Categories
Tag: adonis
Adonis2 inR
Adonis2 inR 0 When I plot my data set in ggplot, I get next to no separation of groups, yet when I run it with Adonis2, I get a p<0.05. What am I doing wrong? I did it before some time ago with a different data set. The difference now…
Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe
Wang, W. T. Revision of Adonis (Ranunculaceae). Bull. Bot. Res. 14, 1–31 (1994). Google Scholar Gao, T. et al. Evaluating the feasibility of using candidate DNA Barcodes in discriminating species of the large Asteraceae family. BMC Evol. Biol. 10, 324 (2016). Article Google Scholar Conti, F. et al. Adonis fucensis…
Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP
ISCA fabrication VeroGray polymer was used to create 3D-printed moulds on an Objet30 3D printer (Stratasys), using previously described protocols32. Each ISCA consisted of 25 wells arranged in a 5 × 5 array. Each 110 µL well possessed a 800-μm-diameter port that connected the inside of the well with the surrounding seawater and…
The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum
Ethics approval and consent to participate The study was approved by the Human Research Ethics Committees of the Children’s Hospital of Soochow University (Reference 2020CS017). All specimens were collected according to the guidelines set by the Children’s Hospital of Soochow University. All authors confirm that all methods were performed in…
Bioconductor – Bioconductor 3.18 Released
Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…
Qiime2 unable to perform ADONIS on multiple variable – Technical Support
Hello,I’ve previously used fragment-insertion plugin without any issues. However, recently as I’m trying generate the tree using rep_seq file generated from vsearch open-reference clustering. I’m getting the following error from the this plugin. And the log file says- Removing /tmp/tmp.etXzw1y7jQ/sepp-tmp-CaHDDnOVOTTraceback (most recent call last):File “/home/turtle/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py”, line 352, in callresults =…
Gut Microbiome of Children with Airway Allergic Disease
Introduction Allergic airway diseases affect many people worldwide, and incidences are still increasing gradually. Allergic rhinitis and allergic asthma, are typical chronic nasopharyngitis respiratory diseases in pediatric, causing an enormous burden of illness and high economic costs to the community.1 Allergic rhinitis and allergic asthma are immunoglobulin E (IgE)-mediated inflammatory…
Qiime2 Python API unifrac dist matrix error: FileNotFoundError: [Errno 2] No such file or directory: ‘ssu’ – Technical Support
Hi all, I am trying to generate an unweighted unifrac with the qiime2 python API and get the following output and error: from qiime2 import Artifact from qiime2.plugins import diversity_lib tab1N=(‘/home/sdegregori/TOL/GMTOLsubsample/GMTOLsong_tablef_V4_N1_pythontest.qza’) phyf=(‘/home/sdegregori/TOL/GMTOLsubsample/GMTOLsong_rooted_treef.qza’) table1N = Artifact.load(tab1N) phylogenyf = Artifact.load(phyf) distance_matrix_result = diversity_lib.methods.unweighted_unifrac(table=table1N,phylogeny=phylogenyf) distance_matrix = distance_matrix_result.distance_matrix distance_matrix.save(‘/home/sdegregori/TOL/GMTOLsubsample/adonis/UW1N.qza’) Running external command line application….
Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China
Wu, Z. Antibiotic Use and Antibiotic Resistance in Food-Producing Animals in China OECD Food, Agriculture and Fisheries Paper No. 134 (OECD, 2019); doi.org/10.1787/4adba8c1-en Looft, T. et al. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl Acad. Sci. USA 109, 1691–1696 (2012). Article ADS CAS PubMed PubMed Central Google…
Human-influenced diets affect the gut microbiome of wild baboons
Field site Akagera National Park (ANP; 1°52’S, 30°42E) lies in eastern Rwanda, along the border with Tanzania. It is roughly 250,000 ha in size and is characterized by woodland, swamps, low mountains and savannah. At least one quarter of the park contains the swamps and lakes of the Kagera River system,…
Evidence of Necromancy during Late Antiquity in the Te’omim Cave | HeritageDaily
The discovery of oil lamps, weapons, and human skulls, suggest that Te’omim Cave was used for necromancy ceremonies during the Late Roman Period. Te’omim Cave, also known as Mŭghâret Umm et Tûeimîn (“the cave of the mother of twins”), is a cave complex in Israel’s Jerusalem Hills east of Beit…
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis
Bacterial strains and growth conditions Rothia aeria CECT9999 (Ra9, isolate D1P7 described in24), was used as a nitrate-reducing probiotic candidate. Prior to the experiment, Brain Heart Infusion (BHI) (Biolife, Deerfield, Illinois, USA) agar plates were inoculated with the strain, incubated for 48 h at 37 °C, and stored at 4 °C for up…
Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil
Study sites Soils were collected from two different sites (ARDEC: Colorado State University’s Agricultural Research, Development and Education Center in Fort Collins, CO; and CPCRC: USDA Columbia Plateau Conservation Research Center in Pendleton, OR). At each site, four replicate plots of no-till corn (ARDEC) or no-till annual wheat (CPCRC) were…
Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding
doi: 10.1111/1755-0998.13812. Online ahead of print. Affiliations Expand Affiliations 1 CBGP, CIRAD, Montpellier SupAgro, INRAE, IRD, University of Montpellier, Montpellier, France. 2 CIRAD, CBGP, Montpellier, France. 3 CBGP, INRAE, Montpellier SupAgro, INRAE, IRD, University of Montpellier, Montpellier, France. Item in Clipboard Marie-Pierre Chapuis et al. Mol Ecol Resour. 2023. Show details…
Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species
Introduction Tropical rainforests in the Amazon basin harbor the highest tree diversity on earth (Ter Steege et al., 2020). Most of this diversity is concentrated in a relatively small number of plant families, including Chrysobalanaceae, Fabaceae, Lauraceae, Lecythidaceae, Malvaceae (sensu lato), Myrtaceae, Rubiaceae, and Sapotaceae, that can comprise > 60%…
Babylon Health ‘may Trade To Zero’
InnovationRx is your weekly digest of healthcare news. To get it in your inbox, subscribe here. Ali Parsa, founder and chief executive officer of Babylon Holdings Limited. © 2022 Bloomberg Finance LP Babylon Holdings Limited, a U.K. and Austin, Texas-based digital health company that went public in a 2021 SPAC…
Low W taxa identified as significant – troubles with workaround – User Support
Dear community. I started working with Qiime2 (2023.2) recently and i am facing some issues with ANCOM/ANCOM-BC. I have read multiple posts in the forum and done the tutorials, but still not sure how to proceed. Originally, i was just running Alpha Diversity, Adonis and PERMANOVA test to analyze my…
Shallow shotgun sequencing reduces technical variation in microbiome analysis
Participant selection and sample collection Informed consent was obtained for five adult volunteers. The study protocols were reviewed and approved by the Advarra Institutional Review Board (Advarra, Inc., Columbia, MD). All analyses were performed according to the relevant guidelines and regulations. Fecal collection was completed by self-sampling, which has proven…
Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods | Environmental Microbiome
O’Neill J. The Review on Antimicrobial Resistance—tackling drug-resistant infections globally: final report and recommendations. 2016. Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet. 2022;399:629–55. Article CAS Google Scholar Laxminarayan R….
Chronic Strongyloides stercoralis infection increases presence of the Ruminococcus torques group in the gut and alters the microbial proteome
Human ethics statement This study was approved by the Human Ethical Review Committee of Khon Kaen University, Thailand (HE641434) following the principles of the Declaration of Helsinki. Before stool samples were collected, participants were required to complete and sign written informed-consent forms. Participants and samples All samples came from residents…
Does the skbio PERMANOVA function have a pairwise option like in qiime2? – General Discussion
Hi all, I know how to run the basic skbio permanova code in python: import skbio as skbskperm=skb.stats.distance.permanova(dm, host_md_test, column=’Host1′, permutations=999) But I only get stats on the overall test. Is there a way to show the pairwise comparisons like in qiime2?I am trying to keep this in python because…
Leveraging 16S rRNA data to uncover vaginal microbial signatures in women with cervical cancer
1 Introduction Cervical cancer (CC) remains the fourth most common cancer in women worldwide, with 604,127 new cases in 2020 and more than 341,831 deaths, accounting for nearly 8% of all female cancer-related deaths annually (Sung et al., 2021). This common infection-related neoplasm and its premalignant precursor are caused by high-risk…