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We report the draft genome assembly of strain 4866-2_S43 isolated from a eucalyptus lesion in Argentina and what until recently was caused by Xanthomonas citri pv. eucalyptorum (Xce). The genome size is 5 188 607 bp, with a G+C content of 64.66%. Comparative analysis reveals that the closest relative of strain 4866-2_S43 is Xce LPF 602, isolated in Brazil. Comparison of the whole genome sequences revealed an average nucleotide identity (ANI) of 99.96% between the two strains. ANIs were determined between the whole genome sequence of strain 4866-2_S43 and the genomes of all currently validated Xanthomonas spp. These results revealed that strain 4866-2_S43 shared >95% similarity with X. citri pv. citri and X. citri pv. phaseoli, and <95% with X. euvesicatoria pv. alfalfae, X. euvesicatoria pv. perforans, and X. euvesicatoria pathovars euvesicatoria and eucalyptii.

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Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages (4,152 prophages + 122 virulent phages, distributed in 46 countries in the world), we show that 91% (875 out of 963) of the prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are not only cosmopolitan but also the most abundant species. We also noted that polylysogens had very divergent prophages, belonging to different prophage species, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. Our study highlights how integrating the host population structure and a solid operational definition of phage species allows us to better appreciate phage diversity and its transmission dynamics. IMPORTANCE: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages, we show that most prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are cosmopolitan and the most abundant species. Prophages in the same bacterial genome are very divergent, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. This study shows how integrating the host population structure and clustering at the species level allows us to better appreciate phage diversity and its transmission dynamics.

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Bacterial wilt, caused by Ralstonia solanacearum, is one of the main challenges for sustainable tomato production in the Amazon region. This study evaluated the potential of bacteria isolated from sediments of the Solimões and Negro rivers for the biocontrol of this disease. From 36 bacteria selected through in vitro antibiosis, three promising isolates were identified: Priestia aryabhattai RN 11, Streptomyces sp. RN 24, and Kitasatospora sp. SOL 195, which inhibited the growth of the phytopathogen by 100%, 87.62%, and 100%, respectively. These isolates also demonstrated the ability to produce extracellular enzymes and plant growth-promoting compounds, such as indole-3-acetic acid (IAA), siderophore, and ammonia. In plant assays, during both dry and rainy seasons, P. aryabhattai RN 11 reduced disease incidence by 40% and 90%, respectively, while promoting the growth of infected plants. Streptomyces sp. RN 24 and Kitasatospora sp. SOL 195 exhibited high survival rates (85-90%) and pathogen suppression in the soil (>90%), demonstrating their potential as biocontrol agents. This study highlights the potential of Amazonian bacteria as biocontrol agents against bacterial wilt, contributing to the development of sustainable management strategies for this important disease.

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Background and Objectives: Pelvic floor muscles (PFM) play a core role in defecation and micturition. Weakening of PFM underlies urogynecological disorders such as pelvic organ prolapse and stress urinary incontinence. Vaginal delivery damages PFM. Muscle trauma implies an inflammatory response mediated by myeloid cells, essential for subsequent recovery. Molecular signaling characterizing the pro-inflammatory phase shifts M1 macrophages to M2 macrophages, which modulate muscle repair. The present study aimed to evaluate histological characteristics and the presence of M1 and M2 macrophages in bulbospongiosus (Bsm) and pubococcygeus muscles (Pcm). Materials and Methods: Muscles from young nulliparous (N) and multiparous rabbits on postpartum days three (M3) and twenty (M20) were excised and histologically processed to measure the myofiber cross-sectional area (CSA) and count the centralized myonuclei in hematoxylin-eosinstained sections. Using immunohistochemistry, M1 and M2 macrophages were estimated in muscle sections. Kruskal-Wallis or one-way ANOVA testing, followed by post hoc tests, were conducted to identify significant differences (p < 0.05). Results: The myofiber CSA of both the Bsm and Pcm of the M3 group were more extensive than those of the N and M20 groups. Centralized myonuclei estimated in sections from both muscles of M20 rabbits were higher than those of N rabbits. Such histological outcomes matched significant increases in HLA-DR immunostaining in M3 rabbits with the CD206 immunostaining in muscle sections from M20 rabbits. Conclusions: A shift from the pro- to anti-inflammatory phase in the bulbospongiosus and pubococcygeus muscles of multiparous rabbits matches with centralized myonuclei, suggesting the ongoing regeneration of muscles.

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Strain FSQ1T was isolated from the rhizosphere of the common bean (Phaseolus vulgaris L.) crop sampled in a commercial field located in the Gabriel Leyva Solano community, which belongs to the Guasave municipality (state of Sinaloa, Mexico). Based on its full-length 16S rRNA gene sequence, strain FSQ1T was assigned to the genus Bacillus (100 % similarity). This taxonomic affiliation was supported by its morphological and metabolic traits. Strain FSQ1T was a Gram-stain-positive bacterium with the following characteristics: rod-shaped cells, strictly aerobic, spore forming, catalase positive, reduced nitrate to nitrite, hydrolysed starch and casein, grew in the presence of lysozyme and 2 % NaCl, utilized citrate, grew at pH 6.0-8.0, produced acid from glucose, was unable to produce indoles from tryptophan, and presented biological control against Sclerotinia sclerotiorum. The whole-genome phylogenetic results showed that strain FSQ1T formed an individual clade in comparison with highly related Bacillus species. In addition, the maximum values for average nucleotide identity and from Genome-to-Genome Distance Calculator analysis were 91.57 and 44.20 %, respectively, with Bacillus spizizenii TU-B-10T. Analysis of its fatty acid content showed the ability of strain FSQ1T to produce fatty acids that are not present in closely related Bacillus species, such as C18 : 0 and C20 : 0. Thus, these results provide strong evidence that strain FSQ1T represents a novel species of the genus Bacillus, for which the name Bacillus mexicanus sp. nov. is proposed. The type strain is FSQ1T (CM-CNRG TB51T=LBPCV FSQ1T).

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La fisura anal es una de las enfermedades más antiguamente descritas, la misma que, ha tenido hasta el momento múltiples tratamientos tanto médicos como quirúrgicos, existiendo controversias en su algoritmo terapéutico. Constituye una de las patologías cuyo diagnóstico y tratamiento corresponde a la Especialidad de Coloproctología, afecta a ambos sexos y a cualquier edad y puede ser aguda o crónica. Proponemos el presente Protocolo para un adecuado manejo de la patología, de manera que sirva de guía en la toma correcta de decisiones basadas en la evidencia y el consenso de quienes integramos la Unidad Técnica de Coloproctología del Hospital de Especialidades Carlos Andrade Marín.

Anal fissure is one of the oldest described diseases, which has so far had multiple medical and surgical treatments, with controversies in its therapeutic algorithm. It is one of the pathologies whose diagnosis and treatment corresponds to the Coloproctology Specialty, it affects both sexes and any age and can be acute or chronic. We propose the present Protocol for an adequate management of the pathology, so that it serves as a guide in the correct decision making based on evidence and consensus of those who integrate the Technical Unit of Coloproctology of the Hospital de Especialidades Carlos Andrade Marín.

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A novel Vibrio strain (CAIM 722T=SW9T=DSM 24596T) was isolated in 2003 from water of a shrimp (Penaeus vannamei) culture pond located in Los Mochis, Sinaloa, Mexico, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence clustered within those of the genus Vibrio, showing high similarity to the type strains of the Porteresiae clade. Multilocus sequence analysis using eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, topA and 16S rRNA) and phylogenetic analysis with 139 single-copy genes showed that the strain forms an independent branch. Whole genome sequencing and genomic analyses (average nucleotide identity, OrthoANI, average amino acid identity and in silico DNA-DNA hybridization) produced values well below the thresholds for species delineation with all methods tested. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strain from related taxa. The results obtained demonstrate that the strain represent a novel species, for which the name Vibrio eleionomae sp. nov. is proposed.

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PURPOSE: The aim of this study was to analyze the sensory and muscle functions of the pelvic floor in women with endometriosis, trying to improve overall knowledge/findings regarding pelvic floor muscle functions in patients with endometriosis. METHODS: Sample size calculated as 92 patients with endometriosis, aged between 18 and 45 years, not virgin, without other causes of pain and could not be pregnant. Patients underwent the Pelvic Floor Sensorial and Muscle Function Exam (EFSMAP). Descriptive data were recorded with mean and standard deviation, median (range), and absolute and relative frequency. The Kolmogorov-Smirnov test was used to observe the normality of quantitative variables. The significance level adopted for this study was 5%. RESULTS: Of 92 women assessed, 93.3% had pain and 75% had increased tone in the levator ani muscle; 50.4% had impaired pelvic floor relaxation with median strength of 3 by the Oxford scale and endurance of 2 s. CONCLUSIONS: The patients had a high prevalence of pain and dysfunction of the pelvic floor muscles, such as low muscle endurance and difficulty to relax. It shows that these patients should be referred to a pelvic floor physiotherapist, as soon as they have the diagnosis of endometriosis, to be assessed to prevent and/or treat pelvic floor impairments.

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The Gram-positive genus Clavibacter is currently divided into seven species (Clavibacter michiganensis, Clavibacter nebraskensis, Clavibacter capsici, Clavibacter sepedonicus, Clavibacter tessellarius, Clavibacter insidiosus and Clavibacter zhangzhiyongii) and three subspecies (C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli). Recent studies have indicated that the taxonomic rank of the subspecies must be re-evaluated. In this research, we assessed the taxonomic position of the three C. michiganensis subspecies and clarified the taxonomic nomenclature of other 75 Clavibacter strains. The complete genomes of the type strains of the three Clavibacter subspecies, the type strain of C. tessellarius and C. nebraskensis A6096 were sequenced using PacBio RSII technology. Application of whole-genome-based computational approaches such as average nucleotide identity (ANI), digital DNA-DNA hybridization, multi-locus sequence analysis of seven housekeeping genes (acnA, atpD, bipA, icdA, mtlD, recA and rpoB), a phylogenomic tree reconstructed from 1 028 core genes, and ANI-based phylogeny provided sufficient justification for raising C. michiganensis subsp. californiensis to the species level. These results led us to propose the establishment of Clavibacter californiensis sp. nov. as a species with its type strain C55T (=CFBP 8216T=ATCC BAA-2691T). Moreover, the orthologous and in silico dot plot analyses, along with the above described bioinformatic strategies, revealed a high degree of similarity between C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli. Based on these analyses, we propose that both subspecies be combined into a single taxon and elevated to the species level as Clavibacter phaseoli sp. nov., with LPPA 982T (= CECT 8144T= LMG 27667T) as the type strain.

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Bradyrhizobium is a heterogeneous bacterial genus capable of establishing symbiotic associations with a broad range of legume hosts, including species of economic and environmental importance. This study was focused on the taxonomic and symbiovar definition of four strains - CNPSo 4026T, WSM 1704T, WSM 1738T and WSM 4400T - previously isolated from nodules of legumes in Western Australia and South Africa. The 16S rRNA gene phylogenetic tree allocated the strains to the Bradyrhizobium elkanii supergroup. The multilocus sequence analysis (MLSA) with partial sequences of six housekeeping genes - atpD, dnaK, glnII, gyrB, recA and rpoB - did not cluster the strains under study as conspecific to any described Bradyrhizobium species. Average nucleotide identity and digital DNA-DNA hybridization values were calculated for the four strains of this study and the closest species according to the MLSA phylogeny with the highest values being 95.46 and 62.20 %, respectively; therefore, both being lower than the species delineation cut-off values. The nodC and nifH phylogenies included strains WSM 1738T and WSM 4400T in the symbiovars retamae and vignae respectively, and also allowed the definition of three new symbiovars, sv. cenepequi, sv. glycinis, and sv. cajani. Analysis of morphophysiological characterization reinforced the identification of four novel proposed Bradyrhizobium species that are accordingly named as follows: Bradyrhizobium cenepequi sp. nov. (CNPSo 4026T=WSM 4798T=LMG 31653T), isolated from Vigna unguiculata; Bradyrhizobium semiaridum sp. nov. (WSM 1704T=CNPSo 4028T=LMG 31654T), isolated from Tephrosia gardneri; Bradyrhizobium hereditatis sp. nov. (WSM 1738T=CNPSo 4025T=LMG 31652T), isolated from Indigofera sp.; and Bradyrhizobium australafricanum sp. nov. (WSM 4400T=CNPSo 4015T=LMG 31648T) isolated from Glycine sp.

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Superior do Instituto Butantan, São Paulo, 2022. Considered by the World Health Organization (WHO) a public problem that affects several countries, oral diseases affect about 3.5 billion people worldwide. There are several common oral diseases present in the population that are caused by bacteria, such as oral cavities, tartar, gingivitis and periodontitis. The mouth is the natural habitat of several bacteria, with more than 700 species known so far. Scenarios like this, characterized by a great complexity of the microbiota, demonstrate the need for accuracy in biological classification, which is essential to characterize the microorganisms present in different physiological situations, especially during pathological events. An accurate classification is also essential for the diagnosis and epidemiological monitoring of infectious diseases. Although there is a consensus that the taxonomic information of a bacterium is contained in its genome, its use for taxonomic purposes has only become more frequent with the advances in new generations of DNA sequencing technologies. In fact, for years the DNA-DNA hybridization method (DDH) was used for the classification of bacteria, however, with advances in genomics, the DDH became an outdated method, opening space for new taxonomic analysis tools, such as the average nucleotide identity (ANI), an analysis considered to be the best option for determining species boundaries and confirming the taxonomic identification of a sample. The main objective of this study was, based on genomic analyzes and the use of bioinformatics tools, to revise the classification of bacterial genera both present in the oral cavity and that contain species that cause oral infections. We chose six genera of bacteria that, according to the literature, have species that are present in oral infections. The genera chosen were: Aggregatibacter, Fusobacterium, Prevotella, Porphyromonas, Selenomonas and Veillonella. In all these genera, inconsistencies were found between the classification described in GenBank and that indicated by the ANI analysis, which allowed us to propose the reclassification of several isolates and propose the creation of new species for all these genera.

Consideradas pela Organização Mundial da Saúde (OMS) um problema de âmbito público que afeta diversos países, as doenças bucais afetam cerca de 3,5 bilhões de pessoas mundialmente. Há diversas enfermidades bucais comuns presentes na população que são ocasionadas por bactérias, como as cáries bucais, tártaro, gengivite e periodontite. A boca é o habitat natural de diversas bactérias, tendo-se conhecimento de mais de 700 espécies. Cenários como este, caracterizados por grande complexidade da microbiota, demonstram a necessidade da precisão da classificação biológica, que é essencial para caracterizar quem são os microorganismos presentes em diferentes situações fisiológicas, especialmente durante eventos patológicos. Uma precisa classificação também é essencial para o diagnóstico e o monitoramento epidemiológico de doenças infecciosas. Embora exista um consenso de que as informações taxonômicas de uma bactéria estejam contidas em seu genoma, a sua utilização para fins taxônomicos só passou a ser mais frequente a partir dos avanços das tecnologias de sequenciamento de DNA de nova geração. De fato, durante anos o método de hibridização DNA-DNA (DDH) foi utilizado para a classificação de bactérias, no entanto, com os avanços da genômica, o DDH se tornou um método ultrapassado, abrindo espaço para novas ferramentas de análise taxonômica, como a identidade média de nucleotídeos (ANI), uma análise considerada como a melhor opção para determinar os limites das espécies e confirmar a identificação taxonômica de uma amostra. O objetivo principal deste estudo foi, a partir de análises genômicas e do uso de ferramentas de bioinformática, revisar a classificação de gêneros bacterianos presentes na cavidade oral e que contenham espécies que acarretam infecções bucais. Escolhemos seis gêneros de bactérias que, de acordo com a literatura, apresentam espécies que estão presente em infecções bucais. Os gêneros escolhidos foram: Aggregatibacter, Fusobacterium, Prevotella, Porphyromonas, Selenomonas e Veillonella. Em todos esses gêneros foram encontradas inconsistências entre a classificação descrita no GenBank e aquela apontada pela análise de ANI, o que nos permitiu propor a reclassificação de diversos isolados e propor a criação de novas espécies para todos esses gêneros.

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Bioinformatics is an important tool in several areas of science, and it can be used for the reclassification of organisms from the Archaea and Bacteria kingdoms. Using tools to calculate the average nucleotide identity, gene annotation and pan-genome analysis, it can be identified possible inconsistencies in the classification of bacteria. It was made a massive analysis of genomic data from two bacterial genera of medical interest Brucella and Micrococcus responsible for causing chronic diseases and nosocomial infections, respectively. The methodology used was nucleotide similarity analysis, genomic annotation, pan-genome analysis and annotation of genes of interest. In this study we propose reclassifications for both genera studied and we point out proposals for new poorly classified species and others not yet identified.

A bioinformática é uma importante ferramenta em diversas áreas da ciência, podendo ser usada para a reclassificação de organismos dos reinos Archaea e Bacteria. A partir do uso de ferramentas de cálculo da identidade média de nucleotídeos, anotação de genes, análise pan-genoma podem ser identificadas possíveis inconsistências na classificação de bactérias. Nesse trabalho, foi realizada uma análise massiva de dados genômicos de dois gêneros bacterianos de interesse médico, Burcella e Micrococcus, responsáveis por causar doenças crônicas e infecções hospitalares, respectivamente. A metodologia utilizada foi a de análise de similaridade nucleotídica, anotação genômica, análise de pan-genoma e anotação de genes de interesse. Neste estudo propomos reclassificações para ambos os gêneros estudados e apontamos propostas de novas espécies classificadas erroneamente e de outras ainda não identificadas.

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Bioinformatics has generated a great impact in the scientific field due to its diverse applications, one of its highlights being the study of genomes through tools that make it possible to carry out sequence alignment, identification of protein families profile, genome annotation and the investigation of presence/absence of resistance and virulence genes based on different databases. A resource that has recently gained prominence in the classification of microorganisms is called ANI (Average Nucleotide Identity), which seeks, through the average nucleotide similarity between genomes, to demarcate boundaries between species. Another relevant resource is the investigation of microorganisms with potential multi-resistance. We used both of these resources to investigate a significative number of isolates of the genus Neisseria and Vibrio, which, in addition to having gone through recent phylogenetic reclassifications, present possible multiresistant species. We sought to identify possible classification inconsistencies of species from the genus Neisseria and Vibrio through ANI, proposing reclassifications when applicable. Another objective was to analyze the presence / absence of resistance and virulence genes through bioinformatics software. Among the investigated species N. sicca LPB0402 and N. perflava LPB0400 need to undergo a reclassification, due to having presented ANI of 99.99%, which define them as the same species. Concerning the genus Vibrio, we suggest with low doubt, that V. lentus 5F79 and V. tasmaniensis 5F79 are the same species, since they present ANI of 99.97%, whereas V. lentus 10N6145B10 with ANI of 95.62% and 95.64% respectively, when compared to these two isolates cited above, should also be included in this same species. As for resistance genes N. lactamica, N. gonorrhoeae, N. meningitidis and especially N. brasiliensis N17716, V. hepatarius DSM19134 and V. cholerae 1Mo have a potential profile of multiresistance; V. mimicus 2011V1073 stood out in terms of virulence. We can conclude that the analysis of the genome of bacterial isolates allowed us to find classification inconsistencies and to generate proposals for reclassification, as well as allowed us to show that isolates not considered of medical interest actually have a large number of genes for vituence and antimicrobial resistance, reason why they should have their vigilance increased.

A bioinformática tem gerado grande impacto no campo científico devido às suas diversas aplicações, sendo um de seus destaques o estudo de genomas por meio de ferramentas que possibilitam realizar alinhamento de sequências, identificação do perfil de famílias de proteínas, anotação de genomas e a investigação da presença/ausência de genes de resistência e virulência baseados em diferentes conjuntos de dados. Um recurso que ganhou destaque recentemente na reclassificação de microrganismos foi a análise por ANI (Average Nucleotide Identity), que busca por meio da média de similaridade nucleotídica entre os genomas, demarcar limites entre espécies. Um outro recurso relevante é a investigação de microrganismos com potencial multirresistência. Utilizando essas duas ferramentas, avaliamos um grande número de isolados dos gêneros Neisseria e Vibrio, que além de terem passado por recentes reclassificações filogenéticas, apresentam potenciais espécies multiresistentes. Buscamos identificar possíveis inconsistências de classificação de espécies dos gêneros Neisseria e Vibrio por meio de ANI, propondo reclassificações quando aplicáveis. Outro objetivo foi analisar a presença/ausência de genes de resistência e virulência por meio de softwares de bioinformática. Dentre as espécies investigadas N. sicca LPB0402 e N. perflava LPB0400 precisam passar por uma reclassificação, devido terem apresentado ANI de 99,99%, o que as define como a mesma espécie. Quanto ao gênero Vibrio sugerimos, com pouca margem de dúvida, que V. lentus 5F79 e V. tasmaniensis 5F79 são a mesma espécie, por apresentarem ANI de 99,97%, podendo V. lentus 10N6145B10 com ANI de 95,62% e 95,64% respectivamente quando comparado comos dois isolados citadas acima, ser incluso nesta mesma espécie. Quanto aos genes de resistência N. lactamica, N. gonorrhoeae, N. meningitidis e principalmente N. brasiliensis N17716, V. hepatarius DSM19134 e V. cholerae 1Mo apresentaram um perfil potencial de multirresistência; V. mimicus 2011V1073 se destacou no quesito virulência Podemos concluir que a análise do genoma de isolados bacterianos nos permitiu encontrar inconsistencias de classificação e gerar propostas de reclassificação, assim como permitiu detectar que isolados não considerados como de interesse médico possuem, na verdade, grande número de genes de vitulência e resistencia antimicromiana, motivo pelo qual devem ter sua vigilância aumentada.

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Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA-DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95-96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, "Bartonella mastomydis," and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) "Bartonella vinsonii" subsp. arupensis and "B. vinsonii" subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 ("Mesorhizobium loti LMG 6,125T"), GCF_003024595.1 ("Mesorhizobium plurifarium LMG 11,892T"), GCF_003096615.1 ("Methylobacterium organophilum DSM 760T"), and GCF_000373025.1 ("R. gallicum R-602 spT") are not from the genuine type strains used for the respective species descriptions; and v) "Xanthobacter autotrophicus" Py2 and "Aminobacter aminovorans" KCTC 2,477T represent cases of misuse of the term "type strain". Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust ("Prokaryotic Clusters"), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

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AIM: To evaluate the pelvic floor (PF) biometry using three-dimensional ultrasound (US) at two-time points of gestational in pregnant women with gestational diabetes mellitus (GDM). METHODS: A prospective cohort study conducted at the Perinatal Diabetes Research Center including 44 pregnant women with GDM and 66 pregnant women without GDM at 24 to 28 weeks of gestation. Three-dimensional transperineal US was performed at 24 to 28 and 34 to 38 weeks of gestation in the lithotomy position at rest. The axial plane of the minimal Levator hiatal dimensions was used to determine Levator ani muscle and Hiatal area (HA) biometry at 24 to 28 and 34 to 38 weeks of gestation. RESULTS: Of the 110 pregnant women, 100 (90.9%) completed the follow-up at 34 to 38 weeks of gestation. The evaluation by US showed a negative biometric change between the two-time points, during pregnancy in women with GDM; in the HA (ß coefficient: estimative of effect in biometric progression according to GDM diagnosis, using the non-GDM group as reference = -6.76; P = .020), anteroposterior diameter (ß = -5.07; P = .019), and Levator ani thickness (ß = -12.34; P = .005). CONCLUSIONS: Pregnant women with GDM had a significantly lower than expected percentage of changes in biometry of Levator ani thickness and HA from 24 to 28 to 34 to 38 weeks of gestation when compared with the group of pregnant women without GDM. GDM alters the morphology of PF structures assessed by three-dimension US. This reported complication may be implicated in adverse birth outcomes and may play a role in the development of PF dysfunction.

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The genus Bradyrhizobium is considered as the probable ancestor lineage of all rhizobia, broadly spread in a variety of ecosystems and with remarkable diversity. A polyphasic study was performed to characterize and clarify the taxonomic position of eight bradyrhizobial strains isolated from indigenous legumes to Western Australia. As expected for the genus, the 16S rRNA gene sequences were highly conserved, but the results of multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed three new distinct clades including the following strains: (1) WSM 1744T, WSM 1736 and WSM 1737; (2) WSM 1791T and WSM 1742; and (3) WSM 1741T, WSM 1735 and WSM 1790. The highest ANI values of the three groups in relation to the closest type strains were 92.4, 92.3 and 93.3 %, respectively, below the threshold of species circumscription. The digital DNA-DNA hybridization analysis also confirmed new species descriptions, with less than 52 % relatedness with the closest type strains. The phylogeny of the symbiotic gene nodC clustered the eight strains into the symbiovar retamae, together with seven Bradyrhizobium type strains, sharing from 94.2-98.1 % nucleotide identity (NI), and less than 88.7 % NI with other related strains and symbiovars. Morpho-physiological, phylogenetics, genomic and symbiotic traits were determined for the new groups and our data support the description of three new species, Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., with WSM 1744T (=CNPSo 4013T=LMG 31646T), WSM 1791T (=CNPSo 4014T=LMG 31647T) and WSM 1741T (=CNPSo 4020T=LMG 31651T) designated as type strains, respectively.

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Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.

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OBJECTIVE: To provide an overview of the hormone actions and receptors expressed in the female pelvic floor muscles, relevant for understanding the pelvic floor disorders. METHODS: We performed a literature review focused on the expression of hormone receptors mainly in the pelvic floor muscles of women and female rats and rabbits. RESULTS: The impairment of the pelvic floor muscles can lead to the onset of pelvic floor dysfunctions, including stress urinary incontinence in women. Hormone milieu is associated with the structure and function alterations of pelvic floor muscles, a notion supported by the fact that these muscles express different hormone receptors. Nuclear receptors, such as steroid receptors, are up till now the most investigated. The present review accounts for the limited studies conducted to elucidate the expression of hormone receptors in pelvic floor muscles in females. CONCLUSION: Hormone receptor expression is the cornerstone in some hormone-based therapies, which require further detailed studies on the distribution of receptors in particular pelvic floor muscles, as well as their association with muscle effectors, involved in the alterations relevant for understanding pelvic floor disorders.

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A polyphasic study was conducted with 11 strains trapped by Mimosa pudica and Phaseolus vulgaris grown in soils of the Brazilian Atlantic Forest. In the phylogenetic analysis of the 16S rRNA gene, one clade of strains (Psp1) showed higher similarity with Paraburkholderia piptadeniae STM7183T (99.6%), whereas the second (Psp6) was closely related to Paraburkholderia tuberum STM678T (99%). An MLSA (multilocus sequence analysis) with four (recA, gyrB, trpB and gltB) housekeeping genes placed both Psp1 and Psp6 strains in new clades, and BOX-PCR profiles indicated high intraspecific genetic diversity within each clade. Values of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) of the whole genome sequences were of 56.9 and 94.4% between the Psp1 strain CNPSo 3157T and P. piptadeniae; and of 49.7% and 92.7% between the Psp6 strain CNPSo 3155T and P. tuberum, below the threshold for species delimitation. In the nodC analysis, Psp1 strains clustered together with P. piptadeniae, while Psp6 did not group with any symbiotic Paraburkholderia. Other phenotypic, genotypic and symbiotic properties were evaluated. The polyphasic analysis supports that the strains represent two novel species, for which the names Paraburkholderia franconis sp. nov. with type strain CNPSo 3157T (= ABIP 241, = LMG 31644) and Paraburkholderia atlantica sp. nov. with type strain CNPSo 3155T (= ABIP 236, = LMG 31643) are proposed.

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BACKGROUND: Levator ani avulsion is defined as the interruption of the insertion of this muscle on the pubic bone. It is currently recognized as an important triggering factor for genital prolapse. Although surgical interventions are available, there are no conservative strategies for this muscular injury. DESCRIPTION: A 40-year-old female presented with urinary incontinence and levator ani avulsion, which was confirmed on transperineal three-dimensional ultrasound (3DUS). Upon referral for physiotherapy, she presented with incorrect and weak contractions of the pelvic floor. Her treatment comprised 13 sessions of intravaginal electrotherapy followed by pelvic floor muscle (PFM) exercises in different positions. At the end of the sessions, another transperineal 3DUS was performed, and it revealed rapprochement of the levator ani muscle. The avulsed levator ani muscle can be reinserted using physiotherapeutic interventions, especially a combination of electrotherapy and PFM exercises. CONCLUSION: Transperineal 3DUS is an important approach for the follow-up of conservative treatment until full recovery.