Tag: PERMANOVA

Functional alterations and predictive capacity of gut microbiome in type 2 diabetes

Diversity and compositional analyses Regarding clinical differences (Table 1), T2DM individuals (mean 69.6 (± 12.3 sd) years) were significantly (p value < 0.01; Wilcoxon rank-sum test) older than the controls (46.9 (± 17.3 sd) years), showed higher BMI (mean 30.9 (± 7.01 sd) vs. mean 26.3 (± 6.12 sd) than the control…

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Benchmarking DNA isolation methods for marine metagenomics

Scheme of the study The overall pipeline of our study is presented in Fig. 1 and is described in detail in the methods section. We processed three types of samples: fresh water, sea sediment, and digestive system of a marine invertebrate M. gigas (“gut flora”). These samples were treated in triplicates…

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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…

Continue Reading Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP

Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment

Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….

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Additional file 1 of Anti-diarrheal drug loperamide induces dysbiosis in zebrafish microbiota via bacterial inhibition

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)….

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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,…

Continue Reading Gut microbiota composition and diversity before, during, and two months after rifamycin-based tuberculosis preventive therapy

Spatial compartmentalisation of bacteria in phoronid microbiomes

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…

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Higher abundance of Campylobacter in the oral microbiome of Japanese patients with moyamoya disease

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…

Continue Reading Higher abundance of Campylobacter in the oral microbiome of Japanese patients with moyamoya disease

Microbiomes associated with Coffea arabica and Coffea canephora in four different floristic domains of Brazil

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…

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Uncovering the relationship between gut microbial dysbiosis, metabolomics, and dietary intake in type 2 diabetes mellitus and in healthy volunteers: a multi-omics analysis

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),…

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Scientists study the effect of grape pomace on the digestive tract microbiota of herbivores

Effect of control (CD) and grape pomace (GP) diets on the bacterial community structure of the gastrointestinal tract (GIT). (A) The rarefaction curve calculated by observed features; (B) Alpha diversity representing species richness and evenness using Chao1 and Shannon indices of CD and GP in GIT; Principal-coordinate analysis (PCoA) of…

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Baseline gut microbiota and metabolome predict durable immunogenicity to SARS-CoV-2 vaccines

Dynamics of immunogenicity at 6 months after BNT162b2 and CoronaVac vaccination From April 2021 to March 2022, we longitudinally followed 161 COVID-19 vaccinees who had received BNT162b2 (N = 121, 65.3% females) or CoronaVac vaccines (N = 40, 72.5% females). BNT162b2 vaccinees were younger compared to CoronaVac vaccinees [median (IQR) in years: 42 (29,…

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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…

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Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts

Study population Among the 60 cases, 28 were male (46.7%) and 32 were female (53.3%) ranging between 1.5 and 90 years of age; most patients were between 19 and 64 years (n = 26; 43.3%) or less than 9 years (n = 16; 26.7%). No difference in the proportion of stool submissions was observed by year, though…

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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…

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Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety

Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…

Continue Reading Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety

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…

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Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

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….

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Course. -Multivariate Data Analysis with R and vegan

News:Course. -Multivariate Data Analysis with R and vegan 0 Dear all, We’re excited to announce that registrations are now open for the next edition of course on Multivariate Data Analysis with R and Vegan taking place online from November 27th to December 1st, 2023. This course will equip you with…

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Inter-comparison of marine microbiome sampling protocols

Environmental communities For the MetaB16SV4V5 sequencing results (n = 60), we initially obtained between 714,103 and 2,841,890 raw reads per sample (median = 1,462,584 reads, IQR = 267,472 reads). The final number of high quality reads attributed to taxonomic lineages ranged between 169,945 and 1,517,860 reads per sample (median = 660 878 reads, IQR = 438 932 reads). Thus, between…

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Microbial genome (Illumina MiSeq) sequencing of drinking water treatment residuals to evaluate compatibility with environmental applications

The clarification of drinking water leads to the production of large quantities of water treatment residuals (WTRs). DNA was extracted from six WTR samples collected from water treatment plants within the UK to compare their bacterial communities and examine whether factors such as coagulant usage (aluminium versus iron salt), the…

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16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling

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…

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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…

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Solved Instructions:Copy, paste, and run the code below on

Instructions: Copy, paste, and run the code below on RStudio to obtain the data for this assignment. This code will create a matrix with 30 columns representing species and 10 rows representing communities. The object will be called “community_matrix” ######### set.seed(2)community1=matrix(sample(0:250,300,replace=T),nrow=10,dimnames=list(paste(“community”,1:10,sep=””),paste(“sp”,1:30,sep=””))) community2=matrix(sample(50:200,300,replace=T),nrow=10,dimnames=list(paste(“community”,11:20,sep=””),paste(“sp”,1:30,sep=””)))community_matrix<- rbind(community1,community2) ####### This code will create a metadata…

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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,…

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Mapping the poultry insectome in and around broiler breeder pullet farms identifies new potential Dipteran vectors of Histomonas meleagridis | Parasites & Vectors

Sampling Four broiler breeder pullet farms in North Alabama belonging to two different companies were selected for this study. Two of them had a history of histomonosis. All farms had closed houses with dirt floors with tunnel ventilation and pine shavings as litter. Each house had about 20,000 pullets. Biosecurity…

Continue Reading Mapping the poultry insectome in and around broiler breeder pullet farms identifies new potential Dipteran vectors of Histomonas meleagridis | Parasites & Vectors

Genetic strategies for sex-biased persistence of gut microbes across human life

Strain dynamics of the gut-associated microbiota within the first 24 months of life Shotgun metagenomics sequencing approaches were applied to the microbiomes of 11 healthy, vaginally delivered, full-term (>37 weeks of gestation) newborns, which were longitudinally sampled at 1-, 6-, 12-, and 24-months following birth (Figs. S1, S2, Supplementary Data 1). Consistent with…

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Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering

Predominant bacteria in sewage do likely not originate from the human gut To identify bacterial genomes from sewage across the world, we used a combination of two different metagenomics genome binners (VAMB24 and MetaBAT225). From 757 samples across 101 different countries (Fig. 1a and Supplementary Fig. 1), we were able to create…

Continue Reading Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering

Patterns and determinants of the global herbivorous mycobiome

Sampling overview A total of 661 samples belonging to 34 species and 9 families of foregut-fermenting ruminant (thereafter ruminant, n = 468), foregut-fermenting pseudoruminant (thereafter pseudoruminant, n = 17), and hindgut fermenters (n = 176) were examined (Fig. 1a, b, Supplementary Data 1). The dataset also provides a high level of replication for a variety of animals (229…

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Characteristics of gut microbiota in patients with metabolic associated fatty liver disease

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…

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Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses

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…

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Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics

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…

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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…

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Microbial diversity in the vaginal microbiota and its link to pregnancy outcomes

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…

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Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities

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)…

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Endophytic bacterial diversity by 16S rRNA gene sequencing of Pak choi roots under fluazinam, Trichoderma harzianum, and Sophora flavescens inoculation

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…

Continue Reading Endophytic bacterial diversity by 16S rRNA gene sequencing of Pak choi roots under fluazinam, Trichoderma harzianum, and Sophora flavescens inoculation

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%…

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Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients

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…

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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…

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Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota

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…

Continue Reading Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota

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…

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Association Between Infant Gut Microbiome and Maternal Vaginal Microbiome by Mode of Delivery

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…

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Comparison of bioinformatics pipelines for eDNA metabarcoding data analysis

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…

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Characterization of rumen microbiome and metabolome from oro-esophageal tubing and rumen cannula in Holstein dairy cows

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…

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Vaginal and neonatal microbiota in pregnant women with preterm premature rupture of membranes and consecutive early onset neonatal sepsis | BMC Medicine

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…

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Impact of high altitude on composition and functional profiling of oral microbiome in Indian male population

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…

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Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

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…

Continue Reading Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

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…

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course MULTIVARIATE DATA ANALYSIS WITH R AND VEGAN

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…

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High-throughput microbial culturomics using automation and machine learning

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),…

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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…

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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…

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Multivariate data analysis with R and vegan

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…

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Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice

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…

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Amoxicillin and thiamphenicol treatments may influence the co-selection of resistance genes in the chicken gut microbiota

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…

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Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature

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…

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Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

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)…

Continue Reading Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

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…

Continue Reading GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants

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…

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Capturing Actively Produced Microbial Volatile Organic Compounds from Human-Associated Samples with Vacuum-Assisted Sorbent Extraction

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…

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Metagenomics technology and microbial community diversity analysis methods

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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Vertical stratification of the air microbiome in the lower troposphere

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…

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Basic logic and use of PERMANOVA for microbiome data

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…

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Biostar Systems

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…

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