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Tag: iTOL
Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein | Parasites & Vectors
Akhoundi M, Downing T, Votypka J, Kuhls K, Lukes J, Cannet A, et al. Leishmania infections: molecular targets and diagnosis. Mol Aspects Med. 2017;57:1–29. Article PubMed Google Scholar Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. A historical overview of the classification, evolution, and…
Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes
Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). Article PubMed Google Scholar Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020). Article ADS Google Scholar Tian, H. et al. A comprehensive quantification of global…
ST23 Klebsiella pneumoniae in China
Introduction Klebsiella pneumoniae (KP), a member of the Enterobacteriaceae family, inhabits aquatic environments and can colonise respiratory and gastrointestinal tracts in humans, making it a significant opportunistic pathogen. It may result in pneumonia, meningitis, urinary tract infections, and bloodstream infections. Hypervirulent Kp (HvKp) is believed to cause severe community-acquired invasive…
Multiple host colonization and differential expansion of multidrug-resistant ST25-Acinetobacter baumannii clades
Features of animal and human isolates of this study On average, sequencing of isolates of this study generated 2.36 M of reads per genome, with an estimated genome size of 4.2 M bases, with a coverage depth of 204X (Table S1). Animal isolates included in this study (n = 33) were found mostly in…
Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes
Yang J, Liu X, Cao S, Dong X, Rao S, Cai K. Understanding esophageal cancer: the challenges and opportunities for the next decade. Front Oncol. 2020;10:1727. Article PubMed PubMed Central Google Scholar Li J, Xu J, Zheng Y, Gao Y, He S, Li H, et al. Esophageal cancer: epidemiology, risk…
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….
Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis
Centers for Disease Control and Prevention (U.S.). Antibiotic Resistance Threats in the United States, 2019. doi.org/10.15620/cdc:82532 (2019). Centers for Disease Control and Prevention. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. doi.org/10.15620/CDC:117915 (2022). Fricks-Lima, J. et al. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from…
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article CAS PubMed Google…
The genomic epidemiology of shigellosis in South Africa
Institue for Health Metrics and Evaluation. Global Burden of Disease. vizhub.healthdata.org/gbd-results/ 2019. Troeger, C. E. et al. Quantifying risks and interventions that have affected the burden of diarrhoea among children younger than 5 years: an analysis of the Global Burden of Disease Study 2017. Lancet Infect. Dis. 20, 37–59 (2020)….
Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius
Khalifa, S. A. M. et al. Overview of bee pollination and Its economic value for crop production. Insects 12 (2021). Vanengelsdorp, D. et al. Colony collapse disorder: a descriptive study. PLoS ONE 4, e6481 (2009). Article ADS PubMed PubMed Central Google Scholar Muli, E. et al. Evaluation of the distribution…
Phenotypic drug-susceptibility profiles and genetic analysis based on whole-genome sequencing of Mycobacterium avium complex isolates in Thailand
Abstract Mycobacterium avium complex (MAC) infections are a significant clinical challenge. Determining drug-susceptibility profiles and the genetic basis of drug resistance is crucial for guiding effective treatment strategies. This study aimed to determine the drug-susceptibility profiles of MAC clinical isolates and to investigate the genetic basis conferring drug resistance using…
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article CAS PubMed Google Scholar Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…
Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance
De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…
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…
Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau
Abebe TD, Naz AA, Léon J (2015) Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.). Front Plant Sci 6:813 Article PubMed PubMed Central Google Scholar Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 Article CAS PubMed …
itol style + color label issue
hi, based on previous post i tried to reproduce some itol style. It’s working but i can’t add color label. library(ape)library(ggtree) …
Detection and characterization of putative hypervirulent Klebsiella pneumoniae isolates in microbiological diagnostics
Navon-Venezia, S., Kondratyeva, K. & Carattoli, A. Klebsiella pneumoniae: A major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol. Rev. 41(3), 252–275 (2017). Article CAS PubMed Google Scholar Marr, C. M. & Russo, T. A. Hypervirulent Klebsiella pneumoniae: A new public health threat. Expert Rev. Anti Infect. Ther. 17(2),…
Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms
Bond, R. & Loeffler, A. What’s happened to Staphylococcus intermedius? Taxonomic revision and emergence of multi-drug resistance. J. Small Anim. Pr. 53, 147–154 (2012). Article CAS Google Scholar Carroll, K. C., Burnham, C. D. & Westblade, L. F. From canines to humans: clinical importance of Staphylococcus pseudintermedius. PLoS Pathog. 17,…
Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo
Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…
Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection
Bacterial strains and phages Escherichia coli DH5a was routinely grown in Lysogeny broth (LB) medium and used for plasmid cloning, while E. coli BL21 (DE3) was used for protein production and the in vivo assays. E. coli phages T5, T7 and Lambda-vir are gifts from Shi Chen lab (Wuhan University,…
Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species
Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, et al. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol. 2021;166:2633–48. Article CAS PubMed Google Scholar Koonin EV, Dolja VV,…
Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock
A total of 178 samples were collected from livestock production systems and were screened for Enterococcus using bile esculin azide agar selective media. Based on the phenotypic colony morphology of brown and a black halo shape, 24 isolates (13.5%) were presumptively identified as Enterococcus spp. The isolates were identified using…
Genetic diversity and phylogenetic analyses of Asian lineage Zika virus whole genome sequences derived from Culex quinquefasciatus mosquitoes and urine of patients during the 2020 epidemic in Thailand
Hayes, E. B. Zika virus outside Africa. Emerg. Infect. Dis. 15(9), 1347–1350. doi.org/10.3201/eid1509.090442 (2009). Article PubMed PubMed Central Google Scholar Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis. 8(1), e2636. doi.org/10.1371/journal.pntd.0002636 (2014). Article CAS PubMed PubMed Central Google…
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…
Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps
de Jonge, P. A., Nobrega, F. L., Brouns, S. J. J. & Dutilh, B. E. Molecular and evolutionary determinants of bacteriophage host range. Trends Microbiol. 27, 51–63 (2019). Article PubMed Google Scholar Cambillau, C. Bacteriophage module reshuffling results in adaptive host range as exemplified by the baseplate model of listerial…
Genomic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae
Introduction Klebsiella pneumoniae (K. pneumoniae), which belongs to the family Enterobacteriaceae, is a common nosocomial pathogen that causes a variety of human infections, including bloodstream infection, respiratory tract infection, urinary tract infection, and abdominal infection.1,2 Carbapenems are generally considered to be a last choice for the treatment of multi-drug resistant…
EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets | BMC Bioinformatics
EasyCGTree was implemented in Perl programming languages (www.perl.org/) and was built using a collection of published reputable tools, including Clustal Omega version 1.2.4 [12]; consense from PHYLIP version 3.698 [13]; FastTree version 2.1 [14]; hmmbuild and hmmsearch from HMMER version 3.0 (hmmer.org/); IQ-TREE version 2.1.1 [15]; trimAl version 1.2 [16];…
Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos
Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…
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:…
Virulence Characteristics of Salmonella Enteritidis
Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…
Genomic insights into Bacillus subtilis MBB3B9 mediated aluminium stress mitigation for enhanced rice growth
Bian, M. et al. Development of gene-specific markers for acid soil/aluminium tolerance in barley (Hordeum vulgare L.). Mol. Breed. 32, 155–164 (2013). Article CAS Google Scholar Kochian, L. V., Piñeros, M. A., Liu, J. & Magalhaes, J. V. Plant adaptation to acid soils: The molecular basis for crop aluminum resistance….
Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago
Nutman, P. S. Centenary lecture. Phil. Trans. R. Soc. B 317, 69–106 (1987). Google Scholar Kelly, S., Radutoiu, S. & Stougaard, J. Legume LysM receptors mediate symbiotic and pathogenic signalling. Curr. Opin. Plant Biol. 39, 152–158 (2017). Article CAS PubMed Google Scholar Roy, S. et al. Celebrating 20 years of…
A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins
Construction of integrated PCEG and PCEP To the best of our knowledge, the present study is the first to develop a comprehensive catalog of plastic-contaminated soils using an integrated bioinformatic workflow. Five datasets were used to produce 53,300,583 unique genes and proteins. Quality control of reads, trimming, assembly, and binning…
Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis
Neilson, J. W. et al. Significant impacts of increasing aridity on the arid soil microbiome. mSystems 2, e00195–e00116 (2017). Article CAS PubMed PubMed Central Google Scholar Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA 109, 21390–21395 (2012). Article …
Extensive natural Agrobacterium-induced transformation in the genus Camellia
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. doi.org/10.1016/S0022-2836(05)80360-2 Article CAS PubMed Google Scholar Cai Y, Meng J, Cui Y, Tian M, Shi Z, Wang J (2022) Transcriptome and targeted hormone metabolome reveal the molecular mechanisms of flower…
A whole new order of bacteria could hold the key to improving biogas production
(A) Dendrogram of all the HQ and GQ MAGs from MICRO4BIOGAS (n=1053), computed with UBCG and visualized with iTOL. The legend shows a classification by different colors corresponding to different phyla, according to the annotation obtained with GTDB-tk (v 2.1.1), and a highlight on MBA03 (within Bacillota). (B) Tree with…
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…
Analysis of drug-resistance characteristics of MDR-TB
Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), continues to pose a significant global public health challenge.1–3 In 2021, there were 10.6 million new TB cases worldwide, with China accounting for 780,000 cases, making it the third highest burden country for TB globally.4 The World Health Organization (WHO) estimates that…
Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections | BMC Genomics
Sheu CC, Chang YT, Lin SY, Chen YH, Hsueh PR. Infections Caused by Carbapenem-Resistant Enterobacteriaceae: An Update on Therapeutic Options. Front Microbiol. 2019;10:80. Article PubMed PubMed Central Google Scholar HammoudiHalat D, Ayoub Moubareck C. The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel)….
Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater | BMC Microbiology
Hydrogeochemical properties of the arsenic-contaminated groundwater The hydrological and geochemical properties of the analyzed GW samples are summarized in Table 2. Temperature, pH, and dissolved oxygen (DO) levels were within acceptable limits for drinking water in all samples. The average temperature and pH of the As-contaminated GW samples were 27.33°C…
Interrogating the viral dark matter of the rumen ecosystem with a global virome database
Gregory, A. C. et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell 177, 1109–1123.e1114 (2019). Article CAS PubMed PubMed Central Google Scholar Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016). Article CAS PubMed Google Scholar Camarillo-Guerrero, L….
Genomic Identified PenR E151V Substitution in BCC
Ya-Chun Liao,1 Yao-Ting Huang,2,* Chien-Hao Tseng,1 Chia-Wei Liu,1 Po-Yu Liu1,3,4,* 1Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; 2Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan; 3Department of Post-Baccalaureate Medicine, National Chung Hsing University, Taichung, Taiwan; 4Genome Center for…
Core-genome multilocus sequence typing for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri
Xanthomonas citri subsp. citri is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry. X. citri subspecies and pathovars are responsible for diseases in soybean, common bean, mango, pomegranate, and cashew. X. citri disease has been tracked using several typing methods, but recent studies…
Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle
Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article CAS PubMed PubMed Central Google Scholar Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…
Multidrug-resistant Providencia rettgeri strain YQ150713.
Introduction Providencia rettgeri is a Gram-negative opportunistic human pathogenic bacterium that belongs to the Proteae bacteria. It is a pathogen commonly found in the hospitals that mainly cause urinary tract infections, pneumonia, bacteremia, neonatal sepsis, eye infections, meningitis, endocarditis, and diarrhea.1–3 The pathogen Providencia rettgeri demonstrates inherent resistance to numerous…
Comparative analysis of carbapenem-resistant K. pneumoniae
Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…
Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species
Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, et al. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun. 2023;14:1127. Article CAS PubMed PubMed Central Google Scholar Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, et…
The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses | Parasites & Vectors
Cowie RH. Annotated catalogue of species of Angiostrongylus and the related genera Gallegostrongylus, Rodentocaulus and Stefanskostrongylus (Nematoda: Metastrongyloidea, Angiostrongylidae). J Helminthol. 2019;93:389–423. Article PubMed Google Scholar de Almeida LR, de Souza JGR, Santos HA, Torres EJL, Vilela R, do V, Cruz OMS, et al. Angiostrongylus minasensis n. sp.: new species…
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 and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community
Dwiyanto, J. et al. Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia. PLoS ONE 17, e0265142 (2022). Article CAS PubMed PubMed Central Google Scholar Farrugia, D. N. et al. The complete genome and phenome of a community-acquired Acinetobacter baumannii. PLoS ONE 8,…
PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes
Salipante, S. J. & Horwitz, M. S. Phylogenetic fate mapping. Proc. Natl Acad. Sci. USA 103, 5448–5453 (2006). Article CAS PubMed PubMed Central Google Scholar Sulston, J. E., Schierenberg, E., White, J. G. & Thomson, J. N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119…
A predicted CRISPR-mediated symbiosis between uncultivated archaea
Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67 (2010). Article CAS PubMed Google Scholar Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047–1050 (2008). Article CAS PubMed Google…
Microorganisms | Free Full-Text | Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates from Diabetic and Non-Diabetic Patients with Pulmonary Tuberculosis
1. Introduction Globally, about 10 million people are estimated to have developed tuberculosis (TB) in 2020 with eight countries accounting for two-thirds of the global total, with India reporting the largest proportion at 26% [1]. Type 2 diabetes mellitus (DM) is becoming a major public health problem globally, especially in…
Enzyme stabilization and thermotolerance function of the intrinsically disordered LEA2 proteins from date palm
Hernández-Sánchez, et al. LEAfing through literature: Late embryogenesis abundant proteins coming of age-achievements and perspectives. J. Exp. Bot. 73, 6525–6546 (2020). Article Google Scholar Graether, S. P. Proteins involved in plant dehydration protection: The late embryogenesis abundant family. Biomolecules 12, 1380 (2022). Article CAS PubMed PubMed Central Google Scholar Dure,…
Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution
Lieph, R., Veloso, F. A. & Holmes, D. S. Thermophiles like hot T. Trends Microbiol. 14, 423–426 (2006). Article CAS PubMed Google Scholar Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015). Article CAS PubMed Google Scholar Kato, S. et…
Insights into peculiar fungal LPMO family members holding a short C-terminal sequence reminiscent of phosphate binding motifs
Floudas, D. et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336, 1715–1719 (2012). Article ADS CAS PubMed Google Scholar Bissaro, B., Várnai, A., Røhr, Å. K. & Eijsink, V. G. H. Oxidoreductases and reactive oxygen species in conversion of lignocellulosic biomass. Microbiol. Mol…
Global scale phylogeography of functional traits and microdiversity in Prochlorococcus
Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. metaSNV: a tool for metagenomic strain level analysis. PLoS ONE. 2017;12:1–9. Article Google Scholar Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11:2639–43. Article PubMed PubMed…
Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring
Pavlov AA, Brown LL, Kasting JF. UV shielding of NH3 and O2 by organic hazes in the Archean atmosphere. J Geophys Res Atmos. 2001;106:23267–87. Article CAS Google Scholar Zahnle KJ. Earth’s earliest atmosphere. Elements. 2006;2:217–22. Article CAS Google Scholar Arias P, Bellouin N, Coppola E, Jones R, Krinner G, Marotzke…
Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor
Crutzen, P. J. The influence of nitrogen oxides on the atmospheric ozone content. Q. J. R. Meteorol. Soc. 96, 320–325 (1970). Article Google Scholar Johnston, H. Reduction of stratospheric ozone by nitrogen oxide catalysts from supersonic transport exhaust. Science 173, 517–522 (1971). Article CAS PubMed Google Scholar Hughes, M. N….
Differential contribution of nitrifying prokaryotes to groundwater nitrification
Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76. Article CAS PubMed Google Scholar Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol. 2018;103:177–89. Article PubMed PubMed Central Google Scholar Lehtovirta-Morley LE Ammonia oxidation: ecology,…
Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities
Rantanen M, Karpechko AY, Lipponen A, Nordling K, Hyvärinen O, Ruosteenoja K, et al. The Arctic has warmed nearly four times faster than the globe since 1979. Commun Earth Environ. 2022;3:1–10. Article Google Scholar Kwok R. Arctic sea ice thickness, volume, and multiyear ice coverage: losses and coupled variability (1958–2018)….
C. ramosum in immunocompetent patient with SARS-CoV-2
Introduction Clostridium ramosum was first identified and characterized in 1898 following its isolation from a patient with pulmonary gangrene and appendicitis.1 This species, initially identified as Bacillus ramosum and later referred to as C. ramosum, was renamed Erysipelatoclostridium ramosum in 2013.2 However, its taxonomic name has not been legally published…
Parallel and convergent genomic changes underlie independent subterranean colonization across beetles
Conway Morris, S. The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften 96, 1313–1337 (2009). Article ADS CAS PubMed Google Scholar Stern, D. L. The genetic causes of convergent evolution. Nat. Rev. Genet. 14, 751–764 (2013). Article CAS PubMed Google Scholar Christiansen, K. Convergence and parallelism in cave entomobryinae….
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…
Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence
Begier, E. et al. Epidemiology of invasive Escherichia coli infection and antibiotic resistance status among patients treated in US hospitals: 2009-2016. Clin. Infect. Dis. Publ. Infect. Dis. Soc. Am. 73, 565–574 (2021). Article CAS Google Scholar Bélanger, L. et al. Escherichia coli from animal reservoirs as a potential source of…
Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16:410–22. doi.org/10.1038/s41579-018-0029-9. Article CAS PubMed Google Scholar Blaxter M. Counting angels with DNA. Nature. 2003;421:122–3. doi.org/10.1038/421122a. Article CAS PubMed Google Scholar Cordier T, Alonso-Sáez L, Apothéloz-Perret-Gentil L, Aylagas…
Growth rate is a dominant factor predicting the rhizosphere effect
Rhizosphere bacteria have shorter predicted doubling times than soil bacteria To investigate whether growth rate potential predictions correlate with rhizosphere enrichment, we re-analyzed previously published metacommunities. These included rhizospheres and associated bulk soil microbiomes from 18 different plant genotypes and conditions such as: Arabidopsis thaliana ecotypes and sister species [9],…
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…
Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR
Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…
High speciation rate of niche specialists in hot springs
Shock EL, Holland M, Meyer-Dombard DA, Amend JP, Osburn GR, Fischer TP. Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA. Geochim Cosmochim Acta. 2010;74:4005–43. Article CAS Google Scholar Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, et al. A comprehensive census…
Genomic characteristics of ESBL-producing E. coli in China
Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…
A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea
Lederberg, J., Cavalli, L. L. & Lederberg, E. M. Sex compatibility in Escherichia Coli. Genetics 37, 720–730 (1952). Article CAS PubMed PubMed Central Google Scholar Elisabeth, G., Günther, M. & Manuel, E. Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 277–301 (2003). Article Google Scholar de la…
Acquisition and carriage of genetically diverse multi-drug resistant gram-negative bacilli in hospitalised newborns in The Gambia
United Nations Inter-agency Group for Child Mortality Estimation. Levels & Trends in Child Mortality: Report 2020, Estimates developed by the United Nations Inter-agency Group for Child Mortality Estimation. New York: United Nations Children’s Fund; 2020. Okomo, U. et al. Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in…
Distribution and diversity of ‘Tectomicrobia’, a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites
Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–69. CAS PubMed PubMed Central Google Scholar Konstantinidis K, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406. PubMed PubMed Central Google Scholar Parks…
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains
Kiu, R. & Hall, L. J. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg. Microbes Infect. 7, 141 (2018). Article PubMed PubMed Central Google Scholar Li, J., Paredes-Sabja, D., Sarker, M. R. & McClane, B. A. Clostridium perfringens sporulation and sporulation-associated toxin production. Microbiol. Spectr. doi.org/10.1128/microbiolspec.TBS-0022-2015…
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae
Elston KM, Leonard SP, Geng P, Bialik SB, Robinson E, Barrick JE. Engineering insects from the endosymbiont out. Trends Microbiol. 2022;30:79–96. Article CAS PubMed Google Scholar Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, et al. Engineered integrative and conjugative elements for efficient and inducible DNA…
Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation
Borzi, A. Le communicazioni intracellulari delle nostochinee. Malpighia – Rassegna mensuale di botanica 1 (1886–1887). Simon, R. D. Cyanophycin granules from the blue-green alga anabaena cylindrica: A reserve material consisting of copolymers of aspartic acid and arginine. Proc. Natl. Acad. Sci. U. S. A. 68, 265–267 (1971). Article ADS CAS …
The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase
Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…
An unusual tandem kinase fusion protein confers leaf rust resistance in wheat
Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…
Genomic and phylogenetic analysis of Klebsiella michiganens
Introduction Multidrug-resistant Enterobacteriaceae infection is a severe threat to public health that is worsening globally and is associated with increasing mortality rates.1 Klebsiella pneumoniae is a significant pathogen that contributes to the dissemination of multidrug-resistant strains in healthcare environments.2 K. michiganensis is a novel specie of pathogenic Klebsiella genus. Since…
Apoptotic gene loss in Cnidaria is associated with transition to parasitism
Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article CAS PubMed PubMed Central Google Scholar Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article CAS PubMed PubMed Central Google Scholar Alberts, B., Johnson, A. & Lewis, J….
HMSS2: an advanced tool for the analysis of sulfur metabolism, including organosulfur compound transformation, in genome and metagenome assemblies
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,…
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 …
Whole spectrum of Aeromonas hydrophila virulence determinants and the identification of novel SNPs using comparative pathogenomics
FAO. The State of World Fisheries and Aquaculture 2022. (FAO, 2022). doi.org/10.4060/cc0461en. Marinho-Neto, F. A. et al. Morphological, microbiological and ultrastructural aspects of sepsis by Aeromonas hydrophila in Piaractus mesopotamicus. PLoS ONE 14, 1–20 (2019). Google Scholar Shirajum-Monir, M., Yusoff, S. M., Mohamad, A. & Ina-Salwany, M. Y. Vaccination of…
Resistance of Nosocomial Acinetobacter baumannii
Chenxing Wei,1,* Jian Chen,1,* Tanveer Muhammad Anwar,2,* Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…
Genome-wide identification and comparative analysis of Dmrt genes in echinoderms
Kopp, A. Dmrt genes in the development and evolution of sexual dimorphism. Trends Genet. 28, 175–184 (2012). Article CAS PubMed PubMed Central Google Scholar Zarkower, D. DMRT genes in vertebrate gametogenesis. Curr. Top. Dev. Biol. 102, 327–356 (2013). Article CAS PubMed Google Scholar Zhang, T. & Zarkower, D. DMRT proteins…
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…
Ceftriaxone resistant Salmonella enterica serovar Paratyphi A identified in a case of enteric fever: first case report from Pakistan | BMC Infectious Diseases
Typhoid GBD, Paratyphoid C. The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Infect Dis. 2019;19(4):369–81. Article Google Scholar Arndt MB, Mosites EM, Tian M, Forouzanfar MH, Mokhdad AH, Meller M, Ochiai RL, Walson JL. Estimating the burden of…
A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
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)….
Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter
PhnD1 proteins in picocyanobacteria are lineage partitioned The predicted phosphonate-binding protein (PhnD1) under study is found within the genome of all 97 sequenced picocyanobacteria strains in the Cyanorak database, comprising cluster CK_860 [20]. While the gene encoding PhnD1 is highly conserved among all picocyanobacterial genomes, our phylogenetic tree reveals it…
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting
Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article CAS PubMed Google Scholar Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…
Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay
Faulde, M. K., Rueda, L. M. & Khaireh, B. A. First record of the Asian malaria vector Anopheles stephensi and its possible role in the resurgence of malaria in Djibouti Horn of Africa. Acta Trop. 139, 39–43 (2014). Article PubMed Google Scholar R, A. et al. Confirmation of the presence…
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….
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…
Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli
Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004). Article CAS PubMed Google Scholar Nataro, J. P. & Kaper, J. B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11, 142–201 (1998). Article CAS PubMed PubMed Central Google Scholar Croxen, M. A….
A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans | BMC Biology
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51. Article CAS PubMed PubMed Central Google Scholar Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, et al. Evolutionary relationships of wild hominids recapitulated…
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…