Tag: Metagenome

The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and…

The soil samples were collected from an orchard situated in Karnataka, India, which were categorized based on their stage of infection (ISI, ASI) and compared with a healthy sample (HSC). Physical examination of the plants, with respect to their roots, leaves, stem and fruits, revealed the presence of root knots…

Revsbech, N. P. et al. Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor. Limnol. Oceanogr.: Methods. 7, 371-381. (2009). Wright, J. J., Konwar, K. M. & Hallam, S. J. Microbial ecology of expanding oxygen minimum zones. Nat. Rev. Microbiol. 10, 381–394 (2012). Article  CAS  PubMed …

Occurrence of prophage sequences in L. casei group genomes The first stage of the analysis involved the identification of prophage-like sequences in 439 genomic sequences of bacterial strains belonging to the following 5 species: L. casei (27), L. paracasei (200), L. rhamnosus (204), L. zeae (6) and L. chiayiensis (2)….

Introduction Severe hospital-acquired pneumonia (SHAP) is the most common acquired infection in the intensive care unit (ICU) and one of the main causes of increased mortality in ICU patients.1,2 Potential multidrug-resistant pathogens are very common in ICU-acquired pneumonia, including Pseudomonas aeruginosa, Acinetobacter spp., methicillin-resistant Staphylococcus aureus (MRSA), and ultrabroad spectrum…

The infant and maternal gut microbiota are defined by different Bifidobacterium species The samples analysed in this study were collected during the MicrobeMom study (ISRCTN5302301420,21), these included samples from the maternal stool, vagina, oral cavity, and breast milk in addition to infant stool (Table 1; Fig. 1a). From the 160 participants recruited,…

1050 SGBs clustered from 8210 high-medium quality metagenome-assembled genomes (MAGs) Over 779 Gb metagenomic sequence data was generated by Illumina HiSeq × Ten platform from 65 TPs samples (Supplementary Table 1). We integrated the above sequencing raw reads with a published metagenomic sequence dataset of 287 captive pigs from Denmark, France…

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…

Amplicon sequencing Microbial community diversity Figure 1 shows the relative abundance of microorganisms at the phylum and genus level for bacteria and fungi based on amplicon sequencing. Firmicutes was the dominant phylum in all samples at the phylum level of bacteria (Fig. 1A). In Daqu, the dominant phyla were mainly Firmicutes (69%),…

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…

Background: Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we…

Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40. Article  CAS  PubMed  Google Scholar  Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the dark: phylogenetic and physiological diversity of chemosynthetic symbioses. Annu Rev Microbiol. 2021;75:695–718….

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)….

Applications are invited for a Research Scientist to join the group of Professor Alison Mather at the Quadram Institute Bioscience (QIB), based in Norwich, UK. Background: Antimicrobial resistance (AMR) has evolved in environmental bacteria over billions of years, producing a vast reservoir of AMR genes that can potentially be transferred…

Resumo:  Although (in the context of bacterial infections) the goal of antibiotic use is to combat and eliminate pathogenic bacteria, hundreds of non-pathogenic bacterial species are also affected when antibiotics are administrated. This results in a selection of bacteria resistant to the class of antibiotic applied. Additionally, with the ability…

image: Some cultivation-based data show beached Sargassum appear to harbor high amounts of Vibrio bacteria. view more  Credit: Brian Lapointe, FAU Harbor Branch A new study uncovers how the interplay between Sargassum spp., plastic marine debris and Vibrio bacteria creates the perfect “pathogen” storm that has implications for both marine life…

Postdoctoral Research Scientist / Senior Postdoctoral Research Scientist Applications are invited for a three-year position, as a Postdoctoral Research Scientist, to join the laboratory of Dr Quince in the High-Resolution Microbiomics group (www.earlham.ac.uk/quince-group) at the Earlham Institute, based in Norwich, UK. Background: The Earlham Institute is committed to an ambitious long-term program…

Abstract Dissimilatory perchlorate reduction is an anaerobic respiratory pathway that in communities might be influenced by metabolic interactions. Because the genes for perchlorate reduction are horizontally transferred, previous studies have been unable to identify uncultivated perchlorate-reducing populations. Here we recovered metagenome-assembled genomes from perchlorate-reducing sediment enrichments and employed a manual…

KEGG MGENOME: T30754 (Metagenome)     MGENOME: T30754 (Metagenome) Help Entry T30754            Meta      Genome                                  Org code GS032 Name GS032 – Mangrove on Isabella Island Annotation GhostKOALAShow organism Data source Original DB Comment /SITE_NAME=”Mangrove on Isabella Island”/FILTER_MIN=0.1/FILTER_MAX=0.8/COLLECTION_TIME=”2004/2/11 11:30″/LATITUDE=-0.5938889/LONGITUDE=-91.06944/SITE_DEPTH=”0.1 m”/SITE_DESCRIPTION=Mangrove/COUNTRY_NAME=ECUADOR/REGION=”Galapagos Islands”/HABITAT_NAME=”saline water”/SEQUENCING_METHOD=”dideoxysequencing (Sanger)”/water_depth=”1.6 m”/temperature=”25.4 C” Statistics Number of protein genes:      628007 Phylum distribution: Function distribution: LinkDB All DBs…

York University researchers stated that wild bees residing in metropolitan settings like Toronto are more likely to experience environmental stresses like more diseases and parasites than those living in rural or even suburban regions based on a recent research. Wild bees increased diseases and parasites in cities (Photo :…

Editorial Medicalfacts/ Janine Budding 16 mei 2023 – 23:35 The cells of our body not only harbor our own hereditary material, but also that of viruses that have invaded. By analyzing this complete metagenome, it is possible to identify the cause of a virus infection. The LUMC is the first…

Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to…

In a recent study published in Nature Microbiology, researchers used shotgun sequencing to extract human reads from deoxyribonucleic acid (DNA) in fecal samples of 343 Japanese individuals comprising the main dataset of this study. They used this gut metagenome data to reconstruct personal information. Some study participants also provided whole…

Researchers from York University have found that wild bees living in cities like Toronto encounter growing environmental challenges such as more pathogens and parasites compared to rural and even suburban areas. The researchers published their findings last Friday in in the journal Global Change Biology. They say alterations in the…

15.05.2023 – 17:14 MGI Tech Co., Ltd. Shenzhen, China (ots/PRNewswire) MGI Tech Co.Ltd. (MGI), a company dedicated to building core tools and technologies to guide LEAD Life Science, recently announced that as part of the “Million Microbiome of Humans Project (MMHP)” officially launched in ARM 2019 a total of 60,000…

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…

Subject participation The study protocol was approved by the ethics committees of Osaka University and related medical institutions as well as the Translational Health Science and Technology Institute (Faridabad). Japanese individuals (n = 343) for whom gut metagenome shotgun sequencing were performed in previous studies were included in this study46,47,48. Among these…

Gut bacteria , gut flora, microbiome. Bacteria inside the small intestine, concept, representation. 3D illustration. Gut bacteria , gut flora, microbiome. Bacteria inside the small intestine, concept, representation. 3D illustration. DNA from stool samples can reveal a person’s sex, ancestry, and whether they carry particular genetic variants, according to research…

ANI | Updated: May 15, 2023 10:24 IST Jena [Germany], May 15 (ANI): The bacteria in the intestine provide information on the amounts of fungi from the possibly pathogenic Candida genus. Surprisingly, among them are lactic acid bacteria, which are known for their ability to guard against fungal diseases.Researchers from…

Background: Over the past years, sequencing technologies have expanded our ability to examine novel microbial metabolisms and diversity previously obscured by isolation approaches. Long-read sequencing promises to revolutionize the metagenomic field and recover less fragmented genomes from environmental samples. Nonetheless, how to best benefit from long-read sequencing and whether long-read…

. 2023 Apr 27;13:1183039. doi: 10.3389/fonc.2023.1183039. eCollection 2023. Affiliations Expand Affiliations 1 Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway. 2 Department of Research, Cancer Registry of Norway, Oslo, Norway. 3 Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway. 4 Department of…

Abstract Deoxynivalenol (DON) is one of the most prevalent food-associated mycotoxins, and is known to cause a variety of adverse health effects on human and animals. Upon oral exposure, the intestine is the main target organ of DON. The current study unraveled that DON exposure (2 mg/kg bw/day or 5…

HMSS2: an advanced tool for the analysis of sulfur metabolism, including organosulfur compound transformation, in genome and metagenome assemblies Abstract The global sulfur cycle has implications for human health, climate change, biogeochemistry, and bioremediation. The organosulfur compounds that participate in this cycle not only represent a vast reservoir of sulfur,…

As urbanization continues to increase, it is expected that two-thirds of the human population will reside in cities by 2050. Urbanization fragments and degrades natural landscapes, threatening wildlife including economically important species such as bees. In this study, we employ whole genome sequencing to characterize the population genetics, metagenome and…

Reteroviruses in shotgun metgaenome data 0 Hi Everyone!! Is it possible to detect RNA viruses from shotgun metagenomics data except for the retroviruses? I am curious because we have found retroviruses from our shotgun metagenome data but that is explainable because the retroviruses have the machinery to integrate into the…

Dick G, Anantharaman K, Baker B, Li M, Reed D, Sheik C. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front Microbiol. 2013;4:124. Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol. 2019;17:271–83. Article  CAS …

Animal rearing and samples collection Our experiment was designed to compare eight female Laiwu pigs (LW) with eight female Lulai pigs (LU) which crossbred between LW and Yorkshire breeds. All pigs were born and raised for approximately two years (715 ± 33 days, Table 1) under uniform housing and feeding conditions at Jing-Qi-Shen…

image: The researchers analysed the DNA of microorganisms in stool samples, and evaluated the data using bioinformatics tools. view more  Credit: Anna Schroll/Leibniz-HKI The bacteria present in the intestine provide information about the quantities of fungi of the potentially disease-causing Candida genus. Among them, and surprisingly, are lactic acid bacteria that…

hi folks, Recently, I’ve been working on developing molecular and computational methods to improve the accuracy of relative abundance estimation of metagenome assembled genomes (MAGs) from NGS datasets. Most of this work is focused on host-associated viral metagenomics, where quite a bit of nucleic acid manipulation and amplification is needed…

1. Introduction Shiga toxin-producing Escherichia coli (STEC) are important zoonotic pathogens comprising more than 400 serotypes (Beutin and Fach, 2015). Pathogenic STEC strains such as enterohemorrhagic E. coli (EHEC) may cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. However, it remains difficult to fully define human pathogenic STEC…

Noone AM, Howlader N, Krapcho M, Miller D, Brest A, Yu M, et al., editors. SEER Cancer Statistics Review, 1975-2015. 2018;Available from: seer.cancer.gov/csr/1975_2015/. Bonadonna G, Brusamolino E, Valagussa P, Rossi A, Brugnatelli L, Brambilla C, et al. Combination chemotherapy as an adjuvant treatment in operable breast cancer. N Engl J…

Preprint Technical Note Version 1 This version is not peer-reviewed Version 1 : Received: 11 May 2023 / Approved: 11 May 2023 / Online: 11 May 2023 (09:25:18 CEST) Ng, W. Metrics for Understanding the Degraded Metagenome of Stomach Cancer Patient . Preprints.org 2023, 2023050835. doi.org/10.20944/preprints202305.0835.v1. Ng, W. Metrics for…

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…

Background The prevalence of type 2 diabetes (T2D) is rapidly increasing worldwide, with an estimated global prevalence of approximately 552 million by 2030.1 Long-term hyperglycemia in T2D patients can lead to vascular endothelial damage, which includes microvascular disease such as diabetic retinopathy and nephropathy, neuropathy, and macrovascular disease including peripheral…

The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to…

Problem while downloading SRA using aspera links 1 while downloading fastq.gz files using aspera command in ubuntu, it’s showing an error message. Session Stop (Error: Server aborted session: No such file or directory) I checked using other aspera commands for fastq.gz files which i have dowloaded 2 weeks ago, same…

Trying to use hmmer to search genes over metagenome assembled genomes 0 Hello I have a hmm file (my genes.hmm) that I want to use to search some genes over some MAGs that I elaborated. For this purpose I installed hmmer and tried to run hmmsearch as the following: First…

Marine environments are home to a staggering diversity of microbial life, the majority of which has yet to be cultivated in a laboratory setting. These microbes are the base of the food chain that supports marine life and key drivers of the planets biogeochemical cycles. Marine microbes also produce biologically…

Manrique, P., Dills, M. & Young, M. J. The human gut phage community and its implications for health and disease. Viruses 9, 141 (2017). Article  PubMed  PubMed Central  Google Scholar  Li, Z. et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J….

@article{9bba3dfc881c483b9abef6bdf5215b8c, title = “MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice”, abstract = “Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic…

La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef  CAS  PubMed  Google Scholar  Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…

L-2-aminobutyric acid (L-2-ABA) is a chiral precursor for the synthesis of anti-epileptic drug levetiracetam and anti-tuberculosis drug ethambutol. Asymmetric synthesis of L-2-ABA by leucine dehydrogenases has been widely developed. However, the limitations of natural enzymes, such as poor stability, low catalytic efficiency, and inhibition of high-concentration substrates, limit large-scale applications….

Metagenomics is a new generation of high-throughput sequencing (NGS) technology that takes the microbial population genome in a specific environment as the research object. Based on the analysis of microbial diversity, population structure and evolutionary relationship, it can further explore the functional activity of microbial population, the relationship between mutual…

software recommendation for metagenome assembly for low abundance bacteria 0 I hope to obtain some MAGs for certain bacteria from my samples. We know they do exit in the samples by 16S amplicon, but the abundance is low. Is there any recommendation about how to assembly the MAGs for these…

In a recent study published in the Nature Journal, researchers described a new method to safely release deoxyribonucleic acid (DNA) trapped inside the ancient tooth and bone artifacts, which was used to analyze and identify the wearer or maker of a deer tooth pendant from the Upper Paleolithic period found…

Introduction Hyperuricemia is a disease caused by irregular purine metabolism, which is always accompanied by excessive production or abnormal excretion of uric acid (UA).1 Most notably, the overall incidence of hyperuricemia in China has been increasing over the past decade with the westernization of eating habits.2,3 However, there are blind…

World J Microbiol Biotechnol . 2023 May 3;39(7):179. doi: 10.1007/s11274-023-03631-2. Affiliations Expand Affiliations 1 Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India. 2 Department of Life Science and Bioinformatics, Hargobind Khurana School of Life Sciences, Assam University, Silchar, Assam, 788011, India. 3…

Align shotgun metagenomics to reference protein database 0 Hi all, I would like to align the shotgun metagenomics data to a set of protein sequences of interest to estimate their abundance in the metagenome. I found [paladin][1] can accomplish this task, which is on the basis of bwa algorithm. However,…

Researchers headed by teams at the Leibniz Institute for Natural Product Research and Infection Biology at the Max Planck Institute for Evolutionary Anthropology, and at Harvard University, have reconstructed the bacterial genomes of previously unknown bacteria, from the calcified dental plaque of human and Neanderthal remains. Using these genetic blueprints,…

Reconstructing the bacterial genomes recovered from the calcified plaque of human and Neanderthal remains has offered new insights into previously undescribed Pleistocene bacterial metabolites, researchers report. The approach expands researchers ability to study microbial natural products, which has otherwise been mostly limited to studying living bacteria. Bioactive small molecules produced…

Dense living communities of hundreds of bacterial species form biofilms on our teeth. Without careful brushing and flossing of this dental plaque, minerals seep in, hardening it into tartar. When proteins in saliva adhere tartar to tooth surfaces, a trip to the dentist is required to hack the stuff off….

Shkoporov, A. N. & Hill, C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe 25, 195–209 (2019). Article  CAS  PubMed  Google Scholar  Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498…

. 2023 May 1;19(5):e1011001. doi: 10.1371/journal.pcbi.1011001. Online ahead of print. Affiliations Expand Affiliations 1 Department of Computer Science, ETH Zürich, Zürich, Switzerland. 2 Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen, Germany. 3 Swiss Institute for Bioinformatics, Lausanne, Switzerland. 4 ETH AI center, ETH Zürich, Zürich, Switzerland….

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…

KEGG T30379: 62936     T30379 (Metagenome): 62936 Help Entry 62936             CDS       T30379                                  Name imidazole glycerol phosphate synthase cyclase subunit   KO K02500   imidazole glycerol-phosphate synthase subunit HisF [EC:4.3.2.10] Best hit Pathway 00340   Histidine metabolism 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 01230   Biosynthesis of amino acids Other DBs LinkDB All DBs Position…

Design of this study In this study, we use 98 MAGs described previously from Guaymas Basin hydrothermal plumes (see Metagenomic datasets and model building in Methods) to understand metabolic interactions and evolution in hydrothermal systems (Refer Supplementary File S1 for the short name references used in this article). Both bacteria and archaea…

Authors: Christopher A. Francis1* (caf@stanford.edu), Katie Langenfeld1, Anna Rasmussen1, Bradley B. Tolar1,5, Linta Reji1,6, Emily Cardarelli1,7, Zach Perzan1, Kristin Boye2, John R. Bargar3, Nicholas Bouskill4 Institutions: 1Stanford University, Stanford, CA; 2SLAC National Accelerator Laboratory, Menlo Park, CA; 3Pacific Northwest National Laboratory, Richland, WA; 4Lawrence Berkeley National Laboratory, Berkeley, CA; 5University…

[Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads 0 Hello everyone, We did a metagenome sequencing on ONT and ran metaFlye to obtain contigs and polished with medaka. Out of the 318 contigs, around 21 contigs were prokaryotic contigs, and two of the contigs had 16S rRNA sequences annotated which…

1. Introduction Since the beginning of extraterrestrial exploration by NASA, planetary protection (PP) has been an important effort to prevent biological forward contamination of non-Earth environments. The Committee on Space Research (COSPAR) has formulated a Planetary Protection Policy with associated implementation requirements as an international standard to protect against interplanetary biological…

AACR 2023 presentation highlights noteworthy diagnostic performance potential using cell-free microbial DNA in diagnosing early-stage lung cancer SAN DIEGO, April 27, 2023–(BUSINESS WIRE)–Highlighting that cancer is no longer considered a sterile disease, Greg Sepich-Poore, Ph.D., Chief Analytic Officer and Co-founder of Micronoma, the first biotech company offering early cancer detection…

Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013)….

Analysis of the Fecal Metagenome in Long-Term Survivors of Pancreas Cancer | PracticeUpdate …

   The great threaten of microbes carried by ballast water calls for figuring out the species composition of the ballast-tank microbial community, where the dark, cold, and anoxic tank environment might select special taxa. In this study, we reconstructed 103 metagenome-assembled genomes (MAGs), including 102 bacteria and one archaea from…

. 2023 Apr 21;21(4):e3002083. doi: 10.1371/journal.pbio.3002083. Online ahead of print. Affiliations Expand Affiliations 1 DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America. 2 Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain. 3 Division of Biostatistics and Computational Biology, University of Iowa College of Dentistry,…

  With Earth Day almost here, it is important to remember that our planet is made up of countless interconnected parts, from vast oceans to the microscopic world of microbes. Despite their tiny size, microorganisms play a massive role in shaping our world. They have a hand in everything from cloud…

de La Torre, S., Snowdon, C. T. & Bejarano, M. Effects of human activities on wild pygmy marmosets in Ecuadorian Amazonia. Biol. Conserv. 94, 153–163 (2000). Article  Google Scholar  Turvey, S. T. & Crees, J. J. Extinction in the Anthropocene. Curr. Biol. 29, R982–R986 (2019). Article  CAS  PubMed  Google Scholar …

Abstract It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a…

For the initial test of this protocol, DNA extraction, PCR, Nanopore library preparation, Nanopore sequencing, and subsequent data analysis were conducted at sea aboard the R/V Atlantic Condor in August 2021 [26]. This investigational effort resulted in the sequencing and analysis of deep sea sediment samples within hours of their…

Ma, Y. et al. Gut microbiota adaptation to high altitude in indigenous animals. Biochem. Biophys. Res. Commun. 516, 120–126 (2019). Article  CAS  PubMed  Google Scholar  Guo, N. et al. Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude. NPJ Biofilms Microbiomes 7, 38 (2021)….

Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Suttle, C. A. Marine viruses — major players in the global…

The human microbiome is a collection of microorganisms that inhabit various parts of the body and play critical roles in maintaining health, including the urogenital tract microbiome. The composition and diversity of the urogenital tract microbiome are influenced by various environmental and genetic factors, and are critical in maintaining…

Baumgart, D. C. & Sandborn, W. J. Inflammatory bowel disease: Clinical aspects and established and evolving therapies. Lancet 369(9573), 1641–1657 (2007). Article  CAS  PubMed  Google Scholar  Baumgart, D. C. The diagnosis and treatment of Crohn’s disease and ulcerative colitis. Deutsches Aerzteblatt Online 106(8), 123–133 (2009). Google Scholar  Conrad, K., Roggenbuck,…

Blume-Werry G, Krab EJ, Olofsson J, Sundqvist MK, Väisänen M, Klaminder J. Invasive earthworms unlock arctic plant nitrogen limitation. Nat Commun. 2020;11:1766. Article  CAS  PubMed  PubMed Central  Google Scholar  Xing Y, Meng X, Wang L, Zhang J, Wu Z, Gong X, et al. Effects of benzotriazole on copper accumulation and…

What is it about? This Research work is about the most controversial antimicrobial agent #Triclosan, which is globally used in hundreds of marketed consumer products since 40 Years. One of the well-known triclosan containing product includes #Colgate_Total_Toothpaste. The excessive use of this biocide in personal care products indicates that everybody…

Back to Bioinformatics Main Menu Mothur GCATemplates available: no Mothur homepage module spider Mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities See syntax for commands when running in command line mode such as in a batch file. mothur.org/wiki/Command_line_mode QIIME GCATemplates available: terra QIIME is an open-source bioinformatics pipeline for…

Credit: CC0 Public Domain A genetic study analyzing the microbiome (bacteria in the gut) of a large nationally representative sample of the Finnish population finds that geographic, demographic, diet, and lifestyle factors are driving the spread of antibiotic resistance in the general population. The most comprehensive study of its kind…

 The Revio system offers faster and more cost-effective long-read sequencing for metagenomcis researchers, allowing for more high-quality and complete microbial datasets and access to new frontiers of discovery.   The best in metagenomics just got better Shotgun metagenomics with PacBio highly accurate long-read sequencing (aka HiFi sequencing) has been the…

The Element AVITI™ System rapidly delivers high-quality, cost-effective data to accelerate cytogenomic research on Phase Genomics’ OncoTerra™ Platform SEATTLE & SAN DIEGO–(BUSINESS WIRE)– Phase Genomics, Inc., a leading developer of cutting-edge genomic solutions, and Element Biosciences, the developer of an innovative DNA sequencing platform disrupting genomics, today released new details…

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…

References [1] Hogerwerf L, Roof I, de Jong MJK, Dijkstra F, van der Hoek W. Animal sources for zoonotic transmission of psittacosis: A systematic review. BMC Infect Dis. 2020;20(1):192.Search in Google Scholar [2] Stokes HS, Berg ML, Bennett ATD. A review of chlamydial infections in wild birds. Pathogens. 2021;10(8):948.Search in…

Agency for Toxic Substances and Disease Registry (ATSDR) (2002) Toxicological profile for copper. Atlanta, GA: Centers for Disease Control Ahemad M (2012) Implications of bacterial resistance against heavy metals in bioremediation: A review. IIOAB J 3:39–46 CAS  Google Scholar  Alcamán-Arias ME, Pedrós-Alió C, Tamames J, Fernández C, Pérez-Pantoja D, Vásquez M,…

doi: 10.1007/s10142-023-01046-8. Affiliations Expand Affiliations 1 Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India. 2 Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India. saleenam@srmist.edu.in. Item in Clipboard Arunmozhi Bharathi Achudhan et al. Funct Integr Genomics….

KEGG T30613: 141471     T30613 (Metagenome): 141471 Help Entry 141471            CDS       T30613                                  Symbol aepY Name phosphonopyruvate decarboxylase   KO Best hit Taxonomy Firmicutes – Clostridia [GN:ral]Taxonomy Pathway 00440   Phosphonate and phosphinate metabolism 00998   Biosynthesis of various secondary metabolites – part 2 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 01120   Microbial metabolism in…

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…

Sci-Hub | A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Acetobacter Lipopolysaccharide Genes Are Necessary for Association with Drosophila melanogaster . G3: Genes|Genomes|Genetics, g3.300530.2017 | 10.1534/g3.117.300530 ◂ ↓ save White, K. M., Matthews, M. K., Hughes, R., Sommer, A. J., Griffitts, J. S., Newell, P. D., & Chaston, J….

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…

With respect to the ionic circumstances, Further education was the next or perhaps last many highly-adsorbed steel out of 27 components assessed. Tests employing Fe-limited artificial marine sea water indicated that expansion of the particular maritime diatom Thalassiosira weissflogii (axenic pressure) had been superior while incubated inside the existence of…

Preprint Review Version 1 This version is not peer-reviewed † These authors contributed equally to work. Version 1 : Received: 9 April 2023 / Approved: 11 April 2023 / Online: 11 April 2023 (08:14:43 CEST) Zehrh, I.; Habiba, U.; Picco, M.R.; Basheer, S.H.; Rehman, U.A.; Haider, O.; Khoso, S. Metagenomics…

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Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article  CAS  PubMed  PubMed Central  Google Scholar  Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…