Categories
Tag: Megahit
Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
The specific environmental/history/collection context The Huseby Klev materials were unearthed and collected by archaeologists (including two of the co-authors of this article) during the excavation of this coastal hunter-fisher-gatherer site in the 90s50. The material assemblage was rich and well preserved: human bones, animal bones, plant remains and pieces of…
Diversity and dissemination of viruses in pathogenic protozoa
Wang, A. L. & Wang, C. C. Viruses of the protozoa. Annu. Rev. Microbiol. 45, 251–263 (1991). Article CAS PubMed Google Scholar Banik, G., Stark, D., Rashid, H. & Ellis, J. Recent advances in molecular biology of parasitic viruses. Infect. Disord. – Drug Targets 14, 155–167 (2015). Article Google Scholar …
A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery
Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article CAS PubMed Google Scholar Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article CAS …
Resin acids play key roles in shaping microbial communities during degradation of spruce bark
Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…
Zea mays genotype influences microbial and viral rhizobiome community structure
Oburger E, Schmidt H. New methods to unravel rhizosphere processes. Trends Plant Sci. 2016;21:243–55. Article CAS PubMed Google Scholar Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot. 2013;100:1689–91. Article PubMed Google Scholar Pratama AA, Terpstra J, de Oliveria ALM,…
Borrelia puertoricensis in opossums (Didelphis marsupialis) from Colombia | Parasites & Vectors
Oppler Z, Keeffe K, McCoy K, Brisson D. Evolutionary genetics of Borrelia. Curr Issues Mol Biol. 2021;42:97–112. doi.org/10.21775/cimb.042.097.2. Article PubMed Google Scholar Margos G, Fingerle V, Cutler S, Gofton A, Stevenson B, Estrada-Peña A. Controversies in bacterial taxonomy: the example of the genus Borrelia. Ticks Tick Borne Dis. 2020;11:101335. doi.org/10.1016/j.ttbdis.2019.101335….
Quast Genome assembly Quality (Galaxy Version 5.2.0+galaxy1) – usegalaxy.org support
Busrak November 29, 2023, 9:55am 1 Hi dear galaxy family, When I put my metagenome single read Megahit assembly data into Quast, I encounter the following error code. How can I solve this problem? Assembly_with_MEGAHIT_on_data_658 /usr/local/opt/quast-5.2.0/metaquast.py –single /jetstream2/scratch/main/jobs/53997042/inputs/dataset_f68c8b4a-bea0-4985-8324-4c64cdbe4d6d.dat –labels Assembly_with_MEGAHIT_on_data_658 -o outputdir –max-ref-num 50 –m 822: Quast on data 196…
Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost
Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article Google Scholar Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…
Shotgun metagenomes from productive lakes in an urban region of Sweden
Williamson, C. E., Saros, J. E., Vincent, W. F. & Smol, J. P. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnology and Oceanography 54, 2273–2282, doi.org/10.4319/lo.2009.54.6_part_2.2273 (2009). Article ADS Google Scholar Cavicchioli, R. et al. 2019. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews…
Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article ADS CAS PubMed PubMed Central Google Scholar Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article Google Scholar Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…
Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]
Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…
Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility
Abstract Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which…
Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective | BMC Genomics
Aslam B, Khurshid M, Arshad MI, Muzammil S, Rasool M, Yasmeen N, Shah T, Chaudhry TH, Rasool MH, Shahid A, et al. Antibiotic resistance: one health one world outlook. Front Cell Infect Microbiol. 2021;11:771510. Article CAS PubMed PubMed Central Google Scholar Ahern PP, Faith JJ, Gordon JI. Mining the human…
What are unbinned contigs ?
What are unbinned contigs ? 1 Hello community, by taking a look into the number of binned contigs from a binning refinement procedure I notice that the number of contigs employed to make bins or MAGs are less than half of the number of contigs produced by the assembly procedure….
Disease-specific loss of microbial cross-feeding interactions in the human gut
Wang, T., Goyal, A., Dubinkina, V. & Maslov, S. Evidence for a multi-level trophic organization of the human gut microbiome. PLOS Comput. Biol. 15, e1007524 (2019). Article ADS PubMed PubMed Central Google Scholar Fischbach, M. A. & Sonnenburg, J. L. Eating for two: how metabolism establishes interspecies interactions in the…
Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales
Quesada A, Vincent WF. Strategies of adaptation by antarctic cyanobacteria to ultraviolet radiation. Eur J Phycol. 1997;32:335–42. Article Google Scholar Genuário DB, Corrêa DM, Komárek J, Fiore MF. Characterization of freshwater benthic biofilm-forming Hydrocoryne (Cyanobacteria) isolates from Antarctica. J Phycol. 2013;49:1142–53. Article PubMed Google Scholar Makhalanyane TP, Valverde A, Gunnigle…
Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle
Falkowski P. G., Raven J. A. Aquatic Photosynthesis (Princeton Univ. Press, 2013). Sanchez-Baracaldo, P., Bianchini, G., Wilson, J. D. & Knoll, A. H. Cyanobacteria and biogeochemical cycles through earth history. Trends Microbiol. 30, 143–157 (2022). Article CAS PubMed Google Scholar Blankenship, R. E. Early evolution of photosynthesis. Plant Physiol. 154,…
Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease | Genome Biology
Zhang L, Wang F, Wang L, Wang W, Liu B, Liu J, Chen M, He Q, Liao Y, Yu X, et al. Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012;379:815–22. Article PubMed Google Scholar Collaboration GBDCKD. Global, regional, and national burden of chronic kidney disease, 1990–2017:…
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples
Tuganbaev, T. et al. Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis. Cell 182, 1441–1459 (2020). Article CAS PubMed Google Scholar Dejea, C. M. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359, 592–597 (2018). Article CAS PubMed PubMed Central Google Scholar Bullman,…
Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium
Rabus, R., Hansen, T. A. & Widdel, F. In Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes. The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., and Thompson F. at (2013). Rabus, R. et al. Chapter Two—A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing…
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…
A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil
Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…
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…
A comprehensive genomic catalog from global cold seeps
Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Pl. Sci. 48, 205–231 (2020). Article ADS CAS Google Scholar Al-Shayeb, B. et al. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature 610, 731–736 (2022). Article ADS CAS PubMed PubMed Central Google Scholar …
Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation
Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…
Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome
Kolstø AB. Dynamic bacterial genome organization. Mol Microbiol. 1997;24:241–8. doi.org/10.1046/j.1365-2958.1997.3501715.x. Article PubMed Google Scholar Snel B, Bork P, Huynen MA. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 2002;12:17–25. doi.org/10.1101/gr.176501. Article CAS PubMed Google Scholar Puigbò P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV….
phylogeny – Variation in 16S rRNA between assemblers – how do I know which is real?
I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So let’s call the bins of interest 1, 2 and 3. The raw reads had…
Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin
Magnabosco C, Lin LH, Dong H, Bomberg M, Ghiorse W, Stan-Lotter H, et al. The biomass and biodiversity of the continental subsurface. Nat Geosci. 2018;11:707–17. Article CAS Google Scholar LaRowe DE, Amend JP. Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings. Am J Sci. 2015;315:167–203. Article …
Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China
Wu, Z. Antibiotic Use and Antibiotic Resistance in Food-Producing Animals in China OECD Food, Agriculture and Fisheries Paper No. 134 (OECD, 2019); doi.org/10.1787/4adba8c1-en Looft, T. et al. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl Acad. Sci. USA 109, 1691–1696 (2012). Article ADS CAS PubMed PubMed Central Google…
Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer
Espedido, B. A., Partridge, S. R. & Iredell, J. R. bla(IMP-4) in different genetic contexts in Enterobacteriaceae isolates from Australia. Antimicrob. Agents Chemother. 52, 2984–2987 (2008). Article CAS PubMed PubMed Central Google Scholar Kizny Gordon, A. et al. Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated…
Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales
Romans, B. W. & Graham, S. A. A deep-time perspective of land–ocean linkages in the sedimentary record. Annu. Rev. doi.org/10.1146/annurev-marine-121211-172426 (2013). Article Google Scholar Smith, S. V. & Hollibaugh, J. T. Coastal metabolism and the ocean organic carbon balance. Rev. Geophys. 31, 75–89 (1993). Article ADS Google Scholar Bauer, J….
A genome catalogue of lake bacterial diversity and its drivers at continental scale
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). Article CAS PubMed PubMed Central Google Scholar Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats….
Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont
Psyllid sampling, tissue collection and DNA isolation Adult D. citri newly emerged (five days old) was initially harvested from Citrus Tachibana uninfected CLas in 2020 at Guangxi province, China, and was successively reared on Murraya paniculata at Guangxi Special Crops Research Institute for more than 15 generations. All cages and…
Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites | BMC Medicine
Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus–infected pneumonia in Wuhan. China JAMA. 2020;323(11):1061–9. Article CAS PubMed Google Scholar Zhao Y, Zhao Z, Wang Y, Zhou Y, Ma Y, Zuo W. Single-cell RNA expression…
Recommendation regarding antibiotic resistance genes in oceanic metagenomic samples
Recommendation regarding antibiotic resistance genes in oceanic metagenomic samples 1 Hello everyone, I am currently working on my final master’s project, which focuses on antibiotic resistance genes in oceanic metagenomic samples. I am facing a challenge as I am using Amazon WorkSpaces, which has limited computational capacity. So far, using…
A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017). Article CAS PubMed Google Scholar Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019). Article CAS PubMed PubMed Central Google…
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017). Article CAS PubMed Google Scholar Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). Article …
Genome-resolved carbon processing potential of tropical peat microbiomes from an oil palm plantation
Dargie, G. C. et al. Age, extent and carbon storage of the central Congo Basin peatland complex. Nature 542, 86–90 (2017). Article ADS CAS PubMed Google Scholar Page, S. E., Rieley, J. O. & Banks, C. J. Global and regional importance of the tropical peatland carbon pool. Global Change Biology…
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants
Awasthi MK, Singh E, Binod P, Sindhu R, Sarsaiya S, Kumar A, et al. Biotechnological strategies for bio-transforming biosolid into resources toward circular bio-economy: a review. Renew Sustain Energy Rev. 2022;156:111987. Article CAS Google Scholar Diamantis V, Eftaxias A, Stamatelatou K, Noutsopoulos C, Vlachokostas C, Aivasidis A. Bioenergy in the…
Not annotated metagenome-assembled genomes recovered from rumen samples from cows
Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the genera Entodinium has been consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that species such as Entodinium caudatum exert, their greater…
Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands
Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev. 2015;39:203–21. Article CAS PubMed Google Scholar Pointing SB, Belnap J. Microbial colonization and controls in dryland systems. Nat Rev Microbiol. 2012;10:551–62. Article CAS PubMed Google Scholar Ji M,…
Error while running Megahit
Error while running Megahit 0 Hi, Myself Abhirami, Currently pursuing Ph.D., for a paper publication currently I’m working on mitogenomic sequences. So as the initial steps, I proceed successfully with fastp (Quality checking), cutadapt, bwa mem (to remove host genome). But, while running megahit, I reached up with many difficulties…
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes
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 …
Long-Read Metagenomics and CAZyme Discovery
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…
Metagenomics-enabled reverse-genetics assembly and characterization of myotis bat morbillivirus
Ethics declaration Animal study was performed following the Guide for the Care and Use of Laboratory Animals. Animal experiment was approved by the Institutional Animal Care and Use Committee of Colorado State University (protocol number 1090) in advance and conducted in compliance with the Association for the Assessment and Accreditation…
filter extract sequences
filter extract sequences 0 Hi, I am a bioinformatics beginner and have very little command line knowledge. I have downloaded raw sequence reads and assembled them with megahit into contigs (‘genome of interest’). I have aligned to this genome several thousand DNA fragments of 100 bases long (probes) using blastn:…
How could I filter a metagenomic assembly file (from Megahit or metaspades) for low coverage/short contigs to enable faster downstream analysis (i.e blastn)
How could I filter a metagenomic assembly file (from Megahit or metaspades) for low coverage/short contigs to enable faster downstream analysis (i.e blastn) 0 Title is pretty selg-explanatory, can i filter down a de-novo metagenomic assembly to make downstream analysis like blastn run faster? metagenomics blast spades megahit assembly •…
Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons
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 …
Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)
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)….
Mirusviruses link herpesviruses to giant viruses
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…
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes
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…
Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments
Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Planet. Sci. 48, 205–231 (2020). Article CAS Google Scholar Feng, D. et al. Cold seep systems in the South China Sea: An overview. J. Asian Earth SCI 168, 3–16 (2018). Article Google Scholar Dubilier, N., Bergin, C….
Linking prokaryotic genome size variation to metabolic potential and environment
Kirchberger PC, Schmidt ML, Ochman H. The ingenuity of bacterial genomes. Annu Rev Microbiol. 2020;74:815–34. Article CAS PubMed Google Scholar Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, et al. A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked…
The persistence and stabilization of auxiliary genes in the human skin virome | Virology Journal
Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66. Article CAS PubMed Google Scholar Suttle CA. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12. Article CAS PubMed Google Scholar Breitbart M. Marine viruses: truth or dare. Ann…
Characterization of a novel papillomavirus identified from a whale (Delphinapterus leucas) pharyngeal metagenomic library | Virology Journal
Van Doorslaer K, Chen Z, Bernard HU, Chan PKS, DeSalle R, Dillner J, Forslund O, Haga T, McBride AA, Villa LL, et al. ICTV Virus Taxonomy Profile: Papillomaviridae. J Gen Virol. 2018;99:989–90. Article CAS PubMed PubMed Central Google Scholar McBride AA. Oncogenic human papillomaviruses. Philos Trans R Soc Lond B…
Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome
Introduction Cyanide-containing compounds are known as nitriles and are widely distributed in the natural environment. They are generated by different plants in various forms, such as ricinine, phenyl acetonitrile, cyanogenic glycosides, and β -cyanoalanine (Sewell et al., 2003). Anthropogenic activities have substantially influenced the production of vast quantities of nitrile…
A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes
Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article CAS PubMed Google Scholar Timmer-Ten Hoor, A. A new type of…
bwa-mem2 vs htslib – compare differences and reviews?
What are some alternatives? When comparing bwa-mem2 and htslib you can also consider the following projects: minimap2 – A versatile pairwise aligner for genomic and spliced nucleotide sequences bowtie2 – A fast and sensitive gapped read aligner genozip – A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF,…
Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome
Manzin, A., Mallus, F., Macera, L., Maggi, F. & Blois, S. Global impact of Torque teno virus infection in wild and domesticated animals. J. Infect. Dev. Countries 9, 562–570 (2015). Article CAS Google Scholar Biagini, P. et al. Family Anelloviridae. In Virus Taxonomy: Ninth Report of the International Committee on…
Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades
Moore CM, Mills MM, Arrigo KR, Berman-Frank I, Bopp L, Boyd PW, et al. Processes and patterns of oceanic nutrient limitation. Nat Geosci. 2013;6:701–10. Article CAS Google Scholar Sohm JA, Webb EA, Capone DG. Emerging patterns of marine nitrogen fixation. Nat Rev Microbiol. 2011;9:499–508. Article CAS PubMed Google Scholar Zehr…
Seasonal activities of the phyllosphere microbiome of perennial crops
Robertson, G. P. et al. Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes. Sci. (80-.) 356, 1–9 (2017). Article Google Scholar Ma, L. et al. The impact of stand age and fertilization on the soil microbiome of Miscanthus × giganteus. Phytobiomes J. 5, 51–59 (2021). Article Google…
Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars
Zhang J, Liu Y, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84. Article CAS PubMed Google Scholar Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots:…
Co-diversification of an intestinal Mycoplasma and its salmonid host
Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol 2016;31:689–99. Article PubMed Google Scholar Groussin M, Mazel F, Alm EJ. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe. 2020;28:12–22. Article CAS PubMed Google Scholar Alberdi A,…
Relation of the number of contigs to the real DNA abundance before sequencing
Relation of the number of contigs to the real DNA abundance before sequencing 0 Hello everyone! I have a problem with my work on contigs. I have searched the literature but have not found anything useful yet. First, total DNA was isolated from a soil sample, then mechanically fragmented (sonication)…
database for better classification of illumina contigs
Forum:database for better classification of illumina contigs 0 hi everyone I have sequenced some filth flies guts using Novoseq and assembled the contigs using megahit. I have assigned taxonomy to the contigs using the NR (which is part of another pipeline, that compares predicted aa to the protein NR) but…
First detection of Ixodiphagus hookeri (Hymenoptera: Encyrtidae) in Ixodes ricinus ticks (Acari: Ixodidae) from multiple locations in Hungary
Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: A review. Front. Public Health doi.org/10.3389/fpubh.2021.715759 (2021). Article Google Scholar Jongejan, F. & Uilenberg, G. The global importance of ticks. Parasitology 129, S3–S14 (2004). Google Scholar Hornok, S., Kováts, D., Horváth, G., Kontschán, J….
Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga
Koonin, E. V. & Dolja, V. V. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol. Mol. Biol. Rev. 78, 278–303 (2014). Article CAS Google Scholar Pritham, E. J., Putliwala, T. & Feschotte, C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and…
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
Data collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….
Unexpected absence of ribosomal protein genes from metagenome-assembled genomes
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article PubMed Google Scholar Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS PubMed Article Google Scholar Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome
Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed PubMed Central Google Scholar Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…
Petabase-scale sequence alignment catalyses viral discovery
Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…
metagenome low alignment rate
metagenome low alignment rate 1 I have 20 metagenome samples which need to be analyzed. I started with one sample for the time being with the below tools/pipelines. After assembling first sample I mapped its reads back to contigs but the alignment rate is pretty low, What could be the…
many reads are not assembled into long contigs
many reads are not assembled into long contigs 2 Hi folks, I am assembling paired-end short metagnenomic reads (150 bp) using metaSpades and Megahit (with default settings). Then I did binning (with various binners and refiners), only 35-40% trimmed clean reads could be mapped to the bins. This is criticized…
Towards the biogeography of prokaryotic genes
1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed Google Scholar 2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS PubMed PubMed Central Google Scholar 3. Mohammad,…