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1.
Curr Biol ; 30(19): R1124-R1130, 2020 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-33022254

RESUMO

Since the first recognition that infectious microbes serve as the causes of many human diseases, physicians and scientists have sought to understand and control their spread. For the past 150+ years, these 'microbe hunters' have learned to combine epidemiological information with knowledge of the infectious agent(s). In this essay, I reflect on the evolution of microbe hunting, beginning with the history of pre-germ theory epidemiological studies, through the microbiological and molecular eras. Now in the genomic age, modern-day microbe hunters are combining pathogen whole-genome sequencing with epidemiological data to enhance epidemiological investigations, advance our understanding of the natural history of pathogens and drivers of disease, and ultimately reshape our plans and priorities for global disease control and eradication. Indeed, as we have seen during the ongoing Covid-19 pandemic, the role of microbe hunters is now more important than ever. Despite the advances already made by microbial genomic epidemiology, the field is still maturing, with many more exciting developments on the horizon.


Assuntos
Bactérias/genética , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/epidemiologia , Epidemiologia Molecular/métodos , Prevenção Primária/métodos , Bactérias/patogenicidade , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Infecções por Coronavirus/epidemiologia , Genoma Bacteriano/genética , Genoma Viral/genética , História do Século XIX , História do Século XX , Humanos , Microbiota/genética , Pandemias , Pneumonia Viral/epidemiologia
2.
Nat Commun ; 11(1): 4708, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948758

RESUMO

While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. Our analysis of this data reveals an absolute protein-to-RNA ratio of 102-104 for bacterial populations and 103-105 for an archaeon, which is more comparable to Eukaryotic representatives' humans and yeast. Furthermore, we use the linearity between the metaproteome and metatranscriptome over time to identify core functional guilds, hence using a fundamental biological feature (i.e., RNA/protein levels) to highlight phenotypical complementarity. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function.


Assuntos
Microbiota/genética , Microbiota/fisiologia , Proteínas/genética , Proteínas/metabolismo , RNA/genética , RNA/metabolismo , Archaea/genética , Archaea/metabolismo , Bactérias/genética , Bactérias/metabolismo , DNA , Perfilação da Expressão Gênica , Genoma Microbiano , Humanos , Metabolômica , Fenótipo , Proteoma , Proteômica , Transcriptoma , Leveduras
3.
Ecotoxicol Environ Saf ; 205: 111267, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32992213

RESUMO

Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.


Assuntos
Actinobacteria/efeitos dos fármacos , Arsênico/toxicidade , Firmicutes/efeitos dos fármacos , Metagenômica/métodos , Proteobactérias/efeitos dos fármacos , Poluentes do Solo/toxicidade , Actinobacteria/citologia , Actinobacteria/genética , Arsênico/análise , Biodegradação Ambiental , Meios de Cultura/química , Farmacorresistência Bacteriana/efeitos dos fármacos , Firmicutes/citologia , Firmicutes/genética , Ouro , Testes de Sensibilidade Microbiana , Microbiota/efeitos dos fármacos , Microbiota/genética , Mineração , Proteobactérias/citologia , Proteobactérias/genética , RNA Ribossômico 16S/genética , Solo/química , Microbiologia do Solo , Poluentes do Solo/análise
4.
Pediatrics ; 146(4)2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32934151

RESUMO

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


Assuntos
Asma/etiologia , Microbiota , Nariz/microbiologia , Aerococcaceae/isolamento & purificação , Fatores Etários , Asma/diagnóstico , Asma/microbiologia , Criança , Pré-Escolar , Feminino , Finlândia , Seguimentos , Perfilação da Expressão Gênica/métodos , Haemophilus/isolamento & purificação , Humanos , Incidência , Lactente , Recém-Nascido , Aprendizado de Máquina , Masculino , Microbiota/genética , Moraxella/isolamento & purificação , Análise Multivariada , Estudos Prospectivos , RNA Ribossômico 16S/genética , Infecções Respiratórias/complicações , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/microbiologia , Risco , Streptococcus/isolamento & purificação
5.
BMC Infect Dis ; 20(1): 610, 2020 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-32811432

RESUMO

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


Assuntos
Microbiota/genética , Doença Pulmonar Obstrutiva Crônica/epidemiologia , Doença Pulmonar Obstrutiva Crônica/microbiologia , Escarro/microbiologia , Streptococcus/genética , Idoso , Idoso de 80 Anos ou mais , Biomarcadores , China/epidemiologia , Estudos de Coortes , Progressão da Doença , Eosinófilos , Feminino , Humanos , Contagem de Leucócitos , Masculino , Pessoa de Meia-Idade , Prevalência , RNA Ribossômico 16S/genética
6.
Medicine (Baltimore) ; 99(30): e21315, 2020 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-32791721

RESUMO

INTRODUCTION: There is evidence that caesarean section (CS) is associated with increased risk of childhood obesity, asthma, and coeliac disease. The gut microbiota of CS-born babies differs to those born vaginally, possibly due to reduced exposure to maternal vaginal bacteria during birth. Vaginal seeding is a currently unproven practice intended to reduce such differences, so that the gut microbiota of CS-born babies is similar to that of babies born vaginally. Our pilot study, which uses oral administration as a novel form of vaginal seeding, will assess the degree of maternal strain transfer and overall efficacy of the procedure for establishing normal gut microbiota development. METHODS AND ANALYSIS: Protocol for a single-blinded, randomized, placebo-controlled pilot study of a previously untested method of vaginal seeding (oral administration) in 30 CS-born babies. A sample of maternal vaginal bacteria is obtained prior to CS, and mixed with 5 ml sterile water to obtain a supernatant. Healthy babies are randomized at 1:1 to receive active treatment (3 ml supernatant) or placebo (3 ml sterile water). A reference group of 15 non-randomized vaginal-born babies are also being recruited. Babies' stool samples will undergo whole metagenomic shotgun sequencing to identify potential differences in community structure between CS babies receiving active treatment compared to those receiving placebo at age 1 month (primary outcome). Secondary outcomes include differences in overall gut community between CS groups (24 hours, 3 months); similarity of CS-seeded and placebo gut profiles to vaginally-born babies (24 hours, 1 and 3 months); degree of maternal vaginal strain transfer in CS-born babies (24 hours, 1 and 3 months); anthropometry (1 and 3 months) and body composition (3 months). ETHICS AND DISSEMINATION: Ethics approval by the Northern A Health and Disability Ethics Committee (18/NTA/49). Results will be published in peer-reviewed journals and presented at international conferences. REGISTRATION: Australian New Zealand Clinical Trials Registry (ACTRN12618000339257).


Assuntos
Cesárea/efeitos adversos , Microbiota/fisiologia , Placebos/administração & dosagem , Vagina/microbiologia , Adulto , Antropometria/métodos , Asma/epidemiologia , Asma/etiologia , Fenômenos Fisiológicos Bacterianos , Composição Corporal , Estudos de Casos e Controles , Doença Celíaca/epidemiologia , Doença Celíaca/etiologia , Parto Obstétrico/tendências , Fezes , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Metagenômica/métodos , Microbiota/genética , Nova Zelândia/epidemiologia , Obesidade Pediátrica/epidemiologia , Obesidade Pediátrica/etiologia , Gravidez
7.
PLoS Biol ; 18(8): e3000788, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32841232

RESUMO

Women with bacterial vaginosis (BV), an imbalance of the vaginal microbiome, are more likely to be colonized by potential pathogens such as Fusobacterium nucleatum, a bacterium linked with intrauterine infection and preterm birth. However, the conditions and mechanisms supporting pathogen colonization during vaginal dysbiosis remain obscure. We demonstrate that sialidase activity, a diagnostic feature of BV, promoted F. nucleatum foraging and growth on mammalian sialoglycans, a nutrient resource that was otherwise inaccessible because of the lack of endogenous F. nucleatum sialidase. In mice with sialidase-producing vaginal microbiotas, mutant F. nucleatum unable to consume sialic acids was impaired in vaginal colonization. These experiments in mice also led to the discovery that F. nucleatum may also "give back" to the community by reinforcing sialidase activity, a biochemical feature of human dysbiosis. Using human vaginal bacterial communities, we show that F. nucleatum supported robust outgrowth of Gardnerella vaginalis, a major sialidase producer and one of the most abundant organisms in BV. These results illustrate that mutually beneficial relationships between vaginal bacteria support pathogen colonization and may help maintain features of dysbiosis. These findings challenge the simplistic dogma that the mere absence of "healthy" lactobacilli is the sole mechanism that creates a permissive environment for pathogens during vaginal dysbiosis. Given the ubiquity of F. nucleatum in the human mouth, these studies also suggest a possible mechanism underlying links between vaginal dysbiosis and oral sex.


Assuntos
Proteínas de Bactérias/genética , Disbiose/microbiologia , Fusobacterium/metabolismo , Gardnerella vaginalis/metabolismo , Neuraminidase/genética , Polissacarídeos/metabolismo , Vaginose Bacteriana/microbiologia , Animais , Proteínas de Bactérias/metabolismo , Técnicas de Tipagem Bacteriana , Disbiose/patologia , Feminino , Fusobacterium/genética , Fusobacterium/isolamento & purificação , Fusobacterium/patogenicidade , Gardnerella vaginalis/genética , Gardnerella vaginalis/isolamento & purificação , Gardnerella vaginalis/patogenicidade , Expressão Gênica , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Microbiota/genética , Neuraminidase/metabolismo , RNA Ribossômico 16S/genética , Ácidos Siálicos/metabolismo , Simbiose/genética , Vagina/microbiologia , Vaginose Bacteriana/patologia
8.
PLoS One ; 15(8): e0236796, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32780734

RESUMO

It is well-known that different plant species, and even plant varieties, promote different assemblages of the microbial communities associated with them. Here, we investigate how microbial communities (bacteria and fungi) undergo changes within the influence of woody plants (two olive cultivars, one tolerant and another susceptible to the soilborne fungal pathogen Verticillium dahliae, plus wild Holm oak) grown in the same soil but with different management (agricultural versus native). By the use of metabarcoding sequencing we determined that the native Holm oak trees rhizosphere bacterial communities were different from its bulk soil, with differences in some genera like Gp4, Gp6 and Solirubrobacter. Moreover, the agricultural management used in the olive orchard led to belowground microbiota differences with respect to the natural conditions both in bulk soils and rhizospheres. Indeed, Gemmatimonas and Fusarium were more abundant in olive orchard soils. However, agricultural management removed the differences in the microbial communities between the two olive cultivars, and these differences were minor respect to the olive bulk soil. According to our results, and at least under the agronomical conditions here examined, the composition and structure of the rhizospheric microbial communities do not seem to play a major role in olive tolerance to V. dahliae.


Assuntos
Microbiota/genética , Olea/microbiologia , Quercus/microbiologia , Microbiologia do Solo , DNA Fúngico/química , DNA Fúngico/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Raízes de Plantas/microbiologia , Análise de Componente Principal , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Rizosfera , Análise de Sequência de DNA , Verticillium/genética , Verticillium/patogenicidade
9.
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
10.
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
11.
Water Res ; 185: 116261, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32791454

RESUMO

Substantial N2O emission results from activated sludge nitrogen removal processes. N2O-reducing organisms possessing NosZ-type N2O reductases have been recognized to play crucial roles in suppressing emission of N2O produced in anoxic activated sludge via denitrification; however, which of the diverse nosZ-possessing organisms function as the major N2O sink in situ remains largely unknown. Here, nosZ genes and transcripts in wastewater microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approaches. A sewage sample was enriched in a batch reactor fed continuous stream of N2 containing 20-10,000 ppmv N2O with excess amount (10 mM) of acetate as the source of carbon and electrons, where 14 genera of potential N2O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primers/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated with the shotgun metagenome analysis results. With these group-specific qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.


Assuntos
Microbiota , Esgotos , Desnitrificação , Metagenoma , Microbiota/genética , Óxido Nitroso/análise , República da Coreia
12.
Ecotoxicol Environ Saf ; 205: 111113, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32836153

RESUMO

Eutrophication is a global problem, and bacterial diversity and community composition are usually affected by eutrophication. However, limited information on the ecological significance of bacterial community during algae blooms of rivers has been given, more studies should be focused on the bacterial diversity and distribution characteristics in eutrophic rivers. In this study, we explored the spatial variations of bacterial biomass, community structure, and their relationship with environmental factors in the eutrophic Xiangxi River. The content of Chlorophyll (Chl) was about 16 mg/L in the midstream (S2, S3), which was in the range of light eutrophication. Significant spatial variation of bacterial community structure was found at different sites and depths (p < 0.05), and the driving environmental factor was found to be nitrogen, mainly detected as total nitrogen (TN), Kjeldahl nitrogen (KN), and ammonia nitrogen (NH4+) (p < 0.05). The midstream sites had some significantly different bacteria, including algicidal bacteria and dominant lineages during algal blooms. This result was consistent with the functional prediction, where significant higher abundance of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was associated with algicidal substances in the midstream. At different water depths, some populations adapted to the surface layer, such as the class Flavobacteriia, and others preferred to inhabit in the bottom layer, such as Betaproteobacteria and Acidobacteria. The bacterial biomass was higher in the bottom layer than that in the surface and middle layer, and temperature and pH were found to be the major driving factors. The bacterial diversity increased with the increasing of depths in most sampling sites according to operational taxonomic units (OTUs), Chao1 and ACE indexes, and PO43- was demonstrated to be the most significant factor. In summary, this study offered the evidence for microbial distribution characteristics across different sites and depths in summer, and its relationship with environmental variables in a eutrophic river.


Assuntos
Monitoramento Ambiental/métodos , Eutrofização , Microbiota , Proteobactérias/crescimento & desenvolvimento , Rios , Biomassa , China , Clorofila/análise , Microbiota/genética , Nitrogênio/análise , Fosfatos/análise , Fósforo/análise , Proteobactérias/classificação , Proteobactérias/genética , RNA Ribossômico 16S/genética , Rios/química , Rios/microbiologia , Estações do Ano , Temperatura
13.
Ecotoxicol Environ Saf ; 204: 111073, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32755736

RESUMO

The high pH and salinity of textile wastewater is a major hindrance to azo dye decolorization. In this study, a mixed bacterial consortium ZW1 was enriched under saline (10% salinity) and alkaline (pH 10.0) conditions to decolorize Methanil Yellow G (MY-G). Consortium ZW1 was mainly composed of Halomonas (49.8%), Marinobacter (30.7%) and Clostridiisalibacter (19.2%). The effects of physicochemical factors were systematically investigated, along with the degradation pathway and metagenome analysis. The co-carbon source was found to be necessary, and the addition of yeast extract led to 93.3% decolorization of 100 mg/L MY-G within 16 h (compared with 1.12% for control). The optimum pH, salinity, temperature and initial dye concentration were 8.0, 5-10%, 40 °C and 100 mg/L, respectively. The typical dye-related degradation enzymes were most effective at 10% salinity. Consortium ZW1 was also able to differentially decolorize five other direct and acidic dyes in a short period. Phototoxicity tests revealed the detoxification of MY-G degradation products. Combining UV-vis, FTIR and GC-MS detection, the MY-G degradation pathway by consortium ZW1 was proposed. Furthermore, metagenomic approach was used to elucidate the functional potential of genes in MY-G biodegradation. These results signify the broad potential application of halo-alkaliphilic consortia in the bioremediation of dyeing wastewater.


Assuntos
Compostos Azo/toxicidade , Corantes/toxicidade , Metagenoma , Microbiota/efeitos dos fármacos , Águas Residuárias , Poluentes Químicos da Água/toxicidade , Purificação da Água/métodos , Compostos Azo/metabolismo , Biodegradação Ambiental , Carbono/metabolismo , Corantes/metabolismo , Microbiota/genética , Salinidade , Temperatura , Indústria Têxtil , Águas Residuárias/química , Águas Residuárias/microbiologia , Poluentes Químicos da Água/metabolismo
14.
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
15.
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
16.
Aquat Toxicol ; 227: 105591, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32853898

RESUMO

The effects of allelopathy and the potential harm of several isolated allelochemicals have been studied in detail. Microorganisms in the phycosphere play an important role in algal growth, decay and nutrient cycling. However, it is unknown and often neglected whether allelochemicals affect the phycosphere. The present study selected a phenolic acid protocatechuic acid (PA) - previously shown to be an allelochemical. We studied PA at a half maximal effective concentration of 0.20 mM (30 mg L-1) against Scrippsiella trochoidea to assess the effect of PA on its phycosphere in an acute time period (48 h). The results showed that: 1) OTUs (operational taxonomic units) in the treatment groups (31.4 ± 0.55) exceeded those of the control groups (28.2 ± 1.30) and the Shannon and Simpson indices were lower than the control groups (3.31 ± 0.08 and 0.84 ± 0.02, 3.45 ± 0.09 and 0.88 ± 0.01); 2) Gammaproteobacteria predominated in the treatment groups (44.71 ± 2.13 %) while Alphaproteobacteria dominated in the controls (67.17 ± 3.87 %); 3) Gammaproteobacteria and Alphaproteobacteria were important biomarkers in the treatment and control groups respectively (LDA > 4.0). PA improved the relative abundance of Alteromonas significantly and decreased the one of Rhodobacteraceae. PICRUSt analysis showed that the decrease of Rhodobacterceae was closely related with the decline of most functional genes in metabolism such as amino acid, carbohydrate, xenobiotics, cofactors and vitamins metabolism after PA-treated.


Assuntos
Alelopatia/efeitos dos fármacos , Dinoflagelados/efeitos dos fármacos , Proliferação Nociva de Algas/efeitos dos fármacos , Hidroxibenzoatos/farmacologia , Microbiota/efeitos dos fármacos , Feromônios/farmacologia , Alelopatia/genética , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Dinoflagelados/genética , Dinoflagelados/crescimento & desenvolvimento , Microbiota/genética , Proteobactérias/efeitos dos fármacos , Proteobactérias/genética , Proteobactérias/isolamento & purificação
17.
Nat Commun ; 11(1): 3831, 2020 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-32737305

RESUMO

Long-term time series have provided evidence that anthropogenic pressures can threaten lakes. Yet it remains unclear how and the extent to which lake biodiversity has changed during the Anthropocene, in particular for microbes. Here, we used DNA preserved in sediments to compare modern micro-eukaryotic communities with those from the end of the 19th century, i.e., before acceleration of the human imprint on ecosystems. Our results obtained for 48 lakes indicate drastic changes in the composition of microbial communities, coupled with a homogenization of their diversity between lakes. Remote high elevation lakes were globally less impacted than lowland lakes affected by local human activity. All functional groups (micro-algae, parasites, saprotrophs and consumers) underwent significant changes in diversity. However, we show that the effects of anthropogenic changes have benefited in particular phototrophic and mixotrophic species, which is consistent with the hypothesis of a global increase of primary productivity in lakes.


Assuntos
DNA/genética , Eucariotos/genética , Sedimentos Geológicos/análise , Lagos/análise , Alveolados/classificação , Alveolados/genética , Alveolados/isolamento & purificação , Biodiversidade , Evolução Biológica , Ecossistema , Eucariotos/classificação , Eucariotos/isolamento & purificação , História do Século XIX , História do Século XX , História do Século XXI , Atividades Humanas/história , Humanos , Microalgas/classificação , Microalgas/genética , Microalgas/isolamento & purificação , Microbiota/genética , Processos Fototróficos/fisiologia , Rhizaria/classificação , Rhizaria/genética , Rhizaria/isolamento & purificação , Estramenópilas/classificação , Estramenópilas/genética , Estramenópilas/isolamento & purificação
18.
BMC Infect Dis ; 20(1): 629, 2020 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-32842982

RESUMO

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


Assuntos
Biodiversidade , Neoplasia Intraepitelial Cervical/epidemiologia , Progressão da Doença , Microbiota/genética , Papillomaviridae/genética , Infecções por Papillomavirus/epidemiologia , Neoplasias do Colo do Útero/epidemiologia , Vagina/microbiologia , Adulto , Idoso , Neoplasia Intraepitelial Cervical/virologia , China/epidemiologia , Estudos de Coortes , Feminino , Humanos , Lactobacillus/genética , Pessoa de Meia-Idade , Infecções por Papillomavirus/virologia , RNA Ribossômico 16S/genética , Neoplasias do Colo do Útero/virologia
19.
PLoS One ; 15(7): e0234906, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32645011

RESUMO

Small intestinal bacterial overgrowth (SIBO) is highly prevalent and is associated with numerous gastrointestinal disorders, but the microbes involved remain poorly defined. Moreover, existing studies of microbiome alterations in SIBO have utilized stool samples, which are not representative of the entire gastrointestinal tract. Therefore, we aimed to determine and compare the duodenal microbiome composition in SIBO and non-SIBO subjects, using duodenal aspirates from subjects undergoing standard-of-care esophagogastroduodenoscopy without colon preparation. Using the recently-redefined cutoff for SIBO of >103 colony forming units per milliliter (CFU/mL), 42 SIBO and 98 non-SIBO subjects were identified. Duodenal samples from SIBO subjects had 4x103-fold higher counts than non-SIBO subjects when plated on MacConkey agar (P<0.0001), and 3.8-fold higher counts when plated on blood agar (P<0.0001). Twenty subjects had also undergone lactulose hydrogen breath tests (LHBTs), of whom 7/20 had SIBO. At the 90-minute timepoint, 4/7 SIBO subjects had positive LHBTs (rise in hydrogen (H2) ≥ 20 ppm above baseline), as compared to 2/13 non-SIBO subjects. 16S ribosomal RNA (rRNA) sequencing revealed that SIBO subjects had 4.31-fold higher relative abundance of Proteobacteria (FDR P<0.0001) and 1.64-fold lower Firmicutes (P<0.0003) than non-SIBO subjects. This increased relative abundance of Proteobacteria correlated with decreased α-diversity in SIBO subjects (Spearman R = 0.4866, P<0.0001) Specific increases in class Gammaproteobacteria correlated with the area-under-the-curve for H2 for 0-90 mins during LHBT (R = 0.630, P = 0.002). Increases in Gammaproteobacteria resulted primarily from higher relative abundances of the family Enterobacteriaceae (FDR P<0.0001), which correlated with the symptom of bloating (Spearman R = 0.185, 2-tailed P = 0.028). Increases in family Aeromonadaceae correlated with urgency with bowel movement (Spearman R = 0.186, 2-tailed P = 0.028). These results validate the >103 CFU/mL cutoff for the definition of SIBO, and also reveal specific overgrowth of Proteobacteria in SIBO vs. non-SIBO subjects, coupled with an altered Proteobacterial profile that correlates with symptom severity. Future research may elucidate host-microbiome interactions underlying these symptoms in SIBO patients.


Assuntos
Duodeno/microbiologia , Microbioma Gastrointestinal/fisiologia , Intestino Delgado/microbiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Infecções Bacterianas/diagnóstico , Endoscopia do Sistema Digestório , Feminino , Trato Gastrointestinal/microbiologia , Humanos , Síndrome do Intestino Irritável/microbiologia , Masculino , Microbiota/genética , Pessoa de Meia-Idade
20.
Nat Commun ; 11(1): 3514, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32665548

RESUMO

Differential abundance (DA) analysis of microbiome data continues to be a challenging problem due to the complexity of the data. In this article we define the notion of "sampling fraction" and demonstrate a major hurdle in performing DA analysis of microbiome data is the bias introduced by differences in the sampling fractions across samples. We introduce a methodology called Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), which estimates the unknown sampling fractions and corrects the bias induced by their differences among samples. The absolute abundance data are modeled using a linear regression framework. This formulation makes a fundamental advancement in the field because, unlike the existing methods, it (a) provides statistically valid test with appropriate p-values, (b) provides confidence intervals for differential abundance of each taxon, (c) controls the False Discovery Rate (FDR), (d) maintains adequate power, and (e) is computationally simple to implement.


Assuntos
Biologia Computacional/métodos , Microbiota/genética , Ecologia , Humanos , Microbiologia
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