Categories
Tag: DADA2
NifH database for taxonomic assignment in qiime2 – General Discussion
JThurston (Josh Thurston) January 19, 2024, 8:05pm 1 Hi all! I’m currently working through a Qiime2 pipeline analysing Illumina miseq paired-end amplicon data. I’ve successfully analysed bacterial (16s) amplicons from importing, filtering through to taxonomic assignment. However, I also have amplicon data for a functional gene (nifH; nitrogenase for N2…
Error produced when trying to assign taxonomy in DADA2 in R – rstudio
I have been trying to assign taxonomy against the MiDAS database in R. In previous steps, I have cleaned up my genetic data using the DADA2 profiles and then use this code to assign taxonomy taxa_midas_genus <- assignTaxonomy(seqtab.nochim, “C:/R/MiDAS.fa”, taxLevels = c(“Kingdom”, “Phylum”, “Class”, “Order”, “Family”, “Genus”), verbose = TRUE,…
Senior Bioinformatics Scientist in Chicago, IL for University of Chicago (UC)
Details Posted: 19-Dec-23 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Chicago, IL Job Description: Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data. Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform. Functional analysis of…
Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout
FAO. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation (FAO, 2022). Google Scholar Hua, K. et al. The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth 3, 316–329 (2019). Article Google Scholar Hardy, R. W. Utilization of plant proteins in fish diets:…
Senior Bioinformatics Scientist @ University of Chicago
Department BSD DFI – Translational Informatics About the Department The Duchossois Family Institute focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact…
DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea
Description This version is to stay up to date with the improvements and increase in 16S rRNA gene sequences (SSU) added to the GTDB release 214.1. Please read this post for the stats on the updates. gtdb.ecogenomic.org/stats/r214 . There has been no change to the RDP-RefSeq reference database If anyone…
Less number of total Species than Genus in 16S data
DADA2’s classifiers might not be able to classify to the species-level, it will keep the taxonomic level ‘higher’ as necessary. Example with some of my fish ASVs: “Eukaryota”,”Chordata”,”Actinopteri”,”Labriformes”,”Labridae”,NA,NA Only family-level classification, no genus/species “Eukaryota”,”Chordata”,”Actinopteri”,”Kurtiformes”,”Apogonidae”,”Apogonichthyoides”,”Apogonichthyoides timorensis” Classified to the species-level So yeah, you might have more genera classified than species if…
Zea mays genotype influences microbial and viral rhizobiome community structure
Oburger E, Schmidt H. New methods to unravel rhizosphere processes. Trends Plant Sci. 2016;21:243–55. Article CAS PubMed Google Scholar Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot. 2013;100:1689–91. Article PubMed Google Scholar Pratama AA, Terpstra J, de Oliveria ALM,…
Lower-limb ulcers in participants with leprosy sequelae
Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…
Survey of the infant male urobiome and genomic analysis of Actinotignum spp.
Wolfe, A. J. et al. Evidence of uncultivated bacteria in the adult female bladder. J. Clin. Microbiol. 50, 1376–1383 (2012). Article PubMed PubMed Central Google Scholar Hilt, E. E. et al. Urine is not sterile: Use of enhanced urine culture techniques to detect resident bacterial flora in the adult female…
qiime2 illegal instruction – Technical Support
Andrea_G (Andrea Gatti) November 28, 2023, 2:19pm 1 Hello, I have to start working on a cluster and I tired to install Qiime2 in a conda environment, but I was reported with an error during Qiime2 installation, specifying: Preparing transaction: done Verifying transaction: – SafetyError: The package for r-base located…
Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis | BMC Infectious Diseases
Wu Z, McGoogan JM. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020;323(13):1239–42. Article CAS PubMed Google Scholar Kesheh MM, Hosseini P, Soltani S, Zandi M. An…
Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020;70:5607–12. Article PubMed PubMed Central Google Scholar Saxena AK, Kumar M, Chakdar H, Anuroopa N, Bagyaraj DJ. Bacillus species in soil…
Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost
Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article Google Scholar Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…
Improving Species Level-taxonomic Assignment from 16S rRNA Sequencing Technologies
Affiliations Expand Affiliations 1 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain. 2 ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain. 3 Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute…
A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing
Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We…
Evaluation of the fresh beef bacterial community through processing retail display conditions using 16S rRNA gene amplification sequencing
Microorganisms are ubiquitous and provide challenges in the food production system. Beyond monitoring for pathogens or food safety hazards, there is a need for understanding and controlling spoilage organisms, and indicators of potential spoilage especially with products that have a more limited shelf-life, such as fresh meat. Arguably, just as…
Count.groups discrepancy? – Commands in mothur
Hi, I’m importing the output from DADA2 fungal ASVs into mothur for clustering, classification and general tidy up.So far, I’ve edited the ASV file to imitate a shared mothur file, then used count.seqs to produce a count.table. However, when using count.groups on the original shared file and the produced count.table,…
Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics
Albone, E. S. Mammalian semiochemistry. The investigation of chemical signals between mammals. 2–5 (1984). Wyatt, T. D. Pheromones and Animal Behaviour: Communication by Smell and Taste (Cambridge University Press, 2003). Book Google Scholar Doty, R. L. Odor-guided behavior in mammals. Experientia 42, 257–271 (1986). Article CAS PubMed Google Scholar Brennan,…
Gut microbiota composition and diversity before, during, and two months after rifamycin-based tuberculosis preventive therapy
Bagcchi, S. WHO’s global tuberculosis report 2022. The Lancet Microbe. 4, e20 (2023). Article PubMed Google Scholar Behr, M. A., Edelstein, P. H. & Ramakrishnan, L. Revisiting the timetable of tuberculosis. BMJ 362, k2738 (2018). Article PubMed PubMed Central Google Scholar Cohen, A., Mathiasen, V. D., Schön, T. & Wejse,…
Large qiime2 table (107 gb) to phyloseq
Large qiime2 table (107 gb) to phyloseq 0 Hello, I’m currently engaged in a microbiome meta-analysis and have combined a dada2 table involving data from 83 different studies. The file size of this merged table is 107GB. However, I’m encountering difficulties reading this file in R to conduct statistical analyses….
dada2 vs TCGAbiolinks – compare differences and reviews?
What are some alternatives? When comparing dada2 and TCGAbiolinks you can also consider the following projects: kraken-biom – Create BIOM-format tables (biom-format.org) from Kraken output (ccb.jhu.edu/software/kraken/, github.com/DerrickWood/kraken). MicrobiomeStat – Supporting Longitudinal Microbiome Analysis in R GTDBTk – GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes….
Using DADA2 for finding viral sequence variants
Using DADA2 for finding viral sequence variants 0 Hello, I decided to use the Dada2 basic pipeline for 16S in order to detect variants in my viral amplicon sequences. I have PCR amplified sequences from a 302 base-pair region of the viral genome. I used the DADA2 pipeline to detect…
Bacterial networks in Atlantic salmon with Piscirickettsiosis
Verschuere, L., Rombaut, G., Sorgeloos, P. & Verstraete, W. Probiotic bacteria as biological control agents in aquaculture. Microbiol. Mol. Biol. Rev. 64(4), 655–671 (2000). Article CAS PubMed PubMed Central Google Scholar Gomez, G. D. & Balczar, J. L. A review on the interactions between gut microbiota and innate immunity of…
Does ASVs IDs from dada2 have specific taxonomic assignments?
Does ASVs IDs from dada2 have specific taxonomic assignments? 1 Hello Community, I’m trying to subset matrices of ASVs’s associations that were produced from 2 different phyloseq objects. For downstream analysis I need to subset the square matrices in a way that the exactly same taxa are contained in both…
Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium
Rabus, R., Hansen, T. A. & Widdel, F. In Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes. The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., and Thompson F. at (2013). Rabus, R. et al. Chapter Two—A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing…
Phyloseq and ASV names between datasets
Hi, I ran DADA2 on 3 16S-datasets , what went well. Then, I imported the output files to phyloseq in R to create some abundances tables, graphs etc. My problem is to correlate the ASV names between the 3 abundance tables. I mean, each ASV will be named ASV1, ASV2…
DeSeq2 normalization 16S
DeSeq2 normalization 16S 0 @88dd97c8 Last seen 10 hours ago United States Hi! I’m a geochemist doing some microbial analyses, so this may be a silly question. I saw a suggestion to use DESeq2 as a means to normalize my 16S rRNA ASV data rather than using rarefaction via sequencing…
feature-classifier not producing an output – Technical Support
Hello, I have a problem with the feature classifier.So I tried this on multiple computers (with intel and AMD chips) and with multiple versions of QIIME2 (QIIME2 2023.5 and 2023.7)So I have a dual boot on my computer with Windows and Linux Ubuntu, newest release. It has 16 GB of…
q2-dada2 -p-pooling-method TRUE for large number of samples then move to R – User Support
Eman (Eman Khalaf) October 8, 2023, 4:50pm 1 Hi, I have many samples (~650) sequenced by PacBio platform. RStudio can not process dada function due to the memory limit of the software. The total size of the samples is 30 GB and I need to use pool=TRUE parameter. So, I…
The recovery of the microbial community after plaque removal depends on periodontal health status
Jin, L. & Group, E. Initiator paper. Interprofessional education and multidisciplinary teamwork for prevention and effective management of periodontal disease. J. Int. Acad. Periodontol. 17, 74–79 (2015). PubMed Google Scholar Kassebaum, N. J. et al. Global burden of severe periodontitis in 1990–2010: a systematic review and meta-regression. J. Dent. Res….
Protistan predation selects for antibiotic resistance in soil bacterial communities
Courtenay M, Castro-Sanchez E, Fitzpatrick M, Gallagher R, Lim R, Morris G. Tackling antimicrobial resistance 2019-2024–the UK’s five-year national action plan. J Hosp Infect. 2019;101:426–7. Article CAS PubMed Google Scholar D’Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, et al. Antibiotic resistance is ancient. Nature. 2011;477:457–61….
18S taxonomy assignment SILVA database formatting
Hi Bioinformatic community, I would like to classify 18S data (V7) of Fungi with assignTaxonomy from dada2. For that I downloaded SILVA_132_SSURef_tax_silva.fasta.gz from the SILVA website and need to format it, what I do with some Linux command line oneliner. But some species in the database have a different number…
Incorporation of long-read 16s rRNA sequences into QIIME2 and ASV generation – Technical Support
Hi all, I am trying to incorporate some complete/near complete 16s rRNA sequences that I have extracted from annotated genomes following some PacBio HiFi metagenomic sequencing I have done. The aim here is to compare these sequences against a V1-V2 16s rRNA sequencing dataset, generating a phylogenetic tree to see…
Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing
Soil incubation and cell extraction Approximately 3 kg of unmanaged marginal soil (pH 8) was collected from the Pacific Northwest National Laboratory field site in Prosser, Washington (46° 15′ 04″ N and 119° 43′ 43″ W) [23], homogenized, sieved (4 mm mesh size), and stored at 4 °C until further processing. Probe specific…
Maximize RStudio memory for DADA2 workflow – General
Hi, I have approximately 1000 16S sequenced samples generated from the PacBio platform, and I am using DADA2 workflow to infer ASVs. The script is halted at dada function step since I use the pooling option dd <- dada(filts, err=err, pool=TRUE, BAND_SIZE=32, OMEGA_A=1e-10, DETECT_SINGLETONS=FALSE, multithread=TRUE) I tried to use different…
The succession of epiphytic microalgae conditions fungal community composition: how chytrids respond to blooms of dinoflagellates
Jones EBG, Suetrong S, Sakayaroj J, Bahkali AH, Abdel-Wahab MA, Boekhout T, et al. Classification of marine Ascomycota, Basidiomycota, Blastocladiomycota and Chytridiomycota. Fungal Divers. 2015;73:1–72. Article Google Scholar Van den Wyngaert S, Ganzert L, Seto K, Rojas-Jimenez K, Agha R, Berger SA, et al. Seasonality of parasitic and saprotrophic zoosporic…
Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels
Bhaduri D, Pal S, Purakayastha TJ, Chakraborty K, Yadav RS, Akhtar MS. Soil quality and plant-microbe interactions in the rhizosphere. In: Lichtfouse E, editor. Sustainable agriculture reviews: volume 17. Cham: Springer International Publishing; 2015. p. 307–35. Mishra S, Singh A, Keswani C, Saxena A, Sarma BK, Singh HB. Harnessing plant-microbe…
Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria
Ramanan R, Kim BH, Cho DH, Oh HM, Kim HS. Algae–bacteria interactions: evolution, ecology and emerging applications. Biotechnol Adv. 2016;34:14–29. Article CAS PubMed Google Scholar Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive earth’s biogeochemical cycles. Science. 2008;320:1034–9. Article CAS PubMed Google Scholar Buchan A, LeCleir GR,…
Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis
Neilson, J. W. et al. Significant impacts of increasing aridity on the arid soil microbiome. mSystems 2, e00195–e00116 (2017). Article CAS PubMed PubMed Central Google Scholar Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA 109, 21390–21395 (2012). Article …
qiime tools import issues (QIIME2 2023.7) – Technical Support
To Whom it May Concern: Hello. I am trying to run a few practice trials on getting sequences from NCBI via q2-fondue prior to a larger scale analysis. The code was working just fine up until dada2 where I encountered a common error that the forum believes is a storage…
Data from: Tephritid fruit fly gut bacterial population and community dynamics following adult emergence
Data include microbial count data (CFUs), 16S-rRNA copy number data (qPCR), and microbial community (microbiome) data from the guts of the invasive tephritid fruit flies, melon fly (Zeugodacus cucurbitae) and medfly (Ceratitis capitata). Resources in this dataset: Resource Title: R code for dada2 processing and stacked bar charts of control…
Bioconductor – Rbec
DOI: 10.18129/B9.bioc.Rbec Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities Bioconductor version: Release (3.17) Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile…
Effects of a postbiotic SLFC non scalp microbiome
Introduction Sensitive scalp is a skin syndrome caused by the hyper-reactivity to environmental stimuli, which might cause inflammatory symptoms and abnormal sensory reactions of the scalp including pruritus, prickling, tightness, pain, and burning, but without visible signs of inflammation.1 Various circumstances, such as the atmospheric environment, heat, pollution, hair care…
issue with qiime dada2 denoise-ccs – Technical Support
Hi,I have 24 clean CCS read datasets and i want to get amplicon sequence variants by running dada2.I got one issue when running dada2 denoise-ccs with QIIME2. When i am running dada2 in qiime2 with all 24 samples:The command I used was: qiime dada2 denoise-ccs –i-demultiplexed-seqs reads_qza/ccs_reads.qza –p-min-len 1200 –p-max-len…
Plugin error from fragment-insertion: – Technical Support
HiI am running the Parkison mice sample data, and I have updated the Qiime2, and my computer have enough capacity. But I still met this problem. Could you please help me deal with it? Plugin error from fragment-insertion: Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-6m4if51o/a3c55eab-dffc-426e-8521-3d193cab2fc0/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/tmp/qiime2-archive-0s212g0k/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta’,…
Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis
Introduction Endophthalmitis is a severe infection in the eye that can occur as a consequence of intraocular surgery, intraocular injections, trauma, the presence of a central venous catheter and systemic infectious diseases such as sepsis, abscesses or urinary tract infection.1 2 Acute bacterial endophthalmitis represents a significant ocular pathology that…
Error: Alpha rarefaction curve after merging the data of two different runs – Technical Support
Hi!I am facing a problem in alpha rarefaction curve plotting. In this study my samples were sequenced in two different runs “under same conditions” using Illumina Platform- MiSeq. For that reason I have merged the data from both the runs using same filtering parameters and following DADA2. Till “phylogeny align-to-tree-mafft-fasttree”…
if I dont know what primers in my sequencing data,How do I use qiime2 – General Discussion
cjj102664 (俊杰 陈) September 10, 2023, 3:52pm 1 Does anyone know,it is necessary to run qiime cutadapt trim-paired before run dada2. Hello @cjj102664. Welcome to the forums! cjj102664: it is necessary to run qiime cutadapt trim-paired before run dada2. Not necessarily! cutadapt will ‘cut adapters’ from your input reads. Some…
The Biostar Herald for Wednesday, September 06, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation
Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…
Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization
Buettgens, M., Blavin, F. & Pan, C. The affordable care act reduced income inequality in the US. Health Aff. 40, 121–129 (2021). Article Google Scholar Chen, E. & Miller, G. E. Socioeconomic status and health: mediating and moderating factors. Annu. Rev. Clin. Psychol. 9, 723–749 (2013). Article PubMed Google Scholar …
Nodulation number tempers the relative importance of stochastic processes in the assembly of soybean root-associated communities
Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. New Phytol. 2015;206:1196–206. doi.org/10.1111/nph.13312. Article PubMed Google Scholar Zhou J, Ning D. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiol Mol Biol Rev. 2017;81. doi.org/10.1128/MMBR.00002-17. Fitzpatrick CR, Salas-González…
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Publicly available mock community sequencing datasets 136 mock community sequencing samples were collected in total from four publicly available sequencing datasets and analyzed in our evaluation. 69 samples are from Lluch et al.33; 33 samples are from Kozich et al.34; 29 samples are from Fouhy et al.35; and 5 samples…
DADA2 denoising not working (First return error 9 then 1 after increasing memory to 16 GB) – Technical Support
Did not find the exact answer to this on the forum; new to QIIME2, apologies. QIIME2-2023.5, running in Conda through university’s central Linux-based system Apply DADA2 denoising qiime dada2 denoise-paired –i-demultiplexed-seqs paired-end-demux.qza –p-trunc-len-f 280 –p-trunc-len-r 220 –p-n-threads 24 –o-representative-sequences rep-seqs-dada.qza –o-table table-dada2.qza –o-denoising-stats dada-stats.qza –verbose R version 4.2.3 (2023-03-15)Loading required…
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity? 0 I was asked to identify which ASVs came from which samples. My understanding is that an ASV can be present in multiple samples but then that led me to the question of whether or…
PacBio 16S pipeline
QIIME2 analysis pipeline 0. activate conda environment conda activate qiime2-2019.10 1. flip sequences to the same direction mkdir raw_data_rc/ mkdir raw_data_cat/ parallel -j 8 ‘seqtk seq -r {} > raw_data_rc/{/.}_rc.fastq’ ::: rawdata/*.fastq parallel -j 8 –link ‘cat {1} {2} > raw_data_cat/{1/.}_cat.fastq’ ::: rawdata/*.fastq ::: raw_data_rc/*_rc.fastq 2. trim primers mkdir trimmed_reads/…
Bugs : r-bioc-dada2 package : Ubuntu
$ remove-package -s mantic -m “Removed from Debian testing, blocking migration of r-bran-bh and r-bioc-dada2 (LP: #2030740)” q2-dada2Removing packages from mantic: q2-dada2 2022.11.2-2 in mantic q2-dada2 2022.11.2-2 in mantic amd64Comment: Removed from Debian testing, blocking migration of r-bran-bh and r-bioc-dada2 (LP: #2030740)Remove [y|N]? y1 package successfully removed. $ remove-package -s mantic -m…
Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales
Romans, B. W. & Graham, S. A. A deep-time perspective of land–ocean linkages in the sedimentary record. Annu. Rev. doi.org/10.1146/annurev-marine-121211-172426 (2013). Article Google Scholar Smith, S. V. & Hollibaugh, J. T. Coastal metabolism and the ocean organic carbon balance. Rev. Geophys. 31, 75–89 (1993). Article ADS Google Scholar Bauer, J….
Microbial community composition of food waste before anaerobic digestion
Kaza, S., Yao, L. C., Bhada-Tata, P. & Van Woerden, F. What a Waste 20: A Global Snapshot of Solid Waste Management to 2050 (World Bank, 2018). doi.org/10.1596/978-1-4648-1329-0. Book Google Scholar Lim, S. L., Lee, L. H. & Wu, T. Y. Sustainability of using composting and vermicomposting technologies for organic…
A genome catalogue of lake bacterial diversity and its drivers at continental scale
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). Article CAS PubMed PubMed Central Google Scholar Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats….
Sample ID in feature table and meta data not in order – Other Bioinformatics Tools
A. I got this error (below) for this code physeq <- qza_to_phyloseq( features = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/dada2_table_16S.qza”, tree = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza”, taxonomy = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/taxonomy.qza”, metadata = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/metadata16S.tsv” )Error in validObject(.Object) : invalid class “phyloseq” object:Component sample names do not match.Try sample_names() As I was trying to look into detail, this was the error,…
Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population | BMC Gastroenterology
Study populations Between 2015 and 2019, stool samples and data were collected from 219 IBD subjects (CD or UC) attending the Internal Medicine Clinics, King Fahd Hospital of the University, Al-Khobar and King Fahad Hospital, Alhafof, Saudi Arabia. Diagnosis of IBD was based on endoscopy (for CD) or colonoscopy (for…
Using Bioconda with Mac M1 Processor?
Hello Everyone! I’m extremely new to bioinformatics, so please understand my complete ignorance to this process. My lab use to utilize Michigan States Ribosomal Database Project (RDP), but it recently stopped being supported and is no longer available. We are attempting to pivot to QIIME 2 to clean up and…
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,…
Diversity and potential plant growth promoting capacity of seed endophytic bacteria of the holoparasite Cistanche phelypaea (Orobanchaceae)
Bodelier, P. L. E. & Dedysh, S. N. Microbiology of wetlands. Front. Microbiol. 4, 79. doi.org/10.3389/fmicb.2013.00079 (2013). Article PubMed PubMed Central Google Scholar Tebbe, D. A. et al. Seasonal and zonal succession of bacterial communities in North Sea salt marsh sediments. Microorganisms 10(5), 859. doi.org/10.3390/microorganisms10050859 (2022). Article CAS PubMed PubMed…
sequence analysis – Can files with different R1 and R2 lengths be trusted?
I received paired end amplicon sequence from a LAB with different lengths for R1 (320) and R2(280). Should I trust this lab to sequence other samples? Also, I had to do a trimming over the R2 at 220(because Phred score was below 30) in the qiime2/DADA2 pipeline. Do you think…
Toxic and non-toxic dinoflagellates host distinct bacterial communities in their phycospheres
Moran, M. A. et al. Deciphering ocean carbon in a changing world. Proc. Natl. Acad. Sci. USA 113, 3143–3151 (2016). Article CAS Google Scholar Ashraf, N., Ahmad, F. & Lu, Y. Synergy between microalgae and microbiome in polluted waters. Trends Microbiol. 31, 9–21 (2023). Article CAS Google Scholar Ramanan, R….
An error was encountered while running DADA2 in R (return code -9) even with 125GB of RAM – Technical Support
Hi everyone, I am using qiime2 for analyzing the microbiome data. I am stuck at the step of using dada2 denoise-paired for quality control processing. For this step I am using the command:qiime dada2 denoise-paired –i-demultiplexed-seqs demux-paired-end.qza –p-trunc-len-f 150 –p-trunc-len-r 150 –o-representative-sequences rep-seqs-dada2.qza –o-table table-dada2.qza –o-denoising-stats stats-dada2.qza –p-n-threads 10 –verbose…
Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring
Pavlov AA, Brown LL, Kasting JF. UV shielding of NH3 and O2 by organic hazes in the Archean atmosphere. J Geophys Res Atmos. 2001;106:23267–87. Article CAS Google Scholar Zahnle KJ. Earth’s earliest atmosphere. Elements. 2006;2:217–22. Article CAS Google Scholar Arias P, Bellouin N, Coppola E, Jones R, Krinner G, Marotzke…
Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support
Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…
Differential contribution of nitrifying prokaryotes to groundwater nitrification
Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76. Article CAS PubMed Google Scholar Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol. 2018;103:177–89. Article PubMed PubMed Central Google Scholar Lehtovirta-Morley LE Ammonia oxidation: ecology,…
Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities
Rantanen M, Karpechko AY, Lipponen A, Nordling K, Hyvärinen O, Ruosteenoja K, et al. The Arctic has warmed nearly four times faster than the globe since 1979. Commun Earth Environ. 2022;3:1–10. Article Google Scholar Kwok R. Arctic sea ice thickness, volume, and multiyear ice coverage: losses and coupled variability (1958–2018)….
Evaluating cpn60 for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis
Mammalian host swab sample selection To investigate mammalian skin microbial communities using the cpn60 gene, 95 representative skin swab samples, already extracted for genomic DNA and sequenced from a previous project [8], were selected for additional amplification and sequencing of the cpn60 gene. This cpn60 gene amplicon dataset contained samples…
Humans as blood-feeding sources in sylvatic triatomines of Chile unveiled by next-generation sequencing | Parasites & Vectors
Kent RJ. Molecular methods for arthropod bloodmeal identification and applications to ecological and vector-borne disease studies. Mol Ecol. 2009;9:4–18. doi.org/10.1111/j.1755-0998.2008.02469.x. Article CAS Google Scholar Gómez-Díaz E, Figuerola J. New perspectives in tracing vector-borne interaction networks. Trends Parasitol. 2010;26:470–6. doi.org/10.1016/j.pt.2010.06.007. Article PubMed Google Scholar Hylton A, Fitzpatrick DM, Suepaul R, Dobson…
Need help in demultiplexing of amplicon data
Need help in demultiplexing of amplicon data 0 Hello all, I have one query to ask. Actually, I have a merged fastq sequence file that contains sequences of 37 samples and all those samples are of my interest, so, instead of treating them as individual samples, I treated them as…
DADA2 error from ITS sequences – Technical Support
Hello there, I’m working with ITS sequences from 45 samples in total. They were sequenced through an Illumina Novaseq 6000 instrument. Using the last version of QIIME2 (2023.5), my problem occurs while I perform the denoising analysis through dada2 with the following command: qiime dada2 denoise-paired –i-demultiplexed-seqs paired-end-demux.qza –p-trunc-len-f 155…
The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton
Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A et al (2019) Revisions to the classification, nomenclature, and diversity of eukaryotes. J Eukaryot Microbiol 66(1):4–119. doi.org/10.1111/jeu.12691 Article PubMed PubMed Central Google Scholar Annenkova NV, Giner CR, Logares R (2020) Tracing the origin of planktonic protists in an…
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…
Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16:410–22. doi.org/10.1038/s41579-018-0029-9. Article CAS PubMed Google Scholar Blaxter M. Counting angels with DNA. Nature. 2003;421:122–3. doi.org/10.1038/421122a. Article CAS PubMed Google Scholar Cordier T, Alonso-Sáez L, Apothéloz-Perret-Gentil L, Aylagas…
Question about 16S rRNA reads we got from a sequencing company
Hi there, We recently had some DNA samples sequenced at Novogene UK: amplicon sequencing of the V3–V4 subregions of the 16S rRNA gene. The final sequencing data was provided to us in ‘RawData’ and ‘CleanData’ formats. The main thing I’m confused about is that the ‘RawData’ doesn’t actually seem to…
An independent evaluation of microbiome 16S rRNA sequence analysis methods in CRC cohort: OTU-clustering, DADA2, and Deblur
1College of Electronics and Information Engineering, School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China, China 2Guangdong Hongyuan Pukong Medical Technology Co., Ltd, Guangzhou 510000, China, China 3Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China, China …
Plugin error from dada2: An error was encountered while running DADA2 in R (return code 1). – Technical Support
Hello everyone,I’m trying to run dada2 denoise-paired on already demultiplexed Novaseq 6000 150 PE 12s sequences (amplicon size 100 bp ca) of fishes. I have already seen some topics about this issue I think. From what I have understands there is something about the new binned quality scores of Novaseq…
Correct 18S data file ffor assing taxonomy
Correct 18S data file ffor assing taxonomy 0 I wan to perform taxonomy identification using assign taxonomy and silva 18 S data set but i got this error message : Error in assignSpecies(seqs, refFasta = refFasta, allowMultiple = allowMultiple, : Incorrect reference file format for assignSpecies (this looks like a…
Error with dada2 while running Parkinson’s Mouse Tutorial – Technical Support
Hi, everyone. I’m new to qiime2 and I have a technical issue. I have the same problem with forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-255/21016 when I ran Parkinson’s Mouse Tutorial, but I noticed the problem didn’t solved in the website above.That’s my error info: Plugin error from dada2: An error was encountered while running DADA2…
16S rRNA gene sequencing of stool samples collected from patients with latent tuberculosis infection before, during, and two months after treatment with 3HP or 4R | BMC Research Notes
LTBI diagnosis and treatment FDOH clients who tested positive on a tuberculin skin test (TST) or interferon-gamma release assay (IGRA) blood test were diagnosed with LTBI following a chest x-ray and symptoms screening to rule out TB disease [6]. Healthy controls were LTBI negative by self-report of a negative TST…
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…
Correct way to remove Nextera adapters from ITS sequences
Correct way to remove Nextera adapters from ITS sequences 0 Hi everyone, I think this question has been coming up a few times but it didn’t help me solve my issue. I have FastQ files from ITS amplicon based metagenomic sequencing (ITS1/2) (300 bp) and FastQC tells me that they…
Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans
Carlson, J. L., Erickson, J. M., Lloyd, B. B. & Slavin, J. L. Health effects and sources of prebiotic dietary fiber. Curr. Dev. Nutr. 2, nzy005 (2018). Article PubMed PubMed Central Google Scholar Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid…
Error with DADA2 running Qiime2 on a mock community – Technical Support
Dear all, I am facing a trouble with a command in Qiime2. I am working with Qiime2 from a singularity container, retrieved from the official website. I am trying to use Q2 on some mock communities, in detail I am testing it on Mockrobiota community 2 (found on @gregcaporaso GitHub…
Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands
Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev. 2015;39:203–21. Article CAS PubMed Google Scholar Pointing SB, Belnap J. Microbial colonization and controls in dryland systems. Nat Rev Microbiol. 2012;10:551–62. Article CAS PubMed Google Scholar Ji M,…
Dada2 in Qiime2: losing reads during merging
Dada2 in Qiime2: losing reads during merging 0 Hi! I am trying to use dada2 on my 16S paired-end sequences, from a 2 x 150 bp illumina run. But I am losing almost all my reads at the merging step. The FASTQC shows excellent data quality and no adapters in…
Dada2 denoise-paired running time over 24hrs and taking more than 4TB temporary space on HPC – Technical Support
I am running DADA2 through QIIME and my demux.qza file is 110GB. After 24Hr I saw it consumed more than 4TB of disk space and the log file is not updating from a certain point.Here I am curious whether it is normal or if there is any glitch and I…
Assigned taxonomy after dada2 only “NAs” or “Mitochondria”
Hi, I followed the dada2 tutorial on 16S and ITS amplicon metagenomic data from soil samples. However, when trying to assign a taxonomic rank to my ASV table using DECIPHER, I only get “NAs”. When using the dada2 native’s Bayesian method, I get “NA” or “Mitochondria” (family). For my 16S…
Subset FASTA file for taxonomy (phylum name) in R
Subset FASTA file for taxonomy (phylum name) in R 2 Dear all, I would like to subset a FASTA file so that I get the sequences belonging to a certain phylum (in my case: Nematoda). The headers of the FASTA file start with the phylum name, so I thought this…
Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment
Klepeis, N. E. et al. The National Human Activity Pattern Survey (NHAPS): A resource for assessing exposure to environmental pollutants. J. Expo. Anal. Environ. Epidemiol. 11, 231–252 (2001). CAS PubMed Google Scholar Richardson, A. et al. Office design and health: A systematic review. N. Z. Med. J. 130, 39–49 (2017)….
An integrated tumor, immune and microbiome atlas of colon cancer
Samples used in this observational cohort study (tumor tissue and matched healthy colon tissue, AC-ICAM cohort) are from patients with colon cancer diagnosed at Leiden University Medical Center, the Netherlands, from 2001 to 2015 that did not object for future use of human tissues for scientific research and that were…
Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing
Introduction Perturbations in the infant gut microbiome during early life affect growth, development, and long-term health (Sherman, 2010; Carl et al., 2014; Tarr and Warner, 2016). Preterm infants have a physiologically and anatomically immature gastrointestinal tract that is known to be more permeable than that of term infants, and their…
Bacterial metatransciptome antimicrobial resistance genes workflow?
Bacterial metatransciptome antimicrobial resistance genes workflow? 0 Hi everyone! I’m trying to analyse some metatranscriptomics data from different samples, the final goal is to determine wether one group of samples has a higher expression of antimicrobial resistance genes. I’m completely new to RNAseq and I have no clue where to…
How to write/use qiime2 script for LSF (bsub) + docker set up? – Technical Support
Hello all, I’m looking for guidance on how to write a non-interactive job script for qiime2. The HPC I have access to uses LSF and docker images, which are both new to me. So far, I have been creating an interactive shell to use qiime2 (I created a .sh file…