Tag: ASVs

Phylogenetic classification of environmental Perkinsea sequences Using a phylogenetic approach, we investigated the diversity and community structure of Perkinsea ASV sequences retrieved from the published EukBank dataset37. We first conducted a phylogenetic analysis using a reference tree derived from an alignment of 1790 characters, which included representative alveolate groups and…

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,…

To understand the microbiome composition and interplay among bacterial communities in different compartments of a coupled freshwater aquaponics system growing flathead grey mullet (Mugil cephalus) and lettuces (Lactuca sativa), 16S rRNA gene amplicon sequencing of the V3–V4 region was analyzed from each compartment (fish intestine, water from the sedimentation tank,…

Grey mullet (family Mugilidae) farming has a tradition of several hundred years both in Oriental and Western countries in extensive and semi-intensive systems; however, there is still scarce information about their performance and nutritional requirements under different rearing systems and conditions28. This group of euryhaline and eurythermal species is generally…

journal contribution posted on 2023-11-12, 04:20 authored by Rebecca J. Stevick, Bianca Audrain, Sébastien Bedu, Nicolas Dray, Jean-Marc Ghigo, David Pérez-Pascual Additional file 1: Supplementary figures: Fig. S1. Sequencing depth and coverage for 16S rRNA gene amplicon data from conventional zebrafish larvae. (A) Number of quality-controlled bacterial sequences per sample. (B)….

By Daniel Vaulot, emeritus senior scientist at the Roscoff Biological Station (CNRS, France) Time and place: Nov. 3, 2023 1:15 PM – 2:15 PM, Room 1402 Daniel Vaulot We are fortunate to have a seminar from Daniel Vaulot, emeritus senior scientist at the Roscoff Biological Station (CNRS, France) and guest…

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…

Phoronids, or horseshoe worms (phylum Phoronida), are marine invertebrates whose life cycle usually involves a pelagic larva and a benthic, sessile adult that bores into soft sediment or hard substrates like rocks or mollusc shells1. Phoronids filter-feed using an arch of tentacles, the lophophore, and protect their vermiform trunk with…

A flow diagram of the study is shown in Fig. 3. Figure 3 Flow diagram of the study. Ethical approval and consent to participant This study was approved by the Institutional Review Board of the Nagoya University Graduate School of Medicine (approval number 2022-0084; approval date, June 3, 2022). Written informed…

General information In total, more than 60 million reads were obtained: 30,700,327 for 16S rDNA/bacteria and 29,920,072 for ITS/fungi. These sequences were distributed across more than 1000 bacterial and fungal genera (Fig. 2). The coverage index10 was above 0.95 for all samples, showing that the sequencing effort was enough to capture…

After processing the data, 20 control samples and 21 Type 2 Diabetes Mellitus samples contained data from all three collected assays (bacteriome, mycobiome, metabolome). The bacteriome data comprised on average 9534 contigs (s.d. ± 3465), ranging from 2032 to 18,320 contigs (786 ASVs). The mycobiome data contained on average 5450 contigs (s.d. ± 4964),…

Data for contigs, MAGs and other files generated using the Northeastern Indian Ocean microbial dataset. Dataset includes: EIO-MAG.tar.gz 675 non-redundant prokaryotic genomes with ≥ 50% completeness and ≤ 5% contamination. EIO-Contigs.tar.gz: the contigs generated from 25 metagenome. Table.S1:Sampling information and environment factors. Table.S2:The ASVs-table and MAG information. Funding This work…

Abstract The two most commonly used approaches to study the composition of environmental protist communities are marker gene metabarcoding and whole genome analysis through metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches have…

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…

#’ Subset a phyloseq object to a set of taxa. #’ #’ This function takes a phyloseq object and a list of taxon ids to be kept, #’ and discards or merges all other taxa. #’ #’ @details #’ This function is essentially a wrapper around \link[phyloseq]{prune_taxa} and #’ \link[phyloseq]{merge_taxa}….

#’ Get the most abundant taxa from a phyloseq object #’ #’ This function identifies the top \eqn{n} taxa in a phyloseq object. Users specify the #’ summary statistic that is used to rank the taxa, e.g. \code{sum}, \code{mean} or #’ \code{median}. Furthermore, it is possible to add one or…

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…

Sets of differentially abundant ASVs identified using ALDEx2 in each experimental variant described in Golebiewski et al. “Colonization of axenic beet by rhizosphere bacteria takes place in discreet phases regardless of bioinculation with next generation bioinoculant“. Files are in the tsv (tab separated values) format. Experimental variants are contained in…

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…

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…

RNA-sequencing and Amplicon-sequencing alignment statistics On average, the total number of reads mapped for all samples in low and high-RFI animals were 303,428,164 and 318,958,134, for Angus (AN); 317,776,686 and 299,963,316 for Charolais (CH); and 328,016,010 and 332,007,994 for Kinsella (KN). The majority of reads were successfully uniquely mapped to…

functional analysis applied on 16S rRNA Gene Metabarcoding data 0 Hello community, I really need your expertise to help me with this question : Actually I’m wondering if it is possible to perform functional analysis on 16S rRNA Gene Metabarcoding data. if it’s the case could you please give some…

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…

Lulu Island waste resource recovery ecosystem The Lulu Island WWTP operated by Metro Vancouver in Richmond, British Columbia, Canada (Longitude: −123.14498° or 123° 8’ 42” W, Latitude: 49.11491° or 49° 6’ 54” N) provides primary and secondary treatment of >30 billion liters of mixed-sourced wastewater from ~200,000 residents each year….

I have QIIME2 outputs (feature table, tree, taxonomy, and metadata) that I’ve imported into R using qiime2R (v. 0.99.6) ‘qza_to_phyloseq’ to create a phyloseq object. My QIIME feature table shows reasonable values for ASV abundance across all samples (n=16; feature table available upon request). Problem: The otu_table the ASV values…

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…

An alteration in gut microbiome diversity occurred in patients with three different inflammatory conditions, suggesting a common pathology, prospective rRNA sequencing of patients’ stool samples showed. Patients with axial spondyloarthritis (SpA), acute anterior uveitis (AAU), and Crohn’s disease had a low concentration of Lachnospiraceae compared with a control group of…

The problem of off-target amplification The widely used standardized protocol for 16S rRNA gene amplicon sequencing7,14 turned out to be inadequate due to robust off-target amplification of human DNA during the analysis of bacteriome in samples of different biopsy sites from the upper gastrointestinal (GI) tract. In samples from all…

Bone biopsy (BEBOP) trial The BeBoP trial is an international multicentre randomised controlled trial, for which inclusions run from 2018 to 2022. In the BeBoP trial we compare the outcomes of DFO treatment based on two diagnostic strategies, percutaneous bone versus ulcer bed biopsy cultures. Only the results of one of these…

The Greengenes reference database has a long history of use for characterizing microbial communities (see McDonald et al. ISMEJ 2011 and DeSantis et al. AEM 2006). It was the 16S rRNA reference used for massive endeavors such as the Human Microbiome Project, the American Gut Project and the Earth Microbiome…

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,…

should remove unassigned genera in 16S rRNA sequencing analysis 0 Hi all, When analyzing 16S rRNA amplicon data from tissue samples, I found some ASVs could not be taxonomically assigned at the genus level. Rather they can be assigned at a higher level. I wonder whether I should remove those…

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…

How to add a refseq() slot to a MAG based phyloseq object ? 0 Hello, I was asked to build a phyloseq object from some metagenome assembled genomes that I built. By far I have created a tax_table() slot from the classification of the MAGs using GTDB-Tk, a out_table() that…

I don’t know why my rarefaction curve for most samples does not reach saturation. Please how can I improve te curve? The curve does not look like most rarefaction curves I see in publications, Please help and I am relatively new to microbiome study. Below is the code I used:…

I’m trying to create a plot showing the abundance of ASVs within control vs true samples. This isn’t an issue with the code since I’ve used it before and it was just working yesterday, but I’ll include it here: # Starting from a phyloseq object called “noMitoChloroMock_physeq” # Set control…

The clinical and physical variables Table 1 presents the general characteristics of the 106 included participants. The mean age was approximately 36 years in both healthy and MAFLD groups. Of the 106 participants, 81 (68 men, 13 women) were in the MAFLD group. Body mass index (BMI) level was significantly lower…

Abstract Amplicon sequencing of small subunit (SSU) rRNA genes is a foundational method for studying microbial communities within various environmental, human, and engineered ecosystems. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification. The low-cost Oxford Nanopore…

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…

Rhizosphere bacteria have shorter predicted doubling times than soil bacteria To investigate whether growth rate potential predictions correlate with rhizosphere enrichment, we re-analyzed previously published metacommunities. These included rhizospheres and associated bulk soil microbiomes from 18 different plant genotypes and conditions such as: Arabidopsis thaliana ecotypes and sister species [9],…

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 …

Geochemical evolution of groundwater in the Canadian Prairie The mean residence time of water in an aquifer is a very important factor influencing its geochemical composition (or facies) (Fig. 2a). Mean residence time, or groundwater age, is determined using radioisotopes such as tritium and 14C and refers to the travel time…

doi: 10.1186/s13104-023-06370-7. Affiliations Expand Affiliations 1 Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32610, USA. nseraphin@ufl.edu. 2 Department of Medicine, Division of Infectious Diseases and Global Medicine, University of Florida, Gainesville, FL, USA. nseraphin@ufl.edu. 3 Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32610, USA. 4 Department of Medicine,…

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…

Engraftment of donor communities prior to dietary treatment Germ-free (GF) female ApoE−/− mice were colonized with fecal samples from one of three human donors (Supplementary Fig. 1). These samples were selected from a repository of fecal specimens previously collected from adults in their mid-seventies36 and were chosen based on (i)…

The samples were collected during some 3,000 dives by scientists aboard research vessel Tara.Credit: Pete West/Tara Ocean Foundation The largest-ever survey of Pacific Ocean corals has found that there’s likely to be more genetic diversity in the world’s coral reefs than researchers previously thought. This assessment is based on a…

too many zeros in 16S rRNA amplicon sequencing data 0 Hi all, I have some 16S rRNA sequencing data from human tissue, which was performed on NovaSeq 6000 platform. I detected ~40000 ASVs in total after removing singletons. However, most ASVs were only present in a few samples. In other…

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…

DNA metabarcoding reads Sequencing of the 44 libraries, together with other 12 libraries (total number of libraries = 56), yielded a total of 1,201,786 raw reads, with an average of 94.29% base calls being quality scores of more than 30.00. After primer trimming, quality filtering, merging of paired reads, and chimera filtering,…

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…

Sociodemographic characteristics of SpA patients and controls The group of individuals analyzed in this study was made up of 32 patients with SpA and seven healthy individuals. Of the SpA patients, 56.2% were male, and at the time of the study, 9.4% reported to smoke, 28.1% smoked, and 15.6% considered…

Hi,is there an option in the dada2 plugin under qiime2 for “priors” specific sequences as reported in the dada2 tutorial for pseudo-pooling?benjjneb.github.io/dada2/pseudo.html Hello Alberto, Welcome to the forums! You can sort of do this within the Qiime2 pipeline.docs.qiime2.org/2023.2/plugins/available/dada2/denoise-paired/ While you can’t provide expected sequences, you can use–p-pooling-method pseudoto enable pseudo-pooling,…

To maximize reproducibility, a list of the reagents and resources used in this study, as well as their source and identifier, is provided in Supplementary Table 5. Experimental model and subject details Oral swab samples were obtained from bottlenose dolphins (Tursiops truncatus) managed by the U.S. Navy MMP Biosciences Division, Space…

All experimental procedures were conducted at the University of Illinois at Urbana-Champaign and followed protocols approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Illinois at Urbana-Champaign under protocol number 17172. All ARRIVE, and IACUC guidelines and regulations were followed during the entire duration of…

Two new Tepidiforma species expand on a small number of cultivated Dehalococcoidia Two bacterial strains were isolated from terrestrial geothermal springs by plating benthic mat and sediment slurries onto R2A medium and were identified by 16S rRNA gene sequencing as members of the recently described genus Tepidiforma [27]. Strain YIM…

タイトル:  A simple method that enhances minority species detection in the microbiota: 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer) 著者:  Nakajima, ArutoYoshida, KeisukeGotoh, AinaKatoh, Toshihiko    Ojima, Miriam N.Sakanaka, Mikiyasu       orcid.org/0000-0002-4223-0926 (unconfirmed)Xiao, Jin-ZhongOdamaki, ToshitakaKatayama, Takane       orcid.org/0000-0003-4009-7874 (unconfirmed) 著者名の別形:  中島, 有登後藤, 愛那加藤, 紀彦尾島, 望美阪中, 幹祥片山, 高嶺 キーワード:  16S metagenome-DRIPα-Type DNA polymerasebiotinylated inhibitory…

​​​​​​​In a recent study published in the Nutrients journal, researchers in the United States investigated the association between caffeine, coffee consumption, and the colonic microbiome. ​​​​​​​ Study: The Association between Caffeine Intake and the Colonic Mucosa-Associated Gut Microbiota in Humans—A Preliminary Investigation. Image Credit:Rawpixel.com/Shutterstock.com Background Caffeine has been extensively consumed in…

Hi, I have some problems trying to convert some zOTUs files I obtained with a Usearch11 protocol to Qiime2 format. I want to do this to compare some results I got with a Qiime2 pipeline. I aim to know the differences between ASVs and zOTUs in my analysis. As a…

Survey of mcrA genes across physicochemically contrasting geothermal features The presence and diversity of Mcr-encoding populations was assessed in 100 geothermal features of YNP via mcrA gene amplicon sequencing. Gene amplicons were recovered from 66 sediment and/or microbial mat samples spanning 39 geothermal features located in the Lower Culex Basin…

Arivale cohort The main study cohort was derived from 6,223 individuals who participated in a wellness program offered by a currently closed commercial company (Arivale, Inc.) between 2015 and 2019. An individual was eligible for enrollment if the individual was over 18 years of age, not pregnant and a resident of…

Principal findings of the study In this re-analysis of fifteen placental microbiota studies, of the ASVs which were ranked in the top five ASVs for relative abundance in any one study, Lactobacillus ASVs were clearly the most prevalent across studies. Yet, Lactobacillus ASV prevalence was explained by background DNA contamination,…

Composition of the vaginal microbiota of PPROM patients The 16S rRNA gene sequencing was performed for 166 vaginal swab samples collected at hospital admission (V0), after antibiotic treatment (V1), and < 24 h before delivery (V2). The overall upstream analyses resulted in 2923 amplicon sequence variants (ASVs) assigned to 20 different phyla and…

This prospective observational study (NCT04803695) complied with the Declaration of Helsinki (current version, Fortaleza, Brazil, October 2013). Our institution’s Internal Review Board approved the study, and all patients gave their written informed consent (No. HCB/2018/0236, Hospital Clinic Barcelona). Sputum samples and DNA extraction Thirty-three sputum samples were collected from patients…

1. Introduction Soil harbors high abundance and diversity of prokaryotic microorganisms, with 1 g of soil containing up to 10 billion microbial cells (Torsvik and Øvreås, 2002) and 103–106 phylotypes (Bickel and Or, 2020), including many microorganisms that play critical biogeochemical roles (Crowther et al., 2019). With continuous expansion of prokaryotic…

Breed differences in animal feed conversion and economic trait performance Throughout the feed intake measurement period, summary statistics shows animals on test had an average DMI of 1.11 kg/d (SD = 0.18), ADG of 0.27 kg/d (SD = 0.1), FCR of 4.04 kg of DMI/ Kg of ADG (SD = 0.1), start weight of 29.60 kg (SD = 3.7), final live weight…

Data-driven culturomics using phenotypes and automation Colony picking is a classic microbiology method for clonally isolating bacterial strains. Colony growth on plates depends on many factors, including the composition of the media (for example, available nutrients), atmospheric conditions (for example, level of oxygenation), presence of inhibitory molecules (for example, antibiotics),…

Sequencing statistics NGS was used across the V3-V4 region of the 16S rRNA gene to sequence 24 environmental samples. The mean number of ASVs per sample obtained after DADA2 was 72,050 ± 31,480, ranging from 22,568 to 143,267. From a total of 1,729,209 contigs remaining after quality control and removal of chimeras,…

Myxococcota and Bdellovibrionota were active constituents of activated sludge microbiota To explore the predating activity and diversity of predatory bacteria in activated sludge, 13C-labeled Escherichia coli and Pseudomonas putida cells (determined as 97.09 and 97.30 atom% 13C, respectively) were added to the sludge microcosms for maximumly eight days of incubation,…

Fmadere (Ferra Madere) February 9, 2023, 3:58am 1 Hello All, A few months ago I ran some 16S sequencing data through Qiime2. I am now attempting to do some further analysis of the data using Valencia, a nearest-centroid based algorithm for the classification of human vaginal microbial community into state…

Ethics statement All animal experiments were performed in compliance with the Regulations for the Care and Use of Laboratory Animals issued by the Ministry of Science and Technology of the People’s Republic of China, which enforces the ethical use of animals. The protocol was approved by Institutional Animal Care and…

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…

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

Volatile fatty acid production and absorption is modulated by diet Animals were adapted to a starch-rich diet by gradually increasing dietary concentrate content from 50 to 90% over the three 100-d experimental periods (Fig. 1A). With both diets, rumen structure and epithelial morphology were robust and rumen pH remained above 6.0…

Subsetting DESEQ2 VST Microbiome Data 1 @f8d5630d Last seen 16 hours ago Germany Hello there, the question is a bit off topic I am currently using DESEQ2 to normalize 16S microbiome data as advised several times in the recent literature. Currently I am facing the problem that I have 16S…

Hi everyone, I am currently in the process of removing unwanted taxa (Kingdom=”Eukaryota”, Family=”Mitochondria”, and Order=”Chloroplast”) from a phyloseq object I created. This phyloseq object was created using my outputs from DADA2 (OTU table, taxonomy table, and metadata file). I have saved a taxonomy table in CSV format at every…

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared…

Phyloseq Objects for different time points 0 Hi I am very new to this microbiome analysis so this might be a very simple question… I have a question related to the microbiome analysis I’m doing. I have microbiome data from 3 different timepoints (T1, T7, and T13), for I made…

How to get normalized count table from DESeq? 1 Hi, I’m using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all <- DESeq(ds.all,fitType = “local”) Then as the results I got 8 ASVs that showed significantly different….

Relative abundance of differentially abundant ASVs after DESeq2 0 Hello, I used DESeq2 to see which ASVs were differentially abundant between different treatments on 16S metabarcoding data. I now want to plot the relative abundance (in %) of those ASVs. However, I am unsure which data would make to most…