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…

Continue Reading Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein | Parasites & Vectors

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…

Continue Reading Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

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…

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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…

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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…

Continue Reading Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes

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….

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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…

Continue Reading Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis

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…

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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)….

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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…

Continue Reading Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius

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…

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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…

Continue Reading Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

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…

Continue Reading Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

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…

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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 …

Continue Reading Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau

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)                                                          …

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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),…

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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,…

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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…

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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,…

Continue Reading Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection

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,…

Continue Reading Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species

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…

Continue Reading Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock

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…

Continue Reading 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

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…

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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…

Continue Reading Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales

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…

Continue Reading Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps

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…

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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];…

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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…

Continue Reading Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos

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:…

Continue Reading Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease | Genome Biology

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…

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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….

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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…

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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…

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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 …

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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…

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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…

Continue Reading A whole new order of bacteria could hold the key to improving biogas production

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 …

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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…

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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…

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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)….

Continue Reading Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections | BMC Genomics

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…

Continue Reading Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater | BMC Microbiology

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….

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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…

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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…

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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…

Continue Reading Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle

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…

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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…

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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…

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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…

Continue Reading The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses | Parasites & Vectors

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…

Continue Reading Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China

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,…

Continue Reading Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community

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…

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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…

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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…

Continue Reading Microorganisms | Free Full-Text | Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates from Diabetic and Non-Diabetic Patients with Pulmonary Tuberculosis

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,…

Continue Reading Enzyme stabilization and thermotolerance function of the intrinsically disordered LEA2 proteins from date palm

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…

Continue Reading Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution

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…

Continue Reading Insights into peculiar fungal LPMO family members holding a short C-terminal sequence reminiscent of phosphate binding motifs

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…

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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…

Continue Reading Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring

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….

Continue Reading Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor

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,…

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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)….

Continue Reading Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

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…

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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….

Continue Reading Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

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…

Continue Reading A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination

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…

Continue Reading Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence

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…

Continue Reading Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors

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],…

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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…

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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…

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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…

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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…

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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…

Continue Reading A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea

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…

Continue Reading Acquisition and carriage of genetically diverse multi-drug resistant gram-negative bacilli in hospitalised newborns in The Gambia

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…

Continue Reading Distribution and diversity of ‘Tectomicrobia’, a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites

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…

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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…

Continue Reading The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae

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 …

Continue Reading Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation

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…

Continue Reading The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

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…

Continue Reading An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

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…

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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….

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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,…

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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 …

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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…

Continue Reading Whole spectrum of Aeromonas hydrophila virulence determinants and the identification of novel SNPs using comparative pathogenomics

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…

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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…

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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…

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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…

Continue Reading Ceftriaxone resistant Salmonella enterica serovar Paratyphi A identified in a case of enteric fever: first case report from Pakistan | BMC Infectious Diseases

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)….

Continue Reading A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

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…

Continue Reading Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter

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…

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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…

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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…

Continue Reading Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay

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….

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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…

Continue Reading The persistence and stabilization of auxiliary genes in the human skin virome | Virology Journal

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….

Continue Reading Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli

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…

Continue Reading A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans | BMC Biology

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…

Continue Reading A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes