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1.
Sci Rep ; 12(1): 10698, 2022 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-35739324

RESUMO

Fusobacteria have been suspected to be pathobionts of colon cancer and inflammatory bowel disease. However, the immunomodulatory properties that affect these inflammatory reactions in dendritic cells (DCs) under anaerobic and aerobic conditions have not yet been characterized. We directly assessed the stimulatory effects of anaerobic commensal bacteria, including fusobacteria, on a human DC line through coculture under aerobic or anaerobic conditions. Under aerobic or anaerobic conditions, stimulation of the DC line with all live commensal bacteria examined, except the probiotic Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus), significantly increased the geometric mean fluorescent intensity (MFI) of marker proteins (HLA-ABC, HLA-DR, CD80, CD86, CD83, or CCR7) on the DC surface. In particular, both Fusobacterium nucleatum (F. nucleatum) and Escherichia coli (E. coli) significantly increased the expression of DC-associated molecules, except for CD83 under both aerobic and anaerobic conditions. The DC line stimulated with Fusobacterium varium (F. varium) significantly increased only CD80, HLA-ABC, and HLA-DR expression under anaerobic conditions. Moreover, differences in the levels of proinflammatory cytokines, such as IL-6, IL-8, and TNF-α, were detected in the DC line stimulated by all live commensal bacteria under either aerobic or anaerobic conditions. Under aerobic conditions, the DC line stimulated with E. coli produced significantly more IL-6, IL-8, and TNF-α than did the cells stimulated with any of the bacteria examined. When E. coli were used to stimulate the DC line under anaerobic conditions, TNF-α was predominantly produced compared to stimulation with any other bacteria. Compared to the DC line stimulated with any other bacteria, the cells stimulated with F. nucleatum showed significantly increased production of IL-6, IL-8 and TNF-α only under anaerobic conditions. In particular, E. coli, F. nucleatum, and F. varium strongly stimulated the DC line, resulting in significantly increased expression of surface molecules associated with DCs and production of inflammatory cytokines.


Assuntos
Células Dendríticas , Fator de Necrose Tumoral alfa , Anaerobiose , Antígeno B7-1/metabolismo , Células Cultivadas , Citocinas/metabolismo , Escherichia coli/metabolismo , Fusobactérias , Antígenos HLA-DR/metabolismo , Humanos , Interleucina-6/metabolismo , Interleucina-8/metabolismo , Fator de Necrose Tumoral alfa/metabolismo
2.
J Infect Chemother ; 28(8): 1165-1167, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35361535

RESUMO

Sneathia sanguinegens is a fastidious, Gram-negative, rod-shape organism rarely isolated from human specimens. In the present report, we describe a case of periprosthetic knee joint infection due to the organism, which occurred in a female patient receiving immunosuppressants for underlying lupus nephritis. The causative organism was isolated from the synovial fluid in the affected knee joint through inoculating the material on chocolate agar and incubation for 15 days under 5% CO2. Moreover, the organism was capable to be subcultured on chocolate agar with incubation for a few days under 5% CO2, demonstrating that this uncommon organism, although generally considered as a strict anaerobe, is culturable in aerobic condition if appropriate media and a sufficient incubation time are given. The patient was treated with intravenous cefepime, an antibiotic highly active to the isolated organism in an in vitro study, in addition to intraarticular debridement and exchanging a polyethylene insert in the affected joint. The antimicrobial therapy with cefepime was given for 19 days and, thereafter, changed with oral levofloxacin. Although the patient showed full recovery after administration of levofloxacin for 100 days, an in vitro study conducted later revealed that levofloxacin was inactive to the isolated organism.


Assuntos
Artrite Infecciosa , Infecções Relacionadas à Prótese , Ágar/uso terapêutico , Antibacterianos/uso terapêutico , Artrite Infecciosa/tratamento farmacológico , Dióxido de Carbono/uso terapêutico , Cefepima , Feminino , Fusobactérias , Bactérias Gram-Negativas , Humanos , Articulação do Joelho , Levofloxacino/uso terapêutico , Infecções Relacionadas à Prótese/complicações , Infecções Relacionadas à Prótese/tratamento farmacológico
3.
Fish Shellfish Immunol ; 124: 332-342, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35430347

RESUMO

The purpose of this study was to evaluate the effects of Cetobacterium somerae XMX-1 fermentation product on gut and liver health and resistance against bacterial infection in genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Fingerling GIFTs (n = 120; initial weight 1.33 ± 0.00 g) were randomly assigned to twelve 90-L tanks (four tanks per diet, 10 fish per tank) with three groups: control group (basal high fat diet), 1% XMX-1 group and 2% XMX-1 group (basal diet supplemented with 10 and 20 g XMX-1/kg feed respectively). After 49 days feeding trial, the growth performance and gut and liver health parameters of tilapia were evaluated. Also the gut microbiota and virome were detected by sequencing. 2% XMX-1 fermentation product had no effect on growth performance. For gut health, the expression of hypoxia-inducible factor-lα (Hif-1α) tend to increase in 1% XMX-1 group (P = 0.053). The expression of intestinal interleukin-6 (IL-6) and tumor growth factor ß (TGF-ß) was significantly down-regulated in 1% and 2% XMX-1 groups (P < 0.05), and the intestinal expression of interleukin-1ß (IL-1ß) had a trend to decrease (P = 0.08) in 1% XMX-1 group versus control. 1% and 2% XMX-1 groups also increased the intestinal expression of tight junction genes Claudin (P = 0.06 and 0.07, respectively). For liver health, XMX-1 fermentation product significantly decreased liver TAG (P < 0.05). Furthermore, the hepatic expression of lipid synthesis gene fatty acid synthase (FAS) was significantly decreased and the expression of lipid catabolism related-gene uncoupling protein 2 (UCP2) was significantly increased in 1% XMX-1 and 2% XMX-1 groups (P < 0.01). And the hepatic expression of IL-1ß and IL-6 significantly decreased in 1% XMX-1 and 2% XMX-1 groups (P < 0.05). XMX-1 fermentation product increased the abundance of Fusobacteria in the gut microbiota and 2% XMX-1 group led to alteration in the virome composition at family level. Lastly, the time of tilapia death post Aeromoans challenge was delayed in 1% XMX-1 and 2% XMX-1 groups compared with control. To sum up, our results show that the dietary supplementation of XMX-1 fermentation product can improve the gut and liver health as well as the resistance against pathogenic bacteria of tilapia.


Assuntos
Infecções Bacterianas , Ciclídeos , Tilápia , Ração Animal/análise , Animais , Ciclídeos/genética , Dieta/veterinária , Suplementos Nutricionais , Fermentação , Fusobactérias/metabolismo , Interleucina-6/metabolismo , Lipídeos , Fígado/metabolismo
4.
Fish Shellfish Immunol ; 120: 56-66, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34780975

RESUMO

Probiotics are widely used in aquafeeds and exhibited beneficial effects on fish by improving host health and resisting pathogens. However, probiotics applied to aquaculture are mainly from terrestrial sources instead of the host animal. The purpose of the work was to evaluate the effects of stabilized fermentation product of commensal Cetobacterium somerae XMX-1 on gut, liver health and antiviral immunity of zebrafish. A total of 240 zebrafish were assigned to the control (fed a basal diet) and XMX-1 group (fed a basal diet with 10 g XMX-1/kg diet). After four weeks feeding, growth performance, feed utilization, hepatic steatosis score, TAG, lipid metabolism related genes and serum ALT were evaluated. Furthermore, serum LPS, the expression of Hif-1α, intestinal inflammation score, antioxidant capability and gut microbiota were tested. The survival rate and the expression of antiviral genes were analyzed after challenge by spring viremia of carp virus (SVCV). Results showed that dietary XMX-1 did not affect growth of zebrafish. However, dietary XMX-1 significantly decreased the level of serum LPS, intestinal inflammation score and intestinal MDA, as well as increased T-AOC and the expression of Hif-1α in zebrafish intestine (p < 0.05). Furthermore, XMX-1 supplementation decreased the relative abundance of Proteobacteria and increased Firmicutes and Actinobacteria. Additionally, XMX-1 supplementation significantly decreased hepatic steatosis score, hepatic TAG, serum ALT and increased the expression of lipolysis genes versus control (p < 0.05). Zebrafish fed XMX-1 diet exhibited higher survival rate after SVCV challenge. Consistently, dietary XMX-1 fermentation product increased the expression of IFNφ2 and IFNφ3 after 2 days of SVCV challenge and the expression of IFNφ1, IFNφ2 and MxC after 4 days of SVCV challenge in the spleen in zebrafish versus control (p < 0.05). In conclusion, our results indicate that dietary XMX-1 can improve liver and gut health, while enhancing antiviral immunity of zebrafish.


Assuntos
Dieta , Fermentação , Fusobactérias , Peixe-Zebra , Ração Animal/análise , Animais , Dieta/veterinária , Trato Gastrointestinal , Inflamação , Lipopolissacarídeos , Fígado , Rhabdoviridae , Peixe-Zebra/imunologia
5.
Microbiol Spectr ; 9(3): e0080221, 2021 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-34787462

RESUMO

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Although dysbiosis of the lung and gut microbiota have been associated with NSCLC, their relative contributions are unclear; in addition, their roles in distant metastasis (DM) are still illusive. We recruited in total 121 participants, including 87 newly diagnosed treatment-naive NSCLC patients of various stages and 34 healthy volunteers, and surveyed their fecal and sputum microbiota. We compared the microbial profiles between groups, identified microbial biomarkers, and generated machine learning models for distinguishing healthy individuals from patients with NSCLC and patients of various stages. We found significant perturbations of gut and sputum microbiota in patients with NSCLC and DM. A machine learning model combining both microbiota (combined model) performed better than an individual data set in patient stratification, with the highest area under the curve (AUC) value of 0.896. Sputum and gut microbiota both contributed to the combined model; in most cases, sputum-only models performed similar to the combined models. Several microbial biomarkers were shared by both microbiotas, indicating their similar roles at distinct body sites. Microbial biomarkers of distinct disease stages were mostly shared, suggesting biomarkers for DM could be acquired early. Furthermore, Pseudomonas aeruginosa, a species previously associated with wound infections, was significantly more abundant in brain metastasis, indicating that distinct types of DMs could have different microbes. Our results indicate that alterations of the sputum microbiota have stronger relationships with NSCLC and DM than the gut and strongly support the feasibility of metagenome-based noninvasive disease diagnosis and risk evaluation. (This study has been registered at ClinicalTrials.gov under registration no. NCT03454685). IMPORTANCE Our survey on gut and sputum microbiota revealed that both were significantly disturbed in non-small cell lung cancer (NSCLC) and associated with distant metastasis (DM) while only the sputum microbiota was associated with non-DM NSCLC. The lung microbiota could therefore have a stronger association with (and thus may contribute more to) disease development than the gut microbiota. Mathematic models using both microbiotas performed better in patient stratification than using individual microbiota. Sputum models, however, performed similar to the combined models, suggesting a convenient, noninvasive diagnostic for NSCLC. Microbial biomarkers of distinct disease stages were mostly shared, suggesting that the same set of microbes were underlying disease progression, and the signals for distant metastasis could be acquired at early stages of the disease. Our results strongly support the feasibility of noninvasive diagnosis of NSCLC, including distant metastasis, are of clinical importance, and should warrant further research on the underlying molecular mechanisms.


Assuntos
Bactérias/classificação , Carcinoma Pulmonar de Células não Pequenas/patologia , Disbiose/microbiologia , Microbioma Gastrointestinal/fisiologia , Neoplasias Pulmonares/patologia , Pulmão/microbiologia , Actinobacteria/isolamento & purificação , Bactérias/isolamento & purificação , Bacteroidetes/isolamento & purificação , Biomarcadores , Fezes/microbiologia , Feminino , Firmicutes/isolamento & purificação , Fusobactérias/isolamento & purificação , Humanos , Masculino , Pessoa de Meia-Idade , Metástase Neoplásica/diagnóstico , Metástase Neoplásica/patologia , Proteobactérias/isolamento & purificação , Escarro/microbiologia
6.
Front Cell Infect Microbiol ; 11: 680643, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34490136

RESUMO

Objective: The role of vaginal microbiota in recurrent spontaneous abortion (RSA) remains unknown. The purpose of this study was to investigate characteristics of vaginal microbiota and the effects of drug treatment on vaginal microbiota of patients with RSA. Methods: A case-control study was performed, in which non-pregnant patients who experienced RSA were selected and divided into untreated and drug-treated groups. Drug-treated patients were subdivided into the metformin group, metformin plus aspirin group, and other drugs group. Healthy women who had live births and never experienced spontaneous abortion were enrolled in the control group. Characteristics of vaginal microbiomes of patients with RSA and healthy women and the impact of drug treatment on the microbiome was evaluated via 16S rRNA gene sequencing of the V3-V4 region using the Illumina MiSeq platform. Results: Women who underwent RSA had lower microbial richness than healthy women. Compared to controls, the relative abundance of seven taxa (Megasphaera, Sneathia sanguinegens, Pseudomonas, Sphingomonas, Rhodococcus, Burkholderia- Caballeronia-Paraburkholderia, and Corynebacterium_1) in the patient's vaginal microbiota changed significantly, which may be closely related to RSA. The composition of the vaginal microbial community in RSA patients was altered by drug treatment. Metformin combined with aspirin treatment significantly increased the relative abundance of vaginal Lactobacillus spp. in patients. Conclusion: An altered vaginal microbiome composition might be associated with RSA, which could be modified by drug treatment. The effect of metformin combined with aspirin on vaginal Lactobacillus is worthy of attention.


Assuntos
Aborto Espontâneo , Microbiota , Preparações Farmacêuticas , Estudos de Casos e Controles , Feminino , Fusobactérias , Humanos , Gravidez , RNA Ribossômico 16S/genética , Vagina
7.
Sci Rep ; 11(1): 17866, 2021 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-34504159

RESUMO

The gastric microbiota in Crohn's disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.


Assuntos
Doença de Crohn/microbiologia , Firmicutes/genética , Microbioma Gastrointestinal/genética , RNA Ribossômico 16S/genética , Bacteroidetes/genética , Doença de Crohn/diagnóstico , Doença de Crohn/genética , Fezes/microbiologia , Fusobactérias/genética , Humanos , Proteobactérias/genética
8.
Biomolecules ; 11(8)2021 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-34439821

RESUMO

Irritable bowel syndrome is not a life-threatening disease, yet it significantly affects the quality of life and contributes to economic loss. It is estimated that even up to 45% of the world's population can suffer from the disease. The first attempts to diagnose irritable bowel syndrome were made at the end of the 19th century; however, establishing appropriate diagnostic criteria and treatment methods is still ongoing. To date, little is known about the etiology of irritable bowel syndrome; however, growing attention is drawn to the intestinal microbiota as a factor in the disease development. For this reason, researchers have conducted many studies on therapies that modulate the microbiota, among which probiotics, prebiotics, and synbiotics are widely studied. To date, most studies have examined probiotics; however, there are also several studies demonstrating the efficacy of prebiotics and synbiotics. The aim of this review was to summarize findings on the usefulness of probiotics, prebiotics, and synbiotics in the treatment of irritable bowel syndrome.


Assuntos
Disbiose/dietoterapia , Microbioma Gastrointestinal/efeitos dos fármacos , Síndrome do Intestino Irritável/dietoterapia , Prebióticos/administração & dosagem , Probióticos/administração & dosagem , Simbióticos/administração & dosagem , Actinobacteria/genética , Actinobacteria/crescimento & desenvolvimento , Actinobacteria/isolamento & purificação , Antibacterianos/efeitos adversos , Bacteroidetes/genética , Bacteroidetes/crescimento & desenvolvimento , Bacteroidetes/isolamento & purificação , Ensaios Clínicos como Assunto , Disbiose/etiologia , Disbiose/microbiologia , Disbiose/patologia , Firmicutes/genética , Firmicutes/crescimento & desenvolvimento , Firmicutes/isolamento & purificação , Fusobactérias/genética , Fusobactérias/crescimento & desenvolvimento , Fusobactérias/isolamento & purificação , Microbioma Gastrointestinal/genética , Humanos , Síndrome do Intestino Irritável/microbiologia , Síndrome do Intestino Irritável/patologia , Proteobactérias/genética , Proteobactérias/crescimento & desenvolvimento , Proteobactérias/isolamento & purificação , Qualidade de Vida
9.
Microbiologyopen ; 10(4): e1215, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34459554

RESUMO

As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less-studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time, to establish a baseline for future studies of host-microbial-environment interactions and monitoring programs. During two consecutive reproductive seasons, 57 fecal samples were collected from seven different JFFS colonies within the Juan Fernandez Archipelago, Chile. Bacterial composition and abundance were characterized by sequencing the V4 region of the 16S rRNA gene. The overall microbiome composition was dominated by five phyla: Firmicutes (40% ±24), Fusobacteria (30% ±17), Bacteroidetes (22% ±10), Proteobacteria (6% ±4), and Actinobacteria (2% ±3). Alpha diversity was higher in Tierras Blancas. However, location was not found to be a dominant driver of microbial composition. Interestingly, the strongest signal in the data was a negative association between the genera Peptoclostridium and Fusobacterium, which explained 29.7% of the total microbial composition variability between samples. The genus Peptoclostridium has not been reported in other pinniped studies, and its role here is unclear, with interpretation challenging due to a lack of information regarding microbiome functionality in marine mammals. As a first insight into the JFFS fecal microbiome, these results contribute towards our understanding of the natural microbial diversity and composition in free-ranging pinnipeds.


Assuntos
Bactérias/classificação , Fezes/microbiologia , Otárias/microbiologia , Microbioma Gastrointestinal/genética , Microbiota/genética , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Animais , Bactérias/genética , Bactérias/isolamento & purificação , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Biodiversidade , Chile , DNA Bacteriano/genética , Firmicutes/classificação , Firmicutes/genética , Firmicutes/isolamento & purificação , Fusobactérias/classificação , Fusobactérias/genética , Fusobactérias/isolamento & purificação , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
10.
Viruses ; 13(7)2021 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-34201869

RESUMO

Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.


Assuntos
Escherichia coli/genética , Fusobactérias/virologia , Prófagos/metabolismo , Proteínas Virais/metabolismo , Clonagem Molecular , Códon , Genoma Viral , Fontes Hidrotermais/microbiologia , Família Multigênica , Filogenia , Prófagos/classificação , Prófagos/genética , Dobramento de Proteína , Estabilidade Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Siphoviridae/classificação , Siphoviridae/genética , Siphoviridae/metabolismo , Temperatura de Transição , Proteínas Virais/química , Proteínas Virais/genética , Proteínas Virais/isolamento & purificação
11.
Protein Sci ; 30(9): 1974-1982, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34191368

RESUMO

Membrane proteins play key roles in cellular signaling and transport, represent the majority of drug targets, and are implicated in many diseases. Their relevance renders them important subjects for structural, biophysical, and functional investigations. However, obtaining membrane proteins in high purities is often challenging with conventional purification steps alone. To address this issue, we present here an approach to increase the purity of α-helical transmembrane proteins. Our approach exploits the Thioredoxin (Trx) tag system, which is able to confer some of its favorable properties, such as high solubility and thermostability, to its fusion partners. Using Trx fusions of transmembrane helical hairpin constructs derived from the human cystic fibrosis transmembrane conductance regulator (CFTR) and a bacterial ATP synthase, we establish conditions for the successful implementation of the selective heat treatment procedure to increase sample purity. We further examine systematically its efficacy with respect to different incubation times and temperatures using quantitative gel electrophoresis. We find that minute-timescale heat treatment of Trx-tagged fusion constructs with temperatures ranging from 50 to 90°C increases the purity of the membrane protein samples from ~60 to 98% even after affinity purification. We show that this single-step approach is even applicable in cases where regular selective heat purification from crude extracts, as reported for Trx fusions to soluble proteins, fails. Overall, our approach is easy to integrate into existing purification strategies and provides a facile route for increasing the purity of membrane protein constructs after purification by standard chromatography approaches.


Assuntos
Complexos de ATP Sintetase/química , Proteínas de Bactérias/química , Regulador de Condutância Transmembrana em Fibrose Cística/química , Subunidades Proteicas/química , Proteínas Recombinantes de Fusão/química , Tiorredoxinas/química , Complexos de ATP Sintetase/genética , Complexos de ATP Sintetase/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Clonagem Molecular , Regulador de Condutância Transmembrana em Fibrose Cística/genética , Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Fusobactérias/química , Fusobactérias/enzimologia , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Temperatura Alta , Humanos , Modelos Moleculares , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Solubilidade , Tiorredoxinas/genética , Tiorredoxinas/metabolismo
12.
Genome Biol ; 22(1): 192, 2021 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-34183041

RESUMO

A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.


Assuntos
Neoplasias Colorretais/microbiologia , DNA Bacteriano/genética , Diabetes Mellitus Tipo 2/microbiologia , Metagenoma , Microbiota/genética , Software , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Estudos de Casos e Controles , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/patologia , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/patologia , Firmicutes/classificação , Firmicutes/genética , Firmicutes/isolamento & purificação , Fusobactérias/classificação , Fusobactérias/genética , Fusobactérias/isolamento & purificação , Humanos , Filogenia , Reação em Cadeia da Polimerase/métodos , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Sequenciamento Completo do Genoma
13.
Front Cell Infect Microbiol ; 11: 622474, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34094994

RESUMO

Background: The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations. Objective: Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women. Methods: Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. Lactobacillus species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing. Results: Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of Lactobacillus iners (p-value All_Trimesters<0.02), Megasphaera sp (p-value1st_Trimester <0.05), Gardnerella vaginalis (p-value2nd_Trimester= 0.01) and Sneathia sanguinegens (p-value2nd_Trimester <0.0001) were identified in preterm samples whereas higher abundance of L. gasseri (p-value3rd_Trimester =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of L. iners, and Megasphaera sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of L. crispatus and L. gasseri indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of L. crispatus and L. gasseri in reducing the risk of PTB. Conclusion: Our findings indicate that the dominance of specific Lactobacillus species and few other facultative anaerobes are associated with birth outcomes.


Assuntos
Nascimento Prematuro , Feminino , Fusobactérias , Humanos , Índia , Recém-Nascido , Lactobacillus , Gravidez , Nascimento Prematuro/epidemiologia , RNA Ribossômico 16S/genética , Vagina
14.
PLoS One ; 16(4): e0250401, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33886647

RESUMO

The Rimac river is the main source of water for Lima, Peru's capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.


Assuntos
Organismos Aquáticos/genética , Arcobacter/genética , Código de Barras de DNA Taxonômico/métodos , Flavobacterium/genética , Fusobactérias/genética , Microbiota/genética , RNA Ribossômico 16S/genética , Rios/microbiologia , Biologia Computacional/métodos , Monitoramento Ambiental/métodos , Peru , Esgotos/microbiologia , Água/análise , Microbiologia da Água , Poluição da Água/análise
15.
Gut Microbes ; 13(1): 1-15, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33840371

RESUMO

The capability of carbohydrate utilization in fish is limited compared to mammals. It has scientific and practical significance to improve the ability of fish to use carbohydrates. The efficiency of dietary carbohydrate utilization varies among fish with different feeding habits, which are associated with differential intestinal microbiota. In this study, we found that zebrafish fed with omnivorous diet (OD) and herbivorous diet (HD) showed better glucose homeostasis compared with carnivorous diet (CD) fed counterpart and the differential glucose utilization efficiency was attributable to the intestinal microbiota. The commensal bacterium Cetobacterium somerae, an acetate producer, was enriched in OD and HD groups, and administration of C. somerae in both adult zebrafish and gnotobiotic larval zebrafish models resulted in improved glucose homeostasis and increased insulin expression, supporting a causative role of C. somerae enrichment in glucose homeostasis in fish. The enrichment of C. somerae was constantly associated with higher acetate levels, and dietary supplementation of acetate promotes glucose utilization in zebrafish, suggesting a contribution of acetate in the function of C. somerae. Furthermore, we found that the beneficial effect of both acetate and C. somerae on glucose homeostasis was mediated through parasympathetic activation. Overall, this work highlights the existence of a C. somerae-brain axis in the regulation of glucose homeostasis in fish and suggests a role of acetate in mediating the axis function. Our results suggest potential strategies for improvement of fish carbohydrate utilization.


Assuntos
Acetatos/metabolismo , Fusobactérias , Glucose/metabolismo , Intestinos/microbiologia , Sistema Nervoso Parassimpático/metabolismo , Peixe-Zebra/metabolismo , Peixe-Zebra/microbiologia , Ração Animal , Animais , Microbioma Gastrointestinal , Homeostase , Interações entre Hospedeiro e Microrganismos , Insulina/metabolismo , Modelos Animais , RNA Ribossômico 16S
16.
Crit Rev Microbiol ; 47(4): 517-542, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33823747

RESUMO

Sneathia is an emerging pathogen implicated in adverse reproductive and perinatal outcomes. Although scarce, recent data suggest that vaginally residing Sneathia becomes pathogenic following its ascension into the upper urogenital tract, amniotic fluid, placenta, and foetal membranes. The role of Sneathia in women's health and disease is generally underappreciated because the cultivation of these bacteria is limited by their complex nutritional requirements, slow growth patterns, and anaerobic nature. For this reason, molecular methods are typically required for the detection and differential diagnosis of Sneathia infections. Here, we review the laboratory methods used for the diagnosis of Sneathia infections, the molecular mechanisms underlying its virulence, and its sensitivity to antibiotics. We further review the evidence of Sneathia's contributions to the pathogenesis of bacterial vaginosis, chorioamnionitis, preterm prelabour rupture of membranes, spontaneous preterm labour, stillbirth, maternal and neonatal sepsis, HIV infection, and cervical cancer. Collectively, growing evidence indicates that Sneathia represents an important yet underappreciated pathogen affecting the development and progression of several adverse clinical conditions diagnosed in pregnant women and their neonates, as well as in non-pregnant women.


Assuntos
Fusobactérias/fisiologia , Infecções por Bactérias Gram-Negativas/microbiologia , Complicações Infecciosas na Gravidez/microbiologia , Vaginose Bacteriana/microbiologia , Animais , Feminino , Fusobactérias/genética , Fusobactérias/isolamento & purificação , Humanos , Gravidez
17.
PLoS One ; 16(4): e0250344, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33872339

RESUMO

Canine acute hemorrhagic diarrhea syndrome (AHDS) has been associated in some studies with Clostridioides perfringens overgrowth and toxin-mediated necrosis of the intestinal mucosa. We aimed to determine the effect of a single fecal microbiota transplantation (FMT) on clinical scores and fecal microbiomes of 1 and 7 dogs with AHDS from New Zealand and South Africa. We hypothesized that FMT would improve AHDS clinical scores and increase microbiota alpha-diversity and short-chain fatty acid (SCFA)-producing microbial communities' abundances in dogs with AHDS after FMT. We sequenced the V3-V4 region of the 16S-rRNA gene in the feces of AHDS FMT-recipients and sham-treated control dogs, and their healthy donors at admission, discharge, and 30 days post-discharge. There were no significant differences in median AHDS clinical scores between FMT-recipients and sham-treated controls at admission or discharge (P = 0.22, P = 0.41). At admission, the Shannon diversity index (SDI) was lower in AHDS dogs than healthy donors (P = 0.002). The SDI did not change from admission to 30 days in sham-treated dogs yet increased in FMT-recipients from admission to discharge (P = 0.04) to levels not different than donors (P = 0.33) but significantly higher than sham-treated controls (P = 0.002). At 30 days, the SDI did not differ between FMT recipients, sham-treated controls, and donors (P = 0.88). Principal coordinate analysis of the Bray-Curtis index separated post-FMT and donor dogs from pre-FMT and sham-treated dogs (P = 0.009) because of increased SCFA-producing genera's abundances after FMT. A single co-abundance subnetwork contained many of the same OTUs found to be differentially abundant in FMT-recipients, and the abundance of this module was increased in FMT-recipients at discharge and 30 days, compared to sham-treated controls. We conclude in this small pilot study FMT did not have any clinical benefit. A single FMT procedure has the potential to increase bacterial communities of SCFA-producing genera important for intestinal health up to 30 days post-FMT.


Assuntos
Clostridioides/patogenicidade , Infecções por Clostridium/terapia , Diarreia/terapia , Transplante de Microbiota Fecal/veterinária , Fezes/microbiologia , Hemorragia Gastrointestinal/terapia , Microbioma Gastrointestinal/fisiologia , Actinobacteria/genética , Actinobacteria/crescimento & desenvolvimento , Actinobacteria/isolamento & purificação , Animais , Bacteroidetes/genética , Bacteroidetes/crescimento & desenvolvimento , Bacteroidetes/isolamento & purificação , Clostridioides/genética , Clostridioides/crescimento & desenvolvimento , Infecções por Clostridium/microbiologia , Infecções por Clostridium/patologia , Infecções por Clostridium/veterinária , Diarreia/microbiologia , Diarreia/patologia , Diarreia/veterinária , Cães , Ácidos Graxos Voláteis/biossíntese , Feminino , Firmicutes/genética , Firmicutes/crescimento & desenvolvimento , Firmicutes/isolamento & purificação , Fusobactérias/genética , Fusobactérias/crescimento & desenvolvimento , Fusobactérias/isolamento & purificação , Hemorragia Gastrointestinal/microbiologia , Hemorragia Gastrointestinal/patologia , Hemorragia Gastrointestinal/veterinária , Mucosa Intestinal/microbiologia , Masculino , Nova Zelândia , Projetos Piloto , Estudos Prospectivos , Proteobactérias/genética , Proteobactérias/crescimento & desenvolvimento , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , África do Sul
18.
Cell Rep Med ; 2(3): 100206, 2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33763652

RESUMO

Extremely low birth weight (ELBW) infants often develop an altered gut microbiota composition, which is related to clinical complications, such as necrotizing enterocolitis and sepsis. Probiotic supplementation may reduce these complications, and modulation of the gut microbiome is a potential mechanism underlying the probiotic effectiveness. In a randomized, double-blind, placebo-controlled trial, we assessed the effect of Lactobacillus reuteri supplementation, from birth to post-menstrual week (PMW)36, on infant gut microbiota. We performed 16S amplicon sequencing in 558 stool samples from 132 ELBW preterm infants at 1 week, 2 weeks, 3 weeks, 4 weeks, PMW36, and 2 years. Probiotic supplementation results in increased bacterial diversity and increased L. reuteri abundance during the 1st month. At 1 week, probiotic supplementation also results in a lower abundance of Enterobacteriaceae and Staphylococcaceae. No effects were found at 2 years. In conclusion, probiotics may exert benefits by modulating the gut microbiota composition during the 1st month in ELBW infants.


Assuntos
Suplementos Nutricionais , Microbioma Gastrointestinal/genética , Recém-Nascido de Peso Extremamente Baixo ao Nascer/crescimento & desenvolvimento , Lactente Extremamente Prematuro/crescimento & desenvolvimento , Lactobacillus reuteri/fisiologia , Probióticos/administração & dosagem , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Biodiversidade , Fezes/microbiologia , Feminino , Firmicutes/classificação , Firmicutes/genética , Firmicutes/isolamento & purificação , Fusobactérias/classificação , Fusobactérias/genética , Fusobactérias/isolamento & purificação , Humanos , Lactente , Masculino , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Verrucomicrobia/classificação , Verrucomicrobia/genética , Verrucomicrobia/isolamento & purificação
19.
ISME J ; 15(3): 833-847, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33208892

RESUMO

Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded 13C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.


Assuntos
Fusobactérias , Sedimentos Geológicos , Anaerobiose , Filogenia , RNA Ribossômico 16S/genética
20.
Environ Microbiol Rep ; 13(6): 899-910, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34668338

RESUMO

Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.


Assuntos
Fusobactérias , Microbiota , Mar Negro , Fusobactérias/genética , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Sulfetos
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