Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 23.633
Filtrar
1.
Tumour Biol ; 43(1): 1-9, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33935124

RESUMEN

BACKGROUND: Oral infections associate statistically with cancer. OBJECTIVE: We hypothesized that certain periodontal microorganisms might specifically link to malignancies in general and set out to investigate this in our ongoing cohort study. METHODS: A sample of 99 clinically examined patients from our cohort of 1676 subjects was used to statistically investigate the associations between harboring periodontal microorganisms Aggregatibacter actinomycetemcomitans (A.a), Porphyromonas gingivalis (P.g), Prevotella intermedia (P.i), Tannerella forsythia (T.f) and Treponema denticola (T.d). We used oral infection indexes and the incidence figures of malignancies as registered in 2008-2016 in the Swedish National Cancer Register. RESULTS: The pathogen A.a showed strong association with malignancy in 32 out of the 99 patients while P.g and P.i were more prevalent among patients without malignancy. In principal component analyses, A.a appeared in the strongest component while the second strongest component consisted of a combination of T.f and T.d. The third component consisted of a combination of P.g and P.i, respectively. Of basic and oral health variables, gingival index appeared to be the strongest expression of inflammation (Eigen value 4.11 and Explained Variance 68.44 percent). CONCLUSIONS: The results partly confirmed our hypothesis by showing that harboring certain periodontal bacteria might link to malignancy. However, the associations are statistical and no conclusions can be drawn about causality.


Asunto(s)
Neoplasias/epidemiología , Periodontitis/epidemiología , Periodontitis/microbiología , Bacterias/clasificación , Bacterias/aislamiento & purificación , Estudios de Cohortes , Estudios Transversales , Femenino , Humanos , Masculino , Persona de Mediana Edad , Neoplasias/diagnóstico , Índice Periodontal , Prevalencia , Suecia/epidemiología
2.
J Med Microbiol ; 70(4)2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33861190

RESUMEN

Introduction. During previous viral pandemics, reported co-infection rates and implicated pathogens have varied. In the 1918 influenza pandemic, a large proportion of severe illness and death was complicated by bacterial co-infection, predominantly Streptococcus pneumoniae and Staphylococcus aureus.Gap statement. A better understanding of the incidence of co-infection in patients with COVID-19 infection and the pathogens involved is necessary for effective antimicrobial stewardship.Aim. To describe the incidence and nature of co-infection in critically ill adults with COVID-19 infection in England.Methodology. A retrospective cohort study of adults with COVID-19 admitted to seven intensive care units (ICUs) in England up to 18 May 2020, was performed. Patients with completed ICU stays were included. The proportion and type of organisms were determined at <48 and >48 h following hospital admission, corresponding to community and hospital-acquired co-infections.Results. Of 254 patients studied (median age 59 years (IQR 49-69); 64.6 % male), 139 clinically significant organisms were identified from 83 (32.7 %) patients. Bacterial co-infections/ co-colonisation were identified within 48 h of admission in 14 (5.5 %) patients; the commonest pathogens were Staphylococcus aureus (four patients) and Streptococcus pneumoniae (two patients). The proportion of pathogens detected increased with duration of ICU stay, consisting largely of Gram-negative bacteria, particularly Klebsiella pneumoniae and Escherichia coli. The co-infection/ co-colonisation rate >48 h after admission was 27/1000 person-days (95 % CI 21.3-34.1). Patients with co-infections/ co-colonisation were more likely to die in ICU (crude OR 1.78,95 % CI 1.03-3.08, P=0.04) compared to those without co-infections/ co-colonisation.Conclusion. We found limited evidence for community-acquired bacterial co-infection in hospitalised adults with COVID-19, but a high rate of Gram-negative infection acquired during ICU stay.


Asunto(s)
Infecciones Bacterianas/epidemiología , Coinfección/epidemiología , Adulto , Anciano , Anciano de 80 o más Años , Bacterias/clasificación , Bacterias/aislamiento & purificación , Infecciones Bacterianas/microbiología , Coinfección/microbiología , Enfermedad Crítica , Infección Hospitalaria/epidemiología , Infección Hospitalaria/microbiología , Inglaterra/epidemiología , Femenino , Hospitalización , Humanos , Unidades de Cuidados Intensivos , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Estudios Retrospectivos , Adulto Joven
3.
Nat Commun ; 12(1): 2089, 2021 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-33828081

RESUMEN

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.


Asunto(s)
Calentamiento Global , Metagenoma , Microbiología del Suelo , Suelo/química , Bacterias/clasificación , Bacterias/genética , California , Carbono/metabolismo , Bosques , Microbiota , Nitrógeno/metabolismo , ARN Ribosómico 16S , Temperatura
4.
J Med Microbiol ; 70(4)2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33856291

RESUMEN

Introduction. Feline odontoclastic resorptive lesion (FORL) is one of the most common and painful oral diseases of the cat. It is characterised by tooth resorption due to destructive activity of odontoclasts. FORL can result in tooth loss. While the aetiology of FORL is not clearly understood, it is thought to be multifactorial and bacteria are likely to play a major role.Hypothesis. Dysbiosis of the normal feline oral microbiota leads to an alteration in commensal bacteria populations, which results in the development of FORL.Aim. The purpose of the current study was to determine the composition of the microbiomes associated with feline oral health and FORL.Methodology. Supragingival plaque was collected from 25 cats with a healthy oral cavity and 40 cats with FORL. DNA was extracted from each sample, the V4 region of the 16S rRNA gene amplified by polymerase chain reaction and amplicons sequenced. Diversity and species richness analyses were performed, principal component analysis was used to explore differences between the oral microbiomes of healthy cats and those with FORL, and linear discriminant analysis effect size was used to assess differences between the groups.Results. The six most abundant bacterial genera identified were Bergeyella, Capnocytophaga, Lampropedia, Morexella, Porphyromonas and Treponema. Two-step cluster analysis of the data identified two FORL sub-groups (FORL-1, FORL-2). The FORL-2 sub-group was very similar to the healthy group, whilst the FORL-1 sub-group was clearly different from both the FORL-2 sub-group and the healthy groups. In this analysis, Capnocytophaga (P <0.001) and Lampropedia (P <0.01) were found at significantly lower levels and Porphyromonas at a slightly higher level in the FORL-1 sub-group compared to the healthy and FORL-2 sub-groups. Microbial diversity was found to be less in the FORL-1 sub-group than in the healthy group. Lampropedia sp., a phosphate-accumulating oral commensal species, was significantly lower in the FORL-1 sub-group.Conclusion. The oral microbiota associated with the FORL-1 sub-group is distinct from that found in the healthy group and FORL-2 sub-group. Lampropedia species may influence the local calcium-phosphate ratio, which could be a factor in tooth and bone resorption observed in FORL.


Asunto(s)
Enfermedades de los Gatos/microbiología , Microbiota , Osteoclastos/patología , Resorción Dentaria/veterinaria , Animales , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Biodiversidad , Enfermedades de los Gatos/patología , Gatos , Femenino , Masculino , Boca/microbiología , Salud Bucal , Resorción Dentaria/microbiología , Resorción Dentaria/patología
5.
Nat Commun ; 12(1): 2009, 2021 03 31.
Artículo en Inglés | MEDLINE | ID: mdl-33790294

RESUMEN

Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.


Asunto(s)
Genoma Bacteriano/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenoma/genética , Metagenómica/métodos , ARN Ribosómico 16S/genética , Aguas del Alcantarillado/microbiología , Bacterias/clasificación , Bacterias/genética , Reactores Biológicos/microbiología , Dinamarca , Microbiota/genética , Filogenia , ARN Ribosómico 23S/genética , ARN Ribosómico 5S/genética , Aguas Residuales/microbiología , Purificación del Agua/métodos
6.
Zoolog Sci ; 38(2): 140-147, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33812353

RESUMEN

Symbiotic associations with beneficial microorganisms endow a variety of host animals with adaptability to the environment. Stable transmission of symbionts across host generations is a key event in the maintenance of symbiotic associations through evolutionary time. However, our understanding of the mechanisms of symbiont transmission remains fragmentary. The deep-sea clam Phreagena okutanii harbors chemoautotrophic intracellular symbiotic bacteria in gill epithelial cells, and depends on these symbionts for nutrition. In this study, we focused on the association of these maternally transmitted symbionts with ovarian germ cells in juvenile female clams. First, we established a sex identification method for small P. okutanii individuals, and morphologically classified female germ cells observed in the ovary. Then, we investigated the association of the endosymbiotic bacteria with germ cells. We found that the symbionts were localized on the outer surface of the cell membrane of primary oocytes and not within the cluster of oogonia. Based on our findings, we discuss the processes and mechanisms of symbiont vertical transmission in P. okutanii.


Asunto(s)
Bacterias/clasificación , Bivalvos/microbiología , Simbiosis/fisiología , Animales , Femenino , Branquias/microbiología , Oocitos/microbiología
7.
Commun Biol ; 4(1): 480, 2021 04 13.
Artículo en Inglés | MEDLINE | ID: mdl-33850296

RESUMEN

The relationship between gut microbes and COVID-19 or H1N1 infections is not fully understood. Here, we compared the gut mycobiota of 67 COVID-19 patients, 35 H1N1-infected patients and 48 healthy controls (HCs) using internal transcribed spacer (ITS) 3-ITS4 sequencing and analysed their associations with clinical features and the bacterial microbiota. Compared to HCs, the fungal burden was higher. Fungal mycobiota dysbiosis in both COVID-19 and H1N1-infected patients was mainly characterized by the depletion of fungi such as Aspergillus and Penicillium, but several fungi, including Candida glabrata, were enriched in H1N1-infected patients. The gut mycobiota profiles in COVID-19 patients with mild and severe symptoms were similar. Hospitalization had no apparent additional effects. In COVID-19 patients, Mucoromycota was positively correlated with Fusicatenibacter, Aspergillus niger was positively correlated with diarrhoea, and Penicillium citrinum was negatively correlated with C-reactive protein (CRP). In H1N1-infected patients, Aspergillus penicilloides was positively correlated with Lachnospiraceae members, Aspergillus was positively correlated with CRP, and Mucoromycota was negatively correlated with procalcitonin. Therefore, gut mycobiota dysbiosis occurs in both COVID-19 patients and H1N1-infected patients and does not improve until the patients are discharged and no longer require medical attention.


Asunto(s)
/fisiopatología , Disbiosis/microbiología , Microbioma Gastrointestinal/fisiología , Gripe Humana/fisiopatología , Adulto , Anciano , Bacterias/clasificación , Bacterias/genética , Heces/microbiología , Femenino , Hongos/clasificación , Hongos/genética , Microbioma Gastrointestinal/genética , Humanos , Subtipo H1N1 del Virus de la Influenza A/fisiología , Gripe Humana/virología , Masculino , Persona de Mediana Edad , Análisis de Secuencia de ADN/métodos
8.
Nat Commun ; 12(1): 2435, 2021 04 23.
Artículo en Inglés | MEDLINE | ID: mdl-33893312

RESUMEN

Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. Certain ARGs appear to be frequently mobilised by different mobile genetic elements. We characterise the phylogenetic reach of these mobilisation elements to predict the potential future dissemination of known ARGs. Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 of 94 predicted mobilisations. We explore transfer barriers beyond mobilisation and show experimentally that physiological constraints of the host can explain why specific genes are largely confined to Gram-negative bacteria although their mobile elements support dissemination to Gram-positive bacteria. Our approach may potentially enable better risk assessment of future resistance gene dissemination.


Asunto(s)
Antibacterianos/farmacología , Bacterias/genética , Farmacorresistencia Bacteriana/genética , Transferencia de Gen Horizontal/genética , Genes Bacterianos/genética , Genoma Bacteriano/genética , Bacterias/clasificación , Filogenia , Especificidad de la Especie
9.
Nat Commun ; 12(1): 2213, 2021 04 13.
Artículo en Inglés | MEDLINE | ID: mdl-33850115

RESUMEN

Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.


Asunto(s)
Bacterias/genética , Genes Bacterianos/genética , Redes y Vías Metabólicas/genética , Metagenómica/métodos , Bacterias/clasificación , Fenómenos Fisiológicos Bacterianos , Biodiversidad , Ecología , Metagenoma , Océano Pacífico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Termodinámica
10.
Nat Commun ; 12(1): 2241, 2021 04 14.
Artículo en Inglés | MEDLINE | ID: mdl-33854066

RESUMEN

Antibiotic-induced modulation of the intestinal microbiota can lead to Clostridioides difficile infection (CDI), which is associated with considerable morbidity, mortality, and healthcare-costs globally. Therefore, identification of markers predictive of CDI could substantially contribute to guiding therapy and decreasing the infection burden. Here, we analyze the intestinal microbiota of hospitalized patients at increased CDI risk in a prospective, 90-day cohort-study before and after antibiotic treatment and at diarrhea onset. We show that patients developing CDI already exhibit significantly lower diversity before antibiotic treatment and a distinct microbiota enriched in Enterococcus and depleted of Ruminococcus, Blautia, Prevotella and Bifidobacterium compared to non-CDI patients. We find that antibiotic treatment-induced dysbiosis is class-specific with beta-lactams further increasing enterococcal abundance. Our findings, validated in an independent prospective patient cohort developing CDI, can be exploited to enrich for high-risk patients in prospective clinical trials, and to develop predictive microbiota-based diagnostics for management of patients at risk for CDI.


Asunto(s)
/fisiología , Infecciones por Clostridium/microbiología , Microbioma Gastrointestinal , Anciano , Antibacterianos/uso terapéutico , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Biomarcadores/análisis , /genética , Infecciones por Clostridium/diagnóstico , Infecciones por Clostridium/tratamiento farmacológico , Femenino , Humanos , Masculino , Persona de Mediana Edad , Estudios Prospectivos
11.
BMC Plant Biol ; 21(1): 127, 2021 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-33663379

RESUMEN

BACKGROUND: Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. RESULTS: In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. CONCLUSIONS: We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.


Asunto(s)
Bacterias/aislamiento & purificación , Dendrobium/microbiología , Plantas Medicinales/microbiología , Rizosfera , Microbiología del Suelo , Bacterias/clasificación , Biodiversidad , Medicamentos Herbarios Chinos , Secuenciación de Nucleótidos de Alto Rendimiento , Microbiota
12.
Ann Agric Environ Med ; 28(1): 61-71, 2021 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-33775069

RESUMEN

INTRODUCTION: Money is the most common item with which we have daily contact. Circulated banknotes and coins can become microbiologically contaminated and act as both a source and a means of spreading such pollutants. MATERIAL AND METHODS: The study was carried out in three money sorting facilities in Poland. Bioaerosol samples were collected using a 6-stage Andersen impactor, and microorganisms deposited on tabletop surfaces were sampled using the swab method. Bacterial and fungal concentrations were calculated and all isolated species were taxonomically identified. RESULTS: The study confirmed that means of payment are active sources of microbial emission in money sorting facilities. The bioaerosol concentrations did not exceed the threshold limit values proposed for this type of office premises. It confirms that ventilation systems in these facilities worked efficiently, protecting them from the migration of microbial contaminants present in both indoor and outdoor (atmospheric) background air. On the other hand, the average concentrations of bacteria and fungi on tabletop surfaces in banknote and coin sorting rooms were above the proposed purity levels for indoor surfaces and should be treated as microbiologically contaminated. Microbiota isolated from the air and surfaces were very diverse and among those strains were bacterial and fungal pathogens that can pose a health threat to exposed individuals. CONCLUSIONS: The results showed that employees in money sorting facilities were exposed to microorganisms that may contribute to the development of adverse health outcomes. To protect them, highly efficient hygienic measures should be introduced in this working environment, to prevent both unwanted pollution and subsequent secondary emission of microbial contaminants from sorted means of payment and tabletop surfaces.


Asunto(s)
Bacterias/aislamiento & purificación , Contaminación de Equipos/estadística & datos numéricos , Hongos/aislamiento & purificación , Microbiología del Aire , Bacterias/clasificación , Bacterias/genética , Bacterias/crecimiento & desarrollo , Hongos/clasificación , Hongos/genética , Hongos/crecimiento & desarrollo , Humanos , Polonia , Lugar de Trabajo
13.
Poult Sci ; 100(4): 100996, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33667869

RESUMEN

The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE). To investigate the composition and functional differences of cecal microbiota between high (n = 30) and low (n = 29) feed conversion ratio (FCR; metric for FE) groups, we performed 16S rRNA gene sequencing and predicted the metagenome function using Phylogenetic Investigation of Communities by Reconstruction of Unobserved Species in yellow broilers. The results showed that the 2 groups had the same prominent microbes but with differing abundance. Firmicutes, Bacteroidetes, and Actinobacteria were 3 prominent bacterial phyla in the cecal microbial community. Although there were no differences in microbial diversity, compositional differences related to FCR were found via linear discriminant analysis (LDA) effect size; the genus Bacteroides had a significantly higher abundance (LDA >2) in the high FE (HFE) group than in the low FE group. Furthermore, genus Bacteroides had a negative FCR-associated correlation (P < 0.05). Oscillospira was positively correlated with Bacteroides in both groups, whereas Dorea was negatively correlated with Bacteroides in the HFE group. Predictive functional analysis revealed that metabolic pathways such as "starch and sucrose metabolism," "phenylalanine, tyrosine and tryptophan biosynthesis," and "carbohydrate metabolism" were significantly enriched in the HFE group. The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.


Asunto(s)
Ciego , Microbioma Gastrointestinal , Alimentación Animal/análisis , Animales , Bacterias/clasificación , Bacterias/genética , Biodiversidad , Ciego/microbiología , Pollos , Filogenia , ARN Ribosómico 16S/genética
14.
Nature ; 592(7852): 138-143, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33731925

RESUMEN

A variety of species of bacteria are known to colonize human tumours1-11, proliferate within them and modulate immune function, which ultimately affects the survival of patients with cancer and their responses to treatment12-14. However, it is not known whether antigens derived from intracellular bacteria are presented by the human leukocyte antigen class I and II (HLA-I and HLA-II, respectively) molecules of tumour cells, or whether such antigens elicit a tumour-infiltrating T cell immune response. Here we used 16S rRNA gene sequencing and HLA peptidomics to identify a peptide repertoire derived from intracellular bacteria that was presented on HLA-I and HLA-II molecules in melanoma tumours. Our analysis of 17 melanoma metastases (derived from 9 patients) revealed 248 and 35 unique HLA-I and HLA-II peptides, respectively, that were derived from 41 species of bacteria. We identified recurrent bacterial peptides in tumours from different patients, as well as in different tumours from the same patient. Our study reveals that peptides derived from intracellular bacteria can be presented by tumour cells and elicit immune reactivity, and thus provides insight into a mechanism by which bacteria influence activation of the immune system and responses to therapy.


Asunto(s)
Antígenos Bacterianos/análisis , Antígenos Bacterianos/inmunología , Bacterias/inmunología , Antígenos HLA/inmunología , Melanoma/inmunología , Melanoma/microbiología , Péptidos/análisis , Péptidos/inmunología , Presentación de Antígeno , Bacterias/clasificación , Bacterias/genética , Línea Celular Tumoral , Técnicas de Cocultivo , Antígenos HLA/análisis , Humanos , Linfocitos Infiltrantes de Tumor/citología , Linfocitos Infiltrantes de Tumor/inmunología , Melanoma/patología , Metástasis de la Neoplasia/inmunología , Filogenia , ARN Ribosómico 16S/genética
15.
Science ; 372(6539)2021 04 16.
Artículo en Inglés | MEDLINE | ID: mdl-33766942

RESUMEN

Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.


Asunto(s)
Animales Salvajes/microbiología , Bacterias , Microbioma Gastrointestinal , Genoma Bacteriano , Metagenoma , Animales , Animales Salvajes/clasificación , Animales Salvajes/fisiología , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Toxinas Bacterianas/metabolismo , Conducta Animal , Biodiversidad , Bases de Datos de Ácidos Nucleicos , Dieta , Ecosistema , Islas Malvinas , Heces/microbiología , Interacciones Microbiota-Huesped , Israel , Madagascar , Metagenómica , Péptido Hidrolasas/genética , Péptido Hidrolasas/metabolismo , Filogenia , Queensland , Uganda
16.
Nat Commun ; 12(1): 1926, 2021 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-33771992

RESUMEN

The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.


Asunto(s)
Microbioma Gastrointestinal/efectos de los fármacos , Infecciones por Helicobacter/tratamiento farmacológico , Helicobacter pylori/efectos de los fármacos , Aprendizaje Automático , Microbiota/efectos de los fármacos , Inhibidores de la Bomba de Protones/uso terapéutico , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Infecciones por Helicobacter/microbiología , Helicobacter pylori/fisiología , Humanos , Dinámica Poblacional , ARN Ribosómico 16S/genética , Estómago/microbiología
17.
Gut Microbes ; 13(1): 1-19, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33685349

RESUMEN

The current pandemic of coronavirus disease (COVID) 2019 constitutes a global public health issue. Regarding the emerging importance of the gut-lung axis in viral respiratory infections, analysis of the gut microbiota's composition and functional activity during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection might be instrumental in understanding and controling COVID 19. We used a nonhuman primate model (the macaque), that recapitulates mild COVID-19 symptoms, to analyze the effects of a SARS-CoV-2 infection on dynamic changes of the gut microbiota. 16S rRNA gene profiling and analysis of ß diversity indicated significant changes in the composition of the gut microbiota with a peak at 10-13 days post-infection (dpi). Analysis of bacterial abundance correlation networks confirmed disruption of the bacterial community at 10-13 dpi. Some alterations in microbiota persisted after the resolution of the infection until day 26. Some changes in the relative bacterial taxon abundance associated with infectious parameters. Interestingly, the relative abundance of Acinetobacter (Proteobacteria) and some genera of the Ruminococcaceae family (Firmicutes) was positively correlated with the presence of SARS-CoV-2 in the upper respiratory tract. Targeted quantitative metabolomics indicated a drop in short-chain fatty acids (SCFAs) and changes in several bile acids and tryptophan metabolites in infected animals. The relative abundance of several taxa known to be SCFA producers (mostly from the Ruminococcaceae family) was negatively correlated with systemic inflammatory markers while the opposite correlation was seen with several members of the genus Streptococcus. Collectively, SARS-CoV-2 infection in a nonhuman primate is associated with changes in the gut microbiota's composition and functional activity.


Asunto(s)
/microbiología , Microbioma Gastrointestinal , Macaca/microbiología , Macaca/virología , Animales , Bacterias/clasificación , Modelos Animales de Enfermedad , Heces , Femenino , Metaboloma , ARN Ribosómico 16S/genética
18.
Int J Mol Sci ; 22(4)2021 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-33672790

RESUMEN

Nonsense mutations turn a coding (sense) codon into an in-frame stop codon that is assumed to result in a truncated protein product. Thus, nonsense substitutions are the hallmark of pseudogenes and are used to identify them. Here we show that in-frame stop codons within bacterial protein-coding genes are widespread. Their evolutionary conservation suggests that many of them are not pseudogenes, since they maintain dN/dS values (ratios of substitution rates at non-synonymous and synonymous sites) significantly lower than 1 (this is a signature of purifying selection in protein-coding regions). We also found that double substitutions in codons-where an intermediate step is a nonsense substitution-show a higher rate of evolution compared to null models, indicating that a stop codon was introduced and then changed back to sense via positive selection. This further supports the notion that nonsense substitutions in bacteria are relatively common and do not necessarily cause pseudogenization. In-frame stop codons may be an important mechanism of regulation: Such codons are likely to cause a substantial decrease of protein expression levels.


Asunto(s)
Codón sin Sentido , Codón de Terminación/genética , Sistemas de Lectura Abierta/genética , Células Procariotas/metabolismo , Bacterias/clasificación , Bacterias/genética , Proteínas Bacterianas/clasificación , Proteínas Bacterianas/genética , Secuencia de Bases , Evolución Molecular , Modelos Genéticos , Filogenia , Mutación Puntual , Seudogenes/genética , Selección Genética , Homología de Secuencia de Ácido Nucleico
19.
Int J Food Microbiol ; 345: 109130, 2021 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-33735781

RESUMEN

Pélardon is an artisanal French raw goat's milk cheese, produced using natural whey as a backslop. The aim of this study was to identify key microbial players involved in the acidification and aroma production of this Protected Designation of Origin cheese. Microbial diversity of samples, collected from the raw milk to 3-month cheese ripening, was determined by culture-dependent (MALDI-TOF analysis of 2877 isolates) and -independent (ITS2 and 16S metabarcoding) approaches and linked to changes in biochemical profiles (volatile compounds and acids). In parallel, potential dominant autochthonous microorganism reservoirs were also investigated by sampling the cheese-factory environment. Complex and increasing microbial diversity was observed by both approaches during ripening although major discrepancies were observed regarding Lactococcus lactis and Lacticaseibacillus paracasei fate. By correlating microbial shifts to biochemical changes, Lactococcus lactis was identified as the main acidifying bacterium, while L. mesenteroides and Geotrichum candidum were prevalent and associated with amino acids catabolism after the acidification step. The three species were dominant in the whey (backslop). In contrast, L. paracasei, Enterococcus faecalis, Penicillium commune and Scopulariopsis brevicaulis, which dominated during ripening, likely originated from the cheese-making environment. All these four species were positively correlated to major volatile compounds responsible for the goaty and earthy Pélardon cheese aroma. Overall, this work highlighted the power of MALDI-TOF and molecular techniques combined with volatilome analyses to dynamically follow and identify microbial communities during cheese-making and successively identify the key-players involved in aroma production and contributing to the typicity of Pélardon cheese.


Asunto(s)
Bacterias/clasificación , Bacterias/metabolismo , Queso/microbiología , Hongos/clasificación , Hongos/metabolismo , Leche/microbiología , Animales , Bacterias/aislamiento & purificación , Enterococcus faecalis/aislamiento & purificación , Enterococcus faecalis/metabolismo , Hongos/aislamiento & purificación , Geotrichum/aislamiento & purificación , Geotrichum/metabolismo , Cabras , Lactobacillus paracasei/aislamiento & purificación , Lactobacillus paracasei/metabolismo , Lactococcus lactis/aislamiento & purificación , Lactococcus lactis/metabolismo , Microbiota , Odorantes/análisis , Penicillium/aislamiento & purificación , Penicillium/metabolismo , Scopulariopsis/aislamiento & purificación , Scopulariopsis/metabolismo , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción
20.
Microbiome ; 9(1): 63, 2021 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-33741058

RESUMEN

BACKGROUND: Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.). RESULTS: A total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The "Candidatus Jiangella antarctica" has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa. CONCLUSIONS: Our findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life. Video abstract.


Asunto(s)
Bacterias/clasificación , Ecosistema , Filogenia , Regiones Antárticas , Bacterias/genética , Historia Antigua , Marte
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA
...