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1.
Food Microbiol ; 122: 104532, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38839238

RESUMO

Penicillium spp. produce a great variety of secondary metabolites, including several mycotoxins, on food substrates. Chestnuts represent a favorable substrate for Penicillium spp. development. In this study, the genomes of ten Penicillium species, virulent on chestnuts, were sequenced and annotated: P. bialowiezense. P. pancosmium, P. manginii, P. discolor, P. crustosum, P. palitans, P. viridicatum, P. glandicola, P. taurinense and P. terrarumae. Assembly size ranges from 27.5 to 36.8 Mb and the number of encoded genes ranges from 9,867 to 12,520. The total number of predicted biosynthetic gene clusters (BGCs) in the ten species is 551. The most represented families of BGCs are non ribosomal peptide synthase (191) and polyketide synthase (175), followed by terpene synthases (87). Genome-wide collections of gene phylogenies (phylomes) were reconstructed for each of the newly sequenced Penicillium species allowing for the prediction of orthologous relationships among our species, as well as other 20 annotated Penicillium species available in the public domain. We investigated in silico the presence of BGCs for 10 secondary metabolites, including 5 mycotoxins, whose production was validated in vivo through chemical analyses. Among the clusters present in this set of species we found andrastin A and its related cluster atlantinone A, mycophenolic acid, patulin, penitrem A and the cluster responsible for the synthesis of roquefortine C/glandicoline A/glandicoline B/meleagrin. We confirmed the presence of these clusters in several of the Penicillium species conforming our dataset and verified their capacity to synthesize them in a chestnut-based medium with chemical analysis. Interestingly, we identified mycotoxin clusters in some species for the first time, such as the andrastin A cluster in P. flavigenum and P. taurinense, and the roquefortine C cluster in P. nalgiovense and P. taurinense. Chestnuts proved to be an optimal substrate for species of Penicillium with different mycotoxigenic potential, opening the door to risks related to the occurrence of multiple mycotoxins in the same food matrix.


Assuntos
Genoma Fúngico , Família Multigênica , Micotoxinas , Penicillium , Filogenia , Metabolismo Secundário , Penicillium/genética , Penicillium/metabolismo , Micotoxinas/metabolismo , Micotoxinas/genética , Contaminação de Alimentos/análise , Patulina/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Nozes/microbiologia , Policetídeo Sintases/genética , Policetídeo Sintases/metabolismo , Microbiologia de Alimentos , Corylus/microbiologia , Compostos Heterocíclicos de 4 ou mais Anéis , Indóis , Piperazinas
2.
Microbes Environ ; 39(2)2024.
Artigo em Inglês | MEDLINE | ID: mdl-38839365

RESUMO

Shigella species are a group of highly transmissible Gram-negative pathogens. Increasing reports of infection with extensively drug-resistant varieties of this stomach bug has convinced the World Health Organization to prioritize Shigella for novel therapeutic interventions. We herein coupled the whole-genome sequencing of a natural isolate of Shigella flexneri with a pangenome ana-lysis to characterize pathogen genomics within this species, which will provide us with an insight into its existing genomic diversity and highlight the root causes behind the emergence of quick vaccine escape variants. The isolated novel strain of S. flexneri contained ~4,500 protein-coding genes, 57 of which imparted resistance to antibiotics. A comparative pan-genomic ana-lysis revealed genomic variability of ~64%, the shared conservation of core genes in central metabolic processes, and the enrichment of unique/accessory genes in virulence and defense mechanisms that contributed to much of the observed antimicrobial resistance (AMR). A pathway ana-lysis of the core genome mapped 22 genes to 2 antimicrobial resistance pathways, with the bulk coding for multidrug efflux pumps and two component regulatory systems that are considered to work synergistically towards the development of resistance phenotypes. The prospective evolvability of Shigella species as witnessed by the marked difference in genomic content, the strain-specific essentiality of unique/accessory genes, and the inclusion of a potent resistance mechanism within the core genome, strengthens the possibility of novel serotypes emerging in the near future and emphasizes the importance of tracking down genomic diversity in drug/vaccine design and AMR governance.


Assuntos
Antibacterianos , Genoma Bacteriano , Genômica , Shigella flexneri , Águas Residuárias , Shigella flexneri/genética , Shigella flexneri/isolamento & purificação , Shigella flexneri/classificação , Shigella flexneri/efeitos dos fármacos , Genoma Bacteriano/genética , Águas Residuárias/microbiologia , Antibacterianos/farmacologia , Filogenia , Sequenciamento Completo do Genoma , Farmacorresistência Bacteriana Múltipla/genética , Virulência/genética
3.
Microbes Environ ; 39(5)2024.
Artigo em Inglês | MEDLINE | ID: mdl-38839370

RESUMO

Microbiologically influenced corrosion refers to the corrosion of metal materials caused or promoted by microorganisms. Although some novel iron-corrosive microorganisms have been discovered in various manmade and natural freshwater and seawater environments, microbiologically influenced corrosion in the deep sea has not been investigated in detail. In the present study, we collected slime-like precipitates composed of corrosion products and microbial communities from a geochemical reactor set on an artificial hydrothermal vent for 14.5 months, and conducted culture-dependent and -independent microbial community ana-lyses with corrosive activity measurements. After enrichment cultivation at 37, 50, and 70°C with zero-valent iron particles, some of the microbial consortia showed accelerated iron dissolution, which was approximately 10- to 50-fold higher than that of the abiotic control. In a comparative ana-lysis based on the corrosion acceleration ratio and amplicon sequencing of the 16S rRNA gene, three types of corrosion were estimated: the methanogen-induced type, methanogen-sulfate-reducing bacteria cooperative type, and sulfate-reducing Firmicutes-induced type. The methanogen-induced and methanogen-sulfate-reducing bacteria cooperative types were observed at 50°C, while the sulfate-reducing Firmicutes-induced type was noted at 37°C. The present results suggest the microbial components associated with microbiologically influenced corrosion in deep-sea hydrothermal systems, providing important insights for the development of future deep-sea resources with metal infrastructures.


Assuntos
Bactérias , Fontes Hidrotermais , Ferro , Consórcios Microbianos , RNA Ribossômico 16S , Água do Mar , Corrosão , Ferro/metabolismo , Ferro/química , Água do Mar/microbiologia , Água do Mar/química , RNA Ribossômico 16S/genética , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Bactérias/isolamento & purificação , Fontes Hidrotermais/microbiologia , Filogenia
4.
Syst Parasitol ; 101(4): 44, 2024 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-38839661

RESUMO

Species of Diolcogaster parasitize Lepidoptera pests of commercial plants. The diversity of this genus is high, but few species of Diolcogaster have been described. The description of a new Diolcogaster species provides information for the biological control using this insect. This study presents the description and key notes on the biology of a new Diolcogaster parasitoid wasp. This species was reared from a caterpillar of Hypercompe brasiliensis collected after feeding on a Gloxinia perennis plant important to floriculture. Two complementary identification analyzes were performed on Diolcogaster adult bodies. The first was the analyses of its external morphology and the second its molecular analysis (mitochondrial DNA). The morphological analysis defined the insect as a new species of Diolcogaster, named Diolcogaster joanesi sp. nov. A maximum-likelihood (ML) analysis partially confirmed the morphological analysis, placing D. joanesi within a cluster including a previously identified species (Diolcogaster choi) and seven other morphospecies. The proximity of D. joanesi to D. choi is discussed and an updated key for all New World species of the xanthaspis group is provided. Twenty-eight adult wasps were obtained (22 females and six males) out of 50 cocoons which larvae emerged from the caterpillar host. The findings contribute to the broader understanding of Diolcogaster in the Neotropics and its potential for the biological control of lepidopteran defoliators.


Assuntos
Controle Biológico de Vetores , Especificidade da Espécie , Vespas , Animais , Brasil , Vespas/classificação , Vespas/anatomia & histologia , Mariposas/parasitologia , Lepidópteros/parasitologia , Filogenia , Larva , Feminino
5.
Artigo em Inglês | MEDLINE | ID: mdl-38842428

RESUMO

In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.


Assuntos
Técnicas de Tipagem Bacteriana , Campylobacter , DNA Bacteriano , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , RNA Ribossômico 16S/genética , Campylobacter/genética , Campylobacter/classificação , Campylobacter/isolamento & purificação , Animais , DNA Bacteriano/genética , Suínos , Ruminantes/microbiologia
6.
J Med Virol ; 96(6): e29711, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38847304

RESUMO

The emerging evidence of human infections with emerging viruses suggests their potential public health importance. A novel taxon of viruses named Statoviruses (for stool-associated Tombus-like viruses) was recently identified in the gastrointestinal tracts of multiple mammals. Here we report the discovery of respiratory Statovirus-like viruses (provisionally named Restviruses) from the respiratory tracts of five patients experiencing acute respiratory disease with Human coronavirus OC43 infection through the retrospective analysis of meta-transcriptomic data. Restviruses shared 53.1%-98.8% identities of genomic sequences with each other and 39.9%-44.3% identities with Statoviruses. The phylogenetic analysis revealed that Restviruses together with a Stato-like virus from nasal-throat swabs of Vietnamese patients with acute respiratory disease, formed a well-supported clade distinct from the taxon of Statoviruses. However, the consistent genome characteristics of Restviruses and Statoviruses suggested that they might share similar evolutionary trajectories. These findings warrant further studies to elucidate the etiological and epidemiological significance of the emerging Restviruses.


Assuntos
Genoma Viral , Filogenia , Infecções Respiratórias , Humanos , China/epidemiologia , Genoma Viral/genética , Infecções Respiratórias/virologia , Infecções Respiratórias/epidemiologia , Masculino , Feminino , Estudos Retrospectivos , Sistema Respiratório/virologia , Pré-Escolar , Adulto , Criança , RNA Viral/genética , Pessoa de Meia-Idade
7.
Microb Genom ; 10(6)2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38847800

RESUMO

Sequence comparison of 16S rRNA PCR amplicons is an established approach to taxonomically identify bacterial isolates and profile complex microbial communities. One potential application of recent advances in long-read sequencing technologies is to sequence entire rRNA operons and capture significantly more phylogenetic information compared to sequencing of the 16S rRNA (or regions thereof) alone, with the potential to increase the proportion of amplicons that can be reliably classified to lower taxonomic ranks. Here we describe GROND (Genome-derived Ribosomal Operon Database), a publicly available database of quality-checked 16S-ITS-23S rRNA operons, accompanied by multiple taxonomic classifications. GROND will aid researchers in analysis of their data and act as a standardised database to allow comparison of results between studies.


Assuntos
Bactérias , Filogenia , RNA Ribossômico 16S , RNA Ribossômico 16S/genética , Bactérias/genética , Bactérias/classificação , RNA Ribossômico 23S/genética , Óperon , Óperon de RNAr/genética , Bases de Dados Genéticas , Bases de Dados de Ácidos Nucleicos , Análise de Sequência de DNA/métodos
8.
Arch Virol ; 169(7): 137, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38847873

RESUMO

The present study focuses on the pathological and molecular characterization of African swine fever virus (ASFV) associated with an outbreak in wild boars in two national parks in southern India in 2022-2023. Significant mortality was observed among free-ranging wild boars at Bandipur National Park, Karnataka, and Mudumalai National Park, Tamil Nadu. Extensive combing operations were undertaken in both national parks, spanning an area of around 100 km2, originating from the reported epicenter, to estimate the mortality rate. Recovered carcasses were pathologically examined, and ASFV isolates was genetically characterized. Our findings suggested spillover infection of ASFV from nearby domestic pigs, and the virus was equally pathogenic in wild boars and domestic pigs. ASFV intrusion was reported in the Northeastern region of the country, which borders China and Myanmar, whereas the current outbreak is very distantly located, in southern India. Molecular data will help in tracing the spread of the virus in the country.


Assuntos
Vírus da Febre Suína Africana , Febre Suína Africana , Surtos de Doenças , Sus scrofa , Animais , Vírus da Febre Suína Africana/genética , Vírus da Febre Suína Africana/isolamento & purificação , Índia/epidemiologia , Suínos , Febre Suína Africana/virologia , Febre Suína Africana/epidemiologia , Febre Suína Africana/mortalidade , Sus scrofa/virologia , Surtos de Doenças/veterinária , Filogenia , Animais Selvagens/virologia
9.
Arch Virol ; 169(7): 136, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38847927

RESUMO

Here, we report the first detection of lymphocystis disease virus (LCDV) in Indian glass fish in the Andaman Islands, India. Microscopic examination revealed the presence of whitish clusters of nodules on the fish's skin, fins, and eyes. The histopathology of the nodules revealed typical hypertrophied fibroblasts. Molecular characterization of the major capsid protein (MCP) gene of the virus showed a significant resemblance to known LCDV sequences from Korea and Iran, with 98.92% and 97.85% sequence identity, respectively. Phylogenetic analysis confirmed that the MCP gene sequence of the virus belonged to genotype V. This study represents the first documented case of LCDV in finfish from the Andaman Islands, emphasizing the necessity for continued monitoring and research on the health of aquatic species in this fragile ecosystem.


Assuntos
Proteínas do Capsídeo , Infecções por Vírus de DNA , Doenças dos Peixes , Iridoviridae , Filogenia , Animais , Doenças dos Peixes/virologia , Índia , Iridoviridae/genética , Iridoviridae/isolamento & purificação , Iridoviridae/classificação , Infecções por Vírus de DNA/virologia , Infecções por Vírus de DNA/veterinária , Proteínas do Capsídeo/genética , Peixes/virologia , Genótipo , Ilhas
10.
PLoS One ; 19(6): e0301343, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38833478

RESUMO

The dinoflagellate Alexandrium catenella is a well-known paralytic shellfish toxin producer that forms harmful algal blooms, repeatedly causing damage to Chilean coastal waters. The causes and behavior of algal blooms are complex and vary across different regions. As bacterial interactions with algal species are increasingly recognized as a key factor driving algal blooms, the present study identifies several bacterial candidates potentially associated with Chilean Alexandrium catenella. This research narrowed down the selection of bacteria from the Chilean A. catenella culture using antibiotic treatment and 16S rRNA metabarcoding analysis. Subsequently, seawater from two Chilean coastal stations, Isla Julia and Isla San Pedro, was monitored for two years to detect Alexandrium species and the selected bacteria, utilizing 16S and 18S rRNA gene metabarcoding analyses. The results suggested a potential association between Alexandrium species and Spongiibacteraceae at both stations. The proposed candidate bacteria within the Spongiibacteraceae family, potentially engaging in mutualistic relationships with Alexandrium species, included the genus of BD1-7 clade, Spongiibbacter, and Zhongshania.


Assuntos
Dinoflagellida , RNA Ribossômico 16S , Simbiose , Dinoflagellida/genética , Dinoflagellida/fisiologia , Chile , RNA Ribossômico 16S/genética , Bactérias/genética , Bactérias/classificação , Proliferação Nociva de Algas , Água do Mar/microbiologia , Filogenia , RNA Ribossômico 18S/genética
11.
PLoS One ; 19(6): e0304621, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38833480

RESUMO

Salmonella enteritidis is a main pathogen responsible for sporadic outbreaks of gastroenteritis, and therefore is an important public health problem. This study investigated the drug resistance and genomic characteristics of S. enteritidis isolated from clinical and food sources in Huzhou, Zhejiang Province, China, from February 1, 2021, to December 30, 2023. In total, 43 S. enteritidis strains isolated during the study period were subjected to virulence gene, drug resistance gene, genetic correlation, antibiotic resistance, and multilocus sequence typing analyses. All 43 isolates were identified as ST11, and contained 108 virulence-related genes. Drug sensitivity analysis of the 43 isolates showed resistance rates of 100% to nalidixic acid and 90.70% to ampicillin and ampicillin/sulbactam. Multidrug resistance is a serious issue, with 81.40% of strains resistant to three or more antibacterial drugs. Genome sequencing indicated that S. enteritidis possessed 23 drug resistance genes, of which 14 were common to all 43 isolates. Phylogenetic analysis based on core genome single-nucleotide polymorphisms divided the 43 S. enteritidis strains into three clusters, with the 10 samples from an outbreak forming an independent branch located in cluster 3.


Assuntos
Antibacterianos , Genoma Bacteriano , Filogenia , Salmonella enteritidis , Salmonella enteritidis/genética , Salmonella enteritidis/efeitos dos fármacos , Salmonella enteritidis/isolamento & purificação , China/epidemiologia , Antibacterianos/farmacologia , Humanos , Tipagem de Sequências Multilocus , Testes de Sensibilidade Microbiana , Infecções por Salmonella/microbiologia , Infecções por Salmonella/epidemiologia , Infecções por Salmonella/tratamento farmacológico , Farmacorresistência Bacteriana Múltipla/genética , Polimorfismo de Nucleotídeo Único , Farmacorresistência Bacteriana/genética , Sequenciamento Completo do Genoma
12.
Sci Rep ; 14(1): 12774, 2024 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-38834652

RESUMO

The diversity of marine cyanobacteria has been extensively studied due to their vital roles in ocean primary production. However, little is understood about the diversity of cyanobacterial species involved in symbiotic relationships. In this study, we successfully sequenced the complete genome of a cyanobacterium in symbiosis with Citharistes regius, a dinoflagellate species thriving in the open ocean. A phylogenomic analysis revealed that the cyanobacterium (CregCyn) belongs to the marine picocyanobacterial lineage, akin to another cyanobacterial symbiont (OmCyn) of a different dinoflagellate closely related to Citharistes. Nevertheless, these two symbionts are representing distinct lineages, suggesting independent origins of their symbiotic lifestyles. Despite the distinct origins, the genome analyses of CregCyn revealed shared characteristics with OmCyn, including an obligate symbiotic relationship with the host dinoflagellates and a degree of genome reduction. In contrast, a detailed analysis of genome subregions unveiled that the CregCyn genome carries genomic islands that are not found in the OmCyn genome. The presence of the genomic islands implies that exogenous genes have been integrated into the CregCyn genome at some point in its evolution. This study contributes to our understanding of the complex history of the symbiosis between dinoflagellates and cyanobacteria, as well as the genomic diversity of marine picocyanobacteria.


Assuntos
Cianobactérias , Dinoflagellida , Genoma Bacteriano , Filogenia , Simbiose , Dinoflagellida/genética , Dinoflagellida/fisiologia , Simbiose/genética , Cianobactérias/genética , Cianobactérias/classificação , Evolução Molecular
13.
Arch Virol ; 169(7): 134, 2024 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-38834736

RESUMO

Anthrax is an acute infectious zoonotic disease caused by Bacillus anthracis, a bacterium that is considered a potential biological warfare agent. Bacillus bacteriophages shape the composition and evolution of bacterial communities in nature and therefore have important roles in the ecosystem community. B. anthracis phages are not only used in etiological diagnostics but also have promising prospects in clinical therapeutics or for disinfection in anthrax outbreaks. In this study, two temperate B. anthracis phages, vB_BanS_A16R1 (A16R1) and vB_BanS_A16R4 (A16R4), were isolated and showed siphovirus-like morphological characteristics. Genome sequencing showed that the genomes of phages A16R1 and A16R4 are 36,569 bp and 40,059 bp in length, respectively. A16R1 belongs to the genus Wbetavirus, while A16R4 belongs to the genus Hubeivirus and is the first phage of that genus found to lyse B. anthracis. Because these two phages can comparatively specifically lyse B. anthracis, they could be used as alternative diagnostic tools for identification of B. anthracis infections.


Assuntos
Fagos Bacilares , Bacillus anthracis , Genoma Viral , Bacillus anthracis/virologia , Genoma Viral/genética , Fagos Bacilares/isolamento & purificação , Fagos Bacilares/genética , Fagos Bacilares/classificação , Siphoviridae/genética , Siphoviridae/isolamento & purificação , Siphoviridae/classificação , Filogenia
14.
Sci Rep ; 14(1): 12861, 2024 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-38834792

RESUMO

The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.


Assuntos
Evolução Molecular , Genoma Mitocondrial , Filogenia , Animais , Genoma Mitocondrial/genética , Hemípteros/genética , Hemípteros/classificação , RNA de Transferência/genética , RNA Ribossômico/genética
15.
Parasites Hosts Dis ; 62(2): 180-192, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38835259

RESUMO

Free-living amoebae (FLA) are found in diverse environments, such as soils, rivers, and seas. Hence, they can be used as bioindicators to assess the water quality based solely on their presence. In this study, we determined the presence of FLA in river water by filtering water samples collected from various sites and culturing the resulting filtrates. FLA were detected in all the water samples with varying quality grades (Grades Ι-V). The significant increase in the size of the amoebae population with the deterioration in the water quality. Monoxenic cultures of the amoebae were performed, and genomic DNAs were isolated, among which 18S rDNAs were sequenced to identify the amoeba species. Of the 12 species identified, 10 belonged to the Acanthamoeba genus; of the remaining 2 species, one was identified as Vannella croatica and the other as a species of Vermamoeba. Acanthamoeba was detected in samples with Grades Ι to VI quality, whereas the Vermamoeba species was present only in Grade Ι water. V. croatica was found exclusively in water with Grade ΙΙ quality. Following morphological observations, genomic DNA was sequenced using 16S rDNA to determine whether the species of Acanthamoeba harbored endosymbionts. Most of the isolated Acanthamoeba contained endosymbionts, among which 4 species of endogenous bacteria were identified and examined using transmission electron microscopy. This study provides evidence that the distribution of amoebae other than Acanthamoeba may be associated with water quality. However, further confirmation will be required based on accurate water quality ratings and assessments using a more diverse range of FLA.


Assuntos
Amoeba , Qualidade da Água , Amoeba/genética , Amoeba/isolamento & purificação , Amoeba/classificação , Filogenia , Rios/parasitologia , DNA de Protozoário/genética , Acanthamoeba/genética , Acanthamoeba/isolamento & purificação , Acanthamoeba/classificação , RNA Ribossômico 18S/genética , DNA Ribossômico/genética , Biodiversidade , Análise de Sequência de DNA/métodos , RNA Ribossômico 16S/genética
16.
Parasites Hosts Dis ; 62(2): 226-237, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38835263

RESUMO

Ticks, blood-sucking ectoparasites, spread diseases to humans and animals. Haemaphysalis longicornis is a significant vector for tick-borne diseases in medical and veterinary contexts. Identifying protective antigens in H. longicornis for an anti-tick vaccine is a key tick control strategy. Enolase, a multifunctional protein, significantly converts D-2-phosphoglycerate and phosphoenolpyruvate in glycolysis and gluconeogenesis in cell cytoplasm. This study cloned a complete open reading frame (ORF) of enolase from the H. longicornis tick and characterized its transcriptional and silencing effect. We amplified the full-length cDNA of the enolase gene using rapid amplification of cDNA ends. The complete cDNA, with an ORF of 1,297 nucleotides, encoded a 432-amino acid polypeptide. Enolase of the Jeju strain H. longicornis exhibited the highest sequence similarity with H. flava (98%), followed by Dermacentor silvarum (82%). The enolase motifs identified included N-terminal and C-terminal regions, magnesium binding sites, and several phosphorylation sites. Reverse transcription-polymerase chain reaction (RT-PCR) analysis indicated that enolase mRNA transcripts were expressed across all developmental stages of ticks and organs such as salivary gland and midgut. RT-PCR showed higher transcript levels in syn-ganglia, suggesting that synganglion nerves influence enolase,s role in tick salivary glands. We injected enolase double-stranded RNA into adult unfed female ticks, after which they were subsequently fed with normal unfed males until they spontaneously dropped off. RNA interference significantly (P<0.05) reduced feeding and reproduction, along with abnormalities in eggs (no embryos) and hatching. These findings suggest enolase is a promising target for future tick control strategies.


Assuntos
Sequência de Aminoácidos , Clonagem Molecular , Ixodidae , Fosfopiruvato Hidratase , Animais , Fosfopiruvato Hidratase/genética , Fosfopiruvato Hidratase/metabolismo , Ixodidae/genética , Ixodidae/enzimologia , Feminino , Dados de Sequência Molecular , Estágios do Ciclo de Vida/genética , Inativação Gênica , Masculino , Filogenia , Sequência de Bases , DNA Complementar/genética , Haemaphysalis longicornis
17.
Gigascience ; 132024 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-38837945

RESUMO

BACKGROUND: Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant constituents praeruptorin (A-E), are the active constituents in the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies have attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and thus the development of better breeding strategies. RESULTS: A telomere-to-telomere (T2T) genome was assembled for P. praeruptorum by combining PacBio HiFi, ONT ultra-long, and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes with genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced 2 whole-genome duplication events. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins. CONCLUSIONS: A T2T genome for P. praeruptorum was obtained, providing molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.


Assuntos
Apiaceae , Cumarínicos , Genoma de Planta , Telômero , Cumarínicos/metabolismo , Apiaceae/genética , Apiaceae/metabolismo , Telômero/genética , Telômero/metabolismo , Evolução Molecular , Filogenia , Genômica/métodos , Vias Biossintéticas/genética
18.
Gigascience ; 132024 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-38837946

RESUMO

BACKGROUND: Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family. FINDINGS: The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. CONCLUSIONS: The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.


Assuntos
Evolução Molecular , Genoma de Planta , Filogenia , Cromossomos de Plantas , Genômica/métodos , Malvaceae/genética
19.
Environ Microbiol Rep ; 16(3): e13260, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38838099

RESUMO

As part of ongoing efforts to discover novel polyhydroxyalkanoate-producing bacterial species, we embarked on characterizing the thermotolerant species, Paracoccus kondratievae, for biopolymer synthesis. Using traditional chemical and thermal characterization techniques, we found that P. kondratievae accumulates poly(3-hydroxybutyrate) (PHB), reaching up to 46.8% of the cell's dry weight after a 24-h incubation at 42°C. Although P. kondratievae is phylogenetically related to the prototypical polyhydroxyalkanoate producer, Paracoccus denitrificans, we observed significant differences in the PHB production dynamics between these two Paracoccus species. Notably, P. kondratievae can grow and produce PHB at elevated temperatures ranging from 42 to 47°C. Furthermore, P. kondratievae reaches its peak PHB content during the early stationary growth phase, specifically after 24 h of growth in a flask culture. This is then followed by a decline in the later stages of the stationary growth phase. The depolymerization observed in this growth phase is facilitated by the abundant presence of the PhaZ depolymerase enzyme associated with PHB granules. We observed the highest PHB levels when the cells were cultivated in a medium with glycerol as the sole carbon source and a carbon-to-nitrogen ratio of 10. Finally, we found that PHB production is induced as an osmotic stress response, similar to other polyhydroxyalkanoate-producing species.


Assuntos
Hidroxibutiratos , Paracoccus , Poliésteres , Hidroxibutiratos/metabolismo , Poliésteres/metabolismo , Paracoccus/metabolismo , Paracoccus/crescimento & desenvolvimento , Paracoccus/genética , Temperatura Alta , Temperatura , Filogenia , Poli-Hidroxibutiratos
20.
Microbiologyopen ; 13(3): e13, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38825966

RESUMO

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.


Assuntos
Bactérias , Trato Gastrointestinal , Sedimentos Geológicos , RNA Ribossômico 16S , Caramujos , Sedimentos Geológicos/microbiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Trato Gastrointestinal/microbiologia , Animais , Caramujos/microbiologia , Alemanha , Dinamarca , Microbioma Gastrointestinal/genética , Microbiologia da Água , Biodiversidade , Estônia , Filogenia , DNA Bacteriano/genética , Análise de Sequência de DNA
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