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1.
Artigo em Chinês | MEDLINE | ID: mdl-33040503

RESUMO

Objective:To compare the nasal microbiota diversity between chronic rhinosinusitis with nasal polyp(CRSwNP) patients and controls, postoperative recurrent with non-recurrent CRSwNP, in order to provide new sight in CRSwNP treatment and prognosis. Method:Forty-eight patients with CRSwNP were recruited as the experimental group, and 33 patients who underwent FESS and had no sinus inflammatory disease, including nasal septum deviation,inverted papilloma, pituitary adenomas, chronic dacryocystitis,or optical canal fractures, were recruited as control group. High-throughput sequencing of 16S rRNA was used to detect the bacterial communities in the nasal secretion which was collected from middle meatus during the operation. The difference of the microbiota diversity between CRSwNP and controls was compared. Patients with CRSwNP were followed up for 1 year after surgery to observe whether they had relapsed or not, and nasal secretions were collected again for bacterial microbiota detection. The difference between postoperative and preoperative microbiota of the non-recurrent CRSwNP were compared, and the difference between postoperative and preoperative microbiota of the recurrent CRSwNP were compared. Result:One year after surgery, 12 cases of CRSwNP recurred(recurrent rate 25%). The clinical history of the recurrent group was longer than that of the non-recurrent group(P=0.018), and the preoperative CT score(P=0.001), nasal polyp size score(P=0.004) and the severity of postnasal drip symptom(P=0.032) in the recurrent group were significantly higher than non-recurrent group. Comparing the preoperative nasal microbiota of CRSwNP with control, there was no significant difference about the richness, α diversity and ß diversity, but the relative abundance of Actinobacteria(FDR P=0.004) and Corynebacterium(FDR P=0.005) of CRSwNP were significantly lower than that of control. After operation, the relative abundance of Actinobacteria(FDR P=0.012) and Corynebacterium(FDR P=0.003) increased, while the Bacteroidetes(FDR P=0.040) decreased in the non-recurrent CRSwNP; However, there was no change in the nasal bacterial microbiota in the recurrent group. Conclusion:CRSwNP was associated with nasal bacterial dysbiosis, and the postoperative improvement of dysbiosis was correlated with the prognosis of CRSwNP.


Assuntos
Microbiota , Pólipos Nasais , Rinite , Sinusite , Humanos , Pólipos Nasais/cirurgia , Recidiva Local de Neoplasia , Prognóstico , RNA Ribossômico 16S/genética , Sinusite/cirurgia
2.
Chemosphere ; 254: 126891, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32957291

RESUMO

Gut microbiota executes many beneficial functions. In this study, the relationship between gut microbiota and ovarian development in the swimming crab P. trituberculatus was explored for the first time. A total of 28 phyla and 422 genera were identified across all samples. However, 105 differential operational taxonomic units, and four differential phyla (Gemmatimonadetes, Actinobacteria, Firmicutes, Marinimicrobia_(SAR406_clade)) were identified. At the genus level, 42 differential genera were identified and 144 bacterial indicators were identified. A key finding was that the relative abundance of 139 indicator bacteria detected in the anisomycin-2 mg/kg group (AK group) was higher than that of blank group (BK group), control group (CK group), SP600125-15 mg/kg group (SK group). In addition, the relative abundance of three indicator bacteria (OTU_236, OTU_1395, OTU_552) detected in the SK group was higher than that of the BK, CK and AK groups. It was also found that the relative abundance of 20 differential genera (Methyloversatilis, Coprococcus_1, Erysipelotrichaceae_UCG_003, Rikenella, Corynebacterium, Ruminiclostridium, Fusicatenibacter, [Eubacterium]_ruminantium_group, Rikenellaceae_RC9_gut_group, Bifidobacterium, Lachnospiraceae_NK4A136_group, Ruminococcaceae_UCG_014, Christensenellaceae_R_7_group, uncultured_Bacteroidales_bacterium, Coprococcus_2, Desulfovibrio, Aggregatibacter, Ambiguous_taxa, Alloprevotella and Ruminococcaceae_NK4A214_group) in the SK, BK, CK, and AK group samples were increasing. These differential genera may reveal the relationship between gut microbial communities and ovarian development in P. trituberculatus after injection with the JNK pathway inhibitor SP600125 or the activator anisomycin. In summary, this study provides a new understanding into the relationship between gut microbiota and ovarian development in response to stimulation with inhibitor or activator.


Assuntos
Braquiúros/fisiologia , Microbioma Gastrointestinal/fisiologia , Animais , Bactérias/genética , Feminino , Microbioma Gastrointestinal/genética , Microbiota , RNA Ribossômico 16S/genética , Natação
3.
Ecotoxicol Environ Saf ; 203: 111047, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32888598

RESUMO

Understanding azo dye degrading enzymes and the encoding of their functional genes is crucial for the elucidation of their molecular mechanisms. In this study, a thermophilic strain capable of degrading azo dye was isolated from the soil near a textile dye manufacturing factory. Based on its morphological, physiological and biochemical properties, as well as 16S rRNA gene sequence analysis, the strain was identified as Anoxybacillus sp. PDR2. The decolorization ratios of 100-600 mg/L Direct Black G (DBG) by strain PDR2 reached 82.12-98.39% within 48 h of dyes. Genome analysis revealed that strain PDR2 contains a circular chromosome of 3791144 bp with a G + C content of 42.48%. The genetic basis of azo dye degradation by strain PDR2 and its capacity to adapt to harsh environments, were further elucidated through bioinformatics analysis. RNA-Seq and qRT-PCR technology confirmed that NAD(P)H-flavin reductase, 2Fe-2S ferredoxin and NAD(P)-dependent ethanol dehydrogenase genes expressed by strain PDR2, were the key genes involved in DBG degradation. The combination of genome and transcriptome analysis was utilized to explore the key genes of strain PDR2 involved in azo dye biodegradation, with these findings providing a valuable theoretical basis for the practical treatment of azo dye wastewater.


Assuntos
Anoxybacillus/isolamento & purificação , Compostos Azo/análise , Corantes/análise , Genes Bacterianos , Microbiologia do Solo , Anoxybacillus/genética , Anoxybacillus/metabolismo , Compostos Azo/metabolismo , Biodegradação Ambiental , China , Corantes/metabolismo , Perfilação da Expressão Gênica , Genômica , RNA Ribossômico 16S/genética , Solo/química , Indústria Têxtil
4.
Medicine (Baltimore) ; 99(39): e22298, 2020 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-32991434

RESUMO

RATIONALE: There are many treatments for chronic hemorrhagic radiation colorectal inflammation, but only a few treatments are supported by high-quality research evidence. Studies have shown that the occurrence and development of radiation proctitis are closely associated with the intestinal flora. Animal studies have indicated that faecal microbiota transplantation (FMT) can improve radiation enteropathy in a mouse model. PATIENT CONCERNS: A 45-year-old female patient suffered from recurrent hematochezia and diarrhea for half a year after radiotherapy and underwent recurrent transfusion treatments. Colonoscopy showed obvious congestion of the sigmoid colon and rectal mucosa, a smooth surface, and bleeding that was easily induced by touch, which are consistent with radiation proctitis. The pathological findings revealed chronic mucosal inflammation. The magnetic resonance imaging examination of the pelvic cavity with a plain scan and enhancement showed changes after radiotherapy and chemotherapy, and no obvious tumor recurrence or metastasis was found. The laboratory examinations excluded pathogen infection. DIAGNOSES: Based on the history and examinations, the final diagnosis of this patient was chronic hemorrhagic radiation proctitis. INTERVENTIONS: The patient was treated with a total of 4 individual courses of FMT. OUTCOMES: After the six-month follow-up, her hematochezia, abdominal pain and diarrhea were relieved. Furthermore, 16S rRNA sequencing of the feces showed that the intestinal bacterial composition of the patient obviously changed after FMT and became similar to that of the donors. LESSONS: This case report shows that FMT can relieve the symptoms of hematochezia and diarrhea by changing the bacterial community structure in patients with chronic hemorrhagic radiation proctitis.


Assuntos
Transplante de Microbiota Fecal/métodos , Hemorragia Gastrointestinal/terapia , Proctite/etiologia , Lesões por Radiação/complicações , Assistência ao Convalescente , Doença Crônica , Colonoscopia/métodos , Diarreia/etiologia , Fezes/microbiologia , Feminino , Humanos , Imagem por Ressonância Magnética/métodos , Pessoa de Meia-Idade , Proctite/diagnóstico , Proctite/patologia , RNA Ribossômico 16S/genética , Lesões por Radiação/diagnóstico por imagem , Lesões por Radiação/patologia , Doadores de Tecidos , Resultado do Tratamento
5.
Pediatrics ; 146(4)2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32934151

RESUMO

OBJECTIVES: Although the airway microbiota is a highly dynamic ecology, the role of longitudinal changes in airway microbiota during early childhood in asthma development is unclear. We aimed to investigate the association of longitudinal changes in early nasal microbiota with the risk of developing asthma. METHODS: In this prospective, population-based birth cohort study, we followed children from birth to age 7 years. The nasal microbiota was tested by using 16S ribosomal RNA gene sequencing at ages 2, 13, and 24 months. We applied an unsupervised machine learning approach to identify longitudinal nasal microbiota profiles during age 2 to 13 months (the primary exposure) and during age 2 to 24 months (the secondary exposure) and examined the association of these profiles with the risk of physician-diagnosed asthma at age 7 years. RESULTS: Of the analytic cohort of 704 children, 57 (8%) later developed asthma. We identified 4 distinct longitudinal nasal microbiota profiles during age 2 to 13 months. In the multivariable analysis, compared with the persistent Moraxella dominance profile during age 2 to 13 months, the persistent Moraxella sparsity profile was associated with a significantly higher risk of asthma (adjusted odds ratio, 2.74; 95% confidence interval, 1.20-6.27). Similar associations were observed between the longitudinal changes in nasal microbiota during age 2 to 24 months and risk of asthma. CONCLUSIONS: Children with an altered longitudinal pattern in the nasal microbiota during early childhood had a high risk of developing asthma. Our data guide the development of primary prevention strategies (eg, early identification of children at high risk and modification of microbiota) for childhood asthma. These observations present a new avenue for risk modification for asthma (eg, microbiota modification).


Assuntos
Asma/etiologia , Microbiota , Nariz/microbiologia , Aerococcaceae/isolamento & purificação , Fatores Etários , Asma/diagnóstico , Asma/microbiologia , Criança , Pré-Escolar , Feminino , Finlândia , Seguimentos , Perfilação da Expressão Gênica/métodos , Haemophilus/isolamento & purificação , Humanos , Incidência , Lactente , Recém-Nascido , Aprendizado de Máquina , Masculino , Microbiota/genética , Moraxella/isolamento & purificação , Análise Multivariada , Estudos Prospectivos , RNA Ribossômico 16S/genética , Infecções Respiratórias/complicações , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/microbiologia , Risco , Streptococcus/isolamento & purificação
6.
BMC Infect Dis ; 20(1): 687, 2020 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948147

RESUMO

BACKGROUND: Vogesella species are common aquatic, Gram-negative rod-shaped bacteria, originally described in 1997. Vogesella perlucida was first isolated from spring water in 2008. Furthermore, bacterial pathogenicity of Vogesella perlucida has never been reported. Here, we report the first case of rare Vogesella perlucida-induced bacteremia in an advanced-age patient with many basic diseases and history of dexamethasone abuse. CASE PRESENTATION: A 71-year-old female was admitted with inflamed upper and lower limbs, rubefaction, pain and fever (about 40 °C). She had been injured in a fall at a vegetable market and then touched river snails with her injury hands. A few days later, soft tissue infection of the patient developed and worsened. Non-pigmented colonies were isolated from blood cultures of the patient. Initially, Vogesella perlucida was wrongly identified as Sphingomonas paucimobilis by Vitek-2 system with GN card. Besides, we failed to obtain an acceptable identification by the MALDI-TOF analysis. Finally, the isolated strain was identified as Vogesella perlucida by 16S rRNA gene sequences. In addition, the patient recovered well after a continuous treatment of levofloxacin for 12 days. CONCLUSION: Traditional microbiological testing system may be inadequate in the diagnosis of rare pathogenic bacteria. Applications of molecular diagnostics techniques have great advantages in clinical microbiology laboratory. By using 16S rRNA gene sequence analysis, we report the the first case of rare Vogesella perlucida-induced bacteremia.


Assuntos
Bacteriemia/microbiologia , Betaproteobacteria/patogenicidade , Infecções dos Tecidos Moles/microbiologia , Idoso , Antibacterianos/uso terapêutico , Bacteriemia/tratamento farmacológico , Técnicas de Tipagem Bacteriana , Betaproteobacteria/classificação , Betaproteobacteria/genética , Betaproteobacteria/isolamento & purificação , Feminino , Humanos , Levofloxacino/uso terapêutico , RNA Ribossômico 16S/genética , Infecções dos Tecidos Moles/tratamento farmacológico , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Vancomicina/uso terapêutico
7.
Nat Commun ; 11(1): 4822, 2020 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-32973149

RESUMO

Abiraterone acetate (AA) is an inhibitor of androgen biosynthesis, though this cannot fully explain its efficacy against androgen-independent prostate cancer. Here, we demonstrate that androgen deprivation therapy depletes androgen-utilizing Corynebacterium spp. in prostate cancer patients and that oral AA further enriches for the health-associated commensal, Akkermansia muciniphila. Functional inferencing elucidates a coinciding increase in bacterial biosynthesis of vitamin K2 (an inhibitor of androgen dependent and independent tumor growth). These results are highly reproducible in a host-free gut model, excluding the possibility of immune involvement. Further investigation reveals that AA is metabolized by bacteria in vitro and that breakdown components selectively impact growth. We conclude that A. muciniphila is a key regulator of AA-mediated restructuring of microbial communities, and that this species may affect treatment response in castrate-resistant cohorts. Ongoing initiatives aimed at modulating the colonic microbiota of cancer patients may consider targeted delivery of poorly absorbed selective bacterial growth agents.


Assuntos
Acetato de Abiraterona/farmacologia , Microbioma Gastrointestinal/efeitos dos fármacos , Neoplasias de Próstata Resistentes à Castração/tratamento farmacológico , Neoplasias da Próstata/tratamento farmacológico , Verrucomicrobia/efeitos dos fármacos , Acetato de Abiraterona/metabolismo , Acetato de Abiraterona/uso terapêutico , Antagonistas de Androgênios/farmacologia , Androgênios/metabolismo , Bactérias/metabolismo , Fezes/microbiologia , Humanos , Masculino , RNA Ribossômico 16S/genética , Verrucomicrobia/genética , Verrucomicrobia/metabolismo , Vitamina K 2/metabolismo , Vitamina K 2/farmacologia
8.
PLoS One ; 15(8): e0237748, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32866195

RESUMO

Soil microbiota are considered a source of undiscovered bioactive compounds, yet cultivation of most bacteria within a sample remains generally unsuccessful. Two main reasons behind the unculturability of bacteria are the presence of cells in a viable but not culturable state (such as dormant cells) and the failure to provide the necessary growth requirements in vitro (leading to the classification of some bacterial taxa as yet-to-be-cultured). The present work focuses on the development of a single procedure that helps distinguish between both phenomena of unculturability based on viability staining coupled with flow cytometry and fluorescence-activated cell sorting. In the selected soil sample, the success rate of cultured bacteria was doubled by selecting viable and metabolically active bacteria. It was determined that most of the uncultured fraction was not dormant or dead but likely required different growth conditions. It was also determined that the staining process introduced changes in the taxonomic composition of the outgrown bacterial biomass, which should be considered for further developments. This research shows the potential of flow cytometry and fluorescence-activated cell sorting applied to soil samples to improve the success rate of bacterial cultivation by estimating the proportion of dormant and yet-to-be-cultured bacteria and by directly excluding dormant cells from being inoculated into growth media.


Assuntos
Bactérias/crescimento & desenvolvimento , Técnicas Microbiológicas/métodos , Microbiota/fisiologia , Microbiologia do Solo , Bactérias/química , Bactérias/genética , Biomassa , Separação Celular/métodos , Meios de Cultura , DNA Bacteriano/isolamento & purificação , Estudos de Viabilidade , Citometria de Fluxo/métodos , Corantes Fluorescentes/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Coloração e Rotulagem/métodos
9.
Zhong Nan Da Xue Xue Bao Yi Xue Ban ; 45(7): 849-855, 2020 Jul 28.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-32879089

RESUMO

The 16S rRNA gene is the most commonly used molecular marker for identifying microorganisms. It is used in sequencing technology, including the first-generation, the second-generation, and the third-generation sequencing technology. A large number of studies on the 16S rRNA gene have contributed to a deeper understanding of oral microbial diversity. In the healthy oral cavity, there is microbial diversity in time and space. With the occurrence or development of oral diseases such as caries, periodontal disease, or halitosis, the microbial diversity will be changed.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Boca , RNA Ribossômico 16S/genética
10.
Mikrobiyol Bul ; 54(3): 404-417, 2020 Jul.
Artigo em Turco | MEDLINE | ID: mdl-32755517

RESUMO

Gram-positive anaerobic cocci (GPAC), a large group of anaerobic bacteria, are the members of the normal microbiota that colonizes the skin and mucosal surfaces of the human body. However, in case of a wound or when the host becomes immunocompromised, GPAC can cause invasive and most frequently mixed infections. GPAC are the second most frequently isolated bacteria in anaerobic infections. Although the studies are limited, GPAC have been reported to develop resistance to antimicrobial drugs. The resistance of the pathogens to the antimicrobials and improper therapy can cause poor clinical outcomes. Therefore, monitoring of the resistance trends of regional clinically important anaerobic bacteria periodically is recommended. In our study, we aimed to determine the antimicrobial susceptibility profiles of clinically important GPAC. A total of 100 non-duplicated pathogenic GPAC isolates were collected from Marmara University Hospital between 2013 and 2015. The isolates were identified by using conventional methods, "matrix-assisted laser desorption ionization-time of flight mass spectrometry system (MALDI-TOF MS)" (VITEK MS; v3.0, bioMerieux, France) and 16S rRNA gene sequencing. Antimicrobial susceptibility test was carried out by the agar dilution method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. The following antimicrobials were tested: penicillin, amoxicillin/ clavulanic acid (AMC), cefoxitin, meropenem, clindamycin, erythromycin, tetracycline, tigecycline, chloramphenicol, moxifloxacin and metronidazole. The minimum inhibitory concentration (MIC) results were interpreted according to the breakpoints described by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Breakpoints recommended by CLSI for cefoxitin, tetracycline and moxifloxacin, and breakpoint recommended by Food and Drug Administration (FDA) for tigecycline were used since there were no EUCAST breakpoints for these antimicrobials. MIC50 and MIC90 values were determined for erythromycin since the breakpoint was not described by EUCAST, CLSI or FDA guidelines. The identification results showed that the strains (n= 100) consisted of five different GPAC genus; Parvomonas (40%), Finegoldia (34%), Peptoniphilus (14%), Peptostreptococcus (10%) and Anaerococcus (1%). All of the organisms were susceptible to meropenem, tigecycline and metronidazole. The isolates were highly susceptible to penicillin, AMC, cefoxitin, and chloramphenicol, since the resistance rates against these antimicrobials were 5% or less. The resistance rates against clindamycin, tetracycline and moxifloxacin were 14%, 31% and 24%, respectively. In total, 11% of the isolates were multidrug resistant. Metronidazole and tigecycline displayed high in vitro activity against GPAC and both are appropriate antimicrobials for the selection of empiric therapy. The effectiveness of meropenem was also found high, but it was observed that this antimicrobial would be more appropriate to use in the treatment of severe mixed infections accompanied by other microorganisms with the resistance potential. Detection of penicillin and AMC resistant isolates, which are frequently used in the treatment of GPAC infection, requires periodic monitoring of the antimicrobial susceptibility patterns of GPAC. The high rates of resistance against clindamycin, tetracycline and moksifloxacin indicated that these antimicrobials should not be used for empirical treatment of infections without prior antimicrobial susceptibility testing. This study is one of the largest susceptibility studies specifically carried out on GPAC to date in Turkey. We believe that our results will provide good surveillance data both for our hospital and our country.


Assuntos
Antibacterianos , Farmacorresistência Bacteriana , Cocos Gram-Positivos , Anaerobiose , Antibacterianos/farmacologia , Cocos Gram-Positivos/efeitos dos fármacos , Cocos Gram-Positivos/genética , Humanos , Testes de Sensibilidade Microbiana , RNA Ribossômico 16S/genética , Turquia
11.
BMC Infect Dis ; 20(1): 610, 2020 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-32811432

RESUMO

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is one of the most prevalent diseases worldwide. Episodes of acute exacerbations of COPD (AECOPD) are associated with disease severity and progression. Although substantial progress has been made in understanding the dynamics of AECOPD, little is known about the sputum microbiome of AECOPD in the Chinese population. METHODS: In this study, we characterized the sputum microbiomes from sputum specimens collected from healthy controls (n = 10), stable (n = 4), AECOPD (n = 36), and recovery (n = 18) stages by sequencing the V3-V4 region of the 16S rRNA gene with a HiSeq sequencer. RESULTS: Streptococcus was the most dominant genus among all the different types of sputum. A random forest model was developed to identify bacterial taxa that differentiate AECOPD samples from others. Most of the top predictors, except Pseudomonas, were less abundant in AECOPD samples. We also developed random forest models to differentiate subtypes of AECOPD based on blood eosinophil counts, the frequency of AECOPD, and sputum eosinophils. Bacterial taxa associated with Pasteurellaceae, Fusobacterium, Solobacterium, Haemophilus, Atopobium, Corynebacterium and Streptococcus, were enriched in the sputum microbiomes of eosinophilic AECOPD. Random forest models also demonstrate that a total of 2 bacterial OTUs were needed to differentiate frequent from non-frequent AECOPDs, and 23 OTUs were enough to accurately predict sputum-eosinophilic (sputum eosinophilic concentration ≥ 3%) AECOPD. CONCLUSION: This study expanded our understanding of the sputum microbiome associated with different subtypes and clinical status of patients with AECOPD in a Chinese cohort, which provides insights into novel and more targeted management of the different subtypes of AECOPD.


Assuntos
Microbiota/genética , Doença Pulmonar Obstrutiva Crônica/epidemiologia , Doença Pulmonar Obstrutiva Crônica/microbiologia , Escarro/microbiologia , Streptococcus/genética , Idoso , Idoso de 80 Anos ou mais , Biomarcadores , China/epidemiologia , Estudos de Coortes , Progressão da Doença , Eosinófilos , Feminino , Humanos , Contagem de Leucócitos , Masculino , Pessoa de Meia-Idade , Prevalência , RNA Ribossômico 16S/genética
12.
Sheng Wu Gong Cheng Xue Bao ; 36(7): 1356-1364, 2020 Jul 25.
Artigo em Chinês | MEDLINE | ID: mdl-32748593

RESUMO

Salinity is the most important factor for the growth of crops. It is an effective method to alleviate the toxic effect caused by salt stress using saline-alkali-tolerant and growth-promoting bacteria in agriculture. Seven salt-tolerant bacteria were screened from saline-alkali soil, and the abilities of EPS production, alkalinity reduction and IAA production of the selected strains were investigated. A dominant strain DB01 was evaluated. The abilities of EPS production, alkalinity reduction and IAA production of strain DB01 were 0.21 g/g, 8.7% and 8.97 mg/L, respectively. The isolate was identified as Halomonas aquamarina by partial sequencing analysis of its 16S rRNA genes, and had the ability to inhibit the growth of Fusarium oxysporum f. sp., Alternaria solani, Phytophthora sojae and Rhizoctonia cerealis. It also could promote root length and germination rate of wheat seedlings under salt stress. Halomonas aquamarina can provide theoretical basis for the development of soil microbial resources and the application in saline-alkali soil improvement.


Assuntos
Álcalis , Raízes de Plantas , Tolerância ao Sal , Microbiologia do Solo , Álcalis/metabolismo , Bactérias/efeitos dos fármacos , Bactérias/genética , Halomonas/genética , Raízes de Plantas/microbiologia , RNA Ribossômico 16S/genética , Tolerância ao Sal/genética , Plântula/crescimento & desenvolvimento , Plântula/microbiologia , Solo/química , Triticum/microbiologia
13.
BMC Infect Dis ; 20(1): 629, 2020 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-32842982

RESUMO

BACKGROUND: In this study, the association between human papillomavirus (HPV) infection and related cervical intraepithelial neoplasia (CIN) or cervical cancer and vaginal microbiome was evaluated in Chinese cohorts. METHODS: The vaginal bacterial composition of five groups, HPV-infected women without CINs (HPV, n = 78), women with low-grade squamous intraepithelial lesions (LSIL, n = 51), women with high-grade squamous intraepithelial lesions (HSIL, n = 23), women with invasive cervical cancer (Cancer, n = 9) and healthy women without HPV infection (Normal, n = 68), was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V3-4) using Illumina MiSeq. RESULTS: HPV infection increased vaginal bacterial richness and diversity regardless of the status of CINs. The vaginal bacterial richness and diversity were further augmented in women with cervical cancer. Lactobacillus was the most abundant genus in all groups. HPV infection had a negative influence on the abundances of Lactobacillus, Gardnerella and Atopobium. Accordingly, HPV infection increased the relative abundance of Prevotella, Bacillus, Anaerococcus, Sneathia, Megasphaera, Streptococcus and Anaerococcus. The increased proportions of Bacillus, Anaerococcus and the reduced abundance of Gradnerella vaginalis were probably related with the progression of CINs severity. HPV infection without CINs or cancerous lesions was strongly associated with Megasphaera. The most abundant bacterium in the LSIL group was Prevotella amnii. However, Prevotella timonensis, Shuttleworthia and Streptococcaceae at the family level were three taxa related to HSIL. Furthermore, more taxa were associated with the Cancer group including Bacillus, Sneathia, Acidovorax, Oceanobacillus profundus, Fusobacterium, Veillonellaceae at the family level, Anaerococcus and Porphyromonas uenonis. Samples in the Normal group were mostly assigned to CST III. HPV infection converted the vaginal bacterial community structure from CST III to CST IV. Furthermore, the proportions of CST IV were gradually augmented with the progression of the severity of CINs. CONCLUSIONS: This work interpreted the differential vaginal bacteria under HPV infection and various precancerous or cancerous lesions in a Chinese cohort. We distinguished the specific microbes and the vaginal bacterial structure that were related with the progression of CINs severity in Chinese women.


Assuntos
Biodiversidade , Neoplasia Intraepitelial Cervical/epidemiologia , Progressão da Doença , Microbiota/genética , Papillomaviridae/genética , Infecções por Papillomavirus/epidemiologia , Neoplasias do Colo do Útero/epidemiologia , Vagina/microbiologia , Adulto , Idoso , Neoplasia Intraepitelial Cervical/virologia , China/epidemiologia , Estudos de Coortes , Feminino , Humanos , Lactobacillus/genética , Pessoa de Meia-Idade , Infecções por Papillomavirus/virologia , RNA Ribossômico 16S/genética , Neoplasias do Colo do Útero/virologia
14.
J Environ Manage ; 274: 111190, 2020 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-32771773

RESUMO

The objectives of this study were to clarify the distribution as well as the removal mechanism of antibiotic resistance genes (ARGs) within three sludge treatment wetlands (STWs) during a loading period of two years. Three STW units were constructed and run during the loading period: Unit 1 (U1) built with aeration tubes, Unit 2 (U2) built with aeration tubes and reeds, and Unit 3 (U3) built with reeds only. All targeted ARGs, intI1, and 16S rRNA were detected in residual sludge in the order of magnitude: 16S rRNA>sul1>intI1>sul2>tetC>tetA>ermB. The abundance of the five targeted ARGs, intI1, and 16S rRNA increased in residual sludge, during the loading period, which may be due to the increase in bacteria caused by the continuous import of exogenous nutrients. However, STWs can also remove ARGs from sewage during the loading period and the mean removal efficiency of five resistance genes was 73.0%. The removal rates of intI1 and 16S rRNA were 73.5% and 78.6%, respectively. Positive correlations were detected in abundance of most ARGs and intI1, as well as 16S rRNA (P < 0.05), indicating intI1 plays a vital part in the propagation of ARGs. The removal of bacteria harboring these genes also occurs in the STW units.


Assuntos
Esgotos , Áreas Alagadas , Animais , Antibacterianos/farmacologia , Resistência Microbiana a Medicamentos/efeitos dos fármacos , Resistência Microbiana a Medicamentos/genética , Genes Bacterianos/genética , RNA Ribossômico 16S/genética , Águas Residuárias/análise
15.
PLoS One ; 15(8): e0236574, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32790770

RESUMO

Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs application are known to influence diversity and function of soil microbial populations. In this study, we investigated the effect of conventional versus organic farming systems at low and high input levels on structure and diversity of prokaryotic microbial communities. Soil samples were collected from the ongoing long-term farming system comparison trials established in 2007 at Chuka and Thika in Kenya. Physicochemical parameters for each sample were analyzed. Total DNA and RNA amplicons of variable region (V4-V7) of the 16S rRNA gene were generated on an Illumina platform using the manufacturer's instructions. Diversity indices and statistical analysis were done using QIIME2 and R packages, respectively. A total of 29,778,886 high quality reads were obtained and assigned to 16,176 OTUs at 97% genetic distance across both 16S rDNA and 16S rRNA cDNA datasets. The results pointed out a histrionic difference in OTUs based on 16S rDNA and 16S rRNA cDNA. Precisely, while 16S rDNA clustered by site, 16S rRNA cDNA clustered by farming systems. In both sites and systems, dominant phylotypes were affiliated to phylum Actinobacteria, Proteobacteria and Acidobacteria. Conventional farming systems showed a higher species richness and diversity compared to organic farming systems, whilst 16S rRNA cDNA datasets were similar. Physiochemical factors were associated differently depending on rRNA and rDNA. Soil pH, electrical conductivity, organic carbon, nitrogen, potassium, aluminium, zinc, iron, boron and micro-aggregates showed a significant influence on the observed microbial diversity. The observed higher species diversity in the conventional farming systems can be attributed to the integration of synthetic and organic agricultural inputs. These results show that the type of inputs used in a farming system not only affect the soil chemistry but also the microbial population dynamics and eventually the functional roles of these microbes.


Assuntos
Agricultura/métodos , Microbiologia do Solo , Acidobacteria/genética , Acidobacteria/isolamento & purificação , DNA Bacteriano/genética , Quênia , Microbiota , Agricultura Orgânica/métodos , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética
16.
PLoS One ; 15(8): e0236932, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32745120

RESUMO

Humanity's reliance on clean water and the ecosystem services provided makes identifying efficient and effective ways to assess the ecological condition of streams ever more important. We used high throughput sequencing of the 16S rRNA region to explore relationships between stream microbial communities, environmental attributes, and assessments of stream ecological condition. Bacteria and archaea in microbial community samples collected from the water column and from stream sediments during spring and summer were used to replicate standard assessments of ecological condition performed with benthic macroinvertebrate collections via the Benthic Index of Biotic Integrity (BIBI). Microbe-based condition assessments were generated at different levels of taxonomic resolution from phylum to OTU (Operational Taxonomic Units) in order to understand appropriate levels of taxonomic aggregation. Stream sediment microbial communities from both spring and summer were much better than the water column at replicating BIBI condition assessment results. Accuracies were as high as 100% on training data used to build the models and up to 80% on validation data used to assess predictions. Assessments using all OTUs usually had the highest accuracy on training data, but were lower on validation data due to overfitting. In contrast, assessments at the order-level had similar performance accuracy for validation data, and a reduced subset of orders also performed well, suggesting the method could be generalized to other watersheds. Subsets of the important orders responded similarly to environmental gradients compared to the entire community, where strong shifts in community structure occurred for known aquatic stressors such as pH, dissolved organic carbon, and nitrate nitrogen. The results suggest the stream microbes may be useful for assessing the ecological condition of streams and especially useful for stream restorations where many eukaryotic taxa have been eliminated due to prior degradation and are unable to recolonize.


Assuntos
Monitorização de Parâmetros Ecológicos/métodos , Microbiota/genética , Rios/microbiologia , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Ecossistema , Monitoramento Ambiental/métodos , Sedimentos Geológicos/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , RNA Ribossômico 16S/genética
17.
PLoS One ; 15(8): e0233325, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32756562

RESUMO

Antibiotics discovery was a significant breakthrough in the field of therapeutic medicines, but the over (mis)use of such antibiotics (in parallel) caused the increasing number of resistant bacterial species at an ever-higher rate. This study was thus devised to assess the multi-drug resistant bacteria present in sanitation-related facilities in human workplaces. In this regard, samples were collected from different gender, location, and source-based facilities, and subsequent antibiotic sensitivity testing was performed on isolated bacterial strains. Four classes of the most commonly used antibiotics i.e., ß-lactam, Aminoglycosides, Macrolides, and Sulphonamides, were evaluated against the isolated bacteria. The antibiotic resistance profile of different (70) bacterial strains showed that the antibiotic resistance-based clusters also followed the grouping based on their isolation sources, mainly the gender. Twenty-three bacterial strains were further selected for their 16s rRNA gene based molecular identification and for phylogenetic analysis to evaluate the taxonomic evolution of antibiotic resistant bacteria (ARB). Moreover, the bacterial resistance to Sulphonamides and beta lactam was observed to be the most and to Aminoglycosides and macrolides as the least. Plasmid curing was also performed for multidrug resistant (MDR) bacterial strains, which significantly abolished the resistance potential of bacterial strains for different antibiotics. These curing results suggested that the antibiotic resistance determinants in these purified bacterial strains are present on respective plasmids. Altogether, the data suggested that the human workplaces are the hotspot for the prevalence of MDR bacteria and thus may serve as the source of horizontal gene transfer and further transmission to other environments.


Assuntos
Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Farmacorresistência Bacteriana Múltipla , Toaletes , Local de Trabalho , Bactérias/genética , Farmacorresistência Bacteriana Múltipla/genética , Microbiologia Ambiental , Feminino , Humanos , Higiene , Masculino , Exposição Ocupacional , Paquistão , Filogenia , Plasmídeos , Prevalência , Fatores R , RNA Ribossômico 16S/genética , Saneamento
18.
PLoS One ; 15(8): e0234839, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32853201

RESUMO

Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.


Assuntos
Gammaproteobacteria/genética , Sedimentos Geológicos/microbiologia , Regiões Árticas , Proteínas de Bactérias/genética , Estuários , Gammaproteobacteria/classificação , Gammaproteobacteria/metabolismo , Genoma Bacteriano , Proteínas de Choque Térmico/genética , Metagenoma , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Svalbard , Transcriptoma
19.
PLoS One ; 15(8): e0236470, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32750057

RESUMO

OBJECTIVES: Spinal cord injury (SCI) is associated with severe autonomic dysfunction. Patients with SCI often suffer from a lack of central nervous system control over the gastrointestinal system. Therefore, we hypothesized that patients with SCI would cause intestinal flora imbalance. We investigated alterations in the fecal microbiome in a group of patients with SCI. METHODS: Microbial communities in the feces of 23 patients and 23 healthy controls were investigated using high-throughput Illumina Miseq sequencing targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene. The relative abundances between the fecal microbiota at the genus level in patients with SCI and healthy individuals were determined using cluster analysis. RESULTS: The structure and quantity of fecal microbiota differed significantly between patients with SCI and healthy controls, but the richness and diversity were not significantly different. A two-dimensional heatmap showed that the relative abundances of forty-five operational taxonomic units (OTUs) were significantly enriched either in SCI or healthy samples. Among these, 18 OTUs were more abundant in healthy controls than in patients with SCI, and 27 OTUs were more abundant in the SCI group than in healthy controls. CONCLUSION: Our study showed that patients with SCI exhibited microbiome dysbiosis.


Assuntos
Disbiose/microbiologia , Fezes/microbiologia , Microbiota/genética , Traumatismos da Medula Espinal/microbiologia , Adulto , Bactérias/classificação , Bactérias/genética , Disbiose/genética , Disbiose/patologia , Feminino , Microbioma Gastrointestinal/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Filogenia , RNA Ribossômico 16S/genética , Traumatismos da Medula Espinal/genética , Traumatismos da Medula Espinal/patologia
20.
Bioresour Technol ; 316: 123909, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32739582

RESUMO

In this study, temporal impacts of thermal, alkaline/acid and thermal-alkaline sludge pre-treatments on digestion performance and microbiome were investigated and compared in methanogenic sludge digesters. Results showed that thermal and alkaline/acid pre-treatments were efficient in releasing intracellular and EPS organic matter, respectively. The thermal-alkaline pre-treatment showed synergistic impacts of both thermal and alkaline/acid pre-treatments by releasing the major portion of sludge organic matter from solid- to liquid-phase, which result in 60-65% organic carbon removal in subsequent sludge digestion and further optimizing digestion temperature had negligible improvement. The 16S rRNA gene-based analyses suggested that organic matter released from sludge pre-treatments is a major deterministic parameter in shaping sludge microbiome. Pre-treatment specific lineages were identified in different sludge digesters, whereas several taxa were identified as common functionally active populations in sludge digestion. This study provided mechanistic insights into impacts of pre-treatments on digestion performance and microbiome in methanogenic sludge digesters.


Assuntos
Euryarchaeota , Microbiota , Anaerobiose , Reatores Biológicos , Metano , RNA Ribossômico 16S/genética , Esgotos , Eliminação de Resíduos Líquidos
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