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1.
Antonie Van Leeuwenhoek ; 112(8): 1147-1159, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30798490

RESUMO

Strain Marseille-P4121T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480T, a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C18:1ω9 (34.4%), C16:0 (30.1%), and C18:0 (19%). The draft genome size of strain Marseille-P4121T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121T (= CECT 9671T = CSUR P4121T) is the type strain of the new species Janibacter massiliensis sp. nov.


Assuntos
Actinobacteria/classificação , Actinobacteria/isolamento & purificação , Descarga Vaginal/microbiologia , Vaginose Bacteriana/microbiologia , Actinobacteria/genética , Actinobacteria/fisiologia , Composição de Bases , Análise por Conglomerados , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Feminino , França , Humanos , Pessoa de Meia-Idade , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
2.
Curr Microbiol ; 75(11): 1419-1428, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29982935

RESUMO

An understanding of the microbial diversity of the human body has generated significant interest in recent years. With the advent of MALDI-TOF mass spectrometry, high-speed sequencing, and the rebirth of microbial culture, knowledge of human microbiota is growing. Using culturomics, a strategy to explore the microbial diversity of samples, coupled with a taxono-genomic strategy, we isolated a new bacterium named Anaerococcus jeddahensis sp. nov. strain SB3T. This strain was isolated from the stool sample of a healthy nomadic Bedouin woman from Saudi Arabia. Here, we describe the characteristics of this organism, and the complete genome sequence and annotation. Strain SB3T is a Gram-positive obligate anaerobic coccus which is non-motile and non-spore forming. Fatty acid analysis shows that the major fatty acid is by far hexadecanoic acid (C16:0; 52%). Its genome is 1,903,534 bp long and has 29.70 mol% of G+C content. It contains 1756 protein-coding genes and 53 RNA genes. These results show that strategy provides a better understanding of the microorganism and that is a good methodology for microbial identification and characterization.


Assuntos
Firmicutes/isolamento & purificação , Composição de Bases , Ácidos Graxos/análise , Ácidos Graxos/metabolismo , Fezes/microbiologia , Feminino , Firmicutes/classificação , Firmicutes/genética , Firmicutes/metabolismo , Microbioma Gastrointestinal , Genoma Bacteriano , Humanos , Filogenia , Arábia Saudita
3.
Antonie Van Leeuwenhoek ; 110(6): 737-750, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28190153

RESUMO

A novel strain, Mt12T (=CSUR P1907 = DSM 100590), was isolated from the fecal sample of a 7-month-old girl from Senegal afflicted with severe acute malnutrition. This bacterium is a strictly anaerobic, spore-forming Gram-stain positive bacillus. The major cellular fatty acid was identified as tetradecanoic acid. Its 16S rRNA gene sequence exhibited 94.9% similarity with that of Crassaminicella profunda strain Ra1766HT, currently the closest species with a validly published name. The draft genome of strain Mt12T is 3,497,275-bp long with a 30.45% of G+C content. 3397 genes were predicted, including 3268 protein-coding genes and 129 RNAs, including eight 16S rRNAs. Genomic comparison with closely related species with an available genome showed a lower quantitative genomic content. The phylogenetic analysis alongside the dDDH values under 30% and phenotypic characteristics suggest that strain Mt12T represents a new genus within the family Clostridiaceae, for which the name Inediibacterium massiliense gen. nov., sp. nov. is proposed.


Assuntos
Clostridiaceae/isolamento & purificação , Microbioma Gastrointestinal , Desnutrição , RNA Ribossômico 16S , Técnicas de Tipagem Bacteriana , Composição de Bases , Clostridiaceae/genética , DNA Bacteriano , Ácidos Graxos , Humanos , Lactente , Filogenia , Análise de Sequência de DNA
4.
Curr Microbiol ; 73(6): 867-877, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27628331

RESUMO

The identification of human-associated bacteria is very important to control infectious diseases. In recent years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial species and/or genera. Using this strategy, strain GM7, a strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese patient. It is a motile coccobacillus without catalase and oxidase activities. The genome of Gabonibacter massiliensis is 3,397,022 bp long with 2880 ORFs and a G+C content of 42.09 %. Of the predicted genes, 2,819 are protein-coding genes, and 61 are RNAs. Strain GM7 differs from the closest genera within the family Porphyromonadaceae both genotypically and in shape and motility. Thus, we propose that strain GM7T (=CSUR P2336 = DSM 101039) is the type strain of the new genus Gabonibacter gen. nov. and the new species G. massiliensis gen. nov., sp. nov.


Assuntos
Bacteroidetes/isolamento & purificação , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Adolescente , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Técnicas de Tipagem Bacteriana , Bacteroidetes/classificação , Bacteroidetes/genética , Composição de Bases , DNA Bacteriano/genética , Genótipo , Humanos , Masculino , Filogenia , RNA Ribossômico 16S/genética
5.
Anaerobe ; 36: 79-87, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26485191

RESUMO

Strain MS1, a Gram-positive, obligately anaerobic, motile and spore-forming rod belonging to the Clostridium genus, was isolated from the feces of a healthy Polynesian male living in French Polynesia. The temperature range for growth was 30-45 °C. We sequenced its complete genome and studied its phenotypic characteristics. The 3,560,738-bp long genome (one chromosome, no plasmid, G + C content 34%) contained 3535 protein-coding and 70 RNA genes. Strain MS1 exhibited a 98.24% 16S rRNA similarity with Clostridium amylolyticum, the phylogenetically closest species. When compared with other Clostridium species with standing in nomenclature, it had an average genomic similarity of 68.8-70%, a unique MALDI-TOF spectrum, and differed in nitrate reduction, motility and L-arabinose and D-lactose metabolism with most of the closest species. Therefore, strain MS1 is sufficiently distinct from type strains of the genus Clostridium to represent a novel species within this genus, for which the name Clostridium polynesiense sp. nov. is proposed. The type strain of C. polynesiense is MS1(T) (= CSUR P630 = DSM 27072).


Assuntos
Clostridium/isolamento & purificação , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Composição de Bases , Clostridium/classificação , Clostridium/genética , Clostridium/metabolismo , Ácidos Graxos/metabolismo , Fezes/microbiologia , Humanos , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Filogenia , Polinésia
6.
Front Aging ; 5: 1368982, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38757145

RESUMO

Hyperbaric Oxygen Therapy (HBOT) utilizes 100% oxygen at high atmospheric pressure for clinical applications. HBOT has proven to be an effective supplementary treatment for a variety of clinical and pathological disorders. HBOT's therapeutic results are based on the physiological effects of increased tissue oxygenation, or improved oxygen bioavailability. HBOT's current indications in illnesses like as wound healing, thermal or radiation burns, and tissue necrosis point to its function in facilitating the regeneration process. Various research has revealed that HBOT plays a function in vascularization, angiogenesis, and collagen production augmentation. Individual regeneration capacity is influenced by both environmental and genetic factors. Furthermore, the regenerating ability of different types of tissues varies, and this ability declines with age. HBOT affects physiological processes at the genetic level by altering gene expression, delaying cell senescence, and assisting in telomere length enhancement. The positive results in a variety of indications, ranging from tissue regeneration to better cognitive function, indicate that it has enormous potential in regenerative and anti-aging therapy.

7.
Ann Med ; 56(1): 2353893, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38753424

RESUMO

BACKGROUND: One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE: In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS: We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS: The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION: The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION: After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.


Assuntos
Biomarcadores Tumorais , Neoplasias , Humanos , Neoplasias/genética , Neoplasias/diagnóstico , Biomarcadores Tumorais/genética , Técnicas de Diagnóstico Molecular/métodos , Detecção Precoce de Câncer/métodos , Predisposição Genética para Doença , Medicina de Precisão/métodos
8.
Cureus ; 16(5): e59934, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38854317

RESUMO

BACKGROUND: The significant global health burden associated with cardiometabolic diseases necessitates a better understanding of the complex interrelationships between metabolic markers and cardiovascular health indicators. Crucial indicators of cardiovascular and metabolic health include metabolic markers such as uric acid and gamma-glutamyl transferase (GGT), as well as blood pressure (BP), triglycerides, total cholesterol, high-density lipoprotein (HDL), and fasting blood glucose. OBJECTIVE: This study aims to investigate the multifactorial relationships among several parameters such as age, BP, lipid profile, body mass index (BMI), fasting blood glucose levels, and specific metabolic enzymes. METHODS: A willing participant who visited the outpatient clinic and was in good health but did not have a history of cardiovascular disease was enrolled in the study. The collected data were subjected to a cross-sectional analysis. Various biochemical and health parameters such as height, weight, BMI, uric acid, triglycerides, HDL, BP, gender, age, and fasting blood glucose were analyzed, and a Pearson correlation coefficient analysis was performed to evaluate the correlations between these variables. RESULTS: Among the 50 study participants, significant Pearson correlations were observed between metabolic health markers such as BP (systolic and diastolic), fasting blood sugar, total cholesterol, triglycerides, HDL, and BMI. Additionally, a positive correlation was found between these metabolic parameters, including the levels of uric acid and liver enzyme GGT. CONCLUSION: This study illustrates the intricate relationships among lipid profiles, liver enzymes, BP, and other metabolic health markers in the general population. Understanding these associations can help create focused interventions and individualized care plans for metabolic and cardiovascular disorders. Our findings address the complexity of cardiometabolic health and its management by identifying multifactorial risk factors linked to metabolic disorders and cardiovascular diseases.

9.
Cureus ; 16(3): e55939, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38601378

RESUMO

Background Instant infections in children due to acute encephalitis syndrome (AES) were reported in a tribal district of Bastar in Chattisgarh, India, between August 2018 and August 2019. Objective The study was conducted to explore the possibility of a viral cause indicating an outbreak. Methods Clinical surveys and serological investigation tests were conducted to identify the viral etiology. The Bastar area in Chhattisgarh reported factors such as paddy fields near homes, a high pig-to-cattle ratio, a significant presence of Culex vishnui mosquitoes, low socioeconomic status, and a lack of health awareness among the tribal people. Result This study, conducted at the Late Baliram Kashyap Memorial Government Medical College in Jagdalpur, Bastar, Chhattisgarh, India, analyzed 128 samples from fever cases out of 213 patients visiting the Japanese encephalitis virus (JEV) testing center. Among these samples, 71 cases exhibited AES, and subsequent JEV IgM ELISA testing identified 18 cases as JEV-positive, signifying recent JEV infections. Notably, the overwhelming majority (94.44%) of JEV-positive patients were under 16 years old, highlighting the heightened vulnerability of children to JEV illness in the Bastar region. Although male patients accounted for 61.11% of the JEV-positive cases compared to 38.88% of female patients, statistical analysis revealed that this gender disparity was not statistically significant (p-value = 0.18). Conclusion The study emphasizes the significance of identifying the etiology and delivering evidence-based care to patients with AES. Improved diagnosis and management of AES may result from a greater comprehension of the advantages and disadvantages associated with the application and administration of common laboratory and diagnostic algorithms.

10.
Cureus ; 16(3): e55365, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38562351

RESUMO

Background The H1N1 flu is a subtype of the influenza A virus, also known as the swine flu. An entirely new strain of the H1N1 virus started sickening people in the 2009-2010 flu season. It was a novel influenza virus combination that can infect humans, pigs, and birds. It was frequently referred to as the "swine flu." The virus may be able to spread for a little while longer in children and individuals with compromised immune systems. Objective The objective is to investigate the outbreaks of H1N1 among young adults in the Bastar District of Chhattisgarh. Methods Collection of the blood samples of 342 individuals between December 2015 and November 2017 was done. Thirty-one cases of Influenza A (H1N1) PDM09 virus infection were identified and confirmed. The molecular relationship between viruses is identified by the real-time polymerase chain reaction (RT-PCR) method. Result The majority of samples (n=13) were sourced from Raipur Medical College, followed by contributions from Durg District Hospital (n=5), Raigarh Medical College (n=4), Rajnandgaon District Hospital (n=3), Jagdalpur Medical College (n=2), Bilaspur Medical College (n=2), and smaller contributions from Dhamtari District Hospital and Gariyabandh Primary Health Care. Among these, 31 samples tested positive for Influenza A (H1N1) PDM 2009 virus, with a slightly higher prevalence among 19 female patients. Age-wise distribution revealed higher proportions of positive cases in the age groups of 0-10 years, 31-40 years, and 21-30 years. In the molecular analysis, 154 samples showed no target amplification, while 125 samples exhibited amplification of only Influenza A without subtype (H1) amplification. Remarkably, 31 patients who tested positive for Influenza A (H1N1) died from the virus; most of the deaths were in children under five and middle-aged adults. Conclusion The detection of Influenza A (H1N1) PDM 2009 virus, especially among females, indicates its persistent circulation. Positive cases were prevalent among younger and middle-aged individuals. Molecular analysis showed subtype variations, with significant fatalities observed in children under five and middle-aged adults, emphasizing the severity of the virus across different age groups. It is advised that in order to keep Indian influenza surveillance up to date and robust, more epidemiological data should be gathered, along with information on risk factors like immunization status, hospitalization, and mortality rates should be estimated, and influenza case subtyping should be improved.

11.
Ann Med ; 56(1): 2407066, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-39311013

RESUMO

BACKGROUND: Tuberculosis (TB) is a bacterial infection that usually affects the lungs, although it can also affect other parts of the body. Vitamin D deficiency and response to treatment have been demonstrated in patients with active TB in several studies, but not in MDR-TB patients, which is a new observation in the present study. OBJECTIVE: To study the time to initial sputum culture conversion and to associate baseline vitamin D levels and response to treatment in patients with PTB Cat I and MDR-TB. METHODS: A total of 897 North Indian participants were recruited and divided into three groups: treatment-naïve PTB Cat I, MDR-TB, and healthy controls. Serum biochemistry, including 25-hydroxyvitamin D and calcium, was measured in all participants with PTB, Cat I, and MDR-TB. RESULTS: PTB Cat I patients had high bacillary load grading at baseline compared to 2nd month followed by 6th month of treatment. More severe chest radiographic features, such as cavitation and the presence of bilateral disease at baseline. Mean sputum smear conversion times were 0.95 ± 0.7 months and culture conversion to negative occurred at a mean time of 0.8 ± 0.7 in PTB Cat I patients compared to MDR-TB patients on average sputum smear and time of 2.4 ± 3 months. Significantly lower mean serum 25-hyroxyvitamin D concentration was found in the 6th month than in the 2nd month and baseline in PTB Cat I. CONCLUSION: Low serum vitamin D deficiency was observed in both groups during treatment and is one of the important factors responsible for susceptibility to TB in both groups; however, its significance is uncertain. Patients with continuous positive sputum for multidrug-resistant tuberculosis (MDR-TB) had a worse prognosis than those with sputum bacteriology conversion. Two months into a treatment regimen, sputum smear conversions may be a useful indicator of an MDR-TB patient's prognosis.


Assuntos
Antituberculosos , Escarro , Tuberculose Resistente a Múltiplos Medicamentos , Tuberculose Pulmonar , Deficiência de Vitamina D , Vitamina D , Humanos , Feminino , Masculino , Vitamina D/sangue , Vitamina D/análogos & derivados , Vitamina D/uso terapêutico , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/sangue , Adulto , Índia/epidemiologia , Antituberculosos/uso terapêutico , Escarro/microbiologia , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/sangue , Deficiência de Vitamina D/tratamento farmacológico , Deficiência de Vitamina D/sangue , Deficiência de Vitamina D/complicações , Pessoa de Meia-Idade , Resultado do Tratamento , Cálcio/sangue , Adulto Jovem , Estudos de Casos e Controles , Mycobacterium tuberculosis/isolamento & purificação
12.
Ann Med ; 55(2): 2291554, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38079515

RESUMO

Background: Tuberculosis (TB) and malnutrition are major global health problems, with multidrug-resistant (MDR) TB complicating international efforts. The role of vitamin D in susceptibility to and as an adjunctive treatment for TB is being studied extensively, although no study has included MDR-TB patients in context to dietary profile with vitamin D levels and sunlight exposure.Objective: This study aimed to estimate vitamin D serum levels and examine their association with dietary intake of vitamin D and sun exposure in patients with MDR-TB.Methods: North Indian participants were enrolled in three groups: MDR-TB, drug-susceptible pulmonary TB (DS-PTB), and healthy controls. All consenting participants underwent the estimation of macro- and micronutrient intake and sunlight exposure using structured questionnaires. Serum biochemistry, including 25-hydroxyvitamin D and calcium levels, was measured, and the correlation between variables was determined.Results: 747 participants were enrolled. Significant differences among the three groups were found in mean serum 25-hydroxyvitamin D levels, body mass index, macronutrient intake, dietary vitamin D and calcium content, and sun exposure index (SEI). All except sun exposure (SEI was highest in DS-PTB patients) were found to follow the trend: MDR-TB < DS-PTB < healthy controls. The mean serum vitamin D levels of all groups were deficient and correlated positively with dietary intake and SEI.Conclusion: In this study's we found significant association of serum vitamin D concentrations, dietary intake and sunlight exposure in MDR-TB, DS-PTB patients and healthy controls. Dietary intake may be more important than sun exposure in determining serum levels. However, the significance of this finding is uncertain. Further studies are required to confirm the association, direction, and potential for vitamin D supplementation to treat or prevent MDR-TB infection.


Assuntos
Tuberculose Resistente a Múltiplos Medicamentos , Tuberculose Pulmonar , Deficiência de Vitamina D , Humanos , Deficiência de Vitamina D/tratamento farmacológico , Deficiência de Vitamina D/epidemiologia , Cálcio/uso terapêutico , Vitamina D , Dieta , Vitaminas , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/complicações , Luz Solar , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/epidemiologia
13.
BMC Infect Dis ; 10: 165, 2010 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-20537163

RESUMO

BACKGROUND: Pulmonary tuberculosis, the most common clinical form of mycobacterial diseases, is a granulomatous disease of the lungs caused by Mycobaterium tuberculosis. A number of genes have been identified in studies of diverse origins to be important in tuberculosis. Of these, both tumor necrosis factor alpha (TNF-alpha) and lymphotoxin alpha (LT-alpha) play important immunoregulatory roles. METHODS: To investigate the association of TNF polymorphisms with tuberculosis in the Asian Indians, we genotyped five potentially functional promoter polymorphisms in the TNFA gene and a LTA_NcoI polymorphism (+252 position) of the LTA gene in a clinically well-defined cohort of North-Indian patients with tuberculosis (N = 185) and their regional controls (N = 155). Serum TNF-alpha (sTNF-alpha) levels were measured and correlated with genotypes and haplotypes. RESULTS: The comparison of the allele frequencies for the various loci investigated revealed no significant differences between the tuberculosis patients and controls. Also, when the patients were sub-grouped into minimal, moderately advanced and far advanced disease on the basis of chest radiographs, TST and the presence/absence of cavitary lesions, none of the polymorphisms showed a significant association with any of the patient sub-groups. Although a significant difference was observed in the serum TNF-alpha levels in the patients and the controls, none of the investigated polymorphisms were found to affect the sTNF-alpha levels. Interestingly, it was observed that patients with minimal severity were associated with lower log sTNF-alpha levels when compared to the patients with moderately advanced and far advanced severity. However, none of these differences were found to be statistically significant. Furthermore, when haplotypes were analyzed, no significant difference was observed. CONCLUSIONS: Thus, our findings exclude the TNF genes as major risk factor for tuberculosis in the North Indians.


Assuntos
Predisposição Genética para Doença , Linfotoxina-alfa/genética , Polimorfismo Genético , Tuberculose/epidemiologia , Tuberculose/genética , Fator de Necrose Tumoral alfa/genética , Adolescente , Adulto , Feminino , Frequência do Gene , Humanos , Índia , Linfotoxina-alfa/imunologia , Masculino , Pessoa de Meia-Idade , Regiões Promotoras Genéticas , Tuberculose/imunologia , Fator de Necrose Tumoral alfa/sangue , Fator de Necrose Tumoral alfa/imunologia , Adulto Jovem
14.
Microbiologyopen ; 8(3): e00661, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-29931836

RESUMO

Three previously unidentified Gram-positive anaerobic coccoid bacteria, strains KhD-2T , KHD4T , and Kh-D5T , isolated from a vaginal swab, were characterized using the taxonogenomics concept. The phylogenic analysis, phenotypic characteristics, and genotypic data presented in this report attest that these three bacteria are distinct from previously known bacterial species with standing in nomenclature and represent three new Peptoniphilus species. Strain KhD-2T is most closely related to Peptoniphilus sp. DNF00840 and Peptoniphilus harei (99.7% and 98.2% identity, respectively); strain KHD4T to Peptoniphilus lacrimalis (96%) and strain Kh-D5T to Peptoniphilus coxii (97.2%). Strains KhD-2T , KHD4T , and Kh-D5T DNA G+C contents are, respectively, 34.23%, 31.87%, and 49.38%; their major fatty acid was C16:0 (41.6%, 32.0%, and 36.4%, respectively). We propose that strains KhD-2T (=CSUR P0125 = DSM 101742), KHD4T (=CSUR P0110 = CECT 9308), and Kh-D5T (=CSUR P2271 = DSM 101839) be the type strains of the new species for which the names Peptoniphilus vaginalis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilu pacaensis sp. nov., are proposed, respectively.


Assuntos
Técnicas de Tipagem Bacteriana , Líquidos Corporais/microbiologia , Firmicutes/classificação , Firmicutes/isolamento & purificação , Vaginose Bacteriana/microbiologia , Adulto , Anaerobiose , Composição de Bases , Citosol/química , Ácidos Graxos/análise , Feminino , Firmicutes/genética , Firmicutes/fisiologia , Humanos , Filogenia , Homologia de Sequência do Ácido Nucleico
15.
Stand Genomic Sci ; 13: 8, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29682169

RESUMO

We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola strain SIT8 (= CSUR P1560). This strain, whose genome is described here, was isolated from the fecal flora of a healthy 28-month-old Senegalese boy. Strain SIT8 is a facultatively anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,824,451-bp long (1 chromosome but no plasmid) contains 2354 protein-coding and 46 RNA genes, including four rRNA genes.

16.
OMICS ; 22(2): 164-175, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-28650741

RESUMO

Culturomics is a new postgenomics field that explores the microbial diversity of the human gut coupled with taxono-genomic strategy. Culturomics, and the microbiome science more generally, are anticipated to transform global health diagnostics and inform the ways in which gut microbial diversity contributes to human health and disease, and by extension, to personalized medicine. Using culturomics, we report in this study the description of strain CB1T ( = CSUR P1334 = DSM 29075), a new species isolated from a stool specimen from a 37-year-old Brazilian woman. This description includes phenotypic characteristics and complete genome sequence and annotation. Strain CB1T is a gram-negative aerobic and motile bacillus, exhibits neither catalase nor oxidase activities, and presents a 98.3% 16S rRNA sequence similarity with Pseudomonas putida. The 4,723,534 bp long genome contains 4239 protein-coding genes and 74 RNA genes, including 15 rRNA genes (5 16S rRNA, 4 23S rRNA, and 6 5S rRNA) and 59 tRNA genes. Strain CB1T was named Pseudomonas massiliensis sp. nov. and classified into the family Pseudomonadaceae. This study demonstrates the usefulness of microbial culturomics in exploration of human microbiota in diverse geographies and offers new promise for incorporating new omics technologies for innovation in diagnostic medicine and global health.


Assuntos
Genoma Bacteriano/genética , Pseudomonas/genética , Adulto , Brasil , Mapeamento Cromossômico/métodos , Feminino , Microbioma Gastrointestinal/genética , Genômica/métodos , Saúde Global , Humanos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/métodos , Sequenciamento Completo do Genoma/métodos
17.
Future Microbiol ; 11(3): 455-66, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26974504

RESUMO

In recent years, the number of multidrug-resistant bacteria has increased rapidly and several epidemics were signaled in different regions of the world. Faced with this situation that presents a major global public health concern, the development and the use of new and rapid technologies is more than urgent. The use of the next-generation sequencing platforms by microbiologists and infectious disease specialists has allowed great progress in the medical field. Here, we review the usefulness of whole-genome sequencing for the detection of virulence and antibiotic resistance associated genes.


Assuntos
Bactérias/genética , Farmacorresistência Bacteriana Múltipla/genética , Genoma Bacteriano , Genômica , Fatores de Virulência/genética , Bactérias/efeitos dos fármacos , Bactérias/patogenicidade , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Virulência/genética
18.
Stand Genomic Sci ; 11: 32, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27087892

RESUMO

Strain G3(T) (CSUR P207 = DSM 26203) was isolated from the fecal sample of a wild gorilla (Gorilla gorilla subsp gorilla) from Cameroon. It is a Gram-positive, facultative anaerobic short rod. This strain exhibits a 16S rRNA sequence similarity of 98.2 % with Microbacterium thalassium, the closest validly published Microbacterium species and member of the family Microbacteriaceae. Moreover, it shows a low MALDI-TOF-MS score (1.1 to 1.3) that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the phenotypic features of this organism, the complete genome sequence and annotation. The 3,692,770 bp long genome (one chromosome but no plasmid) contains 3,505 protein-coding and 61 RNA genes, including 4 rRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G3(T) against the closest Microbacterium genomes range between 19.7 to 20.5, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Microbacterium gorillae sp. nov. that contains the strain G3(T).

19.
OMICS ; 19(12): 766-76, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26669711

RESUMO

Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.


Assuntos
Bacillus/classificação , Bacillus/genética , Microbioma Gastrointestinal , Metagenoma , Metagenômica , Adulto , Bacillus/efeitos dos fármacos , Bacillus/ultraestrutura , Feminino , Genoma Bacteriano , Genômica , Humanos , Metagenômica/métodos , Fenótipo , Filogenia , RNA Ribossômico 16S/genética
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