Tag: PERMANOVA

Time-independent variation is present in 16S GCN evolution To evaluate the extent of time-independent or intraspecific variation in 16S GCN, we examined 5437 pairs of genomes with identical 16S rRNA gene alignments. The 16S GCN differs in 607 (11%) of them, suggesting the presence of significant time-independent variation. For the…

Construction of proteomic content networks from an ultra-deep metaproteomic approach We define the proteomic content network (PCN) of a microbiome sample as a bipartite graph connecting each microbial taxon to all expressed functions from the taxon’s proteome. In order to gain the deepest possible understanding of sample-specific PCN of the…

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…

A prospective study of pregnant women We established a prospective cohort of 2313 pregnant women with the goal of studying the vaginal microbiota, its community composition and the presence of pathogenic bacteria in the peripartum period. Inclusions and data collection were performed in accordance with applicable laws and ethical standards. Ethical…

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)…

Ahemad M, Khan MS (2012) Effect of fungicides on plant growth promoting activities of phosphate solubilizing Pseudomonas putida isolated from mustard (Brassica compestris) rhizosphere. Chemosphere 86(9):945–950. doi.org/10.1016/j.chemosphere.2011.11.013 Article  CAS  PubMed  Google Scholar  Al-Askar AA, Saber WI, Ghoneem KM, Hafez EE, Ibrahim AA (2021) Crude citric acid of Trichoderma asperellum: tomato…

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%…

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560:233–7. Article  CAS  PubMed  Google Scholar  Waldrop MP, Holloway JM, Smith DB, Goldhaber MB, Drenovsky RE, Scow KM, et al. The interacting roles of climate, soils, and…

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…

Detailed reconstruction of the infant gut bacterial composition A total of 10,935 publicly available datasets, retrieved from 40 cohorts from various geographical origins, were subjected to microbial profiling based on short-read taxonomic classification down to the species level (Supplementary Table 1). Collected data were filtered based on a number of…

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…

The following is a summary of “Relationship between the maternal vaginal microbiome and the infant gut microbiome by mode of delivery,” published in the FEBRUARY 2023 issue of Obstetrics and Gynecology by Santos S, et al. For a LEGACY study, researchers sought to determine if there was a correlation between…

The Fraunhofer-Institute for Molecular Biology and Applied Ecology IME conducts research in the field of applied life sciences from a molecular level to entire ecosystems. With its Applied Ecology division located at Schmallenberg the Fraunhofer IME is the Fraunhofer Institute explicitly dedicated to ecological issues and thematically routed in agricultural…

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…

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…

Present study demonstrates the sequencing of V3-V4 regions of 16S rRNA from 31 saliva samples. In total, 1,881,630 sequences were obtained from the 31 samples, with an average sequence length of 251 bp (Table S1). The rarefaction curve of all samples calculated had reached a plateau, suggesting that the sequencing was…

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…

News:course MULTIVARIATE DATA ANALYSIS WITH R AND VEGAN 0 Dear all, registration is now open for the 2nd edition of the course MULTIVARIATE DATA ANALYSIS WITH R AND VEGAN. Dates: online, 24-28 April This course will offer participants a practical introduction to some of the most useful functions available within…

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),…

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…

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…

News:course – Multivariate data analysis with R and vegan 0 Hi all, registration is now open for the 2nd edition of the course “Multivariate data analysis with R and vegan“. Dates: online, April, 24-28 This course will offer participants a practical introduction to some of the most useful functions available…

Classification of snow algae in the ice core based on ITS2 sequences We used high-throughput sequencing to obtain DNA sequences of algae from 19 layers of an ice core drilled on a glacier in central Asia, dated from present time to 8000 years ago (Fig. 1 and Table S1). In total, 17,016…

General description of sequences After the quality filtering step, removal of chimeric fragments, and read merging, a total of 3,378,323 reads with 3007 different features was obtained, with an average of 27,244 sequences per individual sample. After quality filtering, none of the samples was excluded from the analysis of microbial…

Changes of straw degradation characteristics at different culture stages Corn straw degradation ratio Corn straw weight loss in M44 at F1 reached 35.90% at 15 ℃ for 21 days, which was greater than that at F5, F8, and F11 by 2.33%, 3.01%, and 3.35%, respectively. There were no significant differences between…

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)…

GWAS identifies genetic variations associated with agronomic traits in foxtail millet A total of 827 foxtail millet cultivars collected from China were sequenced and genotyped using common single-nucleotide polymorphisms (SNPs) based on a ~423 Mb Setaria italica cv. Zhanggu reference genome (v.2.3)27. In total, 161,562 SNPs were detected after stringent steps…

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…

This protocol describes the extraction of volatile organic compounds from a biological sample with the vacuum-assisted sorbent extraction method, gas chromatography coupled with mass spectrometry using the Entech Sample Preparation Rail, and data analysis. It also describes culture of biological samples and stable isotope probing. This protocol allows us to…

A large number of microorganisms in nature cannot be cultivated under laboratory conditions by pure culture methods, and the technical methods of traditional microbiology limit the research on environmental microorganisms. The rapid development of high-throughput omics technology has enabled humans to have an unprecedented understanding of the complex microbial communities…

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Significance Large-scale meteorological and biological data demonstrate the vertical stratification of airborne biomass. The previously described diel cycle of airborne microorganisms is shown to disappear at height. Atmospheric turbulence and stratification are shown to be defining factors for the scale and boundaries, dynamics, and natural variability of airborne biomass, resulting…

Basic logic and use of PERMANOVA for microbiome data 1 PERMANOVA is frequently used in microbiome studies when analyzing beta diversity. While I know that basics of PERMANOVA are similar to ANOVA (with some differences related to permutation), I have a hard time understanding the logic of this analysis in…

Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 That is good to know that it isn’t just my set of reads…still concerning, though. Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 I was not expecting this — not sure what to make of it…