assessed by 16S rRNA sequencing and analysed with the QIIME software suite. Dietary intake of Fe was assessed using a FFQ at 16 weeks’ gestation. Women were grouped as receiving low (<60 mg/d, n 94) or high (≥60 mg/d; n 65) Fe supplementation. The median supplementary Fe intake in the low group was 10 (interquartile range (IQR) 5–10) v. 60 (IQR 60–60) mg/d in the high group (P<0·001). Dietary Fe intake did not differ between the groups (10·0 (IQR 7·4–13·3) v. 9·8 (IQR 8·2–13·2) mg/d). Fe supplementation did not significantly affect the composition of the faecal microbiome at any taxonomic level. Network analysis showed that the gut microbiota in the low Fe supplementation group had a higher predominance of SCFA producers. Pregnancy multivitamin Fe content has a minor effect on the overall composition of the gut microbiota of overweight and obese pregnant women at 16 weeks’ gestation.
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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 (November 3, 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 fed an assigned diet for 90 d. Three diets were formulated with poultry fat alone or inclusion of 2% fish oil or 2% algae DHA meal. Blood samples were collected after fasting on 0, 30, 60 and 90 d to be analyzed for plasma and red blood cell fatty acid profiles. A fresh fecal sample was collected within 15 min of defecation from each cat to be analyzed for fecal microbiota. Illumina 16S rRNA sequencing from V4 region was completed using MiSeq and analyzed using QIIME 2. Plasma and RBC fatty acid concentrations at baseline were similar among all cats and treatment groups. However, dietary treatment had a significant effect on the concentrations of several fatty acids in plasma and RBC over time. Plasma and RBC concentrations of DHA were greater (P < 0.05) for cats fed the algal DHA diet compared to the control and fish oil diets. Conversely, plasma and RBC concentrations of EPA did not differ among treatments when analyzed as a change from baseline. Beta- and alpha-diversity did not differ among treatments, indicating that 2% fish oil or algal-DHA meal does alter fecal microbiota of cats in contrast with cats fed a poultry fat-based diet.
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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 (November 3, 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 ANOVA in SAS (v.9.4). Following DNA extraction, 16S rRNA gene sequence analysis was conducted in QIIME 2 (v.2020.2) with Kruskall-Wallis tests for alpha diversity, Spearman correlation with forage nutrients, and taxonomic assignment with Greengenes. A random forest classifier and regressor determined ability to predict forage type and nutrients based upon bacterial composition. Statistical significance was set at p ≤ 0.05. Forage water-soluble carbohydrates (WSC) were greatest in CSG and lowest in WSG; neutral detergent fiber (NDF) was greater in HAY than CSG or WSG. Species richness and evenness (Shannon Index) was greater in horses adapted to WSG vs. CSG or HAY and was correlated with WSC (rs = -0.49) and ethanol-soluble carbohydrates (ESCrs = -0.62). The random forest classifier resulted in model accuracy of 1.0 and identified amplicon sequence variants (ASV) most important in prediction of forage type. Sixteen ASV were from the order Clostridiales including Lachnospiraceae, Ruminococcacceae, and Veillonellaceae families and the genus Coprococcus. Other important taxa included Prevotella spp., Streptococcus luteciae, and Fibrobacter succinogenes. The regressor accurately predicted WSC (r2 = 0.95) and ESC (r2 = 0.84), but not NDF (r2 = 0.09). These results suggest that the equine hindgut microbiome is impacted by forage type and soluble carbohydrate content; however, further research is required to determine functional and physiological significance in grazing horses.
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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 (November 5, 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 solid food-fed infants. Results: Considering all time points, breast milk- and mixed-fed infants had lower oral species richness than solid food-fed infants (p = 0.006). Regardless of feeding mode, species richness was lower at birth than at other time points (p = 0.006). Principal coordinates analysis (PCoA) of unique fraction metric (UniFrac) distances indicated that bacterial communities were impacted by feeding method (p < 0.005). Considering all time points, breast-fed infants had higher Streptococcus, while formula-fed infants had higher Actinomyces and Prevotella. Regardless of feeding mode, Propionibacterium, Porphyromonas, Prevotella, Gemella, Granulicatella, Veillonella, Fusobacterium, Leptotrichia, Neisseria, and Haemophilus increased with age, while Cloacibacterium and Dechloromonas decreased with age. Oral fungi were detected in infants but were not impacted by diet. Conclusions: These findings demonstrate that the establishment of oral bacteria depends on dietary composition and age. More research is necessary to determine whether this affects risk of oral caries and other health outcomes later in life.
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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 (February 4, 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 primers that target the Internal Transcribed Spacer 1 (ITS1) region of the fungal genome on an Illumina platform. Sequences were processed using Quantitative Insights Into Molecular Ecology (QIIME 2.0) and taxonomy assigned with the Findley et al. 2013 ITS1 database. The most abundant genera identified were Leptosphaerulina (22.7%), unclassified Pleosporaceae (17.3%), Cladosporium (16.2%), Alternaria (9.8%), unclassified Pleosporales (4.4%), unclassified Montagnulaceae (2.9%), Fusarium (2.5%), and Pestalotiopsis (1.4%). Fungal community composition (Jaccard, R = 0.460, p = 0.001) and structure (Bray-Curtis, R = 0.811, p = 0.001) were significantly different between pastured mares and stabled stallions. The ocular surface of pastured mares had significantly increased fungal species richness and diversity compared to stabled stallions (Shannon p = 0.0224, Chao1 p = 0.0118, Observed OTUs p = 0.0241). Relative abundances of Aspergillus (p = 0.005) and Alternaria spp. (p = 0.002) were significantly increased in the mycobiota of pastured mares. This is the first report to describe the mycobiota of the equine ocular surface. Environmental factors such as housing influence the composition, structure, and richness of the equine ocular surface mycobiota.
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Kinstler, Sydney, Yanshao Li, Phillip Miller, Thomas E. Burkey, Melanie Trenhaile-Gannemann, Samodha C. Fernando, Allison Knoell, and Wesley A. Tom. "151 Effects of carbohydrate source on performance and gastrointestinal microbiota in nursery pigs." Journal of Animal Science 97, Supplement_2 (July 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). Ileal and colonic digesta and mucosa samples were collected on d 0, 14, and 28 (n = 6, 32, and 32, respectively) for analysis of microbial species using IlluminaTMnext generation sequencing. The DNA sequences were filtered through the DADA2 pipeline, Mothur, and QIIME. Pig body weights and feeder weights were also measured on d 0, 7, 14, 21, and 28. Pigs fed DDGS had lower average daily feed intake (ADFI) compared to other treatments during phase 1 (P < 0.05), but there were no differences in average daily gain (ADG) or gain:feed (G:F) among treatment. There were no differences among treatments for ADFI, ADG, or G:F for phase 2 or the overall experimental period. Microbial composition differed significantly among location in the gastrointestinal tract (P < 0.01) and among the digesta and mucosa samples extracted from the ileum and colon. There were no significant changes in the microbiota among diets (P > 0.1). Over time, there was a trend (P = 0.111) for the microbiota to vary; however, there was no interaction between the diet and sampling timepoint. In conclusion, carbohydrate sources did not affect gastrointestinal microbiota composition, ADFI, ADG, or G:F overall in this experiment. However, feed intake during phase 1 differed between DDGS and oat-based carbohydrate sources and microbial species were different between digesta and mucosa in the ileum and colon.
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Arias-Giraldo, Luisa M., Marina Muñoz, Carolina Hernández, Giovanny Herrera, Natalia Velásquez-Ortiz, Omar Cantillo-Barraza, Plutarco Urbano, and Juan David Ramírez. "Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors." PLOS ONE 15, no. 11 (November 12, 2020): e0240916. http://dx.doi.org/10.1371/journal.pone.0240916.
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Triatomines (Hemiptera: Reduviidae) are the insect vectors of Trypanosoma cruzi, the causative agent of Chagas disease. The gut bacterial communities affect the development of T. cruzi inside the vector, making the characterization of its composition important in the understanding of infection development. We collected 54 triatomine bugs corresponding to four genera in different departments of Colombia. DNA extraction and PCR were performed to evaluate T. cruzi presence and to determine the discrete typing unit (DTU) of the parasite. PCR products of the bacterial 16S rRNA gene were pooled and sequenced. Resulting reads were denoised and QIIME 2 was used for the identification of amplicon sequence variants (ASVs). Diversity (alpha and beta diversity) and richness analyses, Circos plots, and principal component analysis (PCA) were also performed. The overall T. cruzi infection frequency was 75.9%, with TcI being the predominant DTU. Approximately 500,000 sequences were analyzed and 27 bacterial phyla were identified. The most abundant phyla were Proteobacteria (33.9%), Actinobacteria (32.4%), Firmicutes (19.6%), and Bacteroidetes (7.6%), which together accounted for over 90% of the gut communities identified in this study. Genera were identified for these main bacterial phyla, revealing the presence of important bacteria such as Rhodococcus, Serratia, and Wolbachia. The composition of bacterial phyla in the gut of the insects was significantly different between triatomine species, whereas no significant difference was seen between the state of T. cruzi infection. We suggest further investigation with the evaluation of additional variables and a larger sample size. To our knowledge, this study is the first characterization of the gut bacterial structure of the main triatomine genera in Colombia.
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Perera, M., N. N. Al-hebshi, I. Perera, D. Ipe, G. C. Ulett, D. J. Speicher, T. Chen, and N. W. Johnson. "Inflammatory Bacteriome and Oral Squamous Cell Carcinoma." Journal of Dental Research 97, no. 6 (April 9, 2018): 725–32. http://dx.doi.org/10.1177/0022034518767118.
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Results from microbiome studies on oral cancer have been inconsistent, probably because they focused on compositional analysis, which does not account for functional redundancy among oral bacteria. Based on functional prediction, a recent study revealed enrichment of inflammatory bacterial attributes in oral squamous cell carcinoma (OSCC). Given the high relevance of this finding to carcinogenesis, we aimed here to corroborate them in a case-control study involving 25 OSCC cases and 27 fibroepithelial polyp (FEP) controls from Sri Lanka. DNA extracted from fresh biopsies was sequenced for the V1 to V3 region with Illumina’s 2 × 300–bp chemistry. High-quality nonchimeric merged reads were classified to the species level with a prioritized BLASTN-based algorithm. Downstream compositional analysis was performed with QIIME (Quantitative Insights into Microbial Ecology) and linear discriminant analysis effect size, while PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was utilized for bacteriome functional prediction. The OSCC tissues tended to have lower species richness and diversity. Genera Capnocytophaga, Pseudomonas, and Atopobium were overrepresented in OSCC, while Lautropia, Staphylococcus, and Propionibacterium were the most abundant in FEP. At the species level, Campylobacter concisus, Prevotella salivae, Prevotella loeschii, and Fusobacterium oral taxon 204 were enriched in OSCC, while Streptococcus mitis, Streptococcus oral taxon 070, Lautropia mirabilis, and Rothia dentocariosa among others were more abundant in FEP. Functionally, proinflammatory bacterial attributes, including lipopolysaccharide biosynthesis and peptidases, were enriched in the OSCC tissues. Thus, while the results in terms of species composition significantly differed from the original study, they were consistent at the functional level, substantiating evidence for the inflammatory nature of the bacteriome associated with OSCC.
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Bycura, Dierdra, Anthony C. Santos, Arron Shiffer, Shari Kyman, Kyle Winfree, Jay Sutliffe, Talima Pearson, Derek Sonderegger, Emily Cope, and J. Gregory Caporaso. "Impact of Different Exercise Modalities on the Human Gut Microbiome." Sports 9, no. 2 (January 21, 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 measurements were conducted. Heart rate ranges for CRE were determined by subjects’ initial VO2max test. RTE weight ranges were established by subjects’ initial 3RM testing for squat, bench press, and bent-over row. Gut microbiota were profiled using 16S rRNA gene sequencing. Microbiome sequence data were analyzed with QIIME 2. CRE resulted in initial changes to the gut microbiome which were not sustained through or after the intervention period, while RTE resulted in no detectable changes to the gut microbiota. For both CRE and RTE, we observe some evidence that the baseline microbiome composition may be predictive of exercise gains. This work suggests that the human gut microbiome can change in response to a new exercise program, but the type of exercise likely impacts whether a change occurs. The changes observed in our CRE intervention resemble a disturbance to the microbiome, where an initial shift is observed followed by a return to the baseline state. More work is needed to understand how sustained changes to the microbiome occur, resulting in differences that have been reported in cross sectional studies of athletes and non-athletes.
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Smith, Brooke N., Stephen A. Fleming, Mei Wang, and Ryan N. Dilger. "52 Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus." Journal of Animal Science 98, Supplement_3 (November 2, 2020): 30–31. http://dx.doi.org/10.1093/jas/skaa054.054.
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Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically-important disease and ingestion of soy isoflavones (ISF) may benefit PRRSV-infected pigs due to demonstrated anti-inflammatory and anti-viral properties. The objective of this study was to quantify long-term effects of ISF consumption on fecal microbiome characteristics under disease challenge. In total, 96 weaned barrows were group-housed in a BSL-2 containment facility and allotted to 1 of 3 experimental treatments that were maintained throughout the wean-to-finish study: non-infected pigs receiving an ISF-devoid control diet (NC, n=24), and infected pigs receiving either the control diet (PC, n=36) or that supplemented with total ISF in excess of 1,600 mg/kg (ISF, n=36) (Table 1). Following a 7-day adaptation, pigs were inoculated intranasally with either a sham-control (PBS) or live PRRSV (1×105 TCID50/mL, strain NADC20). Fecal samples were collected from 48 individual pigs at pre-infection (-2 days post-inoculation, DPI), peak-infection (10 DPI), and post-infection (144 DPI) time-points and extracted DNA was used for 16S bacterial rRNA sequencing. Differences in bacterial communities among diet groups were evaluated using UniFrac distance matrices (weighted and unweighted) in QIIME. All other data were analyzed by one-way ANOVA performed on transformed data using R. Across all time-points, only minimal differences were observed due to ISF alone. At 10 DPI, PRRSV infection reduced Prevotella 9 genera abundance from approximately 20% to less than 10%, but the specific function of this variety in pigs is unclear. The most notable finding was decreased relative abundance of Actinobacteria at 144 DPI between non-infected and infected treatments (P < 0.05), which is consistent with various dysbioses observed in other disease models. Our findings indicate that differences present were mainly due to PRRSV infection and not strongly influenced by ISF ingestion, which implies previously observed performance benefits conferred by dietary ISF are not likely due to changes in microbiome composition.
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Ordiz, M. Isabel, Stefan Janssen, Greg Humphrey, Gail Ackermann, Kevin Stephenson, Sophia Agapova, Oscar Divala, et al. "The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months." American Journal of Clinical Nutrition 111, no. 4 (February 11, 2020): 884–92. http://dx.doi.org/10.1093/ajcn/nqaa011.
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ABSTRACT Background Common bean and cowpea contain about 25% protein and 25% fiber, and are recommended as complementary foods in sub-Saharan Africa. Objective The objective of this study was to determine if a daily legume supplement given to Malawian infants aged 6 to 12 mo alters the 16S configuration of the fecal microbiota as read out by amplicon sequence variants (ASVs). Methods This study was conducted within the context of a randomized, double-blind, controlled clinical trial to assess whether cowpea or common bean supplementation reduced intestinal permeability or increased linear growth. There were 2 village clusters in which the study was conducted. Fresh stool collections were flash frozen from 236 infants at ≤6 time points. The stools were sequenced using Earth Microbiome project protocols and data were processed using Qiime and Qiita, open-source, validated software packages. α-diversity was measured using the Faith's test. The 16S configuration was characterized by determining the weighted UniFrac distances of the ASVs and comparing them using permutational multivariate ANOVA. Results Among the 1249 samples analyzed, the α-diversity of the fecal microbiome was unchanged among subjects after initiation of legume supplementation. Neither cowpea nor common bean altered the overall 16S configuration at any age. The 16S configuration differed between children with adequate and poor linear growth aged from 6 to 9 mo, but no specific ASVs differed in relative abundance. The 16S configuration differed between children with normal and abnormal intestinal permeability at 9 mo, but no specific ASVs differed in relative abundance. Among categorical characteristics of the population associated with different 16S configurations, village cluster was most pronounced. Conclusion Legume supplementation in breastfed, rural African infants did not affect the structure of the gut microbial communities until the children were aged 9 mo. This trial was registered at clinicaltrials.gov as NCT02472262.
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Oba, Patrícia M., Meredith Carroll, Celeste Alexander, Lynn Lye, Amy Somrak, Stephanie Keating, Adrianna Sage, and Kelly S. Swanson. "87 President Oral Presentation Pick: Oral Microbiota Populations of Adult Dogs Consuming Dental Chews Demonstrated to Reduce Dental Plaque and Calculus." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 61–62. http://dx.doi.org/10.1093/jas/skaa278.111.
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Abstract Microbiota play a prominent role in canine periodontal disease, but little is known about the oral microbial community of dogs. We aimed to determine the differences in oral microbiota of dogs consuming dental chews demonstrated to improve oral health outcomes. Twelve adult dogs were used in a replicated 4x4 Latin square design consisting of 28-day periods. Control (CT) dogs consumed diet only, with treatment groups receiving one of three dental chews (BC, DL and GR). At baseline, teeth were cleaned. Teeth were scored for plaque, calculus, and gingivitis at the end of each period by a veterinary dentist blinded to treatments. Breath samples were measured for sulfur compounds throughout each period. Plaque [supragingival (SUP) and subgingival (SUB) plaque] and saliva (SAL) samples were collected for microbiota analysis. Total DNA from saliva and plaque samples was extracted, with 16S rDNA V4 region gene amplicons subjected to Illumina sequencing. Data were analyzed using QIIME 2 and SAS. CT dogs had a higher pocket score, breath sulfur concentrations, and plaque and calculus scores compared to those given chews. Bacterial species richness was highest for CT, with unweighted and weighted PCoA plots showed a clustering of CT dogs vs. those given chews. For all sample types, CT dogs had higher relative abundance of potential pathogenic bacteria (Porphyromonas, Tannerella, and Treponema) and lower relative abundance of bacterial genera associated with oral health (Neisseria, Corynebacterium, Bergeyella, and Moraxella) compared to those given chews. DL reduced Porphyromonas in SUP and SUB samples. DL and GR reduced Treponema in SUP samples. DL increased Corynebacterium in all sample types. BC increased Corynebacterium in SAL samples. DL and GR increased Neisseria and Moraxella in SAL samples. Our results suggest that the dental chews tested beneficially shifted oral microbiota populations, which were associated with improvements in plaque and calculus scores.
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von Schaumburg, Patrick, Sandra L. Rodriguez-Zas, Bruce R. Southy, and Maria R. C. de Godoy. "PSXI-36 Evaluation of fecal microbiota of dogs fed extruded diets containing white and red sorghum as primary carbohydrate source." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 319–20. http://dx.doi.org/10.1093/jas/skaa278.570.
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Abstract Sorghum (Sorghum bicolor) is a cereal grain consisting of either white, yellow, red, brown or black endosperms. In human and pet nutrition, sorghum has gained increased attention as a gluten-free and non-GMO whole-grain option. However, a paucity of information exists about the effect of this cereal grain on the GI microbiome and host health. Therefore, the aim of this study was to evaluate the effects of extruded diets containing corn (CON), white sorghum (WHS) or red sorghum (RES) as the main carbohydrate source on fecal microbiota and metabolites in dogs. Animal care protocol used in this study was approved by the Institutional Care and Use Committee at the University of Illinois. Three diets containing either 30% of CON, WHS, or RES were formulated to meet or exceed the AAFCO (2018) nutrient profile for adult dogs. Nine adult female beagles were randomly assigned to one of the 3 dietary treatments using a replicated 3x3 Latin square design. Each experiment period consisted of 14d (10d of diet adaption and 4d of fecal collection). Fresh fecal samples were collected and allocated for microbial analysis. Illumina 16S rRNA sequencing from V4 region was completed using MiSeq and analyzed using QIIME 2. Linear models were used to evaluate the main effect of treatment. Over 1.8 million sequences were generated. Samples were rarified to 42,160 reads for analysis of diversity and species richness. Beta-diversity did not differ among dogs fed CON, WHS, or RES diets (q- and p-values > 0.05). Similarly, microbial richness was also not affected by treatment. Overall, fecal metabolite concentrations were similar among treatments and did not have a strong correlated with microbial taxa. Our findings indicate that extruded diets using sorghum as a substitute for corn as the main dietary carbohydrate result in similar fecal metabolite profile and microbiota in adult dogs.
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Kable, Mary, Elizabeth Chin, Liping Huang, Charles Stephensen, and Danielle Lemay. "Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy U.S. Adults." Current Developments in Nutrition 4, Supplement_2 (May 29, 2020): 1566. http://dx.doi.org/10.1093/cdn/nzaa062_023.
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Abstract Objectives Lactase persistence (LP) is a heritable trait in which lactose can be digested into adulthood. Lactase non-persisters (LNP) who consume lactose may experience microbial adaptations in response to the undigested lactose. The objective of this study was to determine the interaction between lactose consumption, LP genotype and gut microbiota in an observational cross-sectional study of healthy U.S. adults. Methods ASA24 dietary data and stool samples were collected from healthy U.S. adults genotyped for the lactase persistence SNP ID: rs4988235 (n = 280). Lactose was estimated by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300bp PE) and analyzed using Qiime 2 (v 2019.10). Bacterial sequence counts present at greater than 0.1% of the total data set were analyzed using DESeq2 and LEfSe. Taxa that were differentially abundant by both analyses at the family or genus level are reported here. Results On average 246 ng/uL (3.9 – 646.5ng/uL) DNA was obtained from each sample, yielding 21,470 sequences (10,122 – 56,837). LP genotypes were unevenly distributed by ethnicity and Clostridium (family Lachnospiraceae) was significantly enriched in Asian ethnicities. Therefore, only Caucasian and Hispanic participants were grouped as LP (AA or AG genotype) or LNP (GG genotype) for further analysis. The abundance of Roseburia and family Lachnospriaceae was higher in the upper (>12.4g), relative to lower (< 5.78g), tertile of lactose consumption in LNP adults, but not in LP. Conclusions Increased abundance of Roseburia, a microbe capable of utilizing lactose, in LNP individuals consuming >12.4 g lactose/day suggests that this genus may metabolize lactose in LNP adults. Funding Sources The California Dairy Research Foundation and the United States Department of Agriculture, Agricultural Research Service.
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Mitchell, Allianna, and Cassandra K. Jones. "PSI-34 The Impact of Varying Protein Sources on Feedlot Goat Fecal Microbiome." Journal of Animal Science 97, Supplement_3 (December 2019): 256. http://dx.doi.org/10.1093/jas/skz258.521.
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Abstract The effect of protein sources with different RUP values on feedlot goat fecal microbiome has not been studied. This experiment evaluated the impact of varying protein sources on feedlot goat fecal microbiome. Fourty-five Boer-influenced goats (23.53 kg ± 1.07; approximately 75 d of age) were blocked by body weight and randomly allocated to 1 of 3 treatment diets (15 goats/treatment) with ad libitum feed and water for 42 d. Diets were formulated to be isocaloric and isonitrogenous, with varying primary protein source: 1) 18.7% solvent-extracted soybean meal (SBM), 2) 22.0% expelled soybean meal (SoyPlus), or 3) 34.4% distillers’ dried grains with solubles (DDGS). On d 42, fecal pellets were collected from each goat and stored at -80°C until microbiome sequencing. Samples underwent PCR amplification of the V4 region of the 16S gene and sequencing on Illumina HiSeq 2500 (Illumina Inc., San Diego, CA) by a commercial lab (MR DNA, Shallowater, TX). Data were analyzed using the GLIMMIX procedure of SAS with Turkey’s test for post hoc comparisons. Beta and alpha diversity were analyzed using Qiime with Kruskal-Wallis pairwise comparisons and ANOSIM. Genera, with individual abundance greater than 1%, that were higher (P ≤ 0.05) in SBM-fed goats compared to goats fed DDGS and SoyPlus include Clostridium, Paludibacter, Tannerella, and Methanobrevibacter. At the phylum level, Bacteroidetes was greater in SBM-fed goats compared to DDGS-fed goats (P = 0.04) and Euryarchaeota was more abundant in goats fed SBM compared to DDGS (P = 0.003) and SoyPlus (P = 0.0001). Protein source did not affect β-diversity (r ≈ 0) or α-diversity (P > 0.10). In summary, altering protein source in finishing goat diets created shifts in some phyla and genera, however the diversity within and between microbial communities across treatments were uninfluenced.
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Poudel, Shyam K., Roshan Padmanabhan, Prabhleen Chahal, Madhusudhan Sanaka, Tyler Stevens, Kathryn Guinta, Alok A. Khorana, Davendra Sohal, and Charis Eng. "Microbiome signature of bile from pancreatic and biliary tract cancer patients: A pilot study." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): e15744-e15744. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e15744.
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e15744 Background: Recent studies especially in murine models have linked meta-organismal pathways in the gut microbial community to cancers of the pancreas and the biliary tract. However, data on microbiome in the biliary pool in patients to establish models for oncogenesis in the pancreatobiliary (PB) habitat have been limited. We analyzed bile collected from a pilot series of patients to identify microbiome signatures associated with malignancy. Methods: We collected bile samples from patients during routine endoscopic retrograde cholangiopancreatography in this study approved by the Cleveland Clinic Institutional Review Board for Human Subjects’ Protection. Of 10 patients, there were 5 with pancreatic ductal adenocarcinoma (PDA), 3 with cholangiocarcinoma (CC), 1 with ampullary adenocarcinoma, and 1 with gallstone pancreatitis. DNA was extracted from bile specimens using PowerViral RNA/DNA Isolation kit. Bacterial 16S rRNA gene amplification and library construction were performed according to the 16S Metagenomic Sequencing Library Preparation guide from Illumina. Post-sequencing analysis was done using QIIME (Quantitative Insights Into Microbial Ecology) and MICCA (MICrobial Community Analysis). Results: Most reads were from phyla Firmicutes (57.9%) and Proteobacteria (14.9%). One benign specimen (pancreatitis) separated clearly from the rest showing 98.9% of reads from Clostridium sensu stricto (phylum Firmicutes). Analysis of beta diversity showed six samples clustering tightly. Of these, 5 were PDA and 1 was CC. A second cluster included remaining 3 samples, 2 with CC and 1 with PDA; this latter had higher abundance of phyla Fusobacteria (90.6%) and Verrucomicrobia (92.9%). Conclusions: Select bacteria are differentially increased in malignant and benign PB diseases. Furthermore, distinct microbiome signatures may be associated with cancer in the pancreatic and biliary habitats. We intend to evaluate these findings in larger sample sizes and determine associations with clinical outcomes and response to treatment.
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Borriello, Giorgia, Rubina Paradiso, Carlotta Catozzi, Roberta Brunetti, Paola Roccabianca, Marita Georgia Riccardi, Bianca Cecere, et al. "Cerumen microbial community shifts between healthy and otitis affected dogs." PLOS ONE 15, no. 11 (November 25, 2020): e0241447. http://dx.doi.org/10.1371/journal.pone.0241447.
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Otitis externa is a common multifactorial disease in dogs, characterized by broad and complex modifications of the ear microbiota. The goal of our study was to describe the ear cerumen microbiota of healthy dogs, within the same animal and between different animals, and to compare the cerumen microbiota of otitis affected dogs with that of healthy animals. The present study included 26 healthy dogs, 16 animals affected by bilateral otitis externa and 4 animals affected by monolateral otitis externa. For each animal cerumen samples from the right and left ear were separately collected with sterile swabs, and processed for DNA extraction and PCR amplification of the 16S rRNA gene. Amplicon libraries were sequenced using an Ion Torrent Personal Genome Machine (PGM), and taxonomical assignment and clustering were performed using QIIME 2 software. Our results indicate that the bacterial community of the cerumen in healthy dogs was characterized by extensive variability, with the most abundant phyla represented by Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Fusobacteria. The analysis of both alpha and beta diversity between pairs of left and right ear samples from the same dog within the group of affected animals displayed higher differences than between paired samples across healthy dogs. Moreover we observed reduced bacterial richness in the affected group as compared with controls and increased variability in population structure within otitis affected animals, often associated with the proliferation of a single bacterial taxon over the others. Moreover, Staphylococcus and Pseudomonas resulted to be the bacterial genera responsible for most distances between the two groups, in association with differences in the bacterial community structure. The cerumen microbiota in healthy dogs exhibits a complex bacterial population which undergoes significant modifications in otitis affected animals.
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Kim, Sangmi, Wenhui Zhang, Victoria Pak, Jasmine Ko Aqua, Vicki Stover Hertzberg, Chandler M. Spahr, George M. Slavich, and Jinbing Bai. "How stress, discrimination, acculturation and the gut microbiome affect depression, anxiety and sleep among Chinese and Korean immigrants in the USA: a cross-sectional pilot study protocol." BMJ Open 11, no. 7 (July 2021): e047281. http://dx.doi.org/10.1136/bmjopen-2020-047281.
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IntroductionAlthough a considerable proportion of Asians in the USA experience depression, anxiety and poor sleep, these health issues have been underestimated due to the model minority myth about Asians, the stigma associated with mental illness, lower rates of treatment seeking and a shortage of culturally tailored mental health services. Indeed, despite emerging evidence of links between psychosocial risk factors, the gut microbiome and depression, anxiety and sleep quality, very few studies have examined how these factors are related in Chinese and Korean immigrants in the USA. The purpose of this pilot study was to address this issue by (a) testing the usability and feasibility of the study’s multilingual survey measures and biospecimen collection procedure among Chinese and Korean immigrants in the USA and (b) examining how stress, discrimination, acculturation and the gut microbiome are associated with depression, anxiety and sleep quality in this population.Method and analysisThis is a cross-sectional pilot study among first and second generations of adult Chinese and Korean immigrants in the greater Atlanta area (Georgia, USA). We collected (a) gut microbiome samples and (b) data on psychosocial risk factors, depression, anxiety and sleep disturbance using validated, online surveys in English, Chinese and Korean. We aim to recruit 60 participants (30 Chinese, 30 Korean). We will profile participants’ gut microbiome using 16S rRNA V3-V4 sequencing data, which will be analysed by QIIME 2. Associations of the gut microbiome and psychosocial factors with depression, anxiety and sleep disturbance will be analysed using descriptive and inferential statistics, including linear regression.Ethics and disseminationThis study has been approved by the Institutional Review Board at Emory University (IRB ID: STUDY00000935). Results will be made available to Chinese and Korean community members, the funder and other researchers and the broader scientific community.
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Fatani, Asmaa, JoonHyuk Suh, Jeremie Auger, Yu Wang, and Wendy Dahl. "Effect of Pea Hull Fiber on Uremic Metabolites and Gut Microbiota Composition in Individuals Undergoing Hemodialysis." Current Developments in Nutrition 5, Supplement_2 (June 2021): 1155. http://dx.doi.org/10.1093/cdn/nzab054_010.
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Abstract Objectives The objective was to determine the effects of pea hull fiber intake on serum uremic molecules and microbiota composition of individuals undergoing hemodialysis. Methods A randomized, double-blind, placebo-control, crossover study was conducted with individuals undergoing hemodialysis. Following a 1-week baseline, participants consumed muffins with added pea hull fiber (15 g/d) and control muffins daily for 4 weeks in random order, separated by a 4-week washout. Blood and stool samples were collected during each period. Serum p-cresol sulfate (PCS), indoxyl sulfate (IS) and trimethylamine N-oxide (TMAO) were analyzed by LC–MS/MS and fecal microbiome profile by 16S rRNA gene amplicon sequencing. qPCR for taxa of interest (Akkermansia muciniphila, Faecalibacterium prausnitzii, Bifidobacterium, and Roseburia) was performed. QIIME 2 sample-classifier was used to discover a unique microbiota profile due to the consumption of pea hull fiber. Results Of the 18 participants randomized (50 ± 4 y; eGFR 6.6 ± 0.7 ml/min/1.73m2), 13 completed the study. No significant changes from baseline were observed in serum PCS (3256 ± 505 μmol/L), IS (166 ± 23 μmol/L) or TMAO (96 ± 12 μmol/L), or for the relative quantification of A. muciniphila, F. prausnitzii, Bifidobacterium, and Roseburia, taxa thought to be health enhancing. Taxa that most distinguished the microbiota composition during the pea hull fiber intervention from usual diet periods were enriched Gemmiger, Collinsella and depleted Lactobacillus, Ruminococcus, Coprococcus and Mogibacteriaceae. Given that abundance of Collinsella has been inversely associated with dietary fiber, this finding was unexpected. Conclusions In dialysis patients, added pea hull fiber did not reduce the serum levels of targeted uremic molecules but did alter fecal microbiota composition. Future research in this patient population should explore the efficacy of alternate fiber sources or plant-based dietary patterns for reducing serum levels of uremic toxins. Funding Sources Saskatchewan Pulse Growers.
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Warzecha, C. M., J. A. Coverdale, J. E. Janecka, J. L. Leatherwood, W. E. Pinchak, T. A. Wickersham, and J. C. McCann. "Influence of short-term dietary starch inclusion on the equine cecal microbiome1." Journal of Animal Science 95, no. 11 (November 1, 2017): 5077–90. http://dx.doi.org/10.2527/jas2017.1754.
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Abstract The objective of this study was to determine bacterial community profiles of the equine cecum in response to abrupt inclusion of varying levels of dietary starch. Seven cecally cannulated Quarter Horse geldings (497 to 580 kg) were used in a crossover design with two 28-d periods and a 28-d washout between each. Horses were randomly assigned to dietary treatments consisting of a commercial concentrate offered as fed at either 0.6 (low starch [LS]) or 1.2% BW (high starch [HS]) daily that was divided into 2 meals at 12-h intervals. Prior to the start of each period, horses were allowed ad libitum access to coastal bermudagrass (Cynodon dactylon) hay. Concentrate was fed on d 1 with no adaptation. Cecal fluid was collected on d 1 at h 0 and at 3, 6, 9, and 12 h relative to the initial concentrate meal on d 1. Additional samples were collected 6 h after feeding on d 2, 3, and 7 of each period. Cecal contents were used to determine pH and VFA concentrations and extract microbial DNA. The V4 through V6 region of 16S rRNA gene was amplified using PCR and sequenced on the Roche 454 FLX platform. Sequence analysis was performed with QIIME, and data were analyzed using the MIXED procedure of SAS. Cecal pH tended to decrease (P = 0.09) in horses fed HS in the first 12 h after the first concentrate meal and remained lower (P ≤ 0.05) the following 7 d. Total VFA were greater (P ≤ 0.05) in horses fed HS in the initial 12 h and 7 d after addition of concentrate. Species richness determined using the Chao1 index was unchanged (P > 0.20) over the initial 12 h and decreased (P = 0.01) over 7 d for both treatments. Community diversity determined using the Shannon index tended to decrease (P = 0.06) over the 7 d. Relative abundances of Paraprevotellaceae were greater (P ≤ 0.05) in HS in the first 12 h. Over 7 d, relative abundances of Paraprevotellaceae, Veillonellaceae, and Succinivibrionaceae were greater (P ≤ 0.05) in HS compared with LS. Abrupt and short-term exposure to dietary starch does alter cecal fermentation and microbial community structure in horses, but the impact on horse health is unknown.
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Vickers, Richard, Ellie J. C. Goldstein, Diane Citron, David Snydman, Cheleste M. Thorpe, and Anne V. Kane. "1774. Ridinilazole (RDZ) for Clostridium difficile infection (CDI): Correlation of In Vitro Spectrum of Activity with Human Gut Microbiome Profiles from a Phase 2 Clinical Trial." Open Forum Infectious Diseases 5, suppl_1 (November 2018): S67. http://dx.doi.org/10.1093/ofid/ofy209.159.
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Abstract Background Recurrence of CDI (rCDI) is associated with perturbation of the gut microbiome during treatment with vancomycin (VAN) or metronidazole (MTZ). RDZ is a novel, targeted spectrum antibacterial under investigation to treat CDI and reduce rCDI. Here correlation of in vitro spectrum of activity with preservation of the human gut microbiome and clinical outcomes is presented. Methods Susceptibility testing was to CLSI standards with VAN, MTZ, and fidaxomicin (FDX) comparators. The Phase 2 clinical trial was a double-blind, randomized study of 100 patients assigned 1:1 to 10 days RDZ 200 mg BID or VAN 125 mg QID treatment. Primary endpoint was sustained clinical response (SCR), defined as cure at end of therapy (EOT), and no rCDI for the next 30 days. Relative effects of RDZ and VAN on the gut microbiome were examined by sequencing 16S rDNA amplicons from stool collected at baseline, days 5, 10, 25, and end of study. Bioinformatic analyses were performed in QIIME. Results RDZ C. difficile (N = 50) MIC range was 0.125–0.25 μg/mL. Clostridium spp. showed varied RDZ susceptibility; C. innocuum MIC90 1 μg/mL, C. ramosum and C. perfringens MIC90 >512 μg/mL. VAN showed potent to moderate growth inhibition of all Clostridium spp. (MIC range 1–16 µg/mL). Limited RDZ activity was observed for Gram-positive anaerobes, including Bifidobacteria, Eggerthella, Finegoldia, and Peptostreptococcus (MIC90 >512, >512, 64, and 64 μg/mL) compared with VAN (MIC90 1, 4, 0.5, and 0.5 μg/mL). Bacteroides fragilis MIC90 for RDZ and VAN were >512 and 64 µg/mL, respectively. These in vitro data correlate closely with human microbiome profiles. RDZ reduced C. difficile to below detection with other reductions in abundancy observed in only 2 families from the Clostridia. VAN at EOT resulted in significant losses, often below detection, in 4 Firmicutes families, Actinobacteria, and Bacteroidetes and a 25-fold increase in Proteobacteria abundance. The preservation of the microbiome by RDZ likely accounted for reduced rCDI compared with VAN with RDZ shown to be superior on SCR to VAN with rates of 66.7% and 42.4%, respectively (pre-specified 90% CI 3.1, 39.1). Conclusion These data demonstrate strong translation of in vitro spectrum to human gut microbiome preservation during therapy and support further clinical development of RDZ. Disclosures R. Vickers, Summit Therapeutics: Employee, Salary and Stock options. E. J. C. Goldstein, Summit Therapeutics: Grant Investigator and Scientific Advisor, Consulting fee and Grant recipient. D. Citron, Summit Therapeutics: Grant Investigator, Research grant. D. Snydman, Summit Therapeutics: Grant Investigator, Grant recipient. C. M. Thorpe, Summit Therapeutics: Grant Investigator and Scientific Advisor, Consulting fee and Grant recipient. A. V. Kane, Summit Therapeutics: Grant Investigator, Grant recipient.
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Davis, Erin, Mei Wang, and Sharon Donovan. "Bacterial Co-Occurrence Patterns Between Human Milk and Microbial Sites of Breastfeeding Dyads." Current Developments in Nutrition 4, Supplement_2 (May 29, 2020): 966. http://dx.doi.org/10.1093/cdn/nzaa054_038.
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Abstract Objectives The human milk (HM) microbiota is predicted to originate from the maternal gastrointestinal tract, saliva and breast skin, and infant saliva. Though compositionally distinct, these habitats are strongly associated during breastfeeding. Vertical microbial transmission from mother to infant has been documented, but complex microbial interactions between sites are less clear. Herein, ecological networks between HM bacteria and other microbial sites of breastfeeding dyads were assessed to investigate the origin of the HM microbiota and how it may shape the infant gut microbiota. Methods DNA was extracted from maternal and infant saliva, HM, breast skin, and maternal and infant stool samples collected at 6 weeks postpartum from 33 mother-infant pairs. The V3-V4 region of the 16S rRNA gene was sequenced and taxonomy was assigned using QIIME 2. Co-occurrence patterns among genus-level abundance data were analyzed in CoNet (Cytoscape 3.0). Results Twenty-one significant co-presence relationships were identified between HM and other microbial communities. Associations spanned from six nodes in HM including Corynebacterium, Cutibacterium, Gemella, Rothia, Veillonella, and Actinomyces. Co-presence between Cutibacterium, Veillonella, Actinomyces, and Corynebacterium on skin and HM were identified, supporting breast skin as a principal contributor to the HM microbiota. Interestingly, Bifidobacterium in infant saliva was associated with Gemella and Rothia in HM. The greatest number of relationships existed between HM and infant stool. HM Gemella, Actinomyces, and Corynebacterium were associated with Bacteroides in infant stool; HM Actinomyces was also associated with infant fecal Escherichia-Shigella and Eggerthella. Additional relationships were identified between HM and maternal saliva and fecal microbiota. Conclusions Several unique ecological relationships exist between HM and microbial sites of breastfeeding dyads. Whether these relationships are indicative of proximity, mutualism, or are biomarkers of other host-microbe interactions remains to be determined. These data will be useful to uncover mechanisms driving microbial community organization and potential targets for microbial modulation in this population. Funding Sources National Dairy Council, NIH, The Gerber Foundation, The Doris Kelley Christopher Foundation.
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Daniels, Simon, Jacob Hepworth, and Meriel Moore-Colyer. "The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens." PLOS ONE 15, no. 11 (November 17, 2020): e0242373. http://dx.doi.org/10.1371/journal.pone.0242373.
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Respirable dust in conserved forages can pose problems with equid respiratory health, thus soaking (W) and high temperature steaming (HTS) are employed to reduce the levels in hay. The aim of this study was to characterize the viable bacterial community profile of four hays from two different locations in UK following pre-feeding wetting regimens. Hypothesis: (1) Viable microbial community profile of hays will not differ between different pre-feeding regimens. (2) Hay type and location will not influence microbial community profile. Replicates of each of the four hays were subjected to dry (D), HTS conducted in a HG600, W by submergence in 45 L tap water, 16°C for 12 hours. From each post-treated hay, 100 g samples were chopped and half (n = 36) treated with Propidium monoazide dye, the remaining half untreated. Bacterial DNA were extracted for profiling the V4-V5 region of 16S rRNA gene from all 72 samples, then sequenced on the Illumina MiSeq platform. Bioinformatics were conducted using QIIME pipeline (v1.9.1). Linear discriminate analysis effect size (LEfSe) was used to identify differences in operational taxonomic units and predicted metabolic pathways between hays and regimens. HTS reduced proportions of microbiota compared to W and D hay (P < 0.001, df 3, F 13.91), viability was reduced within regimens (P = 0.017, df 1, F 5.73). Soaking reduced diversity within and between regimens. Core bacterial communities differed between hays and regimens, however pre-feeding regimen had the greatest effect on the bacterial community profile. W and HTS reduced viable bacteria (P< 0.05) known to cause respiratory disease, for HTS both respiratory and dental disease, with the greatest reductions overall from HTS without reducing bacterial diversity. Soaking increased Gram-negative bacteria and reduced bacterial diversity. Collectively these findings add to a body of evidence that suggest HTS is the most suitable pre-feeding regimen of hay for equid health.
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Lin, Ching-Yen, Meredith Carroll, Xiaojing Yang, Sungho Do, Wanting Shi, Thunyaporn Phungviwatnikul, Fei He, and Kelly S. Swanson. "245 Effects of dietary macronutrient content on fecal microbiota populations and metabolite concentrations of healthy adult dogs." Journal of Animal Science 97, Supplement_3 (December 2019): 61–62. http://dx.doi.org/10.1093/jas/skz258.128.
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Abstract Diet is one of the greatest influences on gut microbiota number and activity, and one that can rapidly alter conditions. However, limited information about the longitudinal effects of diet on canine fecal microbiota is available. The objective of this study was to determine the effects of dietary macronutrient content on fecal microbiota populations and metabolites of adult dogs. Twelve adult female beagles (age: 5.16±0.87 yr, BW: 13.37±0.68 kg) were used in a crossover design with two 27-d experimental periods. All dogs were fed a kibble diet (control) from d1–14, and then fed that diet supplemented with fiber (HFD) or changed to a canned diet (CD) from d15–27. Fresh fecal samples were collected on d13, 16, 20, 24, and 27 for measurement of metabolites and microbiota populations. Microbial data were analyzed using QIIME 2. Other data were analyzed using Mixed Models procedure of SAS 9.4. Compared with controls, dogs fed HFD had greater (P < 0.05) daily fiber intake, while dogs fed CD had greater (P < 0.05) daily protein and fat intakes. Fecal acetate, propionate, and total SCFA increased (P < 0.05) after the change to HFD (d16), with concentrations being maintained through d27. Fecal isobutyrate, isovalerate, total BCFA, phenol, and indole increased (P < 0.05) after dogs consumed CD (d16), with concentrations being maintained through d27. When dogs consumed HFD (d16), microbial alpha-diversity increased (P < 0.05) and was maintained through d27, while beta-diversity (weighted UniFrac distance measures) were altered (P < 0.05) and stabilized from d20 to d27. Relative abundances of Firmicutes increased (P < 0.05) by d24, while Fusobacteria decreased (P < 0.05) by d16 and was stable from d20 to d27, in dogs fed HFD. In conclusion, diets affected fecal microbiota and metabolites. Although concentrations of fecal metabolites were stabilized after 2d, fecal microbial populations needed more time to stabilize after diet transition.
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Gataullin, B. I., I. G. Gataullin, Nguyen Thi Nga, A. I. Kolpakov, and O. N. Ilinskaya. "Analysis of the intestinal microbiome in colorectal cancer." Kazan medical journal 102, no. 2 (April 6, 2021): 185–91. http://dx.doi.org/10.17816/kmj2021-185.
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Aim. To conduct a comparative analysis of the microbiome of biopsies of a tumor and normal intestinal epithelium of patients diagnosed with colorectal cancer and to identify of functional activities of the obtained bacterial isolates that affect the development of the tumor.
Methods. The study included 50 patients with malignant neoplasms of the colon: 36 men and 24 women. The mean age of the patients was 64.110.2 years. To analyze the microbiota of the biopsies, DNA samples were obtained from the tissue of the unaffected colon mucosa and tumor of the patients. Bacterial 16S rRNA genes fragments were amplified using bar-coded primer bakt_341f. Metagenomic next-generation sequencing was performed using the MiSeq platform (Illumina, USA). The obtained data were processed by bioinformatic methods using the QIIME package. Recognition of microorganisms depending on the morphotype and gram staining of the microflora was carried out using combination differential media and biochemical tests. Statistical analysis was carried out using Microsoft Excel, Service Pack 2 for Office XP, Statistica 6.0 (StatSoft). A comparative analysis was performed with the Student's t-test and the MannWhitney test in case of unmet conditions of validity. Alpha diversity of bacterial communities was quantified by the Shannon diversity index and the UniFrac distance for beta diversity analysis.
Results. In patients with colorectal cancer, 5 bacterial phyla were isolated, the predominant of which were Firmicutes and Bacteroidetes, while the content of Actinobacteria was low. In addition, a higher number of representatives of Fusobacteria was observed in the tumor tissue compared to the tissue of a healthy mucosa, at a distance of 5 centimeters proximal to the tumor. The results of this study indicate that the microbiome of a tumor and a healthy mucosa fundamentally differ from each other not only in morphotype and gram staining but also in antagonistic, hemolytic and ribonucleolytic activities.
Conclusion. Colonization of the tumor by dominant aggressive Gram-negative bacteria leads to significant changes in the tumor microbiome composition compared with normal mucosa, whose representatives are displaced from the damaged epithelium by more aggressive strains.
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Poudel, Shyam K., Roshan Padmanabhan, Kathryn Guinta, Tyler Stevens, Madhusudhan Sanaka, Prabhleen Chahal, Davendra Sohal, Alok A. Khorana, and Charis Eng. "Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease." Journal of Clinical Oncology 39, no. 3_suppl (January 20, 2021): 417. http://dx.doi.org/10.1200/jco.2021.39.3_suppl.417.
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417 Background: In pancreaticobiliary (PB) cancers, there is a paucity of data on predictive and pathophysiologic role of the biliary microbiome. We analyzed bile collected from patients with benign and malignant PB diseases to identify microbiomic signatures associated with malignancy. Methods: We collected bile samples from consenting patients during routine endoscopic retrograde cholangiopancreatography at the Cleveland Clinic, approved by the Institutional Review Board. DNA was extracted from bile specimens using PowerViral RNA/DNA Isolation kit. Bacterial 16S rRNA gene amplification and library construction were performed according to the 16S Metagenomic Sequencing Library Preparation guide from Illumina. Post-sequencing analysis was done using QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq and mixMC packages. Results: Of 46 enrolled patients, 32 had PB cancers including pancreatic (N = 25), cholangiocarcinoma (N = 6), and gallbladder (N = 1). The rest (N = 14) had benign PB diseases including acute and chronic pancreatitis, and gallstones. Using multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs), we found a predominance of genera Dicekeya (p = 0.0002), [ Eubacterium] hallii group (p = 0.0007) , Bacteroides (p = 0.00099) , Faecalibacterium (p = 0.007) , Facklamia (p = 0.013) , Peptococcus (p = 0.013) , Bergeyella (p = 0.0024) , Lachnospira (p = 0.026) , and Lactobacillus (p = 0.025) in bile samples from PB cancers as compared to benign PB diseases. Furthermore, bile samples from patients with pancreatic cancer showed an increased abundance of genera Enterobacter, Parabacteroides, Atopobium, Alloprevotella, Prevotella 7, Acinetobacter, Bergeyella, Clostridium sensu stricto, Lactobacillus, and Rothia; and a decreased abundance of genera Tannerella, Peptococcus, Colinsella, Capnocytophaga, Achromobacter, Ruminococcus 2, Bacteroides, Alistipes, Barnesiella,, Lachnoclostridium, Lautropia, Akkermansia, and Christensenellaceae R-7 group as compared to bile samples from patients with cholangiocarcinoma. Conclusions: Distinct microbiome signatures are associated with benign and malignant PB diseases. There is a difference in the relative abundance of OTUs in bile samples between patients with benign PB diseases vs PB cancers, and between pancreatic cancer vs cholangiocarcinoma. Our findings raise the possibility that either these OTUs have a role in carcinogenesis, or that changes in the microenvironment of benign PB diseases differ from PB cancers leading to distinct separation of the OTU clusters. Further studies to explore and validate our findings are needed.
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Shen, Chwan-Li, Rui Wang, Moamen Elmassry, Volker Neugebauer, and Abdul Hamood. "Dietary Ginger Root Extract Supplementation Mitigated Diabetic Peripheral Neuropathy in Streptozotocin-Induced Diabetic Rats by Modulating Gut Microbiota." Current Developments in Nutrition 5, Supplement_2 (June 2021): 1179. http://dx.doi.org/10.1093/cdn/nzab054_034.
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Abstract Objectives Diabetic peripheral neuropathy (DPN) is a prevalent complication of diabetes with no effective treatment currently. The relationship between gut microbiota and neurological diseases, including DNP, has received increasing attention. Previous studies have shown gingerol-enriched gingerol (GEG) has potential pain-reduction and prebiotic abilities due to its anti-inflammatory capacity. This study examined the effect of GEG on pain sensitivity and gut microbiota in DNP rats. Methods Thirty-three male rats were randomly divided into 3 groups: control group (low-fat diet), DPN group (high-fat diet plus single dose of streptozotocin at 36 mg/kg BW), and DPN + GEG at 0.75% in diet for 6 weeks. Von Frey test was used for for pain assessment. 16S rRNA gene sequencing was done from cecal samples and microbiome data analysis was performed using QIIME 2. Results Relative to the control group, the DNP group showed increased pain hypersensitivity, measured as decreased mechanical withdrawal thresholds. GEG supplementation mitigated pain sensitivity in DNP-treated animals. Principal component analysis showed that GEG treatment shifts the microbiome profile from control and DNP samples. Although GEG did not alter the richness of the microbiome, it significantly increased the alpha-diversity in terms of evenness in comparison to DNP (P < 0.05). Using Kruskal–Wallis test followed by the post-hoc Dunn's test, we identified 9 specific taxa, and their abundance was significantly altered among the control, DNP, and DNP + GEG groups (P < 0.05). In comparison to the control group, the DNP group reduced the relative abundance of Eubacterium coprostanoligenes, Lachnospiraceae, Oscillospiraceae, and Peptococcceae, while DNP increased the abundance of Muribaculum intestinale. Relative to DNP group, the DNP + GEG treatment reversed DNP's effect and reduced the abundance of Muribaculum intestinale to a level similar to the control group. GEG treatment increased the abundance of Acinetobacter, Azospirillum, Colidextribacter, and Fournierella. Conclusions This study demonstrated that GEG supplementation not only reduced pain but also favored the composition of gut microbiome in the DNP model, suggesting targeting gut microbiota by GEG may represent a new therapeutic strategy for the management of DNP. Funding Sources Texas Tech University Health Sciences Center.
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Singla, Shyamli, Justin Wong, Shuang Jiang, Sarah Hussain, Laura Coughlin, Xiaowei Zhan, and Andrew Y. Koh. "Serum Citrulline As a Biomarker for Blood Stream Infections in Pediatric Hematopoietic Stem Cell Transplant Patients." Blood 134, Supplement_1 (November 13, 2019): 3268. http://dx.doi.org/10.1182/blood-2019-127061.
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Background: Invasive microbial infections remain a major cause of morbidity and mortality in hematopoietic stem cell transplant (HSCT) patients. Microbes residing in the GI tract are believed to be the source of mucosal barrier injury-associated blood stream infections (mBSI) in HSCT and cancer patients. Three host factors are critical for preventing microbial translocation from the gut: neutrophils, intact gut barrier function, and gut microbiota homeostasis. Currently there are no reliable biomarkers that can identify patients who will develop mBSIs. Objectives/Hypothesis: Since all HSCT patients develop severe neutropenia (ANC<100), we hypothesized that HSCT patients who develop mBSI will have more impaired gut barrier function and a greater imbalance in gut microbiota populations (as evidenced by depletion of beneficial obligate anaerobe commensals) compared to counterparts who do not develop mBSI. Methods: We designed a prospective, non-randomized, case control pilot study for HSCT patients < 20 years of age. Serum citrulline, which has been used as a surrogate to measure overall gut function, was obtained 1-2 times weekly. Bacterial genomic DNA was isolated from stool samples collected every 7 days. Amplicons (16S rRNA V4 variable region) were generated and sequenced using the Illumina MiSeq platform. Microbial taxonomic assignments were determined using QIIME software and further characterized into relative abundances of obligate (beneficial commensal) versus facultative (pathogenic) anaerobes. Clinical characteristics were recorded. Results: Of the 78 HSCT patients enrolled on the study, 27% (21 patients) developed BSI. Of the patients with confirmed blood stream infections, 16 patients were categorized as mBSI, and ultimately 11 patients were included in our analysis. 48 patients did not develop a BSI and had evaluable citrulline levels and constituted our control group. Patients with mBSI had a more significant decline in citrulline levels during the period from the start of conditioning to the development of mBSIs (linear mixed effect model, p = 0.048, likelihood ratio test) compared to counterparts without mBSI. We found no significant association between levels of facultative (pathogenic) anaerobes and the development of mBSI in this cohort. Conclusions: Decreased citrulline levels, which suggest impaired gut epithelial function, are associated with the development of severe, invasive bacterial infections. These data suggest that measuring citrulline may have utility as a biomarker for predicting mBSI in HSCT patients. Disclosures Koh: Merck: Consultancy.