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1.
Nat Commun ; 11(1): 4982, 2020 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-33020474

RESUMO

Nonalcoholic fatty liver disease (NAFLD) is associated with obesity but also found in non-obese individuals. Gut microbiome profiles of 171 Asians with biopsy-proven NAFLD and 31 non-NAFLD controls are analyzed using 16S rRNA sequencing; an independent Western cohort is used for external validation. Subjects are classified into three subgroups according to histological spectra of NAFLD or fibrosis severity. Significant alterations in microbiome diversity are observed according to fibrosis severity in non-obese, but not obese, subjects. Ruminococcaceae and Veillonellaceae are the main microbiota associated with fibrosis severity in non-obese subjects. Furthermore, stool bile acids and propionate are elevated, especially in non-obese subjects with significant fibrosis. Fibrosis-related Ruminococcaceae and Veillonellaceae species undergo metagenome sequencing, and four representative species are administered in three mouse NAFLD models to evaluate their effects on liver damage. This study provides the evidence for the role of the microbiome in the liver fibrosis pathogenesis, especially in non-obese subjects.


Assuntos
Bactérias/isolamento & purificação , Microbioma Gastrointestinal/fisiologia , Hepatopatia Gordurosa não Alcoólica/microbiologia , Hepatopatia Gordurosa não Alcoólica/patologia , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Ácidos e Sais Biliares/análise , Ácidos e Sais Biliares/metabolismo , Biomarcadores , Fezes/química , Fezes/microbiologia , Fibrose , Microbioma Gastrointestinal/genética , Humanos , Cirrose Hepática/diagnóstico , Cirrose Hepática/metabolismo , Cirrose Hepática/microbiologia , Cirrose Hepática/patologia , Camundongos , Hepatopatia Gordurosa não Alcoólica/metabolismo , Obesidade/metabolismo , Obesidade/microbiologia , Obesidade/patologia , Propionatos/análise , Propionatos/metabolismo , RNA Ribossômico 16S/genética , Reprodutibilidade dos Testes
2.
Nat Commun ; 11(1): 4635, 2020 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-32934239

RESUMO

Providing insight into one's health status from a gut microbiome sample is an important clinical goal in current human microbiome research. Herein, we introduce the Gut Microbiome Health Index (GMHI), a biologically-interpretable mathematical formula for predicting the likelihood of disease independent of the clinical diagnosis. GMHI is formulated upon 50 microbial species associated with healthy gut ecosystems. These species are identified through a multi-study, integrative analysis on 4347 human stool metagenomes from 34 published studies across healthy and 12 different nonhealthy conditions, i.e., disease or abnormal bodyweight. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of disease presence (or absence) compared to α-diversity indices. Validation on 679 samples from 9 additional studies results in a balanced accuracy of 73.7% in distinguishing healthy from non-healthy groups. Our findings suggest that gut taxonomic signatures can predict health status, and highlight how data sharing efforts can provide broadly applicable discoveries.


Assuntos
Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Nível de Saúde , Bactérias/classificação , Bactérias/genética , Fezes/microbiologia , Humanos , Metagenoma , Microbiota
3.
Zhongguo Zhong Yao Za Zhi ; 45(15): 3726-3739, 2020 Aug.
Artigo em Chinês | MEDLINE | ID: mdl-32893565

RESUMO

This study is to explore the effect of Qingfei Paidu Decoction(QPD) on the host metabolism and gut microbiome of rats with metabolomics and 16 S rDNA sequencing. Based on 16 S rDNA sequencing of gut microbiome and metabolomics(GC-MS and LC-MS/MS), we systematically studied the serum metabolites profile and gut microbiota composition of rats treated with QPD for continued 5 days by oral gavage. A total of 23 and 43 differential metabolites were identified based on QPD with GC-MS and LC-MS/MS, respectively. The involved metabolic pathways of these differential metabolites included glycerophospholipid metabolism, linoleic acid metabolism, TCA cycle and pyruvate metabolism. Meanwhile, we found that QPD significantly regulated the composition of gut microbiota in rats, such as enriched Romboutsia, Turicibacter, and Clostridium_sensu_stricto_1, and decreased norank_f_Lachnospiraceae. Our current study indicated that short-term intervention of QPD could significantly regulate the host metabolism and gut microbiota composition of rats dose-dependently, suggesting that the clinical efficacy of QPD may be related with the regulation on host metabolism and gut microbiome.


Assuntos
Medicamentos de Ervas Chinesas/farmacologia , Microbioma Gastrointestinal/efeitos dos fármacos , Animais , Bactérias/classificação , Cromatografia Líquida , Metabolômica , Ratos , Espectrometria de Massas em Tandem
4.
Nat Commun ; 11(1): 4887, 2020 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-32985497

RESUMO

The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population's persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.


Assuntos
Bactérias/metabolismo , Bactérias/classificação , Bactérias/genética , Evolução Biológica , Ecossistema , Redes e Vias Metabólicas , Filogenia , Água do Mar/microbiologia , Microbiologia do Solo
5.
Nat Commun ; 11(1): 4827, 2020 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-32973167

RESUMO

In bacteria, translation re-initiation is crucial for synthesizing proteins encoded by genes that are organized into operons. The mechanisms regulating translation re-initiation remain, however, poorly understood. We now describe the ribosome termination structure (RTS), a conserved and stable mRNA secondary structure localized immediately downstream of stop codons, and provide experimental evidence for its role in governing re-initiation efficiency in a synthetic Escherichia coli operon. We further report that RTSs are abundant, being associated with 18%-65% of genes in 128 analyzed bacterial genomes representing all phyla, and are selectively depleted when translation re-initiation is advantageous yet selectively enriched so as to insulate translation when re-initiation is deleterious. Our results support a potentially universal role for the RTS in controlling translation termination-insulation and re-initiation across bacteria.


Assuntos
Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica , Óperon/genética , RNA Mensageiro/química , RNA Mensageiro/fisiologia , Bactérias/classificação , Bactérias/genética , Códon de Terminação/metabolismo , Escherichia coli/metabolismo , Genes Bacterianos/genética , Iniciação Traducional da Cadeia Peptídica , Estrutura Secundária de Proteína , RNA Mensageiro/genética , Ribossomos/metabolismo
6.
Nat Commun ; 11(1): 4717, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948774

RESUMO

Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.


Assuntos
Ecologia , Aquecimento Global , Pradaria , Microbiota , Animais , Bactérias/classificação , Biodiversidade , Secas , Modelos Biológicos , Filogenia , Sensibilidade e Especificidade
7.
Nat Commun ; 11(1): 4721, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948775

RESUMO

The importance of soil age as an ecosystem driver across biomes remains largely unresolved. By combining a cross-biome global field survey, including data for 32 soil, plant, and microbial properties in 16 soil chronosequences, with a global meta-analysis, we show that soil age is a significant ecosystem driver, but only accounts for a relatively small proportion of the cross-biome variation in multiple ecosystem properties. Parent material, climate, vegetation and topography predict, collectively, 24 times more variation in ecosystem properties than soil age alone. Soil age is an important local-scale ecosystem driver; however, environmental context, rather than soil age, determines the rates and trajectories of ecosystem development in structure and function across biomes. Our work provides insights into the natural history of terrestrial ecosystems. We propose that, regardless of soil age, changes in the environmental context, such as those associated with global climatic and land-use changes, will have important long-term impacts on the structure and function of terrestrial ecosystems across biomes.


Assuntos
Biota , Ecossistema , Solo/química , Bactérias/classificação , Biodiversidade , Biomassa , Clima , Fungos/classificação , Microbiota , Plantas/classificação , Fatores de Tempo
8.
Mol Genet Genomics ; 295(6): 1517-1528, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32803300

RESUMO

Increasing studies have revealed strong links among gut microbiota, health status, and shrimp development, but they mainly focus on the microbiota of Pacific white shrimp, Penaeus vannamei, during life stages from juveniles to adults. Little is known about shrimp microbiota dynamics at early developmental stages. In this study, with an aim to profile shrimp microbiota and its dynamics at stages nauplius, zoea, mysis, and early postlarva, we conducted a survey for the successful breeding processes in a commercial hatchery in China, sampled 33 samples including larval/postlarval shrimp, suspended substance in rearing water (SSRW), and nutrition supplements (i.e., algae and brine shrimp larvae) at stages N5, Z2, M2, and P2. The associated bacterial communities were sequenced and comparatively analyzed using high-throughput sequencing of bacterial 16S rRNA genes. Our case study results showed that bacterial community structures and compositions were strikingly different at stages N5, Z2, and P2, indicating the shift of microbiota at the three stages. Many taxa within Gamma-, Alphaproteobacteria, and Flavobacteriia classes were observed to be stage-specifically abundant and identified as taxonomic biomarkers potentially used to differentiate among shrimp at different early developmental stages. Summing up, these results shed light on larval/postlarval microbiota and its dynamics at different early developmental stages, highlighting the potential roles of shrimp development in microbiota formation and shifting.


Assuntos
Bactérias/classificação , Bactérias/genética , Larva/microbiologia , Microbiota/genética , Penaeidae/microbiologia , RNA Ribossômico 16S/análise , Animais , Bactérias/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , Larva/crescimento & desenvolvimento , Metagenômica , Penaeidae/crescimento & desenvolvimento , Tanques , RNA Ribossômico 16S/genética
9.
J Environ Public Health ; 2020: 4609164, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32733576

RESUMO

Air pollution has been a major challenge worldwide particularly in the developing world. Improper waste disposal and management may result in microbial air pollution. In advanced countries, landfill sites are far from neighborhoods; however, the opposite is observed for landfill sites in the developing world. In Accra, some landfill sites are 100 meters from neighborhoods. The aim of this study was to assess the microbial air quality and associated environmental health hazards of landfill sites in selected districts in the Greater Accra Region of Ghana. A random sampling method was employed to select sampling sites across the dry and wet seasons from landfills and their corresponding neighborhoods. Results obtained showed a higher total count (CFU/m3) of bacteria and fungi in the air at the landfill sites than neighborhoods. Statistically significant variation (p < 0.05) in bacterial and fungal concentrations over two seasons was found for both landfills and neighborhoods. However, bacterial concentrations were significantly higher than fungal concentrations (p < 0.05) across seasons for all locations. Staphylococcus epidermidis was the highest (15.6 %) occurring microbe at both landfill sites and neighborhoods. This was followed by Staphylococcus aureus (12.7%). Other bacteria and fungi of public health importance such as Pseudomonas aeruginosa, Escherichia coli, Aspergillus flavus, and Aspergillus niger were also isolated from the study sites, above the WHO recommended levels. In conclusion, the landfill waste disposal and its close proximity to neighborhoods as observed in this study pose a potential environmental health risk, with dire implications for public health and safety. The government must enact and implement policies to regulate waste management and to ensure public safety.


Assuntos
Microbiologia do Ar , Poluentes Atmosféricos/análise , Instalações de Eliminação de Resíduos , Poluentes Atmosféricos/normas , Bactérias/classificação , Bactérias/isolamento & purificação , Monitoramento Ambiental , Fungos/classificação , Fungos/isolamento & purificação , Gana , Saúde Pública , Eliminação de Resíduos , Medição de Risco
10.
PLoS One ; 15(7): e0236936, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32735609

RESUMO

The Roux-en-Y gastric bypass (RYGB) remains the most effective treatment for morbidly obese patients to lower body weight and improve glycemic control. There is recent evidence that the mycobiome (fungal microbiome) can aggravate disease severity in a number of diseases including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) and hepatitis; moreover, a dysbiotic fungal microbiota has been reported in the obese. We characterized fungal and bacterial microbial composition in fecal samples of 16 morbidly obese patients before and three months after RYGB surgery and compared with nine healthy controls. We found that RYGB surgery induced a clear alteration in structure and composition of the gut fungal and bacterial microbiota. Beta diversity analysis revealed significant differences in bacterial microbiota between obese patients before surgery and healthy controls (P < 0.005) and a significant, unidirectional shift in RYGB patients after surgery (P < 0.001 vs. before surgery). In contrast, there was no significant difference in fungal microbiota between groups but individually specific changes after RYGB surgery. Interestingly, RYGB surgery induced a significant reduction in fungal alpha diversity namely Chao1, Sobs, and Shannon diversity index (P<0.05, respectively) which contrasts the trend for uniform changes in bacteria towards increased richness and diversity post-surgery. We did not observe any inter-kingdom relations in RYGB patients but in the healthy control cohort and there were several correlations between fungi and bacteria and clinical parameters (P<0.05, respectively) that warrant further research. Our study identifies changes in intestinal fungal communities in RYGB patients that are distinct to changes in the bacterial microbiota.


Assuntos
Derivação Gástrica , Microbioma Gastrointestinal , Obesidade Mórbida , Adulto , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , DNA Intergênico , Fezes/microbiologia , Feminino , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Microbioma Gastrointestinal/genética , Microbioma Gastrointestinal/fisiologia , Genes Bacterianos , Genes Fúngicos , Humanos , Masculino , Metagenômica , Microbiota , Pessoa de Meia-Idade , Micobioma , Obesidade Mórbida/microbiologia , Obesidade Mórbida/cirurgia , Projetos Piloto , RNA Ribossômico 16S/genética
11.
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
12.
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
13.
Virology ; 548: 200-212, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32763491

RESUMO

The intestinal microbiota is crucial to intestinal homeostasis. Porcine epidemic diarrhea virus (PEDV) is high pathogenic to intestines, causing diarrhea, even death in piglets. To investigate the detailed relationship between PEDV infection and intestinal microbiota, the composition and distribution of intestinal microbiota from pigs were first analyzed using 16S rRNA sequencing technology. The results demonstrated that the composition and distribution of microbes in different intestinal segments were quite similar between 1-week-old and 2-week-old piglets but different from 4-week-old (weaned) piglets. Then piglets at different ages were inoculated with PEDV. The results showed that the 1-week-old piglets exhibited the most severe pathogenicity comparing to the other age groups. Further investigations indicated that Lactobacillus, Escherichia coli, and Lactococcus in the intestinal microbiota of piglets were significantly changed by PEDV infection. These results strengthen our understanding of viruses influencing intestinal microbes and remind us of the potential association between PEDV and intestinal microbes.


Assuntos
Infecções por Coronavirus/virologia , Microbioma Gastrointestinal , Vírus da Diarreia Epidêmica Suína/fisiologia , Doenças dos Suínos/virologia , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Infecções por Coronavirus/microbiologia , Fezes/microbiologia , Intestinos/microbiologia , Vírus da Diarreia Epidêmica Suína/genética , Suínos , Doenças dos Suínos/microbiologia
14.
PLoS Comput Biol ; 16(8): e1008135, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32810127

RESUMO

Social interaction between microbes can be described at many levels of details: from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing an appropriate level to model microbial communities without losing generality remains a challenge. Here we show that modeling cross-feeding interactions at an intermediate level between genome-scale metabolic models of individual species and consumer-resource models of ecosystems is suitable to experimental data. We applied our modeling framework to three published examples of multi-strain Escherichia coli communities with increasing complexity: uni-, bi-, and multi-directional cross-feeding of either substitutable metabolic byproducts or essential nutrients. The intermediate-scale model accurately fit empirical data and quantified metabolic exchange rates that are hard to measure experimentally, even for a complex community of 14 amino acid auxotrophies. By studying the conditions of species coexistence, the ecological outcomes of cross-feeding interactions, and each community's robustness to perturbations, we extracted new quantitative insights from these three published experimental datasets. Our analysis provides a foundation to quantify cross-feeding interactions from experimental data, and highlights the importance of metabolic exchanges in the dynamics and stability of microbial communities.


Assuntos
Microbiota , Bactérias/classificação , Bactérias/metabolismo , Modelos Biológicos
15.
PLoS One ; 15(8): e0237603, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32841261

RESUMO

BACKGROUND/PURPOSE: To date, studies examining polymicrobial infections in ocular disease have mostly been limited to keratitis or endophthalmitis. We characterized polybacterial infections compared to monobacterial infections in prior clinical studies evaluating besifloxacin ophthalmic suspension 0.6% for the treatment of bacterial conjunctivitis and report on associated microbiological outcomes. METHODS: In this post-hoc analysis, microbiological data for subjects with conjunctivitis due to one or more than one bacterial species in three previous studies (two vehicle-, one active-controlled) of besifloxacin were extracted. Bacterial species identified at baseline were deemed causative if their colony count equaled or exceeded species-specific prespecified threshold criteria. In subjects with polybacterial infections, the fold-increase over threshold was used to rank order the contribution of individual species. Baseline pathogens and their minimum inhibitory concentrations (MICs) for common ophthalmic antibiotics were compared by infection type, as were microbial eradication rates following treatment with besifloxacin. RESULTS: Of 1041 subjects with culture-confirmed conjunctivitis, 17% had polybacterial and 83% had monobacterial conjunctivitis at baseline. In polybacterial compared to monobacterial infections, Haemophilus influenzae and Streptococcus pneumoniae were identified less frequently as the dominant infecting species (P = 0.042 and P<0.001, respectively), whereas Streptococcus mitis/S. mitis group was identified more frequently as dominant (P<0.001). Viral coinfection was also identified more frequently in polybacterial infections (P<0.001). Staphylococcus aureus was the most common coinfecting species in polybacterial infections and the second most common dominant species in such infections. With few exceptions, MICs for individual species were comparable regardless of infection type. Clinical microbial eradication rates with besifloxacin were high regardless of infection type (P≤0.016 vs vehicle at follow-up visits). CONCLUSIONS: Approximately one in five subjects with bacterial conjunctivitis are infected with more than one bacterial species underscoring the need for a broad-spectrum antibiotic for such infections. Besifloxacin treatment resulted in robust eradication rates of these infections comparable to monobacterial infections. TRIAL REGISTRATION: NCT000622908, NCT00347932, NCT00348348.


Assuntos
Antibacterianos/uso terapêutico , Azepinas/uso terapêutico , Bactérias/classificação , Bactérias/efeitos dos fármacos , Conjuntivite Bacteriana/tratamento farmacológico , Fluoroquinolonas/uso terapêutico , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Conjuntivite Bacteriana/microbiologia , Conjuntivite Bacteriana/patologia , Método Duplo-Cego , Feminino , Seguimentos , Humanos , Lactente , Recém-Nascido , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Prognóstico , Estudos Prospectivos , Adulto Jovem
16.
PLoS Negl Trop Dis ; 14(8): e0008615, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32813707

RESUMO

The mosquito microbiome alters the physiological traits of medically important mosquitoes, which can scale to impact how mosquito populations sustain disease transmission. The mosquito microbiome varies significantly within individual mosquitoes and among populations, however the ecological and environmental factors that contribute to this variation are poorly understood. To further understand the factors that influence variation and diversity of the mosquito microbiome, we conducted a survey of the bacterial microbiome in the medically important mosquito, Aedes albopictus, on the high Pacific island of Maui, Hawai'i. We detected three bacterial Phyla and twelve bacterial families: Proteobacteria, Acitinobacteria, and Firmicutes; and Anaplasmataceae, Acetobacteraceae, Enterobacteriaceae, Burkholderiaceae, Xanthobacteraceae, Pseudomonadaceae, Streptomycetaceae, Staphylococcaceae, Xanthomonadaceae, Beijerinckiaceae, Rhizobiaceae, and Sphingomonadaceae. The Ae. albopictus bacterial microbiota varied among geographic locations, but temperature and rainfall were uncorrelated with this spatial variation. Infection status with an ampicomplexan pathosymbiont Ascogregarina taiwanensis was significantly associated with the composition of the Ae. albopictus bacteriome. The bacteriomes of mosquitoes with an A. taiwanensis infection were more likely to include several bacterial symbionts, including the most abundant lineage of Wolbachia sp. Other symbionts like Asaia sp. and several Enterobacteriaceae lineages were less prevalent in A. taiwanensis-infected mosquitoes. This highlights the possibility that inter- and intra-domain interactions may structure the Ae. albopictus microbiome.


Assuntos
Aedes/microbiologia , Aedes/parasitologia , Bactérias/classificação , Microbiota/fisiologia , Infecções Protozoárias em Animais/microbiologia , Doenças dos Animais , Animais , Apicomplexa , Bactérias/genética , Interações Hospedeiro-Parasita , Larva/microbiologia , Larva/parasitologia , Simbiose
17.
Nat Commun ; 11(1): 3870, 2020 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-32747621

RESUMO

Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.


Assuntos
Biodiversidade , Ecossistema , Microbiologia do Solo , Solo/parasitologia , Animais , Bactérias/classificação , Bactérias/metabolismo , Biomassa , Clima , Fungos/classificação , Fungos/metabolismo , Geografia , Concentração de Íons de Hidrogênio , Nematoides/classificação , Nematoides/metabolismo , Oligoquetos/classificação , Oligoquetos/metabolismo , Solo/química , Temperatura
18.
Nat Commun ; 11(1): 4322, 2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32859898

RESUMO

Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease.


Assuntos
Doença de Crohn/metabolismo , Doença de Crohn/microbiologia , Microbioma Gastrointestinal/fisiologia , Enxofre/metabolismo , Adolescente , Adulto , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Doença de Crohn/tratamento farmacológico , Modelos Animais de Doenças , Fezes/microbiologia , Feminino , Transplante de Células-Tronco Hematopoéticas , Humanos , Interleucina-10/genética , Masculino , Metagenoma , Camundongos , Camundongos Knockout , RNA Ribossômico 16S/genética , Indução de Remissão , Adulto Jovem
19.
PLoS One ; 15(8): e0237869, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32810164

RESUMO

Abrupt dietary changes, as can be common when managing horses, may lead to compositional changes in gut microbiota, which may result in digestive or metabolic disturbances. The aim of this study was to describe and compare the faecal microbiota of ponies abruptly changed from pasture grazing ad libitum to a restricted hay-only diet and vice versa. The experiment consisted of two, 14-day periods. Faecal samples were collected on day 0 and days 1-3,7,14 after abrupt dietary change from grass to hay and from hay to grass. Microbial populations were characterised by sequencing the V3-V4 region of the 16S rRNA gene using the Illumina MiSeq platform, 4,777,315 sequences were obtained from 6 ponies. Further analyses were performed to characterise the microbiome as well as the relative abundance of microbiota present. The results of this study suggest that the faecal microbiota of mature ponies is highly diverse, and the relative abundances of individual taxa change in response to abrupt changes in diet. The faecal microbiota of ponies maintained on a restricted amount of hay-only was similar to that of the ponies fed solely grass ad libitum in terms of richness and phylogenetic diversity; however, it differed significantly in terms of the relative abundances at distinct taxonomic levels. Class Bacilli, order Lactobacillales, family Lactobacillaceae, and genus Lactobacillus were presented in increased relative abundance on day 2 after an abrupt dietary change from hay to grass compared to all other experimental days (P <0.05). Abrupt changes from grass to hay and vice versa affect the faecal microbial community structure; moreover, the order of dietary change appears to have a profound effect in the first few days following the transition. An abrupt dietary change from hay to grass may represent a higher risk for gut disturbances compared to abrupt change from grass to hay.


Assuntos
Dieta/veterinária , Fezes/microbiologia , Cavalos/microbiologia , Microbiota , Poaceae , Animais , Bactérias/classificação , Bactérias/genética , Biodiversidade , Análise Discriminante , Microbiota/genética , Filogenia , Análise de Componente Principal , Análise de Sequência de DNA
20.
PLoS One ; 15(8): e0237779, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32834004

RESUMO

Microbiome data consists of operational taxonomic unit (OTU) counts characterized by zero-inflation, over-dispersion, and grouping structure among samples. Currently, statistical testing methods are commonly performed to identify OTUs that are associated with a phenotype. The limitations of statistical testing methods include that the validity of p-values/q-values depend sensitively on the correctness of models and that the statistical significance does not necessarily imply predictivity. Predictive analysis using methods such as LASSO is an alternative approach for identifying associated OTUs and for measuring the predictability of the phenotype variable with OTUs and other covariate variables. We investigate three strategies of performing predictive analysis: (1) LASSO: fitting a LASSO multinomial logistic regression model to all OTU counts with specific transformation; (2) screening+GLM: screening OTUs with q-values returned by fitting a GLMM to each OTU, then fitting a GLM model using a subset of selected OTUs; (3) screening+LASSO: fitting a LASSO to a subset of OTUs selected with GLMM. We have conducted empirical studies using three simulation datasets generated using Dirichlet-multinomial models and a real gut microbiome data related to Parkinson's disease to investigate the performance of the three strategies for predictive analysis. Our simulation studies show that the predictive performance of LASSO with appropriate variable transformation works remarkably well on zero-inflated data. Our results of real data analysis show that Parkinson's disease can be predicted based on selected OTUs after the binary transformation, age, and sex with high accuracy (Error Rate = 0.199, AUC = 0.872, AUPRC = 0.912). These results provide strong evidences of the relationship between Parkinson's disease and the gut microbiome.


Assuntos
Bactérias/classificação , Interpretação Estatística de Dados , Microbioma Gastrointestinal/genética , Modelos Biológicos , Doença de Parkinson/diagnóstico , Adulto , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Bactérias/genética , Bactérias/isolamento & purificação , Estudos de Coortes , Simulação por Computador , DNA Bacteriano/isolamento & purificação , Conjuntos de Dados como Assunto , Feminino , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Doença de Parkinson/microbiologia , Valor Preditivo dos Testes , Prognóstico , RNA Ribossômico 16S/genética , Fatores Sexuais
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